From 04c2a2d06a450cb08e63bce890c99d347d0b9b4c Mon Sep 17 00:00:00 2001 From: Kenneth Jung Date: Thu, 30 Apr 2020 11:05:08 -0700 Subject: [PATCH 001/151] Reject fractional values outside of (0.0, 1.0) --- .../sdk/io/gcp/bigquery/BigQueryStorageStreamSource.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/bigquery/BigQueryStorageStreamSource.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/bigquery/BigQueryStorageStreamSource.java index f76a4328dfcb..d460c5d3ca40 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/bigquery/BigQueryStorageStreamSource.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/bigquery/BigQueryStorageStreamSource.java @@ -288,6 +288,11 @@ public BoundedSource splitAtFraction(double fraction) { source.stream.getName(), fraction); + if (fraction <= 0.0 || fraction >= 1.0) { + LOG.info("BigQuery Storage API does not support splitting at fraction {}", fraction); + return null; + } + SplitReadStreamRequest splitRequest = SplitReadStreamRequest.newBuilder() .setOriginalStream(source.stream) From 778e0f9cfa0bb8f456524619ea40b25c24bcb5de Mon Sep 17 00:00:00 2001 From: Esun Kim Date: Fri, 8 May 2020 20:09:40 -0700 Subject: [PATCH 002/151] Upgrades gcsio to 2.1.3 --- .../main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy b/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy index eaf79fbdd696..ac53a23daf4a 100644 --- a/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy +++ b/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy @@ -382,7 +382,7 @@ class BeamModulePlugin implements Plugin { def generated_grpc_ga_version = "1.85.1" def google_auth_version = "0.19.0" def google_clients_version = "1.30.9" - def google_cloud_bigdataoss_version = "2.1.2" + def google_cloud_bigdataoss_version = "2.1.3" def google_cloud_core_version = "1.92.2" def google_cloud_spanner_version = "1.49.1" def google_cloud_datacatalog_version = "0.32.1" From 3e70f16d1abd92c27eb6f54330a7427429827074 Mon Sep 17 00:00:00 2001 From: Sam Rohde Date: Wed, 22 Apr 2020 16:11:26 -0700 Subject: [PATCH 003/151] Make GroupByKey a primitive Move old implementation to DirectRunner. Change-Id: I9aaf3c00ed7e9606f10e417f0a504a5fc63ee68b --- sdks/python/apache_beam/pipeline_test.py | 18 +-- .../runners/dataflow/dataflow_runner.py | 16 ++- .../runners/dataflow/dataflow_runner_test.py | 117 +++++++++++------- .../runners/direct/direct_runner.py | 86 +++++++++++++ .../interactive/pipeline_analyzer_test.py | 2 +- .../interactive/pipeline_instrument_test.py | 12 +- .../fn_api_runner/fn_runner_test.py | 4 +- sdks/python/apache_beam/transforms/core.py | 45 +------ 8 files changed, 187 insertions(+), 113 deletions(-) diff --git a/sdks/python/apache_beam/pipeline_test.py b/sdks/python/apache_beam/pipeline_test.py index 0011109f5d25..a7e0eac9c860 100644 --- a/sdks/python/apache_beam/pipeline_test.py +++ b/sdks/python/apache_beam/pipeline_test.py @@ -27,7 +27,6 @@ from builtins import object from builtins import range -import mock from nose.plugins.attrib import attr import apache_beam as beam @@ -370,9 +369,7 @@ def raise_exception(exn): # pylint: disable=expression-not-assigned p | Create([ValueError('msg')]) | Map(raise_exception) - @mock.patch( - 'apache_beam.runners.direct.direct_runner._get_transform_overrides') - def test_ptransform_overrides(self, file_system_override_mock): + def test_ptransform_overrides(self): class MyParDoOverride(PTransformOverride): def matches(self, applied_ptransform): return isinstance(applied_ptransform.transform, DoubleParDo) @@ -382,15 +379,12 @@ def get_replacement_transform(self, ptransform): return TripleParDo() raise ValueError('Unsupported type of transform: %r' % ptransform) - def get_overrides(unused_pipeline_options): - return [MyParDoOverride()] + p = Pipeline() + pcoll = p | beam.Create([1, 2, 3]) | 'Multiply' >> DoubleParDo() + assert_that(pcoll, equal_to([3, 6, 9])) - file_system_override_mock.side_effect = get_overrides - - # Specify DirectRunner as it's the one patched above. - with Pipeline(runner='BundleBasedDirectRunner') as p: - pcoll = p | beam.Create([1, 2, 3]) | 'Multiply' >> DoubleParDo() - assert_that(pcoll, equal_to([3, 6, 9])) + p.replace_all([MyParDoOverride()]) + p.run() def test_ptransform_override_type_hints(self): class NoTypeHintOverride(PTransformOverride): diff --git a/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py b/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py index 07c5f8809fc7..4c02168cee58 100644 --- a/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py +++ b/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py @@ -278,7 +278,7 @@ def group_by_key_input_visitor(): class GroupByKeyInputVisitor(PipelineVisitor): """A visitor that replaces `Any` element type for input `PCollection` of - a `GroupByKey` or `_GroupByKeyOnly` with a `KV` type. + a `GroupByKey` with a `KV` type. TODO(BEAM-115): Once Python SDk is compatible with the new Runner API, we could directly replace the coder instead of mutating the element type. @@ -289,8 +289,8 @@ def enter_composite_transform(self, transform_node): def visit_transform(self, transform_node): # Imported here to avoid circular dependencies. # pylint: disable=wrong-import-order, wrong-import-position - from apache_beam.transforms.core import GroupByKey, _GroupByKeyOnly - if isinstance(transform_node.transform, (GroupByKey, _GroupByKeyOnly)): + from apache_beam.transforms.core import GroupByKey + if isinstance(transform_node.transform, GroupByKey): pcoll = transform_node.inputs[0] pcoll.element_type = typehints.coerce_to_kv_type( pcoll.element_type, transform_node.full_label) @@ -840,7 +840,11 @@ def apply_WriteToBigQuery(self, transform, pcoll, options): transform.write_disposition, kms_key=transform.kms_key)) + # TODO(srohde): Remove this after internal usages have been removed. def apply_GroupByKey(self, transform, pcoll, options): + return transform.expand(pcoll) + + def _verify_gbk_coders(self, transform, pcoll): # Infer coder of parent. # # TODO(ccy): make Coder inference and checking less specialized and more @@ -858,11 +862,13 @@ def apply_GroupByKey(self, transform, pcoll, options): coders.registry.verify_deterministic( coder.key_coder(), 'GroupByKey operation "%s"' % transform.label) - return pvalue.PCollection.from_(pcoll) - def run_GroupByKey(self, transform_node, options): input_tag = transform_node.inputs[0].tag input_step = self._cache.get_pvalue(transform_node.inputs[0]) + + # Verify that the GBK's parent has a KV coder. + self._verify_gbk_coders(transform_node.transform, transform_node.inputs[0]) + step = self._add_step( TransformNames.GROUP, transform_node.full_label, transform_node) step.add_property( diff --git a/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py b/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py index 87f8785e394e..0791b49a983d 100644 --- a/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py +++ b/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py @@ -55,7 +55,6 @@ from apache_beam.transforms import environments from apache_beam.transforms import window from apache_beam.transforms.core import Windowing -from apache_beam.transforms.core import _GroupByKeyOnly from apache_beam.transforms.display import DisplayDataItem from apache_beam.typehints import typehints @@ -315,53 +314,46 @@ def test_remote_runner_display_data(self): def test_no_group_by_key_directly_after_bigquery(self): remote_runner = DataflowRunner() - p = Pipeline( - remote_runner, - options=PipelineOptions([ - '--dataflow_endpoint=ignored', - '--job_name=test-job', - '--project=test-project', - '--staging_location=ignored', - '--temp_location=/dev/null', - '--no_auth' - ])) - rows = p | beam.io.Read(beam.io.BigQuerySource('dataset.faketable')) with self.assertRaises(ValueError, msg=('Coder for the GroupByKey operation' '"GroupByKey" is not a key-value coder: ' 'RowAsDictJsonCoder')): - unused_invalid = rows | beam.GroupByKey() + with beam.Pipeline(runner=remote_runner, + options=PipelineOptions(self.default_properties)) as p: + # pylint: disable=expression-not-assigned + p | beam.io.Read( + beam.io.BigQuerySource('dataset.faketable')) | beam.GroupByKey() def test_group_by_key_input_visitor_with_valid_inputs(self): p = TestPipeline() pcoll1 = PCollection(p) pcoll2 = PCollection(p) pcoll3 = PCollection(p) - for transform in [_GroupByKeyOnly(), beam.GroupByKey()]: - pcoll1.element_type = None - pcoll2.element_type = typehints.Any - pcoll3.element_type = typehints.KV[typehints.Any, typehints.Any] - for pcoll in [pcoll1, pcoll2, pcoll3]: - applied = AppliedPTransform(None, transform, "label", [pcoll]) - applied.outputs[None] = PCollection(None) - DataflowRunner.group_by_key_input_visitor().visit_transform(applied) - self.assertEqual( - pcoll.element_type, typehints.KV[typehints.Any, typehints.Any]) + + pcoll1.element_type = None + pcoll2.element_type = typehints.Any + pcoll3.element_type = typehints.KV[typehints.Any, typehints.Any] + for pcoll in [pcoll1, pcoll2, pcoll3]: + applied = AppliedPTransform(None, beam.GroupByKey(), "label", [pcoll]) + applied.outputs[None] = PCollection(None) + DataflowRunner.group_by_key_input_visitor().visit_transform(applied) + self.assertEqual( + pcoll.element_type, typehints.KV[typehints.Any, typehints.Any]) def test_group_by_key_input_visitor_with_invalid_inputs(self): p = TestPipeline() pcoll1 = PCollection(p) pcoll2 = PCollection(p) - for transform in [_GroupByKeyOnly(), beam.GroupByKey()]: - pcoll1.element_type = str - pcoll2.element_type = typehints.Set - err_msg = ( - r"Input to 'label' must be compatible with KV\[Any, Any\]. " - "Found .*") - for pcoll in [pcoll1, pcoll2]: - with self.assertRaisesRegex(ValueError, err_msg): - DataflowRunner.group_by_key_input_visitor().visit_transform( - AppliedPTransform(None, transform, "label", [pcoll])) + + pcoll1.element_type = str + pcoll2.element_type = typehints.Set + err_msg = ( + r"Input to 'label' must be compatible with KV\[Any, Any\]. " + "Found .*") + for pcoll in [pcoll1, pcoll2]: + with self.assertRaisesRegex(ValueError, err_msg): + DataflowRunner.group_by_key_input_visitor().visit_transform( + AppliedPTransform(None, beam.GroupByKey(), "label", [pcoll])) def test_group_by_key_input_visitor_for_non_gbk_transforms(self): p = TestPipeline() @@ -404,10 +396,6 @@ def test_gbk_then_flatten_input_visitor(self): flat = (none_str_pc, none_int_pc) | beam.Flatten() _ = flat | beam.GroupByKey() - # This may change if type inference changes, but we assert it here - # to make sure the check below is not vacuous. - self.assertNotIsInstance(flat.element_type, typehints.TupleConstraint) - p.visit(DataflowRunner.group_by_key_input_visitor()) p.visit(DataflowRunner.flatten_input_visitor()) @@ -596,6 +584,15 @@ def test_combine_values_translation(self): self.assertIn( u'CombineValues', set(step[u'kind'] for step in job_dict[u'steps'])) + def _find_step(self, job, step_name): + job_dict = json.loads(str(job)) + maybe_step = [ + s for s in job_dict[u'steps'] + if s[u'properties'][u'user_name'] == step_name + ] + self.assertTrue(maybe_step, 'Could not find step {}'.format(step_name)) + return maybe_step[0] + def expect_correct_override(self, job, step_name, step_kind): """Expects that a transform was correctly overriden.""" @@ -615,14 +612,7 @@ def expect_correct_override(self, job, step_name, step_kind): "user_name": step_name + ".out" }] - job_dict = json.loads(str(job)) - maybe_step = [ - s for s in job_dict[u'steps'] - if s[u'properties'][u'user_name'] == step_name - ] - self.assertTrue(maybe_step, 'Could not find step {}'.format(step_name)) - - step = maybe_step[0] + step = self._find_step(job, step_name) self.assertEqual(step[u'kind'], step_kind) # The display data here is forwarded because the replace transform is @@ -663,6 +653,43 @@ def test_read_pubsub_translation(self): self.expect_correct_override( runner.job, u'ReadFromPubSub/Read', u'ParallelRead') + def test_gbk_translation(self): + runner = DataflowRunner() + with beam.Pipeline(runner=runner, + options=PipelineOptions(self.default_properties)) as p: + # pylint: disable=expression-not-assigned + p | beam.Create([(1, 2)]) | beam.GroupByKey() + + expected_output_info = [{ + "encoding": { + "@type": "kind:windowed_value", + "component_encodings": [{ + "@type": "kind:pair", + "component_encodings": [{ + "@type": "kind:varint" + }, + { + "@type": "kind:stream", + "component_encodings": [{ + "@type": "kind:varint" + }], + "is_stream_like": True + }], + "is_pair_like": True + }, { + "@type": "kind:global_window" + }], + "is_wrapper": True + }, + "output_name": "out", + "user_name": "GroupByKey.out" + }] # yapf: disable + + gbk_step = self._find_step(runner.job, u'GroupByKey') + self.assertEqual(gbk_step[u'kind'], u'GroupByKey') + self.assertEqual( + gbk_step[u'properties']['output_info'], expected_output_info) + class CustomMergingWindowFn(window.WindowFn): def assign(self, assign_context): diff --git a/sdks/python/apache_beam/runners/direct/direct_runner.py b/sdks/python/apache_beam/runners/direct/direct_runner.py index 5181ad734ff0..fb80f19b5d3b 100644 --- a/sdks/python/apache_beam/runners/direct/direct_runner.py +++ b/sdks/python/apache_beam/runners/direct/direct_runner.py @@ -234,7 +234,89 @@ def get_replacement_transform(self, transform): from apache_beam.runners.direct.test_stream_impl import _ExpandableTestStream return _ExpandableTestStream(transform) + class GroupByKeyPTransformOverride(PTransformOverride): + """A ``PTransformOverride`` for ``GroupByKey``. + + This replaces the Beam implementation as a primitive. + """ + def matches(self, applied_ptransform): + # Imported here to avoid circular dependencies. + # pylint: disable=wrong-import-order, wrong-import-position + from apache_beam.transforms.core import GroupByKey + if (isinstance(applied_ptransform.transform, GroupByKey) and + not getattr(applied_ptransform.transform, 'override', False)): + self.input_type = applied_ptransform.inputs[0].element_type + return True + return False + + def get_replacement_transform(self, ptransform): + # Imported here to avoid circular dependencies. + # pylint: disable=wrong-import-order, wrong-import-position + from apache_beam.transforms.core import GroupByKey + + # Subclass from GroupByKey to inherit all the proper methods. + class GroupByKey(GroupByKey): + override = True + + def expand(self, pcoll): + # Imported here to avoid circular dependencies. + # pylint: disable=wrong-import-order, wrong-import-position + from apache_beam.coders import typecoders + from apache_beam.typehints import trivial_inference + + input_type = pcoll.element_type + if input_type is not None: + # Initialize type-hints used below to enforce type-checking and to + # pass downstream to further PTransforms. + key_type, value_type = trivial_inference.key_value_types(input_type) + # Enforce the input to a GBK has a KV element type. + pcoll.element_type = typehints.typehints.coerce_to_kv_type( + pcoll.element_type) + typecoders.registry.verify_deterministic( + typecoders.registry.get_coder(key_type), + 'GroupByKey operation "%s"' % self.label) + + reify_output_type = typehints.KV[ + key_type, typehints.WindowedValue[value_type]] # type: ignore[misc] + gbk_input_type = ( + typehints. + KV[key_type, + typehints.Iterable[ + typehints.WindowedValue[ # type: ignore[misc] + value_type]]]) + gbk_output_type = typehints.KV[key_type, + typehints.Iterable[value_type]] + + # pylint: disable=bad-continuation + return ( + pcoll + | 'ReifyWindows' >> ( + ParDo(self.ReifyWindows()).with_output_types( + reify_output_type)) + | 'GroupByKey' >> ( + _GroupByKeyOnly().with_input_types( + reify_output_type).with_output_types(gbk_input_type)) + | ( + 'GroupByWindow' >> + _GroupAlsoByWindow(pcoll.windowing).with_input_types( + gbk_input_type).with_output_types(gbk_output_type))) + else: + # The input_type is None, run the default + return ( + pcoll + | 'ReifyWindows' >> ParDo(self.ReifyWindows()) + | 'GroupByKey' >> _GroupByKeyOnly() + | 'GroupByWindow' >> _GroupAlsoByWindow(pcoll.windowing)) + + # Infer the correct type. + return GroupByKey().with_output_types( + ptransform.infer_output_type(self.input_type)) + overrides = [ + # This needs to be the first and the last override. Other overrides depend + # on the GroupByKey implementation to be composed of _GroupByKeyOnly and + # _GroupAlsoByWindow. + GroupByKeyPTransformOverride(), SplittableParDoOverride(), ProcessKeyedElementsViaKeyedWorkItemsOverride(), CombinePerKeyOverride(), @@ -253,6 +335,10 @@ def get_replacement_transform(self, transform): except ImportError: pass + # This also needs to be last because other transforms apply GBKs which need to + # be translated into a DirectRunner-compatible transform. + overrides.append(GroupByKeyPTransformOverride()) + return overrides diff --git a/sdks/python/apache_beam/runners/interactive/pipeline_analyzer_test.py b/sdks/python/apache_beam/runners/interactive/pipeline_analyzer_test.py index fdc9145aef10..5cf0921ac804 100644 --- a/sdks/python/apache_beam/runners/interactive/pipeline_analyzer_test.py +++ b/sdks/python/apache_beam/runners/interactive/pipeline_analyzer_test.py @@ -219,7 +219,7 @@ def test_read_cache_expansion(self): pipeline_proto = to_stable_runner_api(p) pipeline_info = pipeline_analyzer.PipelineInfo(pipeline_proto.components) - pcoll_id = 'ref_PCollection_PCollection_12' # Output PCollection of Square + pcoll_id = 'ref_PCollection_PCollection_10' # Output PCollection of Square cache_label1 = pipeline_info.cache_label(pcoll_id) analyzer = pipeline_analyzer.PipelineAnalyzer( diff --git a/sdks/python/apache_beam/runners/interactive/pipeline_instrument_test.py b/sdks/python/apache_beam/runners/interactive/pipeline_instrument_test.py index 8ef6f8c65cf7..9f2684e8e83f 100644 --- a/sdks/python/apache_beam/runners/interactive/pipeline_instrument_test.py +++ b/sdks/python/apache_beam/runners/interactive/pipeline_instrument_test.py @@ -69,7 +69,7 @@ def test_cacheable_key_without_version_map(self): _, ctx = p.to_runner_api(use_fake_coders=True, return_context=True) self.assertEqual( instr.cacheable_key(init_pcoll, instr.pcolls_to_pcoll_id(p, ctx)), - str(id(init_pcoll)) + '_ref_PCollection_PCollection_10') + str(id(init_pcoll)) + '_ref_PCollection_PCollection_8') def test_cacheable_key_with_version_map(self): p = beam.Pipeline(interactive_runner.InteractiveRunner()) @@ -94,8 +94,8 @@ def test_cacheable_key_with_version_map(self): instr.cacheable_key( init_pcoll_2, instr.pcolls_to_pcoll_id(p2, ctx), - {'ref_PCollection_PCollection_10': str(id(init_pcoll))}), - str(id(init_pcoll)) + '_ref_PCollection_PCollection_10') + {'ref_PCollection_PCollection_8': str(id(init_pcoll))}), + str(id(init_pcoll)) + '_ref_PCollection_PCollection_8') def test_cache_key(self): p = beam.Pipeline(interactive_runner.InteractiveRunner()) @@ -131,19 +131,19 @@ def test_cacheables(self): pipeline_instrument._cacheable_key(init_pcoll): instr.Cacheable( var='init_pcoll', version=str(id(init_pcoll)), - pcoll_id='ref_PCollection_PCollection_10', + pcoll_id='ref_PCollection_PCollection_8', producer_version=str(id(init_pcoll.producer)), pcoll=init_pcoll), pipeline_instrument._cacheable_key(squares): instr.Cacheable( var='squares', version=str(id(squares)), - pcoll_id='ref_PCollection_PCollection_11', + pcoll_id='ref_PCollection_PCollection_9', producer_version=str(id(squares.producer)), pcoll=squares), pipeline_instrument._cacheable_key(cubes): instr.Cacheable( var='cubes', version=str(id(cubes)), - pcoll_id='ref_PCollection_PCollection_12', + pcoll_id='ref_PCollection_PCollection_10', producer_version=str(id(cubes.producer)), pcoll=cubes) }) diff --git a/sdks/python/apache_beam/runners/portability/fn_api_runner/fn_runner_test.py b/sdks/python/apache_beam/runners/portability/fn_api_runner/fn_runner_test.py index 2a507da8c0c3..5deb4f6be44d 100644 --- a/sdks/python/apache_beam/runners/portability/fn_api_runner/fn_runner_test.py +++ b/sdks/python/apache_beam/runners/portability/fn_api_runner/fn_runner_test.py @@ -1190,7 +1190,7 @@ def has_mi_for_ptransform(mon_infos, ptransform): # postgbk monitoring infos labels = { - monitoring_infos.PCOLLECTION_LABEL: 'ref_PCollection_PCollection_8' + monitoring_infos.PCOLLECTION_LABEL: 'ref_PCollection_PCollection_6' } self.assert_has_counter( postgbk_mis, monitoring_infos.ELEMENT_COUNT_URN, labels, value=1) @@ -1198,7 +1198,7 @@ def has_mi_for_ptransform(mon_infos, ptransform): postgbk_mis, monitoring_infos.SAMPLED_BYTE_SIZE_URN, labels) labels = { - monitoring_infos.PCOLLECTION_LABEL: 'ref_PCollection_PCollection_9' + monitoring_infos.PCOLLECTION_LABEL: 'ref_PCollection_PCollection_7' } self.assert_has_counter( postgbk_mis, monitoring_infos.ELEMENT_COUNT_URN, labels, value=5) diff --git a/sdks/python/apache_beam/transforms/core.py b/sdks/python/apache_beam/transforms/core.py index 92b88f95e244..e1cbf97ebaf4 100644 --- a/sdks/python/apache_beam/transforms/core.py +++ b/sdks/python/apache_beam/transforms/core.py @@ -2226,50 +2226,11 @@ def infer_output_type(self, input_type): key_type, typehints.WindowedValue[value_type]]] # type: ignore[misc] def expand(self, pcoll): - # This code path is only used in the local direct runner. For Dataflow - # runner execution, the GroupByKey transform is expanded on the service. - input_type = pcoll.element_type - if input_type is not None: - # Initialize type-hints used below to enforce type-checking and to pass - # downstream to further PTransforms. - key_type, value_type = trivial_inference.key_value_types(input_type) - # Enforce the input to a GBK has a KV element type. - pcoll.element_type = typehints.KV[key_type, value_type] - typecoders.registry.verify_deterministic( - typecoders.registry.get_coder(key_type), - 'GroupByKey operation "%s"' % self.label) - - reify_output_type = typehints.KV[ - key_type, typehints.WindowedValue[value_type]] # type: ignore[misc] - gbk_input_type = ( - typehints.KV[ - key_type, - typehints.Iterable[typehints.WindowedValue[ # type: ignore[misc] - value_type]]]) - gbk_output_type = typehints.KV[key_type, typehints.Iterable[value_type]] - - # pylint: disable=bad-continuation - return ( - pcoll - | 'ReifyWindows' >> - (ParDo(self.ReifyWindows()).with_output_types(reify_output_type)) - | 'GroupByKey' >> ( - _GroupByKeyOnly().with_input_types( - reify_output_type).with_output_types(gbk_input_type)) - | ( - 'GroupByWindow' >> - _GroupAlsoByWindow(pcoll.windowing).with_input_types( - gbk_input_type).with_output_types(gbk_output_type))) - else: - # The input_type is None, run the default - return ( - pcoll - | 'ReifyWindows' >> ParDo(self.ReifyWindows()) - | 'GroupByKey' >> _GroupByKeyOnly() - | 'GroupByWindow' >> _GroupAlsoByWindow(pcoll.windowing)) + return pvalue.PCollection.from_(pcoll) def infer_output_type(self, input_type): - key_type, value_type = trivial_inference.key_value_types(input_type) + key_type, value_type = (typehints.typehints.coerce_to_kv_type( + input_type).tuple_types) return typehints.KV[key_type, typehints.Iterable[value_type]] def to_runner_api_parameter(self, unused_context): From 7283332a8f158f10fdaed946e42823cdfbdd1f24 Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 12 May 2020 13:52:21 -0700 Subject: [PATCH 004/151] wip: add stubs for create, update write methods --- .../beam/sdk/io/gcp/healthcare/FhirIO.java | 272 +++++++++++++++++- .../gcp/healthcare/HealthcareApiClient.java | 11 +- .../healthcare/HttpHealthcareApiClient.java | 114 +++++++- 3 files changed, 378 insertions(+), 19 deletions(-) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java index 13609a5ed63d..29ec6fafc2b2 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java @@ -46,12 +46,13 @@ import org.apache.beam.sdk.io.fs.MoveOptions.StandardMoveOptions; import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions; import org.apache.beam.sdk.io.fs.ResourceId; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.ConditionalUpdate.ConditionalUpdateFn; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.ExecuteBundles.ExecuteBundlesFn; import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException; import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO; import org.apache.beam.sdk.metrics.Counter; import org.apache.beam.sdk.metrics.Metrics; import org.apache.beam.sdk.options.ValueProvider; -import org.apache.beam.sdk.transforms.Create; import org.apache.beam.sdk.transforms.DoFn; import org.apache.beam.sdk.transforms.GroupIntoBatches; import org.apache.beam.sdk.transforms.PTransform; @@ -221,7 +222,7 @@ public static class Result implements POutput, PInput { PCollectionTuple pct; /** - * Create FhirIO.Read.Result form PCollectionTuple with OUT and DEAD_LETTER tags. + * ConditionalUpdate FhirIO.Read.Result form PCollectionTuple with OUT and DEAD_LETTER tags. * * @param pct the pct * @return the read result @@ -479,7 +480,7 @@ private Result( if (failedFiles == null) { failedFiles = (PCollection>) - pipeline.apply(Create.empty(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); + pipeline.apply(org.apache.beam.sdk.transforms.Create.empty(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } this.failedFiles = failedFiles; } @@ -577,7 +578,7 @@ private static Write.Builder write(String fhirStore) { } /** - * Create Method creates a single FHIR resource. @see * * @param fhirStore the hl 7 v 2 store @@ -664,7 +665,7 @@ public Result expand(PCollection input) { input .apply( "Execute FHIR Bundles", - ParDo.of(new ExecuteBundles.ExecuteBundlesFn(this.getFhirStore()))) + ParDo.of(new ExecuteBundlesFn(this.getFhirStore()))) .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of())); } return Result.in(input.getPipeline(), failedBundles); @@ -675,7 +676,7 @@ public Result expand(PCollection input) { * Writes each bundle of elements to a new-line delimited JSON file on GCS and issues a * fhirStores.import Request for that file. This is intended for batch use only to facilitate * large backfills to empty FHIR stores and should not be used with unbounded PCollections. If - * your use case is streaming checkout using {@link ExecuteBundles} to more safely execute bundles + * your use case is streaming checkout using {@link ConditionalUpdate} to more safely execute bundles * as transactions which is safer practice for a use on a "live" FHIR store. */ public static class Import extends Write { @@ -796,7 +797,7 @@ public Write.Result expand(PCollection input) { // failed / rescheduled ImportFn::importBatch. input .getPipeline() - .apply(Create.of(Collections.singletonList(tempGcsPath))) + .apply(org.apache.beam.sdk.transforms.Create.of(Collections.singletonList(tempGcsPath))) .apply("Wait On File Writing", Wait.on(failedBodies)) .apply("Wait On FHIR Importing", Wait.on(failedFiles)) .apply( @@ -1104,4 +1105,261 @@ public void executeBundles(ProcessContext context) { } } } + + public static class Create extends PTransform, Write.Result> { + private final String fhirStore; + private final String type; + private final boolean ifNoneExist; + + /** + * Instantiates a new Execute bundles. + * @param fhirStore the fhir store + * @param type + * @param ifNoneExist + */ + Create(ValueProvider fhirStore, String type, boolean ifNoneExist) { + this.fhirStore = fhirStore.get(); + this.type = type; + this.ifNoneExist = ifNoneExist; + } + + /** + * Instantiates a new Execute bundles. + * + * @param fhirStore the fhir store + */ + Create(String fhirStore, String type, boolean ifNoneExist) { + this.fhirStore = fhirStore; + this.type = type; + this.ifNoneExist = ifNoneExist; + } + + @Override + public FhirIO.Write.Result expand(PCollection input) { + return Write.Result.in( + input.getPipeline(), + input + .apply(ParDo.of(new CreateFn(fhirStore, type, ifNoneExist))) + .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); + } + + /** The type Write Fhir fn. */ + static class CreateFn extends DoFn> { + + private Counter failedBundles = Metrics.counter(CreateFn.class, "failed-bundles"); + private transient HealthcareApiClient client; + private final ObjectMapper mapper = new ObjectMapper(); + /** The Fhir store. */ + private final String fhirStore; + private final String type; + private final boolean ifNoneExist; + + /** + * Instantiates a new Write Fhir fn. + * @param fhirStore the Fhir store + * @param type + * @param ifNoneExist + */ + CreateFn(String fhirStore, String type, boolean ifNoneExist) { + this.fhirStore = fhirStore; + this.type = type; + this.ifNoneExist = ifNoneExist; + } + + /** + * Initialize healthcare client. + * + * @throws IOException the io exception + */ + @Setup + public void initClient() throws IOException { + this.client = new HttpHealthcareApiClient(); + } + + /** + * Execute Bundles. + * + * @param context the context + */ + @ProcessElement + public void create(ProcessContext context) { + String body = context.element(); + try { + // Validate that data was set to valid JSON. + mapper.readTree(body); + client.fhirCreate(fhirStore, type, body, ifNoneExist); + } catch (IOException | HealthcareHttpException e) { + failedBundles.inc(); + context.output(HealthcareIOError.of(body, e)); + } + } + } + } + + public static class Update extends PTransform, Write.Result> { + private final String fhirStore; + private final String resourceName; + + /** + * Instantiates a new Execute bundles. + * @param fhirStore the fhir store + * @param resourceName + * @param conditional + */ + Update(ValueProvider fhirStore, String resourceName, boolean conditional) { + this.fhirStore = fhirStore.get(); + this.resourceName = resourceName; + } + + /** + * Instantiates a new Execute bundles. + * + * @param fhirStore the fhir store + */ + Update(String fhirStore, String resourceName, boolean conditional) { + this.fhirStore = fhirStore; + this.resourceName = resourceName; + } + + @Override + public FhirIO.Write.Result expand(PCollection input) { + return Write.Result.in( + input.getPipeline(), + input + .apply(ParDo.of(new UpdateFn(fhirStore, resourceName))) + .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); + } + + /** The type Write Fhir fn. */ + static class UpdateFn extends DoFn> { + + private Counter failedBundles = Metrics.counter(UpdateFn.class, "failed-bundles"); + private transient HealthcareApiClient client; + private final ObjectMapper mapper = new ObjectMapper(); + /** The Fhir store. */ + private final String fhirStore; + private final String resourceName; + + /** + * Instantiates a new Write Fhir fn. + * @param fhirStore the Fhir store + * @param resourceName + */ + UpdateFn(String fhirStore, String resourceName) { + this.fhirStore = fhirStore; + this.resourceName = resourceName; + } + + /** + * Initialize healthcare client. + * + * @throws IOException the io exception + */ + @Setup + public void initClient() throws IOException { + this.client = new HttpHealthcareApiClient(); + } + + /** + * ConditionalUpdate resources. + * + * @param context the context + */ + @ProcessElement + public void update(ProcessContext context) { + String body = context.element(); + try { + // Validate that data was set to valid JSON. + mapper.readTree(body); + client.fhirUpdate(fhirStore, resourceName, body); + } catch (IOException | HealthcareHttpException e) { + failedBundles.inc(); + context.output(HealthcareIOError.of(body, e)); + } + } + } + } + + public static class ConditionalUpdate extends PTransform, Write.Result> { + private final String fhirStore; + private final String type; + + /** + * Instantiates a new Execute bundles. + * @param fhirStore the fhir store + * @param type + */ + ConditionalUpdate(ValueProvider fhirStore, String type, boolean conditional) { + this.fhirStore = fhirStore.get(); + this.type = type; + } + + /** + * Instantiates a new Execute bundles. + * + * @param fhirStore the fhir store + */ + ConditionalUpdate(String fhirStore, String type, boolean conditional) { + this.fhirStore = fhirStore; + this.type = type; + } + + @Override + public FhirIO.Write.Result expand(PCollection input) { + return Write.Result.in( + input.getPipeline(), + input + .apply(ParDo.of(new ConditionalUpdateFn(fhirStore, type))) + .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); + } + + /** The type Write Fhir fn. */ + static class ConditionalUpdateFn extends DoFn> { + + private Counter failedBundles = Metrics.counter(ConditionalUpdateFn.class, "failed-bundles"); + private transient HealthcareApiClient client; + private final ObjectMapper mapper = new ObjectMapper(); + /** The Fhir store. */ + private final String fhirStore; + private final String type; + + /** + * Instantiates a new Write Fhir fn. + * @param fhirStore the Fhir store + * @param type + */ + ConditionalUpdateFn(String fhirStore, String type) { + this.fhirStore = fhirStore; + this.type = type; + } + + /** + * Initialize healthcare client. + * + * @throws IOException the io exception + */ + @Setup + public void initClient() throws IOException { + this.client = new HttpHealthcareApiClient(); + } + + /** + * ConditionalUpdate resources. + * + * @param context the context + */ + @ProcessElement + public void conditionalUpdate(ProcessContext context) { + String body = context.element(); + try { + // Validate that data was set to valid JSON. + mapper.readTree(body); + client.fhirConditionalUpdate(fhirStore, type, body); + } catch (IOException | HealthcareHttpException e) { + failedBundles.inc(); + context.output(HealthcareIOError.of(body, e)); + } + } + } + } } diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java index 458760741915..8e35560014f3 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java @@ -80,7 +80,7 @@ ListMessagesResponse makeHL7v2ListRequest( IngestMessageResponse ingestHL7v2Message(String hl7v2Store, Message msg) throws IOException; /** - * Create hl 7 v 2 message message. + * ConditionalUpdate hl 7 v 2 message message. * * @param hl7v2Store the hl 7 v 2 store * @param msg the msg @@ -106,6 +106,15 @@ Operation pollOperation(Operation operation, Long sleepMs) HttpBody executeFhirBundle(String fhirStore, String bundle) throws IOException, HealthcareHttpException; + HttpBody fhirCreate(String fhirStore, String type, String resource, boolean ifNoneExist) + throws IOException, HealthcareHttpException; + + HttpBody fhirConditionalUpdate(String fhirStore, String relativeResourceName, String resource) + throws IOException, HealthcareHttpException; + + HttpBody fhirUpdate(String fhirStore, String type, String resource) + throws IOException, HealthcareHttpException; + /** * Read fhir resource http body. * diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java index 909f18843949..ab3d9e965760 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java @@ -47,6 +47,7 @@ import java.net.URISyntaxException; import java.text.ParseException; import java.util.ArrayList; +import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Map; @@ -54,6 +55,7 @@ import java.util.stream.Collectors; import javax.annotation.Nullable; import org.apache.beam.sdk.extensions.gcp.util.RetryHttpRequestInitializer; +import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.FhirHttpRequest.Method; import org.apache.beam.sdk.util.ReleaseInfo; import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Strings; import org.apache.http.HttpEntity; @@ -85,7 +87,7 @@ public class HttpHealthcareApiClient implements HealthcareApiClient, Serializabl private static final String FHIRSTORE_HEADER_ACCEPT_CHARSET = "utf-8"; private static final Logger LOG = LoggerFactory.getLogger(HttpHealthcareApiClient.class); private transient CloudHealthcare client; - private transient HttpClient httpClient; + public transient HttpClient httpClient; private transient GoogleCredentials credentials; /** @@ -283,7 +285,7 @@ public Operation pollOperation(Operation operation, Long sleepMs) throws InterruptedException, IOException { LOG.debug(String.format("started opertation %s. polling until complete.", operation.getName())); while (operation.getDone() == null || !operation.getDone()) { - // Update the status of the operation with another request. + // ConditionalUpdate the status of the operation with another request. Thread.sleep(sleepMs); // Pause between requests. operation = client.projects().locations().datasets().operations().get(operation.getName()).execute(); @@ -291,19 +293,65 @@ public Operation pollOperation(Operation operation, Long sleepMs) return operation; } - @Override - public HttpBody executeFhirBundle(String fhirStore, String bundle) - throws IOException, HealthcareHttpException { + static class FhirHttpRequest { + private final String fhirStore; + private final String payload; + private Method method; + private String pathSuffix; + private Map headers; + + + enum Method { + POST, + PUT + } + + FhirHttpRequest(String fhirStore, @Nullable String payload) { + this.fhirStore = fhirStore; + this.payload = payload; + this.method = Method.POST; + this.headers = new HashMap<>(); + } + + public static FhirHttpRequest of(String fhirStore, String payload) { + return new FhirHttpRequest(fhirStore, payload); + } + + public FhirHttpRequest setPathSuffix(String pathSuffix){ + this.pathSuffix = pathSuffix; + return this; + } + + public FhirHttpRequest setHeaders(Map headers){ + this.headers = headers; + return this; + } + + public FhirHttpRequest setMethod(Method method){ + this.method = method; + return this; + } + + + + } + + public HttpBody executeFhirHttpRequest(FhirHttpRequest fhirHttpRequest) throws IOException, HealthcareHttpException { if (httpClient == null || client == null) { initClient(); } credentials.refreshIfExpired(); - StringEntity requestEntity = new StringEntity(bundle, ContentType.APPLICATION_JSON); + StringEntity requestEntity = new StringEntity(fhirHttpRequest.payload, ContentType.APPLICATION_JSON); URI uri; try { + String baseFhirUri= client.getRootUrl() + "v1beta1/" + fhirHttpRequest.fhirStore + "/fhir"; + String uriString = baseFhirUri; + if (!Strings.isNullOrEmpty(fhirHttpRequest.pathSuffix)){ + uriString += fhirHttpRequest.pathSuffix; + } uri = - new URIBuilder(client.getRootUrl() + "v1beta1/" + fhirStore + "/fhir") + new URIBuilder(uriString) .setParameter("access_token", credentials.getAccessToken().getTokenValue()) .build(); } catch (URISyntaxException e) { @@ -311,8 +359,17 @@ public HttpBody executeFhirBundle(String fhirStore, String bundle) throw new IllegalArgumentException(e); } - HttpUriRequest request = - RequestBuilder.post() + RequestBuilder requestBuilder; + switch (fhirHttpRequest.method){ + case PUT: + requestBuilder = RequestBuilder.put(); + break; + case POST: + default: + requestBuilder = RequestBuilder.post(); + } + + HttpUriRequest request = requestBuilder .setUri(uri) .setEntity(requestEntity) .addHeader("User-Agent", USER_AGENT) @@ -321,6 +378,11 @@ public HttpBody executeFhirBundle(String fhirStore, String bundle) .addHeader("Accept", FHIRSTORE_HEADER_ACCEPT) .build(); + // Add headers + for (Map.Entry header: fhirHttpRequest.headers.entrySet()){ + request.addHeader(header.getKey(), header.getValue()); + } + HttpResponse response = httpClient.execute(request); HttpEntity responseEntity = response.getEntity(); String content = EntityUtils.toString(responseEntity); @@ -333,6 +395,36 @@ public HttpBody executeFhirBundle(String fhirStore, String bundle) return responseModel; } + @Override + public HttpBody executeFhirBundle(String fhirStore, String bundle) + throws IOException, HealthcareHttpException { + return executeFhirHttpRequest(FhirHttpRequest.of(fhirStore, bundle)); + } + + @Override + public HttpBody fhirCreate(String fhirStore, String type, String resource, boolean ifNoneExist) + throws IOException, HealthcareHttpException { + return executeFhirHttpRequest(FhirHttpRequest.of(fhirStore, resource).setPathSuffix("/" + type)); + } + + @Override + public HttpBody fhirConditionalUpdate(String fhirStore, String type, String resource) + throws IOException, HealthcareHttpException { + return executeFhirHttpRequest( + FhirHttpRequest.of(fhirStore, resource) + .setPathSuffix("/" + type) + .setMethod(Method.PUT)); + } + + @Override + public HttpBody fhirUpdate(String fhirStore, String relativeResourceName, String resource) + throws IOException, HealthcareHttpException { + return executeFhirHttpRequest( + FhirHttpRequest.of(fhirStore, resource) + .setPathSuffix("/" + relativeResourceName) + .setMethod(Method.PUT)); + } + /** * Wraps {@link HttpResponse} in an exception with a statusCode field for use with {@link * HealthcareIOError}. @@ -352,7 +444,7 @@ public static class HealthcareHttpException extends Exception { } /** - * Create Exception of {@link HttpResponse}. + * ConditionalUpdate Exception of {@link HttpResponse}. * * @param response the HTTP response * @return the healthcare http exception @@ -408,7 +500,7 @@ public void initialize(HttpRequest request) throws IOException { private void initClient() throws IOException { credentials = GoogleCredentials.getApplicationDefault(); - // Create a HttpRequestInitializer, which will provide a baseline configuration to all requests. + // ConditionalUpdate a HttpRequestInitializer, which will provide a baseline configuration to all requests. HttpRequestInitializer requestInitializer = new AuthenticatedRetryInitializer( credentials.createScoped( From 2e17e06c1e41df3addaeb065e12fb6d8040f7bf3 Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 12 May 2020 15:35:05 -0700 Subject: [PATCH 005/151] wip --- .../beam/sdk/io/gcp/healthcare/FhirIO.java | 54 +++++++++++-------- .../sdk/io/gcp/healthcare/HL7v2Message.java | 2 + .../gcp/healthcare/HealthcareApiClient.java | 2 +- .../healthcare/HttpHealthcareApiClient.java | 13 ++++- 4 files changed, 45 insertions(+), 26 deletions(-) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java index 29ec6fafc2b2..c546a0726ec2 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java @@ -57,6 +57,7 @@ import org.apache.beam.sdk.transforms.GroupIntoBatches; import org.apache.beam.sdk.transforms.PTransform; import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.transforms.SerializableFunction; import org.apache.beam.sdk.transforms.Wait; import org.apache.beam.sdk.transforms.WithKeys; import org.apache.beam.sdk.transforms.windowing.BoundedWindow; @@ -1109,29 +1110,28 @@ public void executeBundles(ProcessContext context) { public static class Create extends PTransform, Write.Result> { private final String fhirStore; private final String type; - private final boolean ifNoneExist; + private SerializableFunction ifNoneExistFunction; - /** - * Instantiates a new Execute bundles. - * @param fhirStore the fhir store - * @param type - * @param ifNoneExist - */ - Create(ValueProvider fhirStore, String type, boolean ifNoneExist) { + Create(ValueProvider fhirStore, String type) { this.fhirStore = fhirStore.get(); this.type = type; - this.ifNoneExist = ifNoneExist; } - /** - * Instantiates a new Execute bundles. - * - * @param fhirStore the fhir store - */ - Create(String fhirStore, String type, boolean ifNoneExist) { + Create(String fhirStore, String type) { this.fhirStore = fhirStore; this.type = type; - this.ifNoneExist = ifNoneExist; + } + + /** This should be function that reads an resource string and extracts an + * If-None-Exists query for conditional create. + * Typically this will just be extracting an ID. + * + * https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/create + * */ + public Create withIfNotExistFunction( + SerializableFunction ifNoneExistFunction){ + this.ifNoneExistFunction = ifNoneExistFunction; + return this; } @Override @@ -1139,7 +1139,7 @@ public FhirIO.Write.Result expand(PCollection input) { return Write.Result.in( input.getPipeline(), input - .apply(ParDo.of(new CreateFn(fhirStore, type, ifNoneExist))) + .apply(ParDo.of(new CreateFn(fhirStore, type, ifNoneExistFunction))) .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } @@ -1152,20 +1152,22 @@ static class CreateFn extends DoFn> { /** The Fhir store. */ private final String fhirStore; private final String type; - private final boolean ifNoneExist; + private SerializableFunction ifNoneExistFunction; /** * Instantiates a new Write Fhir fn. - * @param fhirStore the Fhir store + * @param fhirStore the Fhir store * @param type - * @param ifNoneExist + * @param ifNoneExistFunction */ - CreateFn(String fhirStore, String type, boolean ifNoneExist) { + CreateFn(String fhirStore, String type, + SerializableFunction ifNoneExistFunction) { this.fhirStore = fhirStore; this.type = type; - this.ifNoneExist = ifNoneExist; + this.ifNoneExistFunction = ifNoneExistFunction; } + /** * Initialize healthcare client. * @@ -1187,7 +1189,12 @@ public void create(ProcessContext context) { try { // Validate that data was set to valid JSON. mapper.readTree(body); - client.fhirCreate(fhirStore, type, body, ifNoneExist); + if (ifNoneExistFunction != null){ + String ifNoneExistQuery = ifNoneExistFunction.apply(body); + client.fhirCreate(fhirStore, type, body, ifNoneExistQuery); + } else{ + client.fhirCreate(fhirStore, type, body, null); + } } catch (IOException | HealthcareHttpException e) { failedBundles.inc(); context.output(HealthcareIOError.of(body, e)); @@ -1333,6 +1340,7 @@ static class ConditionalUpdateFn extends DoFn> this.type = type; } + /** * Initialize healthcare client. * diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2Message.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2Message.java index 8e846db5b57d..5cf3d2cdbfea 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2Message.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2Message.java @@ -22,8 +22,10 @@ import java.io.IOException; import java.util.Map; import javax.annotation.Nullable; +import org.apache.beam.sdk.coders.DefaultCoder; /** The type HL7v2 message to wrap the {@link Message} model. */ +@DefaultCoder(HL7v2MessageCoder.class) public class HL7v2Message { private static final String schematizedDataKey = "schematizedData"; private static final String schematizedDataPrefix = "{data="; diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java index 8e35560014f3..efa594112ee4 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java @@ -106,7 +106,7 @@ Operation pollOperation(Operation operation, Long sleepMs) HttpBody executeFhirBundle(String fhirStore, String bundle) throws IOException, HealthcareHttpException; - HttpBody fhirCreate(String fhirStore, String type, String resource, boolean ifNoneExist) + HttpBody fhirCreate(String fhirStore, String type, String resource, @Nullable String ifNoneExist) throws IOException, HealthcareHttpException; HttpBody fhirConditionalUpdate(String fhirStore, String relativeResourceName, String resource) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java index ab3d9e965760..a8582dd2971e 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java @@ -402,9 +402,18 @@ public HttpBody executeFhirBundle(String fhirStore, String bundle) } @Override - public HttpBody fhirCreate(String fhirStore, String type, String resource, boolean ifNoneExist) + public HttpBody fhirCreate(String fhirStore, String type, String resource, + @Nullable String ifNoneExist) throws IOException, HealthcareHttpException { - return executeFhirHttpRequest(FhirHttpRequest.of(fhirStore, resource).setPathSuffix("/" + type)); + Map headers = new HashMap<>(); + if (Strings.isNullOrEmpty(ifNoneExist)) { + headers.put("If-None-Exist", ifNoneExist); + } + return executeFhirHttpRequest( + FhirHttpRequest.of(fhirStore, resource) + .setPathSuffix("/" + type) + .setHeaders(headers) + ); } @Override From 5510822b0b3928c44af98853c12b870a32ca08d6 Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Wed, 13 May 2020 10:59:48 -0700 Subject: [PATCH 006/151] remove unused method from FhirIOTest --- .../sdk/io/gcp/healthcare/FhirIOTest.java | 21 ------------------- 1 file changed, 21 deletions(-) diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTest.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTest.java index 976c55fcb76c..f06e27cd3017 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTest.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTest.java @@ -88,25 +88,4 @@ public void test_FhirIO_failedWrites() { private static final long NUM_ELEMENTS = 11; private static final long BATCH_SIZE = 5; - private static ArrayList> createTestData() { - String[] scientists = { - "Einstein", - "Darwin", - "Copernicus", - "Pasteur", - "Curie", - "Faraday", - "Newton", - "Bohr", - "Galilei", - "Maxwell" - }; - ArrayList> data = new ArrayList<>(); - for (int i = 0; i < NUM_ELEMENTS; i++) { - int index = i % scientists.length; - KV element = KV.of("key", scientists[index]); - data.add(element); - } - return data; - } } From 986de56ec3178ea85fc6ac5c1bab56ec920e60a1 Mon Sep 17 00:00:00 2001 From: Sam Rohde Date: Wed, 13 May 2020 14:14:36 -0700 Subject: [PATCH 007/151] Move ReifyWindows etc to DirectRunner, don't subclass from GBK Change-Id: I9a54cbaadf3968dbb48167cc669088212680d336 --- .../runners/dataflow/dataflow_runner_test.py | 4 + .../runners/direct/direct_runner.py | 194 +++++++++++------- .../runners/direct/transform_evaluator.py | 5 +- sdks/python/apache_beam/transforms/core.py | 68 ------ 4 files changed, 132 insertions(+), 139 deletions(-) diff --git a/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py b/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py index 0791b49a983d..b09f38d3427d 100644 --- a/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py +++ b/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py @@ -396,6 +396,10 @@ def test_gbk_then_flatten_input_visitor(self): flat = (none_str_pc, none_int_pc) | beam.Flatten() _ = flat | beam.GroupByKey() + # This may change if type inference changes, but we assert it here + # to make sure the check below is not vacuous. + self.assertNotIsInstance(flat.element_type, typehints.TupleConstraint) + p.visit(DataflowRunner.group_by_key_input_visitor()) p.visit(DataflowRunner.flatten_input_visitor()) diff --git a/sdks/python/apache_beam/runners/direct/direct_runner.py b/sdks/python/apache_beam/runners/direct/direct_runner.py index fb80f19b5d3b..8fa6c902900d 100644 --- a/sdks/python/apache_beam/runners/direct/direct_runner.py +++ b/sdks/python/apache_beam/runners/direct/direct_runner.py @@ -50,10 +50,10 @@ from apache_beam.transforms.core import CombineValuesDoFn from apache_beam.transforms.core import DoFn from apache_beam.transforms.core import ParDo -from apache_beam.transforms.core import _GroupAlsoByWindow -from apache_beam.transforms.core import _GroupAlsoByWindowDoFn -from apache_beam.transforms.core import _GroupByKeyOnly from apache_beam.transforms.ptransform import PTransform +from apache_beam.transforms.window import WindowedValue +from apache_beam.typehints import trivial_inference +from apache_beam.typehints.decorators import TypeCheckError # Note that the BundleBasedDirectRunner and SwitchingDirectRunner names are # experimental and have no backwards compatibility guarantees. @@ -135,6 +135,57 @@ def visit_transform(self, applied_ptransform): V = typing.TypeVar('V') +@typehints.with_input_types(typing.Tuple[K, V]) +@typehints.with_output_types(typing.Tuple[K, typing.Iterable[V]]) +class _GroupByKeyOnly(PTransform): + """A group by key transform, ignoring windows.""" + def infer_output_type(self, input_type): + key_type, value_type = trivial_inference.key_value_types(input_type) + return typehints.KV[key_type, typehints.Iterable[value_type]] + + def expand(self, pcoll): + self._check_pcollection(pcoll) + return PCollection.from_(pcoll) + + +@typehints.with_input_types(typing.Tuple[K, typing.Iterable[V]]) +@typehints.with_output_types(typing.Tuple[K, typing.Iterable[V]]) +class _GroupAlsoByWindow(ParDo): + """The GroupAlsoByWindow transform.""" + def __init__(self, windowing): + super(_GroupAlsoByWindow, self).__init__(_GroupAlsoByWindowDoFn(windowing)) + self.windowing = windowing + + def expand(self, pcoll): + self._check_pcollection(pcoll) + return PCollection.from_(pcoll) + + +class _GroupAlsoByWindowDoFn(DoFn): + # TODO(robertwb): Support combiner lifting. + + def __init__(self, windowing): + super(_GroupAlsoByWindowDoFn, self).__init__() + self.windowing = windowing + + def infer_output_type(self, input_type): + key_type, windowed_value_iter_type = trivial_inference.key_value_types( + input_type) + value_type = windowed_value_iter_type.inner_type.inner_type + return typehints.Iterable[typehints.KV[key_type, + typehints.Iterable[value_type]]] + + def start_bundle(self): + # pylint: disable=wrong-import-order, wrong-import-position + from apache_beam.transforms.trigger import create_trigger_driver + # pylint: enable=wrong-import-order, wrong-import-position + self.driver = create_trigger_driver(self.windowing, True) + + def process(self, element): + k, vs = element + return self.driver.process_entire_key(k, vs) + + @typehints.with_input_types(typing.Tuple[K, V]) @typehints.with_output_types(typing.Tuple[K, typing.Iterable[V]]) class _StreamingGroupByKeyOnly(_GroupByKeyOnly): @@ -172,6 +223,75 @@ def from_runner_api_parameter(unused_ptransform, payload, context): context.windowing_strategies.get_by_id(payload.value)) +@typehints.with_input_types(typing.Tuple[K, typing.Iterable[V]]) +@typehints.with_output_types(typing.Tuple[K, typing.Iterable[V]]) +class _GroupByKey(PTransform): + """The DirectRunner GroupByKey implementation.""" + class ReifyWindows(DoFn): + def process( + self, element, window=DoFn.WindowParam, timestamp=DoFn.TimestampParam): + try: + k, v = element + except TypeError: + raise TypeCheckError( + 'Input to GroupByKey must be a PCollection with ' + 'elements compatible with KV[A, B]') + + return [(k, WindowedValue(v, timestamp, [window]))] + + def infer_output_type(self, input_type): + key_type, value_type = trivial_inference.key_value_types(input_type) + return typehints.Iterable[typehints.KV[ + key_type, typehints.WindowedValue[value_type]]] # type: ignore[misc] + + def expand(self, pcoll): + # Imported here to avoid circular dependencies. + # pylint: disable=wrong-import-order, wrong-import-position + from apache_beam.coders import typecoders + + input_type = pcoll.element_type + if input_type is not None: + # Initialize type-hints used below to enforce type-checking and to + # pass downstream to further PTransforms. + key_type, value_type = trivial_inference.key_value_types(input_type) + # Enforce the input to a GBK has a KV element type. + pcoll.element_type = typehints.typehints.coerce_to_kv_type( + pcoll.element_type) + typecoders.registry.verify_deterministic( + typecoders.registry.get_coder(key_type), + 'GroupByKey operation "%s"' % self.label) + + reify_output_type = typehints.KV[ + key_type, typehints.WindowedValue[value_type]] # type: ignore[misc] + gbk_input_type = ( + typehints. + KV[key_type, + typehints.Iterable[ + typehints.WindowedValue[ # type: ignore[misc] + value_type]]]) + gbk_output_type = typehints.KV[key_type, typehints.Iterable[value_type]] + + # pylint: disable=bad-continuation + return ( + pcoll + | 'ReifyWindows' >> + (ParDo(self.ReifyWindows()).with_output_types(reify_output_type)) + | 'GroupByKey' >> ( + _GroupByKeyOnly().with_input_types( + reify_output_type).with_output_types(gbk_input_type)) + | ( + 'GroupByWindow' >> + _GroupAlsoByWindow(pcoll.windowing).with_input_types( + gbk_input_type).with_output_types(gbk_output_type))) + else: + # The input_type is None, run the default + return ( + pcoll + | 'ReifyWindows' >> ParDo(self.ReifyWindows()) + | 'GroupByKey' >> _GroupByKeyOnly() + | 'GroupByWindow' >> _GroupAlsoByWindow(pcoll.windowing)) + + def _get_transform_overrides(pipeline_options): # A list of PTransformOverride objects to be applied before running a pipeline # using DirectRunner. @@ -243,74 +363,10 @@ def matches(self, applied_ptransform): # Imported here to avoid circular dependencies. # pylint: disable=wrong-import-order, wrong-import-position from apache_beam.transforms.core import GroupByKey - if (isinstance(applied_ptransform.transform, GroupByKey) and - not getattr(applied_ptransform.transform, 'override', False)): - self.input_type = applied_ptransform.inputs[0].element_type - return True - return False + return isinstance(applied_ptransform.transform, GroupByKey) def get_replacement_transform(self, ptransform): - # Imported here to avoid circular dependencies. - # pylint: disable=wrong-import-order, wrong-import-position - from apache_beam.transforms.core import GroupByKey - - # Subclass from GroupByKey to inherit all the proper methods. - class GroupByKey(GroupByKey): - override = True - - def expand(self, pcoll): - # Imported here to avoid circular dependencies. - # pylint: disable=wrong-import-order, wrong-import-position - from apache_beam.coders import typecoders - from apache_beam.typehints import trivial_inference - - input_type = pcoll.element_type - if input_type is not None: - # Initialize type-hints used below to enforce type-checking and to - # pass downstream to further PTransforms. - key_type, value_type = trivial_inference.key_value_types(input_type) - # Enforce the input to a GBK has a KV element type. - pcoll.element_type = typehints.typehints.coerce_to_kv_type( - pcoll.element_type) - typecoders.registry.verify_deterministic( - typecoders.registry.get_coder(key_type), - 'GroupByKey operation "%s"' % self.label) - - reify_output_type = typehints.KV[ - key_type, typehints.WindowedValue[value_type]] # type: ignore[misc] - gbk_input_type = ( - typehints. - KV[key_type, - typehints.Iterable[ - typehints.WindowedValue[ # type: ignore[misc] - value_type]]]) - gbk_output_type = typehints.KV[key_type, - typehints.Iterable[value_type]] - - # pylint: disable=bad-continuation - return ( - pcoll - | 'ReifyWindows' >> ( - ParDo(self.ReifyWindows()).with_output_types( - reify_output_type)) - | 'GroupByKey' >> ( - _GroupByKeyOnly().with_input_types( - reify_output_type).with_output_types(gbk_input_type)) - | ( - 'GroupByWindow' >> - _GroupAlsoByWindow(pcoll.windowing).with_input_types( - gbk_input_type).with_output_types(gbk_output_type))) - else: - # The input_type is None, run the default - return ( - pcoll - | 'ReifyWindows' >> ParDo(self.ReifyWindows()) - | 'GroupByKey' >> _GroupByKeyOnly() - | 'GroupByWindow' >> _GroupAlsoByWindow(pcoll.windowing)) - - # Infer the correct type. - return GroupByKey().with_output_types( - ptransform.infer_output_type(self.input_type)) + return _GroupByKey() overrides = [ # This needs to be the first and the last override. Other overrides depend diff --git a/sdks/python/apache_beam/runners/direct/transform_evaluator.py b/sdks/python/apache_beam/runners/direct/transform_evaluator.py index bc6f397968ba..6421b3935e6c 100644 --- a/sdks/python/apache_beam/runners/direct/transform_evaluator.py +++ b/sdks/python/apache_beam/runners/direct/transform_evaluator.py @@ -45,6 +45,7 @@ from apache_beam.runners.common import DoFnState from apache_beam.runners.dataflow.native_io.iobase import _NativeWrite # pylint: disable=protected-access from apache_beam.runners.direct.direct_runner import _DirectReadFromPubSub +from apache_beam.runners.direct.direct_runner import _GroupByKeyOnly from apache_beam.runners.direct.direct_runner import _StreamingGroupAlsoByWindow from apache_beam.runners.direct.direct_runner import _StreamingGroupByKeyOnly from apache_beam.runners.direct.direct_userstate import DirectUserStateContext @@ -106,7 +107,7 @@ def __init__(self, evaluation_context): core.Flatten: _FlattenEvaluator, core.Impulse: _ImpulseEvaluator, core.ParDo: _ParDoEvaluator, - core._GroupByKeyOnly: _GroupByKeyOnlyEvaluator, + _GroupByKeyOnly: _GroupByKeyOnlyEvaluator, _StreamingGroupByKeyOnly: _StreamingGroupByKeyOnlyEvaluator, _StreamingGroupAlsoByWindow: _StreamingGroupAlsoByWindowEvaluator, _NativeWrite: _NativeWriteEvaluator, @@ -176,7 +177,7 @@ def should_execute_serially(self, applied_ptransform): True if executor should execute applied_ptransform serially. """ if isinstance(applied_ptransform.transform, - (core._GroupByKeyOnly, + (_GroupByKeyOnly, _StreamingGroupByKeyOnly, _StreamingGroupAlsoByWindow, _NativeWrite)): diff --git a/sdks/python/apache_beam/transforms/core.py b/sdks/python/apache_beam/transforms/core.py index e1cbf97ebaf4..665d7ec4ebea 100644 --- a/sdks/python/apache_beam/transforms/core.py +++ b/sdks/python/apache_beam/transforms/core.py @@ -2208,23 +2208,6 @@ class GroupByKey(PTransform): The implementation here is used only when run on the local direct runner. """ - class ReifyWindows(DoFn): - def process( - self, element, window=DoFn.WindowParam, timestamp=DoFn.TimestampParam): - try: - k, v = element - except TypeError: - raise TypeCheckError( - 'Input to GroupByKey must be a PCollection with ' - 'elements compatible with KV[A, B]') - - return [(k, WindowedValue(v, timestamp, [window]))] - - def infer_output_type(self, input_type): - key_type, value_type = trivial_inference.key_value_types(input_type) - return typehints.Iterable[typehints.KV[ - key_type, typehints.WindowedValue[value_type]]] # type: ignore[misc] - def expand(self, pcoll): return pvalue.PCollection.from_(pcoll) @@ -2247,57 +2230,6 @@ def runner_api_requires_keyed_input(self): return True -@typehints.with_input_types(typing.Tuple[K, V]) -@typehints.with_output_types(typing.Tuple[K, typing.Iterable[V]]) -class _GroupByKeyOnly(PTransform): - """A group by key transform, ignoring windows.""" - def infer_output_type(self, input_type): - key_type, value_type = trivial_inference.key_value_types(input_type) - return typehints.KV[key_type, typehints.Iterable[value_type]] - - def expand(self, pcoll): - self._check_pcollection(pcoll) - return pvalue.PCollection.from_(pcoll) - - -@typehints.with_input_types(typing.Tuple[K, typing.Iterable[V]]) -@typehints.with_output_types(typing.Tuple[K, typing.Iterable[V]]) -class _GroupAlsoByWindow(ParDo): - """The GroupAlsoByWindow transform.""" - def __init__(self, windowing): - super(_GroupAlsoByWindow, self).__init__(_GroupAlsoByWindowDoFn(windowing)) - self.windowing = windowing - - def expand(self, pcoll): - self._check_pcollection(pcoll) - return pvalue.PCollection.from_(pcoll) - - -class _GroupAlsoByWindowDoFn(DoFn): - # TODO(robertwb): Support combiner lifting. - - def __init__(self, windowing): - super(_GroupAlsoByWindowDoFn, self).__init__() - self.windowing = windowing - - def infer_output_type(self, input_type): - key_type, windowed_value_iter_type = trivial_inference.key_value_types( - input_type) - value_type = windowed_value_iter_type.inner_type.inner_type - return typehints.Iterable[typehints.KV[key_type, - typehints.Iterable[value_type]]] - - def start_bundle(self): - # pylint: disable=wrong-import-order, wrong-import-position - from apache_beam.transforms.trigger import create_trigger_driver - # pylint: enable=wrong-import-order, wrong-import-position - self.driver = create_trigger_driver(self.windowing, True) - - def process(self, element): - k, vs = element - return self.driver.process_entire_key(k, vs) - - class Partition(PTransformWithSideInputs): """Split a PCollection into several partitions. From 04f256a2c455a5dc3f319c1d0ba9304530774a2b Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Wed, 13 May 2020 14:22:47 -0700 Subject: [PATCH 008/151] draft conditional create and update transforms --- .../beam/sdk/io/gcp/healthcare/FhirIO.java | 401 ++++++++++++------ .../gcp/healthcare/HealthcareApiClient.java | 4 +- .../healthcare/HttpHealthcareApiClient.java | 42 +- .../sdk/io/gcp/healthcare/FhirIOWriteIT.java | 2 + 4 files changed, 306 insertions(+), 143 deletions(-) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java index 38c257c224b4..3ad15ee78515 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java @@ -17,6 +17,7 @@ */ package org.apache.beam.sdk.io.gcp.healthcare; +import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkArgument; import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkState; import com.fasterxml.jackson.databind.ObjectMapper; @@ -84,49 +85,43 @@ * *

Reading

* - *

FHIR resources can be read with {@link FhirIO.Read}, which supports use cases where you have a - * ${@link PCollection} of message IDS. This is appropriate for reading the Fhir notifications from - * a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases where you have a manually - * prepared list of messages that you need to process (e.g. in a text file read with {@link - * org.apache.beam.sdk.io.TextIO}*) . + *

FHIR resources can be read with {@link FhirIO.Read}, which supports use cases where you have + * a ${@link PCollection} of message IDS. This is appropriate for reading the Fhir notifications + * from a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases where you have a + * manually prepared list of messages that you need to process (e.g. in a text file read with {@link + * org.apache.beam.sdk.io.TextIO}**) . * - *

Fetch Resource contents from Fhir Store based on the {@link PCollection} of message ID strings - * {@link FhirIO.Read.Result} where one can call {@link Read.Result#getResources()} to retrieve a - * {@link PCollection} containing the successfully fetched {@link String}s and/or {@link - * FhirIO.Read.Result#getFailedReads()}* to retrieve a {@link PCollection} of {@link - * HealthcareIOError}* containing the resource ID that could not be fetched and the exception as a + *

Fetch Resource contents from Fhir Store based on the {@link PCollection} of message ID + * strings {@link FhirIO.Read.Result} where one can call {@link Read.Result#getResources()} to + * retrieve a {@link PCollection} containing the successfully fetched {@link String}s and/or {@link + * FhirIO.Read.Result#getFailedReads()}** to retrieve a {@link PCollection} of {@link + * HealthcareIOError}** containing the resource ID that could not be fetched and the exception as a * {@link HealthcareIOError}, this can be used to write to the dead letter storage system of your * choosing. This error handling is mainly to transparently surface errors where the upstream {@link - * PCollection}* contains IDs that are not valid or are not reachable due to permissions issues. + * PCollection}** contains IDs that are not valid or are not reachable due to permissions issues. * *

Writing

* *

Write Resources can be written to FHIR with two different methods: Import or Execute Bundle. * - *

Execute Bundle This is best for use cases where you are writing to a non-empty FHIR store with - * other clients or otherwise need referential integrity (e.g. A Streaming HL7v2 to FHIR ETL + *

Execute Bundle This is best for use cases where you are writing to a non-empty FHIR store + * with other clients or otherwise need referential integrity (e.g. A Streaming HL7v2 to FHIR ETL * pipeline). * - * @see https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/executeBundle> - *

Import This is best for use cases where you are populating an empty FHIR store with no - * other clients. It is faster than the execute bundles method but does not respect referential - * integrity and the resources are not written transactionally (e.g. a historicaly backfill on a - * new FHIR store) This requires each resource to contain a client provided ID. It is important - * that when using import you give the appropriate permissions to the Google Cloud Healthcare - * Service Agent - * @see https://cloud.google.com/healthcare/docs/how-tos/permissions-healthcare-api-gcp-products#fhir_store_cloud_storage_permissions> - * @see https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores/import> - * A {@link PCollection} of {@link String} can be ingested into an Fhir store using {@link - * FhirIO.Write#fhirStoresImport(String, String, String, FhirIO.Import.ContentStructure)} This - * will return a {@link FhirIO.Write.Result} on which you can call {@link - * FhirIO.Write.Result#getFailedBodies()} to retrieve a {@link PCollection} of {@link - * HealthcareIOError} containing the {@link String} that failed to be ingested and the - * exception. - *

Example - * 

{@code
+ * @see https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/executeBundle>
+ * 
Import This is best for use cases where you are populating an empty FHIR store with no
+ * other clients. It is faster than the execute bundles method but does not respect referential
+ * integrity and the resources are not written transactionally (e.g. a historicaly backfill on a new
+ * FHIR store) This requires each resource to contain a client provided ID. It is important that
+ * when using import you give the appropriate permissions to the Google Cloud Healthcare Service
+ * Agent
+ * @see https://cloud.google.com/healthcare/docs/how-tos/permissions-healthcare-api-gcp-products#fhir_store_cloud_storage_permissions>
+ * @see https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores/import>
+ * A {@link PCollection} of {@link String} can be ingested into an Fhir store using {@link
+ * FhirIO.Write#fhirStoresImport(String, String, String, FhirIO.Import.ContentStructure)} This will
+ * return a {@link FhirIO.Write.Result} on which you can call {@link
+ * FhirIO.Write.Result#getFailedBodies()} to retrieve a {@link PCollection} of {@link
+ * HealthcareIOError} containing the {@link String} that failed to be ingested and the     exception.     
Example     
{@code
  * Pipeline pipeline = ...
  *
  * // Tail the FHIR store by retrieving resources based on Pub/Sub notifications.
@@ -161,8 +156,7 @@
  * // Alternatively you could use import for high throughput to a new store.
  * FhirIO.Write.Result writeResult =
  *     output.apply("Import FHIR Resources", FhirIO.executeBundles(options.getNewFhirStore()));
- * }***
- * 

+ * }***
*/ public class FhirIO { @@ -213,19 +207,27 @@ public static Import importResources( return new Import(fhirStore, tempDir, deadLetterDir, contentStructure); } - /** The type Read. */ + /** + * The type Read. + */ public static class Read extends PTransform, FhirIO.Read.Result> { private static final Logger LOG = LoggerFactory.getLogger(Read.class); - /** Instantiates a new Read. */ + /** + * Instantiates a new Read. + */ public Read() {} - /** The type Result. */ + /** + * The type Result. + */ public static class Result implements POutput, PInput { private PCollection resources; private PCollection> failedReads; - /** The Pct. */ + /** + * The Pct. + */ PCollectionTuple pct; /** @@ -287,9 +289,13 @@ public void finishSpecifyingOutput( String transformName, PInput input, PTransform transform) {} } - /** The tag for the main output of Fhir Messages. */ + /** + * The tag for the main output of Fhir Messages. + */ public static final TupleTag OUT = new TupleTag() {}; - /** The tag for the deadletter output of Fhir Messages. */ + /** + * The tag for the deadletter output of Fhir Messages. + */ public static final TupleTag> DEAD_LETTER = new TupleTag>() {}; @@ -304,7 +310,7 @@ public FhirIO.Read.Result expand(PCollection input) { *

This DoFn consumes a {@link PCollection} of notifications {@link String}s from the FHIR * store, and fetches the actual {@link String} object based on the id in the notification and * will output a {@link PCollectionTuple} which contains the output and dead-letter {@link - * PCollection}*. + * PCollection}**. * *

The {@link PCollectionTuple} output will contain the following {@link PCollection}: * @@ -312,14 +318,16 @@ public FhirIO.Read.Result expand(PCollection input) { *

  • {@link FhirIO.Read#OUT} - Contains all {@link PCollection} records successfully read * from the Fhir store. *
  • {@link FhirIO.Read#DEAD_LETTER} - Contains all {@link PCollection} of {@link - * HealthcareIOError}* of message IDs which failed to be fetched from the Fhir store, with + * HealthcareIOError}** of message IDs which failed to be fetched from the Fhir store, with * error message and stacktrace. * */ static class FetchResourceJsonString extends PTransform, FhirIO.Read.Result> { - /** Instantiates a new Fetch Fhir message DoFn. */ + /** + * Instantiates a new Fetch Fhir message DoFn. + */ public FetchResourceJsonString() {} @Override @@ -330,7 +338,9 @@ public FhirIO.Read.Result expand(PCollection resourceIds) { .withOutputTags(FhirIO.Read.OUT, TupleTagList.of(FhirIO.Read.DEAD_LETTER)))); } - /** DoFn for fetching messages from the Fhir store with error handling. */ + /** + * DoFn for fetching messages from the Fhir store with error handling. + */ static class ReadResourceFn extends DoFn { private Counter failedMessageGets = @@ -341,7 +351,9 @@ static class ReadResourceFn extends DoFn { private HealthcareApiClient client; private ObjectMapper mapper; - /** Instantiates a new Hl 7 v 2 message get fn. */ + /** + * Instantiates a new Hl 7 v 2 message get fn. + */ ReadResourceFn() {} /** @@ -392,20 +404,30 @@ private String fetchResource(HealthcareApiClient client, String resourceId) } } - /** The type Write. */ + /** + * The type Write. + */ @AutoValue public abstract static class Write extends PTransform, Write.Result> { - /** The tag for the failed writes to FHIR store`. */ + /** + * The tag for the failed writes to FHIR store`. + */ public static final TupleTag> FAILED_BODY = new TupleTag>() {}; - /** The tag for the files that failed to FHIR store`. */ + /** + * The tag for the files that failed to FHIR store`. + */ public static final TupleTag> FAILED_FILES = new TupleTag>() {}; - /** The tag for temp files for import to FHIR store`. */ + /** + * The tag for temp files for import to FHIR store`. + */ public static final TupleTag TEMP_FILES = new TupleTag() {}; - /** The enum Write method. */ + /** + * The enum Write method. + */ public enum WriteMethod { /** * Execute Bundle Method executes a batch of requests as a single transaction @see . + * FHIR stores. . */ IMPORT } - /** The type Result. */ + /** + * The type Result. + */ public static class Result implements POutput { private final Pipeline pipeline; private final PCollection> failedBodies; @@ -430,6 +453,7 @@ public static class Result implements POutput { * Creates a {@link FhirIO.Write.Result} in the given {@link Pipeline}. @param pipeline the * pipeline * + * @param pipeline the pipeline * @param failedBodies the failed inserts * @return the result */ @@ -437,6 +461,14 @@ static Result in(Pipeline pipeline, PCollection> faile return new Result(pipeline, failedBodies, null); } + /** + * In result. + * + * @param pipeline the pipeline + * @param failedBodies the failed bodies + * @param failedFiles the failed files + * @return the result + */ static Result in( Pipeline pipeline, PCollection> failedBodies, @@ -526,7 +558,9 @@ private Result( */ abstract Optional getImportGcsDeadLetterPath(); - /** The type Builder. */ + /** + * The type Builder. + */ @AutoValue.Builder abstract static class Builder { @@ -606,6 +640,14 @@ public static Write fhirStoresImport( .build(); } + /** + * Fhir stores import write. + * + * @param fhirStore the fhir store + * @param gcsDeadLetterPath the gcs dead letter path + * @param contentStructure the content structure + * @return the write + */ public static Write fhirStoresImport( String fhirStore, String gcsDeadLetterPath, @@ -618,6 +660,15 @@ public static Write fhirStoresImport( .build(); } + /** + * Fhir stores import write. + * + * @param fhirStore the fhir store + * @param gcsTempPath the gcs temp path + * @param gcsDeadLetterPath the gcs dead letter path + * @param contentStructure the content structure + * @return the write + */ public static Write fhirStoresImport( ValueProvider fhirStore, ValueProvider gcsTempPath, @@ -694,8 +745,8 @@ public Result expand(PCollection input) { * Writes each bundle of elements to a new-line delimited JSON file on GCS and issues a * fhirStores.import Request for that file. This is intended for batch use only to facilitate * large backfills to empty FHIR stores and should not be used with unbounded PCollections. If - * your use case is streaming checkout using {@link ConditionalUpdate} to more safely execute bundles - * as transactions which is safer practice for a use on a "live" FHIR store. + * your use case is streaming checkout using {@link ConditionalUpdate} to more safely execute + * bundles as transactions which is safer practice for a use on a "live" FHIR store. */ public static class Import extends Write { @@ -729,6 +780,13 @@ public static class Import extends Write { } } + /** + * Instantiates a new Import. + * + * @param fhirStore the fhir store + * @param deadLetterGcsPath the dead letter gcs path + * @param contentStructure the content structure + */ Import( ValueProvider fhirStore, ValueProvider deadLetterGcsPath, @@ -741,6 +799,7 @@ public static class Import extends Write { this.contentStructure = contentStructure; } } + /** * Instantiates a new Import. * @@ -863,7 +922,9 @@ public void delete(@Element Metadata path) { return Write.Result.in(input.getPipeline(), failedBodies, failedFiles); } - /** The Write bundles to new line delimited json files. */ + /** + * The Write bundles to new line delimited json files. + */ static class WriteBundlesToFilesFn extends DoFn { private final String fhirStore; @@ -921,6 +982,7 @@ public void initFile() throws IOException { * Add to batch. * * @param context the context + * @param window the window * @throws IOException the io exception */ @ProcessElement @@ -958,7 +1020,9 @@ public void closeFile(FinishBundleContext context) throws IOException { } } - /** Import batches of new line delimited json files to FHIR Store. */ + /** + * Import batches of new line delimited json files to FHIR Store. + */ static class ImportFn extends DoFn>, HealthcareIOError> { @@ -970,6 +1034,14 @@ static class ImportFn private HealthcareApiClient client; private final String fhirStore; + /** + * Instantiates a new Import fn. + * + * @param fhirStore the fhir store + * @param tempGcsPath the temp gcs path + * @param deadLetterGcsPath the dead letter gcs path + * @param contentStructure the content structure + */ ImportFn( String fhirStore, String tempGcsPath, @@ -985,6 +1057,11 @@ static class ImportFn } } + /** + * Init. + * + * @throws IOException the io exception + */ @Setup public void init() throws IOException { tempDir = @@ -998,6 +1075,10 @@ public void init() throws IOException { /** * Move files to a temporary subdir (to provide common prefix) to execute import with single * GCS URI. + * + * @param element the element + * @param output the output + * @throws IOException the io exception */ @ProcessElement public void importBatch( @@ -1043,9 +1124,13 @@ public void importBatch( } } - /** The enum Content structure. */ + /** + * The enum Content structure. + */ public enum ContentStructure { - /** If the content structure is not specified, the default value BUNDLE will be used. */ + /** + * If the content structure is not specified, the default value BUNDLE will be used. + */ CONTENT_STRUCTURE_UNSPECIFIED, /** * The source file contains one or more lines of newline-delimited JSON (ndjson). Each line is @@ -1058,14 +1143,20 @@ public enum ContentStructure { * a single resource. */ RESOURCE, - /** The entire file is one JSON bundle. The JSON can span multiple lines. */ + /** + * The entire file is one JSON bundle. The JSON can span multiple lines. + */ BUNDLE_PRETTY, - /** The entire file is one JSON resource. The JSON can span multiple lines. */ + /** + * The entire file is one JSON resource. The JSON can span multiple lines. + */ RESOURCE_PRETTY } } - /** The type Execute bundles. */ + /** + * The type Execute bundles. + */ public static class ExecuteBundles extends PTransform, Write.Result> { private final String fhirStore; @@ -1096,7 +1187,9 @@ public FhirIO.Write.Result expand(PCollection input) { .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } - /** The type Write Fhir fn. */ + /** + * The type Write Fhir fn. + */ static class ExecuteBundlesFn extends DoFn> { private Counter failedBundles = Metrics.counter(ExecuteBundlesFn.class, "failed-bundles"); @@ -1144,27 +1237,47 @@ public void executeBundles(ProcessContext context) { } } + /** + * {@link PTransform} for Creating FHIR resources. + * https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/create + */ public static class CreateResources extends PTransform, Write.Result> { private final String fhirStore; private final String type; - private SerializableFunction ifNoneExistFunction; + private SerializableFunction ifNoneExistFunction; + /** + * Instantiates a new Create resources transform. + * + * @param fhirStore the fhir store + * @param type the type + */ CreateResources(ValueProvider fhirStore, String type) { this.fhirStore = fhirStore.get(); this.type = type; } + /** + * Instantiates a new Create resources. + * + * @param fhirStore the fhir store + * @param type the type + */ CreateResources(String fhirStore, String type) { this.fhirStore = fhirStore; this.type = type; } - /** This should be function that reads an resource string and extracts an - * If-None-Exists query for conditional create. - * Typically this will just be extracting an ID. + /** + * This adds a {@link SerializableFunction} that reads an resource string and extracts an + * If-None-Exists query for conditional create. Typically this will just be extracting an ID + * to look for. * * https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/create - * */ + * + * @param ifNoneExistFunction the if none exist function + * @return the create resources + */ public CreateResources withIfNotExistFunction( SerializableFunction ifNoneExistFunction){ this.ifNoneExistFunction = ifNoneExistFunction; @@ -1180,23 +1293,15 @@ public FhirIO.Write.Result expand(PCollection input) { .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } - /** The type Write Fhir fn. */ static class CreateFn extends DoFn> { private Counter failedBundles = Metrics.counter(CreateFn.class, "failed-bundles"); private transient HealthcareApiClient client; private final ObjectMapper mapper = new ObjectMapper(); - /** The Fhir store. */ private final String fhirStore; private final String type; private SerializableFunction ifNoneExistFunction; - /** - * Instantiates a new Write Fhir fn. - * @param fhirStore the Fhir store - * @param type - * @param ifNoneExistFunction - */ CreateFn(String fhirStore, String type, SerializableFunction ifNoneExistFunction) { this.fhirStore = fhirStore; @@ -1204,22 +1309,11 @@ static class CreateFn extends DoFn> { this.ifNoneExistFunction = ifNoneExistFunction; } - - /** - * Initialize healthcare client. - * - * @throws IOException the io exception - */ @Setup public void initClient() throws IOException { this.client = new HttpHealthcareApiClient(); } - /** - * Execute Bundles. - * - * @param context the context - */ @ProcessElement public void create(ProcessContext context) { String body = context.element(); @@ -1240,62 +1334,80 @@ public void create(ProcessContext context) { } } + /** + * {@link PTransform} for Updating FHIR resources resources. + * + * https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/update + */ public static class UpdateResources extends PTransform, Write.Result> { private final String fhirStore; - private final String resourceName; + private SerializableFunction resourceNameFunction; + public static final TupleTag UPDATE_RESULTS = new TupleTag() {}; /** - * Instantiates a new Execute bundles. - * @param fhirStore the fhir store - * @param resourceName - * @param conditional + * Instantiates a new Update resources. + * + * @param fhirStore the fhir store */ - UpdateResources(ValueProvider fhirStore, String resourceName, boolean conditional) { + UpdateResources(ValueProvider fhirStore) { this.fhirStore = fhirStore.get(); - this.resourceName = resourceName; } /** - * Instantiates a new Execute bundles. + * Add a {@link SerializableFunction} to extract a resource name from the input element. + * + * @param resourceNameFunction the resource name function + * @return the update resources + */ + public UpdateResources withResourceNameFunction( + SerializableFunction resourceNameFunction){ + this.resourceNameFunction = resourceNameFunction; + return this; + } + + /** + * Instantiates a new Update resources. * * @param fhirStore the fhir store */ - UpdateResources(String fhirStore, String resourceName, boolean conditional) { + UpdateResources(String fhirStore){ this.fhirStore = fhirStore; - this.resourceName = resourceName; } @Override public FhirIO.Write.Result expand(PCollection input) { + checkArgument(resourceNameFunction == null, + "resourceNameFunction must be set when using FhirIO.UpdateResources"); return Write.Result.in( input.getPipeline(), input - .apply(ParDo.of(new UpdateFn(fhirStore, resourceName))) + .apply(ParDo.of(new UpdateFn(fhirStore, resourceNameFunction))) .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } - /** The type Write Fhir fn. */ + /** + * The type Update fn. + */ static class UpdateFn extends DoFn> { - private Counter failedBundles = Metrics.counter(UpdateFn.class, "failed-bundles"); + private Counter failedUpdates = Metrics.counter(UpdateFn.class, "failed-updates"); private transient HealthcareApiClient client; private final ObjectMapper mapper = new ObjectMapper(); - /** The Fhir store. */ private final String fhirStore; - private final String resourceName; + private SerializableFunction resourceNameFunction; /** - * Instantiates a new Write Fhir fn. - * @param fhirStore the Fhir store - * @param resourceName + * Instantiates a new Update fn. + * + * @param fhirStore the fhir store */ - UpdateFn(String fhirStore, String resourceName) { + UpdateFn(String fhirStore, SerializableFunction resourceNameFunction) { this.fhirStore = fhirStore; - this.resourceName = resourceName; + this.resourceNameFunction = resourceNameFunction; } /** - * Initialize healthcare client. + * Init client. * * @throws IOException the io exception */ @@ -1305,7 +1417,7 @@ public void initClient() throws IOException { } /** - * ConditionalUpdate resources. + * Update. * * @param context the context */ @@ -1315,23 +1427,31 @@ public void update(ProcessContext context) { try { // Validate that data was set to valid JSON. mapper.readTree(body); - client.fhirUpdate(fhirStore, resourceName, body); + String resourceName = resourceNameFunction.apply(body); + HttpBody result = client.fhirUpdate(fhirStore, resourceName, body); + context.output(UPDATE_RESULTS, result.getData()); } catch (IOException | HealthcareHttpException e) { - failedBundles.inc(); + failedUpdates.inc(); context.output(HealthcareIOError.of(body, e)); } } } } + /** + * The type Conditional update. + */ public static class ConditionalUpdate extends PTransform, Write.Result> { private final String fhirStore; private final String type; + private SerializableFunction searchParametersFunction; /** - * Instantiates a new Execute bundles. - * @param fhirStore the fhir store - * @param type + * Instantiates a new Conditional update. + * + * @param fhirStore the fhir store + * @param type the type + * @param conditional the conditional */ ConditionalUpdate(ValueProvider fhirStore, String type, boolean conditional) { this.fhirStore = fhirStore.get(); @@ -1339,9 +1459,23 @@ public static class ConditionalUpdate extends PTransform, Wr } /** - * Instantiates a new Execute bundles. + * With search parameters function conditional update. + * + * @param searchParametersFunction the search parameters function + * @return the conditional update + */ + public ConditionalUpdate withSearchParametersFunction( + SerializableFunction> searchParametersFunction){ + this.searchParametersFunction = searchParametersFunction; + return this; + } + + /** + * Instantiates a new Conditional update. * * @param fhirStore the fhir store + * @param type the type + * @param conditional the conditional */ ConditionalUpdate(String fhirStore, String type, boolean conditional) { this.fhirStore = fhirStore; @@ -1350,36 +1484,46 @@ public static class ConditionalUpdate extends PTransform, Wr @Override public FhirIO.Write.Result expand(PCollection input) { + if (searchParametersFunction == null){ + throw new IllegalArgumentException( + "FhirIO.ConditionalUpdate should always be called with a searchParametersFunction." + + "If this does not meet your use case consider usiing FhirIO.UpdateResources."); + } return Write.Result.in( input.getPipeline(), input - .apply(ParDo.of(new ConditionalUpdateFn(fhirStore, type))) + .apply(ParDo.of(new ConditionalUpdateFn(fhirStore, type, searchParametersFunction))) .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } - /** The type Write Fhir fn. */ + /** + * The type Conditional update fn. + */ static class ConditionalUpdateFn extends DoFn> { private Counter failedBundles = Metrics.counter(ConditionalUpdateFn.class, "failed-bundles"); private transient HealthcareApiClient client; private final ObjectMapper mapper = new ObjectMapper(); - /** The Fhir store. */ private final String fhirStore; private final String type; + private SerializableFunction> searchParametersFunction; /** - * Instantiates a new Write Fhir fn. - * @param fhirStore the Fhir store - * @param type + * Instantiates a new Conditional update fn. + * + * @param fhirStore the fhir store + * @param type the type + * @param searchParametersFunction the search parameters function */ - ConditionalUpdateFn(String fhirStore, String type) { + ConditionalUpdateFn(String fhirStore, String type, + SerializableFunction> searchParametersFunction) { this.fhirStore = fhirStore; this.type = type; + this.searchParametersFunction = searchParametersFunction; } - /** - * Initialize healthcare client. + * Init client. * * @throws IOException the io exception */ @@ -1389,7 +1533,7 @@ public void initClient() throws IOException { } /** - * ConditionalUpdate resources. + * Conditional update. * * @param context the context */ @@ -1399,7 +1543,8 @@ public void conditionalUpdate(ProcessContext context) { try { // Validate that data was set to valid JSON. mapper.readTree(body); - client.fhirConditionalUpdate(fhirStore, type, body); + Map searchParameters = searchParametersFunction.apply(body); + client.fhirConditionalUpdate(fhirStore, type, body, searchParameters); } catch (IOException | HealthcareHttpException e) { failedBundles.inc(); context.output(HealthcareIOError.of(body, e)); diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java index efa594112ee4..6606f19facf9 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java @@ -27,6 +27,7 @@ import com.google.api.services.healthcare.v1beta1.model.Operation; import java.io.IOException; import java.text.ParseException; +import java.util.Map; import javax.annotation.Nullable; import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException; @@ -109,7 +110,8 @@ HttpBody executeFhirBundle(String fhirStore, String bundle) HttpBody fhirCreate(String fhirStore, String type, String resource, @Nullable String ifNoneExist) throws IOException, HealthcareHttpException; - HttpBody fhirConditionalUpdate(String fhirStore, String relativeResourceName, String resource) + HttpBody fhirConditionalUpdate(String fhirStore, String relativeResourceName, String resource, + Map searchParameters) throws IOException, HealthcareHttpException; HttpBody fhirUpdate(String fhirStore, String type, String resource) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java index a8582dd2971e..50c598858e33 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java @@ -60,6 +60,7 @@ import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Strings; import org.apache.http.HttpEntity; import org.apache.http.HttpResponse; +import org.apache.http.NameValuePair; import org.apache.http.client.HttpClient; import org.apache.http.client.methods.HttpUriRequest; import org.apache.http.client.methods.RequestBuilder; @@ -68,6 +69,7 @@ import org.apache.http.entity.StringEntity; import org.apache.http.impl.client.DefaultHttpRequestRetryHandler; import org.apache.http.impl.client.HttpClients; +import org.apache.http.message.BasicNameValuePair; import org.apache.http.util.EntityUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -299,6 +301,7 @@ static class FhirHttpRequest { private Method method; private String pathSuffix; private Map headers; + private Map parameters; enum Method { @@ -332,7 +335,10 @@ public FhirHttpRequest setMethod(Method method){ return this; } - + public FhirHttpRequest setParameters(Map parameters){ + this.parameters= parameters; + return this; + } } @@ -364,25 +370,32 @@ public HttpBody executeFhirHttpRequest(FhirHttpRequest fhirHttpRequest) throws I case PUT: requestBuilder = RequestBuilder.put(); break; - case POST: + case POST: // fallthrough default: requestBuilder = RequestBuilder.post(); } - HttpUriRequest request = requestBuilder - .setUri(uri) - .setEntity(requestEntity) - .addHeader("User-Agent", USER_AGENT) - .addHeader("Content-Type", FHIRSTORE_HEADER_CONTENT_TYPE) - .addHeader("Accept-Charset", FHIRSTORE_HEADER_ACCEPT_CHARSET) - .addHeader("Accept", FHIRSTORE_HEADER_ACCEPT) - .build(); + // add common headers + requestBuilder + .setUri(uri) + .setEntity(requestEntity) + .addHeader("User-Agent", USER_AGENT) + .addHeader("Content-Type", FHIRSTORE_HEADER_CONTENT_TYPE) + .addHeader("Accept-Charset", FHIRSTORE_HEADER_ACCEPT_CHARSET) + .addHeader("Accept", FHIRSTORE_HEADER_ACCEPT); + + // add additional headers + for (Map.Entry param: fhirHttpRequest.parameters.entrySet()){ + requestBuilder.addParameter(param.getKey(), param.getValue()); + } - // Add headers - for (Map.Entry header: fhirHttpRequest.headers.entrySet()){ - request.addHeader(header.getKey(), header.getValue()); + // add additional parameters + for (Map.Entry param: fhirHttpRequest.headers.entrySet()){ + requestBuilder.addHeader(param.getKey(), param.getValue()); } + HttpUriRequest request = requestBuilder.build(); + HttpResponse response = httpClient.execute(request); HttpEntity responseEntity = response.getEntity(); String content = EntityUtils.toString(responseEntity); @@ -417,11 +430,12 @@ public HttpBody fhirCreate(String fhirStore, String type, String resource, } @Override - public HttpBody fhirConditionalUpdate(String fhirStore, String type, String resource) + public HttpBody fhirConditionalUpdate(String fhirStore, String type, String resource, Map searchParameters) throws IOException, HealthcareHttpException { return executeFhirHttpRequest( FhirHttpRequest.of(fhirStore, resource) .setPathSuffix("/" + type) + .setParameters(searchParameters) .setMethod(Method.PUT)); } diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java index 24677ca3fb56..e8e06c60493c 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java @@ -126,4 +126,6 @@ public void testFhirIO_Import() { pipeline.run().waitUntilFinish(); } + + // TODO(jaketf) add IT for conditional create, update, conditional update transforms. } From 0aa92fe0a808e0f6669725ece6db5bd07591c3cf Mon Sep 17 00:00:00 2001 From: Sam Rohde Date: Wed, 13 May 2020 14:49:05 -0700 Subject: [PATCH 009/151] remove references to _GroupByKeyOnly Change-Id: I0917d6495074204761d91579e5e5572401042a18 --- sdks/python/apache_beam/transforms/ptransform_test.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/sdks/python/apache_beam/transforms/ptransform_test.py b/sdks/python/apache_beam/transforms/ptransform_test.py index ee007ff653f6..1cdd273fb3c4 100644 --- a/sdks/python/apache_beam/transforms/ptransform_test.py +++ b/sdks/python/apache_beam/transforms/ptransform_test.py @@ -52,7 +52,6 @@ from apache_beam.testing.util import equal_to from apache_beam.transforms import WindowInto from apache_beam.transforms import window -from apache_beam.transforms.core import _GroupByKeyOnly from apache_beam.transforms.display import DisplayData from apache_beam.transforms.display import DisplayDataItem from apache_beam.transforms.ptransform import PTransform @@ -680,7 +679,7 @@ def test_group_by_key_only_input_must_be_kv_pairs(self): with self.assertRaises(typehints.TypeCheckError) as cm: with TestPipeline() as pipeline: pcolls = pipeline | 'A' >> beam.Create(['a', 'b', 'f']) - pcolls | 'D' >> _GroupByKeyOnly() + pcolls | 'D' >> beam.GroupByKey() expected_error_prefix = ( 'Input type hint violation at D: expected ' @@ -1233,7 +1232,7 @@ def test_group_by_key_only_output_type_deduction(self): | ( 'Pair' >> beam.Map(lambda x: (x, ord(x))).with_output_types( typing.Tuple[str, str])) - | _GroupByKeyOnly()) + | beam.GroupByKey()) # Output type should correctly be deduced. # GBK-only should deduce that Tuple[A, B] is turned into @@ -1261,7 +1260,7 @@ def test_group_by_key_only_does_not_type_check(self): ( self.p | beam.Create([1, 2, 3]).with_output_types(int) - | 'F' >> _GroupByKeyOnly()) + | 'F' >> beam.GroupByKey()) self.assertStartswith( e.exception.args[0], @@ -1309,7 +1308,7 @@ def test_pipeline_checking_gbk_insufficient_type_information(self): self.p | 'Nums' >> beam.Create(range(5)).with_output_types(int) | 'ModDup' >> beam.Map(lambda x: (x % 2, x)) - | _GroupByKeyOnly()) + | beam.GroupByKey()) self.assertEqual( 'Pipeline type checking is enabled, however no output ' @@ -2244,7 +2243,7 @@ def test_pardo_type_inference(self): def test_gbk_type_inference(self): self.assertEqual( typehints.Tuple[str, typehints.Iterable[int]], - _GroupByKeyOnly().infer_output_type(typehints.KV[str, int])) + beam.GroupByKey().infer_output_type(typehints.KV[str, int])) def test_pipeline_inference(self): created = self.p | beam.Create(['a', 'b', 'c']) From b1b612fdafd5a10aa417cd47421b405efc449f8a Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Wed, 13 May 2020 15:30:09 -0700 Subject: [PATCH 010/151] generify and document new interfaces for conditional create and conditional update --- .../beam/sdk/io/gcp/healthcare/FhirIO.java | 295 ++++++++++++------ 1 file changed, 198 insertions(+), 97 deletions(-) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java index 3ad15ee78515..e5efde50d587 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java @@ -48,6 +48,7 @@ import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions; import org.apache.beam.sdk.io.fs.ResourceId; import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.ExecuteBundles.ExecuteBundlesFn; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Write.Result; import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException; import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO; import org.apache.beam.sdk.metrics.Counter; @@ -121,9 +122,20 @@ * FhirIO.Write#fhirStoresImport(String, String, String, FhirIO.Import.ContentStructure)} This will * return a {@link FhirIO.Write.Result} on which you can call {@link * FhirIO.Write.Result#getFailedBodies()} to retrieve a {@link PCollection} of {@link - * HealthcareIOError} containing the {@link String} that failed to be ingested and the exception.

    Example 

    {@code
+ * HealthcareIOError} containing the {@link String} that failed to be ingested and the     exception.
+ *
+ * 
    Conditional Creating / Updating Resources
    
+ * {@link FhirIO} supports interfaces for conditional update.
+ * These can be useful to handle scenarios where an executeBundle failed. For example if you tried
+ * to create a resource that already exists you can grab the faield bodies of your
+ * {@link FhirIO.ExecuteBundles} transform with {@link Result#getFailedBodies()} perform some logic
+ * on the reason for failures and if appropriate route this to {@link FhirIO.ConditionalUpdate} or
+ * {@link FhirIO.CreateResources} to take the appropriate action on your FHIR store.
+ *
+ * 
    Example     
    {@code
  * Pipeline pipeline = ...
  *
+ * // [Begin Reading]
  * // Tail the FHIR store by retrieving resources based on Pub/Sub notifications.
  * FhirIO.Read.Result readResult = p
  *   .apply("Read FHIR notifications",
@@ -133,8 +145,11 @@
  * // happily retrived messages
  * PCollection resources = readResult.getResources();
  * // message IDs that couldn't be retrieved + error context
+ *
  * PCollection> failedReads = readResult.getFailedReads();
+ * // [End Reading]
  *
+ * // [Beign Writing]
  * failedReads.apply("Write Message IDs / Stacktrace for Failed Reads to BigQuery",
  *     BigQueryIO
  *         .write()
@@ -145,17 +160,53 @@
  * FhirIO.Write.Result writeResult =
  *     output.apply("Execute FHIR Bundles", FhirIO.executeBundles(options.getExistingFhirStore()));
  *
+ * // Alternatively you could use import for high throughput to a new store.
+ * FhirIO.Write.Result writeResult =
+ *     output.apply("Import FHIR Resources", FhirIO.executeBundles(options.getNewFhirStore()));
+ * // [End Writing ]
+ *
  * PCollection> failedBundles = writeResult.getFailedInsertsWithErr();
  *
+ * // [Begin Writing to Dead Letter Queue]
  * failedBundles.apply("Write failed bundles to BigQuery",
  *     BigQueryIO
  *         .write()
  *         .to(option.getBQFhirExecuteBundlesDeadLetterTable())
  *         .withFormatFunction(new HealthcareIOErrorToTableRow()));
+ * // [End Writing to Dead Letter Queue]
+ *
+ * // Alternatively you may want to handle DeadLetter with conditional update
+ * // [Begin Reconciliation with Conditional Update]
+ * failedBundles
+ *     .apply("Reconcile with Conditional Update",
+ *         FhirIO.ConditionalUpdate(fhirStore)
+ *             .withFormatBodyFunction(HealthcareIOError::getDataResource)
+ *             .withTypeFunction((HealthcareIOError err) -> {
+ *               String body = err.getDataResource();
+ *               // TODO(user) insert logic to exctract type.
+ *               return params;
+ *             })
+ *             .withSearchParametersFunction((HealthcareIOError err) -> {
+ *               String body = err.getDataResource();
+ *               Map params = new HashMap();
+ *               // TODO(user) insert logic to exctract search query parameters.
+ *               return params;
+ *             });
+ * // [End Reconciliation with Conditional Update]
+ *
+ * // Alternatively you may want to handle DeadLetter with conditional create
+ * // [Begin Reconciliation with Conditional Update]
+ * failedBundles
+ *     .apply("Reconcile with Conditional Create",
+ *         FhirIO.CreateResources(fhirStore)
+ *             .withFormatBodyFunction(HealthcareIOError::getDataResource)
+ *             .withIfNotExistsFunction((HealthcareIOError err) -> {
+ *               String body = err.getDataResource();
+ *               // TODO(user) insert logic to exctract a query to be used in If-Not-Exists header.
+ *               return params;
+ *             });
+ * // [End Reconciliation with Conditional Update]
  *
- * // Alternatively you could use import for high throughput to a new store.
- * FhirIO.Write.Result writeResult =
- *     output.apply("Import FHIR Resources", FhirIO.executeBundles(options.getNewFhirStore()));
  * }*** 
    
  */
 public class FhirIO {
@@ -231,7 +282,7 @@ public static class Result implements POutput, PInput {
       PCollectionTuple pct;
 
       /**
-       * ConditionalUpdate FhirIO.Read.Result form PCollectionTuple with OUT and DEAD_LETTER tags.
+       * FhirIO.Read.Result form PCollectionTuple with OUT and DEAD_LETTER tags.
        *
        * @param pct the pct
        * @return the read result
@@ -617,7 +668,7 @@ private static Write.Builder write(String fhirStore) {
     }
 
     /**
-     * ConditionalUpdate Method creates a single FHIR resource. @see 
      *
      * @param fhirStore the hl 7 v 2 store
@@ -745,7 +796,7 @@ public Result expand(PCollection input) {
    * Writes each bundle of elements to a new-line delimited JSON file on GCS and issues a
    * fhirStores.import Request for that file. This is intended for batch use only to facilitate
    * large backfills to empty FHIR stores and should not be used with unbounded PCollections. If
-   * your use case is streaming checkout using {@link ConditionalUpdate} to more safely execute
+   * your use case is streaming checkout using {@link Import} to more safely execute
    * bundles as transactions which is safer practice for a use on a "live" FHIR store.
    */
   public static class Import extends Write {
@@ -1239,12 +1290,15 @@ public void executeBundles(ProcessContext context) {
 
   /**
    * {@link PTransform} for Creating FHIR resources.
+   *
    * https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/create
    */
-  public static class CreateResources extends PTransform, Write.Result> {
+  public static class CreateResources extends PTransform, Write.Result> {
     private final String fhirStore;
     private final String type;
-    private SerializableFunction ifNoneExistFunction;
+    private SerializableFunction ifNoneExistFunction;
+    private SerializableFunction formatBodyFunction;
+    private static final Logger LOG = LoggerFactory.getLogger(CreateResources.class);
 
     /**
      * Instantiates a new Create resources transform.
@@ -1279,33 +1333,57 @@ public static class CreateResources extends PTransform, Writ
      * @return the create resources
      */
     public CreateResources withIfNotExistFunction(
-        SerializableFunction ifNoneExistFunction){
+        SerializableFunction ifNoneExistFunction){
       this.ifNoneExistFunction = ifNoneExistFunction;
       return this;
     }
 
+    /**
+     * With format body function create resources.
+     *
+     * @param formatBodyFunction the format body function
+     * @return the create resources
+     */
+    public CreateResources withFormatBodyFunction(
+        SerializableFunction formatBodyFunction){
+      this.formatBodyFunction= formatBodyFunction;
+      return this;
+    }
+
     @Override
-    public FhirIO.Write.Result expand(PCollection input) {
+    public FhirIO.Write.Result expand(PCollection input) {
+      checkArgument(
+          formatBodyFunction != null,
+          "FhirIO.CreateResources should always be called with a "
+              + "withFromatBodyFunction");
+
+      if (ifNoneExistFunction == null){
+        LOG.info("ifNoneExistFunction was null will create resources unconditionally");
+      }
+
       return Write.Result.in(
           input.getPipeline(),
           input
-              .apply(ParDo.of(new CreateFn(fhirStore, type, ifNoneExistFunction)))
+              .apply(ParDo.of(new CreateFn(fhirStore, type, formatBodyFunction, ifNoneExistFunction)))
               .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of())));
     }
 
-    static class CreateFn extends DoFn> {
+    static class CreateFn extends DoFn> {
 
       private Counter failedBundles = Metrics.counter(CreateFn.class, "failed-bundles");
       private transient HealthcareApiClient client;
       private final ObjectMapper mapper = new ObjectMapper();
       private final String fhirStore;
       private final String type;
-      private SerializableFunction ifNoneExistFunction;
+      private SerializableFunction ifNoneExistFunction;
+      private SerializableFunction formatBodyFunction;
 
       CreateFn(String fhirStore, String type,
-          SerializableFunction ifNoneExistFunction) {
+          SerializableFunction formatBodyFunction,
+          @Nullable SerializableFunction ifNoneExistFunction) {
         this.fhirStore = fhirStore;
         this.type = type;
+        this.formatBodyFunction= formatBodyFunction;
         this.ifNoneExistFunction = ifNoneExistFunction;
       }
 
@@ -1316,14 +1394,15 @@ public void initClient() throws IOException {
 
       @ProcessElement
       public void create(ProcessContext context) {
-        String body = context.element();
+        T input = context.element();
+        String body = formatBodyFunction.apply(input);
         try {
           // Validate that data was set to valid JSON.
-          mapper.readTree(body);
+          mapper.readTree(input.toString());
           if (ifNoneExistFunction != null){
-            String ifNoneExistQuery = ifNoneExistFunction.apply(body);
+            String ifNoneExistQuery = ifNoneExistFunction.apply(input);
             client.fhirCreate(fhirStore, type, body, ifNoneExistQuery);
-          } else{
+          } else {
             client.fhirCreate(fhirStore, type, body, null);
           }
         } catch (IOException | HealthcareHttpException e) {
@@ -1339,10 +1418,12 @@ public void create(ProcessContext context) {
    *
    * https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/update
    */
-  public static class UpdateResources extends PTransform, Write.Result> {
+  public static class UpdateResources extends PTransform, Write.Result> {
     private final String fhirStore;
-    private SerializableFunction resourceNameFunction;
+    private SerializableFunction formatBodyFunction;
+    private SerializableFunction resourceNameFunction;
     public static final TupleTag UPDATE_RESULTS = new TupleTag() {};
+    private static final Logger LOG = LoggerFactory.getLogger(UpdateResources.class);
 
     /**
      * Instantiates a new Update resources.
@@ -1360,11 +1441,23 @@ public static class UpdateResources extends PTransform, Writ
      * @return the update resources
      */
     public UpdateResources withResourceNameFunction(
-        SerializableFunction resourceNameFunction){
+        SerializableFunction resourceNameFunction){
       this.resourceNameFunction = resourceNameFunction;
       return this;
     }
 
+    /**
+     * With format body function update resources.
+     *
+     * @param formatBodyFunction the format body function
+     * @return the update resources
+     */
+    public UpdateResources withFormatBodyFunction(
+        SerializableFunction formatBodyFunction){
+      this.formatBodyFunction = formatBodyFunction;
+      return this;
+    }
+
     /**
      * Instantiates a new Update resources.
      *
@@ -1375,59 +1468,48 @@ public UpdateResources withResourceNameFunction(
     }
 
     @Override
-    public FhirIO.Write.Result expand(PCollection input) {
+    public FhirIO.Write.Result expand(PCollection input) {
+      checkArgument(
+          formatBodyFunction != null,
+          "FhirIO.UpdateResources should always be called with a "
+              + "withFormatBodyFunction.");
       checkArgument(resourceNameFunction == null,
           "resourceNameFunction must be set when using FhirIO.UpdateResources");
       return Write.Result.in(
           input.getPipeline(),
           input
-              .apply(ParDo.of(new UpdateFn(fhirStore, resourceNameFunction)))
+              .apply(ParDo.of(new UpdateFn(fhirStore, formatBodyFunction, resourceNameFunction)))
               .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of())));
     }
 
-    /**
-     * The type Update fn.
-     */
-    static class UpdateFn extends DoFn> {
+    static class UpdateFn extends DoFn> {
 
       private Counter failedUpdates = Metrics.counter(UpdateFn.class, "failed-updates");
       private transient HealthcareApiClient client;
       private final ObjectMapper mapper = new ObjectMapper();
       private final String fhirStore;
-      private SerializableFunction resourceNameFunction;
+      private SerializableFunction formatBodyFunction;
+      private SerializableFunction resourceNameFunction;
 
-      /**
-       * Instantiates a new Update fn.
-       *
-       * @param fhirStore the fhir store
-       */
-      UpdateFn(String fhirStore, SerializableFunction resourceNameFunction) {
+      UpdateFn(String fhirStore, SerializableFunction formatBodyFunction, SerializableFunction resourceNameFunction) {
         this.fhirStore = fhirStore;
+        this.formatBodyFunction = formatBodyFunction;
         this.resourceNameFunction = resourceNameFunction;
       }
 
-      /**
-       * Init client.
-       *
-       * @throws IOException the io exception
-       */
       @Setup
       public void initClient() throws IOException {
         this.client = new HttpHealthcareApiClient();
       }
 
-      /**
-       * Update.
-       *
-       * @param context the context
-       */
       @ProcessElement
       public void update(ProcessContext context) {
-        String body = context.element();
+        T input = context.element();
+        String body = formatBodyFunction.apply(input);
         try {
           // Validate that data was set to valid JSON.
           mapper.readTree(body);
-          String resourceName = resourceNameFunction.apply(body);
+          String resourceName = resourceNameFunction.apply(input);
           HttpBody result = client.fhirUpdate(fhirStore, resourceName, body);
           context.output(UPDATE_RESULTS, result.getData());
         } catch (IOException | HealthcareHttpException e) {
@@ -1439,23 +1521,23 @@ public void update(ProcessContext context) {
   }
 
   /**
-   * The type Conditional update.
+   * {@link PTransform} to perform Conditional updates on the FHIR store.
+   *
+   * https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/conditionalUpdate
    */
-  public static class ConditionalUpdate extends PTransform, Write.Result> {
+  public static class ConditionalUpdate extends PTransform, Write.Result> {
     private final String fhirStore;
-    private final String type;
-    private SerializableFunction searchParametersFunction;
+    private SerializableFunction> searchParametersFunction;
+    private SerializableFunction typeFunction;
+    private SerializableFunction formatBodyFunction;
 
     /**
      * Instantiates a new Conditional update.
      *
      * @param fhirStore the fhir store
-     * @param type the type
-     * @param conditional the conditional
      */
-    ConditionalUpdate(ValueProvider fhirStore, String type, boolean conditional) {
+    ConditionalUpdate(ValueProvider fhirStore) {
       this.fhirStore = fhirStore.get();
-      this.type = type;
     }
 
     /**
@@ -1465,88 +1547,107 @@ public static class ConditionalUpdate extends PTransform, Wr
      * @return the conditional update
      */
     public ConditionalUpdate withSearchParametersFunction(
-        SerializableFunction> searchParametersFunction){
+        SerializableFunction> searchParametersFunction){
       this.searchParametersFunction = searchParametersFunction;
       return this;
     }
 
+    /**
+     * With type function conditional update.
+     *
+     * @param typeFunction the type function
+     * @return the conditional update
+     */
+    public ConditionalUpdate withTypeFunction(
+        SerializableFunction typeFunction){
+      this.typeFunction = typeFunction;
+      return this;
+    }
+
+    /**
+     * With format body function conditional update.
+     *
+     * @param formatBodyFunction the format body function
+     * @return the conditional update
+     */
+    public ConditionalUpdate withFormatBodyFunction(
+        SerializableFunction formatBodyFunction){
+      this.formatBodyFunction = formatBodyFunction;
+      return this;
+    }
+
     /**
      * Instantiates a new Conditional update.
      *
      * @param fhirStore the fhir store
-     * @param type the type
-     * @param conditional the conditional
      */
-    ConditionalUpdate(String fhirStore, String type, boolean conditional) {
+    ConditionalUpdate(String fhirStore) {
       this.fhirStore = fhirStore;
-      this.type = type;
     }
 
+
     @Override
-    public FhirIO.Write.Result expand(PCollection input) {
-      if (searchParametersFunction == null){
-        throw new IllegalArgumentException(
-            "FhirIO.ConditionalUpdate should always be called with a searchParametersFunction."
-                + "If this does not meet your use case consider usiing FhirIO.UpdateResources.");
-      }
+    public FhirIO.Write.Result expand(PCollection input) {
+      checkArgument(
+          typeFunction != null,
+          "FhirIO.ConditionalUpdate should always be called with a "
+              + "withTypeFunction.");
+      checkArgument(
+          formatBodyFunction != null,
+          "FhirIO.ConditionalUpdate should always be called with a "
+              + "withFormatBodyFunction.");
+      checkArgument(
+          searchParametersFunction != null,
+          "FhirIO.ConditionalUpdate should always be called with a "
+              + "withSearchParametersFunction. If this does not meet your use case consider usiing "
+              + "FhirIO.UpdateResources.");
+
+
       return Write.Result.in(
           input.getPipeline(),
           input
-              .apply(ParDo.of(new ConditionalUpdateFn(fhirStore, type, searchParametersFunction)))
+              .apply(ParDo.of(new ConditionalUpdateFn(
+                  fhirStore, typeFunction, searchParametersFunction, formatBodyFunction)))
               .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of())));
     }
 
-    /**
-     * The type Conditional update fn.
-     */
-    static class ConditionalUpdateFn extends DoFn> {
+    static class ConditionalUpdateFn extends DoFn> {
 
-      private Counter failedBundles = Metrics.counter(ConditionalUpdateFn.class, "failed-bundles");
+      private Counter failedConditionalUpdates = Metrics.counter(ConditionalUpdateFn.class,
+          "failed-conditional-updates");
       private transient HealthcareApiClient client;
       private final ObjectMapper mapper = new ObjectMapper();
       private final String fhirStore;
-      private final String type;
-      private SerializableFunction> searchParametersFunction;
+      private SerializableFunction> searchParametersFunction;
+      private SerializableFunction typeFunction;
+      private SerializableFunction formatBodyFunction;
 
-      /**
-       * Instantiates a new Conditional update fn.
-       *
-       * @param fhirStore the fhir store
-       * @param type the type
-       * @param searchParametersFunction the search parameters function
-       */
-      ConditionalUpdateFn(String fhirStore, String type,
-          SerializableFunction> searchParametersFunction) {
+      ConditionalUpdateFn(String fhirStore, SerializableFunction typeFunction,
+          SerializableFunction> searchParametersFunction,
+          SerializableFunction formatBodyFunction) {
         this.fhirStore = fhirStore;
-        this.type = type;
+        this.typeFunction = typeFunction;
         this.searchParametersFunction = searchParametersFunction;
+        this.formatBodyFunction = formatBodyFunction;
       }
 
-      /**
-       * Init client.
-       *
-       * @throws IOException the io exception
-       */
       @Setup
       public void initClient() throws IOException {
         this.client = new HttpHealthcareApiClient();
       }
 
-      /**
-       * Conditional update.
-       *
-       * @param context the context
-       */
       @ProcessElement
       public void conditionalUpdate(ProcessContext context) {
-        String body = context.element();
+        T input = context.element();
+        String type = typeFunction.apply(input);
+        String body = formatBodyFunction.apply(input);
         try {
           // Validate that data was set to valid JSON.
           mapper.readTree(body);
-          Map searchParameters = searchParametersFunction.apply(body);
+          Map searchParameters = searchParametersFunction.apply(input);
           client.fhirConditionalUpdate(fhirStore, type, body, searchParameters);
         } catch (IOException | HealthcareHttpException e) {
-          failedBundles.inc();
+          failedConditionalUpdates.inc();
           context.output(HealthcareIOError.of(body, e));
         }
       }

From cc405fdc375de0b73797c06f16522f374d511909 Mon Sep 17 00:00:00 2001
From: Sam Rohde 
Date: Wed, 13 May 2020 16:25:25 -0700
Subject: [PATCH 011/151] add back the ReifyWindows to the GBK, some internal
 tests depend on it.

Change-Id: Ibce789eaa56ca93842d94cd23bd6d4aadb05e08d
---
 .../runners/direct/direct_runner.py           | 26 +++----------------
 sdks/python/apache_beam/transforms/core.py    | 17 ++++++++++++
 2 files changed, 21 insertions(+), 22 deletions(-)

diff --git a/sdks/python/apache_beam/runners/direct/direct_runner.py b/sdks/python/apache_beam/runners/direct/direct_runner.py
index 8fa6c902900d..51b064a88114 100644
--- a/sdks/python/apache_beam/runners/direct/direct_runner.py
+++ b/sdks/python/apache_beam/runners/direct/direct_runner.py
@@ -51,9 +51,7 @@
 from apache_beam.transforms.core import DoFn
 from apache_beam.transforms.core import ParDo
 from apache_beam.transforms.ptransform import PTransform
-from apache_beam.transforms.window import WindowedValue
 from apache_beam.typehints import trivial_inference
-from apache_beam.typehints.decorators import TypeCheckError
 
 # Note that the BundleBasedDirectRunner and SwitchingDirectRunner names are
 # experimental and have no backwards compatibility guarantees.
@@ -227,23 +225,6 @@ def from_runner_api_parameter(unused_ptransform, payload, context):
 @typehints.with_output_types(typing.Tuple[K, typing.Iterable[V]])
 class _GroupByKey(PTransform):
   """The DirectRunner GroupByKey implementation."""
-  class ReifyWindows(DoFn):
-    def process(
-        self, element, window=DoFn.WindowParam, timestamp=DoFn.TimestampParam):
-      try:
-        k, v = element
-      except TypeError:
-        raise TypeCheckError(
-            'Input to GroupByKey must be a PCollection with '
-            'elements compatible with KV[A, B]')
-
-      return [(k, WindowedValue(v, timestamp, [window]))]
-
-    def infer_output_type(self, input_type):
-      key_type, value_type = trivial_inference.key_value_types(input_type)
-      return typehints.Iterable[typehints.KV[
-          key_type, typehints.WindowedValue[value_type]]]  # type: ignore[misc]
-
   def expand(self, pcoll):
     # Imported here to avoid circular dependencies.
     # pylint: disable=wrong-import-order, wrong-import-position
@@ -274,8 +255,9 @@ def expand(self, pcoll):
       # pylint: disable=bad-continuation
       return (
           pcoll
-          | 'ReifyWindows' >>
-          (ParDo(self.ReifyWindows()).with_output_types(reify_output_type))
+          | 'ReifyWindows' >> (
+              ParDo(beam.GroupByKey.ReifyWindows()).with_output_types(
+                  reify_output_type))
           | 'GroupByKey' >> (
               _GroupByKeyOnly().with_input_types(
                   reify_output_type).with_output_types(gbk_input_type))
@@ -287,7 +269,7 @@ def expand(self, pcoll):
       # The input_type is None, run the default
       return (
           pcoll
-          | 'ReifyWindows' >> ParDo(self.ReifyWindows())
+          | 'ReifyWindows' >> ParDo(beam.GroupByKey.ReifyWindows())
           | 'GroupByKey' >> _GroupByKeyOnly()
           | 'GroupByWindow' >> _GroupAlsoByWindow(pcoll.windowing))
 
diff --git a/sdks/python/apache_beam/transforms/core.py b/sdks/python/apache_beam/transforms/core.py
index 665d7ec4ebea..fe87117d1e43 100644
--- a/sdks/python/apache_beam/transforms/core.py
+++ b/sdks/python/apache_beam/transforms/core.py
@@ -2208,6 +2208,23 @@ class GroupByKey(PTransform):
 
   The implementation here is used only when run on the local direct runner.
   """
+  class ReifyWindows(DoFn):
+    def process(
+        self, element, window=DoFn.WindowParam, timestamp=DoFn.TimestampParam):
+      try:
+        k, v = element
+      except TypeError:
+        raise TypeCheckError(
+            'Input to GroupByKey must be a PCollection with '
+            'elements compatible with KV[A, B]')
+
+      return [(k, WindowedValue(v, timestamp, [window]))]
+
+    def infer_output_type(self, input_type):
+      key_type, value_type = trivial_inference.key_value_types(input_type)
+      return typehints.Iterable[typehints.KV[
+          key_type, typehints.WindowedValue[value_type]]]  # type: ignore[misc]
+
   def expand(self, pcoll):
     return pvalue.PCollection.from_(pcoll)
 

From 9be5a29ba3ffc632b049fd18299be40f19ab74aa Mon Sep 17 00:00:00 2001
From: Ahmet Altay 
Date: Fri, 15 May 2020 11:26:25 -0700
Subject: [PATCH 012/151] Updated Videos and Podcasts page

---
 .../resources/videos-and-podcasts.md          | 20 ++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/website/www/site/content/en/documentation/resources/videos-and-podcasts.md b/website/www/site/content/en/documentation/resources/videos-and-podcasts.md
index b1d0a0bb6371..651cd8856cd8 100644
--- a/website/www/site/content/en/documentation/resources/videos-and-podcasts.md
+++ b/website/www/site/content/en/documentation/resources/videos-and-podcasts.md
@@ -65,6 +65,24 @@ Presented by Frances Perry, *Apache Beam PPMC member*
 
 The following resources present Apache Beam partnerships.
 
+### Distributed Processing for Machine Learning Production Pipelines 
+
+Flink Forward, 2020
+
+Presented by Ahmet Altay, Robert Crowe, Reza Rokni
+
+
+
    
+
+### TensorFlow Extended: An End-to-End Machine Learning Platform for TensorFlow 
+
+Spark+AI, San Francisco, 2019
+
+Presented by Konstantinos Katsiapis, Ahmet Altay
+
+
+
    
+
 ### Flink and Beam: Current State & Roadmap
 
 Flink Forward, Berlin, 2016
@@ -129,4 +147,4 @@ Your browser does not support the audio element.
 
 ## Next Steps
 
-* Take a self-paced tour through our [Learning Resources](/documentation/resources/learning-resources).
\ No newline at end of file
+* Take a self-paced tour through our [Learning Resources](/documentation/resources/learning-resources).

From 301c32b0d45377172c571e3a01dba4bfcd4f467a Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Fri, 15 May 2020 17:38:42 -0400
Subject: [PATCH 013/151] Update Beam website to release 2.21.0.

---
 website/www/site/config.toml                         | 2 +-
 website/www/site/content/en/get-started/downloads.md | 7 +++++++
 website/www/site/static/.htaccess                    | 2 +-
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/website/www/site/config.toml b/website/www/site/config.toml
index 9c4bcd179672..5211e364a950 100644
--- a/website/www/site/config.toml
+++ b/website/www/site/config.toml
@@ -104,7 +104,7 @@ github_project_repo = "https://github.com/apache/beam"
 
 [params]
 description = "Apache Beam is an open source, unified model and set of language-specific SDKs for defining and executing data processing workflows, and also data ingestion and integration flows, supporting Enterprise Integration Patterns (EIPs) and Domain Specific Languages (DSLs). Dataflow pipelines simplify the mechanics of large-scale batch and streaming data processing and can run on a number of runtimes like Apache Flink, Apache Spark, and Google Cloud Dataflow (a cloud service). Beam also brings DSL in different languages, allowing users to easily implement their data integration processes."
-release_latest = "2.20.0"
+release_latest = "2.21.0"
 # The repository and branch where the files live in Github or Colab. This is used
 # to serve and stage from your local branch, but publish to the master branch.
 #   e.g. https://github.com/{{< param branch_repo >}}/path/to/notebook.ipynb
diff --git a/website/www/site/content/en/get-started/downloads.md b/website/www/site/content/en/get-started/downloads.md
index 76a032c89369..14ae4d683162 100644
--- a/website/www/site/content/en/get-started/downloads.md
+++ b/website/www/site/content/en/get-started/downloads.md
@@ -87,6 +87,13 @@ versions denoted `0.x.y`.
 
 ## Releases
 
+### 2.21.0 (2020-05-xx)
+Official [source code download](http://www.apache.org/dyn/closer.cgi/beam/2.21.0/apache-beam-2.21.0-source-release.zip).
+[SHA-512](https://downloads.apache.org/beam/2.21.0/apache-beam-2.21.0-source-release.zip.sha512).
+[signature](https://downloads.apache.org/beam/2.21.0/apache-beam-2.21.0-source-release.zip.asc).
+
+[Release notes](https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12319527&version=12347143).
+
 ### 2.20.0 (2020-04-15)
 Official [source code download](http://www.apache.org/dyn/closer.cgi/beam/2.20.0/apache-beam-2.20.0-source-release.zip).
 [SHA-512](https://downloads.apache.org/beam/2.20.0/apache-beam-2.20.0-source-release.zip.sha512).
diff --git a/website/www/site/static/.htaccess b/website/www/site/static/.htaccess
index 2ccc960afe4e..916c7558eb66 100644
--- a/website/www/site/static/.htaccess
+++ b/website/www/site/static/.htaccess
@@ -21,4 +21,4 @@ RewriteRule ^(.*)$ https://beam.apache.org/$1 [L,R=301]
 # The following redirect maintains the previously supported URLs.
 RedirectMatch permanent "/documentation/sdks/(javadoc|pydoc)(.*)" "https://beam.apache.org/releases/$1$2"
 # Keep this updated to point to the current release.
-RedirectMatch "/releases/([^/]+)/current(.*)" "https://beam.apache.org/releases/$1/2.20.0$2"
+RedirectMatch "/releases/([^/]+)/current(.*)" "https://beam.apache.org/releases/$1/2.21.0$2"

From ad15754e746c10e615ba88f5d00f79a2dca09894 Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Fri, 15 May 2020 19:53:41 -0400
Subject: [PATCH 014/151] Add blog post announcing the Beam 2.21.0 release.

---
 CHANGES.md                                    |  3 +-
 .../www/site/content/en/blog/beam-2.21.0.md   | 97 +++++++++++++++++++
 2 files changed, 99 insertions(+), 1 deletion(-)
 create mode 100644 website/www/site/content/en/blog/beam-2.21.0.md

diff --git a/CHANGES.md b/CHANGES.md
index 29db42c152ce..c55967a18bfb 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -75,7 +75,7 @@
 
 * Fixed X (Java/Python) ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)).
 
-# [2.21.0] - Unreleased (In Progress)
+# [2.21.0] - 2020-05-xx
 
 ## Highlights
 
@@ -139,6 +139,7 @@ conversion to beam schema options. *Remark: Schema aware is still experimental.*
 ## Deprecations
 * Java SDK: Beam Schema FieldType.getMetadata is now deprecated and is replaced by the Beam
 Schema Options, it will be removed in version `2.23.0`. ([BEAM-9704](https://issues.apache.org/jira/browse/BEAM-9704))
+* The `--zone` option in the Dataflow runner is now deprecated. Please use `--worker_zone` instead. ([BEAM-9716](https://issues.apache.org/jira/browse/BEAM-9716))
 
 ## Known Issues
 
diff --git a/website/www/site/content/en/blog/beam-2.21.0.md b/website/www/site/content/en/blog/beam-2.21.0.md
new file mode 100644
index 000000000000..286d71b6a20b
--- /dev/null
+++ b/website/www/site/content/en/blog/beam-2.21.0.md
@@ -0,0 +1,97 @@
+---
+title:  "Apache Beam 2.21.0"
+date:   2020-05-xx 00:00:01 -0800
+categories: 
+  - blog
+authors:
+  - ibzib
+---
+
+
+We are happy to present the new 2.21.0 release of Beam. This release includes both improvements and new functionality.
+See the [download page](/get-started/downloads/#xxxx-xxxx) for this release.
+For more information on changes in 2.21.0, check out the
+[detailed release notes](https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12319527&version=12347143).
+
+## I/Os
+* Python: Deprecated module `apache_beam.io.gcp.datastore.v1` has been removed
+as the client it uses is out of date and does not support Python 3
+([BEAM-9529](https://issues.apache.org/jira/browse/BEAM-9529)).
+Please migrate your code to use
+[apache_beam.io.gcp.datastore.**v1new**](https://beam.apache.org/releases/pydoc/current/apache_beam.io.gcp.datastore.v1new.datastoreio.html).
+See the updated
+[datastore_wordcount](https://github.com/apache/beam/blob/master/sdks/python/apache_beam/examples/cookbook/datastore_wordcount.py)
+for example usage.
+* Python SDK: Added integration tests and updated batch write functionality for Google Cloud Spanner transform ([BEAM-8949](https://issues.apache.org/jira/browse/BEAM-8949)).
+
+## New Features / Improvements
+* Python SDK will now use Python 3 type annotations as pipeline type hints.
+([#10717](https://github.com/apache/beam/pull/10717))
+
+    If you suspect that this feature is causing your pipeline to fail, calling
+    `apache_beam.typehints.disable_type_annotations()` before pipeline creation
+    will disable is completely, and decorating specific functions (such as 
+    `process()`) with `@apache_beam.typehints.no_annotations` will disable it
+    for that function.
+
+    More details will be in 
+    [Ensuring Python Type Safety](https://beam.apache.org/documentation/sdks/python-type-safety/)
+    and an upcoming
+    [blog post](https://beam.apache.org/blog/python/typing/2020/03/06/python-typing.html).
+
+* Java SDK: Introducing the concept of options in Beam Schema’s. These options add extra 
+context to fields and schemas. This replaces the current Beam metadata that is present 
+in a FieldType only, options are available in fields and row schemas. Schema options are
+fully typed and can contain complex rows. *Remark: Schema aware is still experimental.*
+([BEAM-9035](https://issues.apache.org/jira/browse/BEAM-9035))
+* Java SDK: The protobuf extension is fully schema aware and also includes protobuf option
+conversion to beam schema options. *Remark: Schema aware is still experimental.*
+([BEAM-9044](https://issues.apache.org/jira/browse/BEAM-9044))
+* Added ability to write to BigQuery via Avro file loads (Python) ([BEAM-8841](https://issues.apache.org/jira/browse/BEAM-8841))
+
+    By default, file loads will be done using JSON, but it is possible to
+    specify the temp_file_format parameter to perform file exports with AVRO.
+    AVRO-based file loads work by exporting Python types into Avro types, so
+    to switch to Avro-based loads, you will need to change your data types
+    from Json-compatible types (string-type dates and timestamp, long numeric
+    values as strings) into Python native types that are written to Avro
+    (Python's date, datetime types, decimal, etc). For more information
+    see https://cloud.google.com/bigquery/docs/loading-data-cloud-storage-avro#avro_conversions.
+* Added integration of Java SDK with Google Cloud AI VideoIntelligence service 
+([BEAM-9147](https://issues.apache.org/jira/browse/BEAM-9147))
+* Added integration of Java SDK with Google Cloud AI natural language processing API
+([BEAM-9634](https://issues.apache.org/jira/browse/BEAM-9634))
+* `docker-pull-licenses` tag was introduced. Licenses/notices of third party dependencies will be added to the docker images when `docker-pull-licenses` was set. 
+  The files are added to `/opt/apache/beam/third_party_licenses/`. 
+  By default, no licenses/notices are added to the docker images. ([BEAM-9136](https://issues.apache.org/jira/browse/BEAM-9136))
+
+ 
+## Breaking Changes
+
+* Dataflow runner now requires the `--region` option to be set, unless a default value is set in the environment ([BEAM-9199](https://issues.apache.org/jira/browse/BEAM-9199)). See [here](https://cloud.google.com/dataflow/docs/concepts/regional-endpoints) for more details.
+* HBaseIO.ReadAll now requires a PCollection of HBaseIO.Read objects instead of HBaseQuery objects ([BEAM-9279](https://issues.apache.org/jira/browse/BEAM-9279)).
+* ProcessContext.updateWatermark has been removed in favor of using a WatermarkEstimator ([BEAM-9430](https://issues.apache.org/jira/browse/BEAM-9430)).
+* Coder inference for PCollection of Row objects has been disabled ([BEAM-9569](https://issues.apache.org/jira/browse/BEAM-9569)).
+* Go SDK docker images are no longer released until further notice.
+
+## Deprecations
+* Java SDK: Beam Schema FieldType.getMetadata is now deprecated and is replaced by the Beam
+Schema Options, it will be removed in version `2.23.0`. ([BEAM-9704](https://issues.apache.org/jira/browse/BEAM-9704))
+* The `--zone` option in the Dataflow runner is now deprecated. Please use `--worker_zone` instead. ([BEAM-9716](https://issues.apache.org/jira/browse/BEAM-9716))
+
+
+## List of Contributors
+
+According to git shortlog, the following people contributed to the 2.21.0 release. Thank you to all contributors!
+
+Aaron Meihm, Adrian Eka, Ahmet Altay, AldairCoronel, Alex Van Boxel, Alexey Romanenko, Andrew Crites, Andrew Pilloud, Ankur Goenka, Badrul (Taki) Chowdhury, Bartok Jozsef, Boyuan Zhang, Brian Hulette, brucearctor, bumblebee-coming, Chad Dombrova, Chamikara Jayalath, Chie Hayashida, Chris Gorgolewski, Chuck Yang, Colm O hEigeartaigh, Curtis "Fjord" Hawthorne, Daniel Mills, Daniel Oliveira, David Yan, Elias Djurfeldt, Emiliano Capoccia, Etienne Chauchot, Fernando Diaz, Filipe Regadas, Gleb Kanterov, Hai Lu, Hannah Jiang, Harch Vardhan, Heejong Lee, Henry Suryawirawan, Hk-tang, Ismaël Mejía, Jacoby, Jan Lukavský, Jeroen Van Goey, jfarr, Jozef Vilcek, Kai Jiang, Kamil Wasilewski, Kenneth Knowles, KevinGG, Kyle Weaver, Kyoungha Min, Luke Cwik, Maximilian Michels, Michal Walenia, Ning Kang, Pablo Estrada, paul fisher, Piotr Szuberski, Reuven Lax, Robert Bradshaw, Robert Burke, Rose Nguyen, Rui Wang, Sam Rohde, Sam Whittle, Spoorti Kundargi, Steve Koonce, sunjincheng121, Ted Yun, Tesio, Thomas Weise, Tomo Suzuki, Udi Meiri, Valentyn Tymofieiev, Vasu Nori, Yichi Zhang, yoshiki.obata, Yueyang Qiu

From eea7d10a5fcdaf700ab3f9593cca78e65799166b Mon Sep 17 00:00:00 2001
From: Jacob Ferriero 
Date: Mon, 18 May 2020 12:20:37 -0700
Subject: [PATCH 015/151] move bundle test resources

---
 ...Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json | 0
 .../Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json    | 0
 ...nesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json | 0
 .../Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json | 0
 .../Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json   | 0
 .../DSTU2/hospitalInformation1586309771387.json                   | 0
 .../DSTU2/practitionerInformation1586309771387.json               | 0
 ...erson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json | 0
 ...Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json | 0
 .../Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json | 0
 ...Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json | 0
 ...ymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json | 0
 .../R4/hospitalInformation1586368892823.json                      | 0
 .../R4/practitionerInformation1586368892823.json                  | 0
 ...ander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json | 0
 ...l991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json | 0
 .../Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json     | 0
 .../Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json    | 0
 ...annette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json | 0
 ...Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json | 0
 .../STU3/hospitalInformation1586298239556.json                    | 0
 .../STU3/practitionerInformation1586298239556.json                | 0
 22 files changed, 0 insertions(+), 0 deletions(-)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/DSTU2/Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/DSTU2/Ernesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/DSTU2/Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/DSTU2/Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/DSTU2/hospitalInformation1586309771387.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/DSTU2/practitionerInformation1586309771387.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/R4/Emerson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/R4/Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/R4/Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/R4/Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/R4/Seymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/R4/hospitalInformation1586368892823.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/R4/practitionerInformation1586368892823.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/STU3/Alexander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/STU3/Basil991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/STU3/Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/STU3/Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/STU3/Dannette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/STU3/Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/STU3/hospitalInformation1586298239556.json (100%)
 rename sdks/java/io/google-cloud-platform/src/test/resources/{ => transactional_bundles}/STU3/practitionerInformation1586298239556.json (100%)

diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Ernesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/Ernesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Ernesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/Ernesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/hospitalInformation1586309771387.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/hospitalInformation1586309771387.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/hospitalInformation1586309771387.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/hospitalInformation1586309771387.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/practitionerInformation1586309771387.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/practitionerInformation1586309771387.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/practitionerInformation1586309771387.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/DSTU2/practitionerInformation1586309771387.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/Emerson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/Emerson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/R4/Emerson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/Emerson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/R4/Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/R4/Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/R4/Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/Seymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/Seymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/R4/Seymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/Seymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/hospitalInformation1586368892823.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/hospitalInformation1586368892823.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/R4/hospitalInformation1586368892823.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/hospitalInformation1586368892823.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/practitionerInformation1586368892823.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/practitionerInformation1586368892823.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/R4/practitionerInformation1586368892823.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/R4/practitionerInformation1586368892823.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Alexander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Alexander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/STU3/Alexander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Alexander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Basil991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Basil991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/STU3/Basil991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Basil991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/STU3/Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/STU3/Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Dannette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Dannette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/STU3/Dannette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Dannette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/STU3/Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/hospitalInformation1586298239556.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/hospitalInformation1586298239556.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/STU3/hospitalInformation1586298239556.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/hospitalInformation1586298239556.json
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/practitionerInformation1586298239556.json b/sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/practitionerInformation1586298239556.json
similarity index 100%
rename from sdks/java/io/google-cloud-platform/src/test/resources/STU3/practitionerInformation1586298239556.json
rename to sdks/java/io/google-cloud-platform/src/test/resources/transactional_bundles/STU3/practitionerInformation1586298239556.json

From 6cf105ae5823e01b793fb4ddbb346342cd606634 Mon Sep 17 00:00:00 2001
From: Sam Rohde 
Date: Mon, 18 May 2020 12:40:43 -0700
Subject: [PATCH 016/151] Add to/from_runner_api_parameters to WriteToBigQuery

Change-Id: Ifd969174d5a7744766173f35fd6b65a72ebfd924
---
 sdks/python/apache_beam/io/gcp/bigquery.py    | 72 +++++++++++++++++++
 .../apache_beam/io/gcp/bigquery_test.py       | 67 +++++++++++++++++
 2 files changed, 139 insertions(+)

diff --git a/sdks/python/apache_beam/io/gcp/bigquery.py b/sdks/python/apache_beam/io/gcp/bigquery.py
index fd6b37087484..f0ad45715c49 100644
--- a/sdks/python/apache_beam/io/gcp/bigquery.py
+++ b/sdks/python/apache_beam/io/gcp/bigquery.py
@@ -271,6 +271,8 @@ def compute_table_name(row):
 from apache_beam.transforms import ParDo
 from apache_beam.transforms import PTransform
 from apache_beam.transforms.display import DisplayDataItem
+from apache_beam.transforms.sideinputs import SIDE_INPUT_PREFIX
+from apache_beam.transforms.sideinputs import get_sideinput_index
 from apache_beam.transforms.window import GlobalWindows
 from apache_beam.utils import retry
 from apache_beam.utils.annotations import deprecated
@@ -1390,6 +1392,9 @@ def __init__(
         and
         https://cloud.google.com/bigquery/docs/loading-data-cloud-storage-json.
     """
+    self._table = table
+    self._dataset = dataset
+    self._project = project
     self.table_reference = bigquery_tools.parse_table_reference(
         table, dataset, project)
     self.create_disposition = BigQueryDisposition.validate_create(
@@ -1517,6 +1522,73 @@ def display_data(self):
       res['table'] = DisplayDataItem(tableSpec, label='Table')
     return res
 
+  def to_runner_api_parameter(self, context):
+    from apache_beam.internal import pickler
+
+    # It'd be nice to name these according to their actual
+    # names/positions in the orignal argument list, but such a
+    # transformation is currently irreversible given how
+    # remove_objects_from_args and insert_values_in_args
+    # are currently implemented.
+    def serialize(side_inputs):
+      return {(SIDE_INPUT_PREFIX + '%s') % ix:
+              si.to_runner_api(context).SerializeToString()
+              for ix,
+              si in enumerate(side_inputs)}
+
+    table_side_inputs = serialize(self.table_side_inputs)
+    schema_side_inputs = serialize(self.schema_side_inputs)
+
+    config = {
+        'table': self._table,
+        'dataset': self._dataset,
+        'project': self._project,
+        'schema': self.schema,
+        'create_disposition': self.create_disposition,
+        'write_disposition': self.write_disposition,
+        'kms_key': self.kms_key,
+        'batch_size': self.batch_size,
+        'max_file_size': self.max_file_size,
+        'max_files_per_bundle': self.max_files_per_bundle,
+        'custom_gcs_temp_location': self.custom_gcs_temp_location,
+        'method': self.method,
+        'insert_retry_strategy': self.insert_retry_strategy,
+        'additional_bq_parameters': self.additional_bq_parameters,
+        'table_side_inputs': table_side_inputs,
+        'schema_side_inputs': schema_side_inputs,
+        'triggering_frequency': self.triggering_frequency,
+        'validate': self._validate,
+        'temp_file_format': self._temp_file_format,
+    }
+    return 'beam:transform:write_to_big_query:v0', pickler.dumps(config)
+
+  @PTransform.register_urn('beam:transform:write_to_big_query:v0', bytes)
+  def from_runner_api(unused_ptransform, payload, context):
+    from apache_beam.internal import pickler
+    from apache_beam.portability.api.beam_runner_api_pb2 import SideInput
+
+    config = pickler.loads(payload)
+
+    def deserialize(side_inputs):
+      deserialized_side_inputs = {}
+      for k, v in side_inputs.items():
+        side_input = SideInput()
+        side_input.ParseFromString(v)
+        deserialized_side_inputs[k] = side_input
+
+      # This is an ordered list stored as a dict (see the comments in
+      # to_runner_api_parameter above).
+      indexed_side_inputs = [(
+          get_sideinput_index(tag),
+          pvalue.AsSideInput.from_runner_api(si, context)) for tag,
+                             si in deserialized_side_inputs.items()]
+      return [si for _, si in sorted(indexed_side_inputs)]
+
+    config['table_side_inputs'] = deserialize(config['table_side_inputs'])
+    config['schema_side_inputs'] = deserialize(config['schema_side_inputs'])
+
+    return WriteToBigQuery(**config)
+
 
 class _PassThroughThenCleanup(PTransform):
   """A PTransform that invokes a DoFn after the input PCollection has been
diff --git a/sdks/python/apache_beam/io/gcp/bigquery_test.py b/sdks/python/apache_beam/io/gcp/bigquery_test.py
index 8c2bfe8f0d76..5c0597869517 100644
--- a/sdks/python/apache_beam/io/gcp/bigquery_test.py
+++ b/sdks/python/apache_beam/io/gcp/bigquery_test.py
@@ -584,6 +584,73 @@ def test_schema_autodetect_not_allowed_with_avro_file_loads(self):
                 schema=beam.io.gcp.bigquery.SCHEMA_AUTODETECT,
                 temp_file_format=bigquery_tools.FileFormat.AVRO))
 
+  def test_to_from_runner_api(self):
+    """Tests that serialization of WriteToBigQuery is correct.
+
+    This is not intended to be a change-detector test. As such, this only tests
+    the more complicated serialization logic of parameters: ValueProviders,
+    callables, and side inputs.
+    """
+    FULL_OUTPUT_TABLE = 'test_project:output_table'
+
+    p = TestPipeline(
+        additional_pipeline_args=["--experiments=use_beam_bq_sink"])
+
+    # Used for testing side input parameters.
+    table_record_pcv = beam.pvalue.AsDict(
+        p | "MakeTable" >> beam.Create([('table', FULL_OUTPUT_TABLE)]))
+
+    # Used for testing value provider parameters.
+    schema = value_provider.StaticValueProvider(str, '"a:str"')
+
+    original = WriteToBigQuery(
+        table=lambda _,
+        side_input: side_input['table'],
+        table_side_inputs=(table_record_pcv, ),
+        schema=schema)
+
+    # pylint: disable=expression-not-assigned
+    p | 'MyWriteToBigQuery' >> original
+
+    # Run the pipeline through to generate a pipeline proto from an empty
+    # context. This ensures that the serialization code ran.
+    pipeline_proto, context = TestPipeline.from_runner_api(
+        p.to_runner_api(), p.runner, p.get_pipeline_options()).to_runner_api(
+            return_context=True)
+
+    # Find the transform from the context.
+    write_to_bq_id = [
+        k for k,
+        v in pipeline_proto.components.transforms.items()
+        if v.unique_name == 'MyWriteToBigQuery'
+    ][0]
+    deserialized_node = context.transforms.get_by_id(write_to_bq_id)
+    deserialized = deserialized_node.transform
+    self.assertIsInstance(deserialized, WriteToBigQuery)
+
+    # Test that the serialization of a value provider is correct.
+    self.assertEqual(original.schema, deserialized.schema)
+
+    # Test that the serialization of a callable is correct.
+    self.assertEqual(
+        deserialized._table(None, {'table': FULL_OUTPUT_TABLE}),
+        FULL_OUTPUT_TABLE)
+
+    # Test that the serialization of a side input is correct.
+    self.assertEqual(
+        len(original.table_side_inputs), len(deserialized.table_side_inputs))
+    original_side_input_data = original.table_side_inputs[0]._side_input_data()
+    deserialized_side_input_data = deserialized.table_side_inputs[
+        0]._side_input_data()
+    self.assertEqual(
+        original_side_input_data.access_pattern,
+        deserialized_side_input_data.access_pattern)
+    self.assertEqual(
+        original_side_input_data.window_mapping_fn,
+        deserialized_side_input_data.window_mapping_fn)
+    self.assertEqual(
+        original_side_input_data.view_fn, deserialized_side_input_data.view_fn)
+
 
 @unittest.skipIf(HttpError is None, 'GCP dependencies are not installed')
 class BigQueryStreamingInsertTransformTests(unittest.TestCase):

From e80ee15f8f76f126d83a9a20ed837c985c09c934 Mon Sep 17 00:00:00 2001
From: Jacob Ferriero 
Date: Mon, 18 May 2020 15:20:10 -0700
Subject: [PATCH 017/151] wip

---
 .../sdk/transforms/SerializableFunction.java  |   3 +-
 .../beam/sdk/io/gcp/healthcare/FhirIO.java    | 101 ++++-
 .../sdk/io/gcp/healthcare/FhirIOTestUtil.java |   5 +-
 .../sdk/io/gcp/healthcare/FhirIOWriteIT.java  |  65 ++++
 .../resources/resources/DSTU2/CarePlan.ndjson |   3 +
 .../resources/resources/DSTU2/Claim.ndjson    |  25 ++
 .../resources/DSTU2/Condition.ndjson          |   4 +
 .../resources/DSTU2/DiagnosticReport.ndjson   |   1 +
 .../resources/DSTU2/Encounter.ndjson          |  16 +
 .../resources/DSTU2/ImagingStudy.ndjson       |   1 +
 .../resources/DSTU2/Immunization.ndjson       |   9 +
 .../resources/DSTU2/MedicationOrder.ndjson    |   9 +
 .../resources/DSTU2/Observation.ndjson        |  54 +++
 .../resources/DSTU2/Organization.ndjson       |   2 +
 .../resources/resources/DSTU2/Patient.ndjson  |   1 +
 .../resources/DSTU2/Practitioner.ndjson       |   2 +
 .../resources/DSTU2/Procedure.ndjson          |   7 +
 .../hospitalInformation1589831190233.json     | 183 +++++++++
 .../practitionerInformation1589831190233.json | 135 +++++++
 .../resources/resources/R4/CarePlan.ndjson    |   3 +
 .../resources/resources/R4/CareTeam.ndjson    |   3 +
 .../test/resources/resources/R4/Claim.ndjson  |  25 ++
 .../resources/resources/R4/Condition.ndjson   |   4 +
 .../resources/R4/DiagnosticReport.ndjson      |  17 +
 .../resources/R4/DocumentReference.ndjson     |  16 +
 .../resources/resources/R4/Encounter.ndjson   |  16 +
 .../resources/R4/ExplanationOfBenefit.ndjson  |  16 +
 .../resources/R4/ImagingStudy.ndjson          |   1 +
 .../resources/R4/Immunization.ndjson          |   9 +
 .../resources/resources/R4/Location.ndjson    |   2 +
 .../resources/R4/MedicationRequest.ndjson     |   9 +
 .../resources/resources/R4/Observation.ndjson |  54 +++
 .../resources/R4/Organization.ndjson          |   2 +
 .../resources/resources/R4/Patient.ndjson     |   1 +
 .../resources/R4/Practitioner.ndjson          |   2 +
 .../resources/R4/PractitionerRole.ndjson      |   2 +
 .../resources/resources/R4/Procedure.ndjson   |   7 +
 .../resources/resources/R4/Provenance.ndjson  |   1 +
 .../R4/hospitalInformation1589831190233.json  | 318 ++++++++++++++++
 .../practitionerInformation1589831190233.json | 354 ++++++++++++++++++
 .../resources/resources/STU3/CarePlan.ndjson  |   3 +
 .../resources/resources/STU3/Claim.ndjson     |  25 ++
 .../resources/resources/STU3/Condition.ndjson |   4 +
 .../resources/STU3/DiagnosticReport.ndjson    |   1 +
 .../resources/resources/STU3/Encounter.ndjson |  16 +
 .../STU3/ExplanationOfBenefit.ndjson          |  16 +
 .../resources/STU3/ImagingStudy.ndjson        |   1 +
 .../resources/STU3/Immunization.ndjson        |   9 +
 .../resources/STU3/MedicationRequest.ndjson   |   9 +
 .../resources/STU3/Observation.ndjson         |  54 +++
 .../resources/STU3/Organization.ndjson        |   2 +
 .../resources/resources/STU3/Patient.ndjson   |   1 +
 .../resources/STU3/Practitioner.ndjson        |   2 +
 .../resources/resources/STU3/Procedure.ndjson |   7 +
 .../hospitalInformation1589831190233.json     | 234 ++++++++++++
 .../practitionerInformation1589831190233.json | 135 +++++++
 56 files changed, 1994 insertions(+), 13 deletions(-)
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/CarePlan.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Claim.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Condition.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/DiagnosticReport.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Encounter.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/ImagingStudy.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Immunization.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/MedicationOrder.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Observation.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Organization.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Patient.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Practitioner.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Procedure.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/hospitalInformation1589831190233.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/practitionerInformation1589831190233.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/CarePlan.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/CareTeam.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Claim.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Condition.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/DiagnosticReport.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/DocumentReference.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Encounter.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/ExplanationOfBenefit.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/ImagingStudy.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Immunization.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Location.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/MedicationRequest.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Observation.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Organization.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Patient.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Practitioner.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/PractitionerRole.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Procedure.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Provenance.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/hospitalInformation1589831190233.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/practitionerInformation1589831190233.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/CarePlan.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Claim.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Condition.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/DiagnosticReport.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Encounter.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/ExplanationOfBenefit.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/ImagingStudy.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Immunization.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/MedicationRequest.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Observation.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Organization.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Patient.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Practitioner.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Procedure.ndjson
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/hospitalInformation1589831190233.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/practitionerInformation1589831190233.json

diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java
index a1dba9e688fe..3dbe893eef4e 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java
@@ -17,6 +17,7 @@
  */
 package org.apache.beam.sdk.transforms;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import java.io.Serializable;
 
 /**
@@ -35,5 +36,5 @@ public interface SerializableFunction
     extends ProcessFunction, Serializable {
   /** Returns the result of invoking this function on the given input. */
   @Override
-  OutputT apply(InputT input);
+  OutputT apply(InputT input) throws JsonProcessingException;
 }
diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
index e7edee513735..5446c58dc40c 100644
--- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
+++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
@@ -1250,6 +1250,27 @@ public void executeBundles(ProcessContext context) {
     }
   }
 
+  /**
+   * Create resources fhir io . create resources.
+   *
+   * @param  the type parameter
+   * @param fhirStore the fhir store
+   * @return the fhir io . create resources
+   */
+  public static  FhirIO.CreateResources createResources(ValueProvider fhirStore){
+    return new CreateResources(fhirStore);
+  }
+
+  /**
+   * Create resources fhir io . create resources.
+   *
+   * @param  the type parameter
+   * @param fhirStore the fhir store
+   * @return the fhir io . create resources
+   */
+  public static  FhirIO.CreateResources createResources(String fhirStore){
+    return new CreateResources(fhirStore);
+  }
   /**
    * {@link PTransform} for Creating FHIR resources.
    *
@@ -1257,31 +1278,27 @@ public void executeBundles(ProcessContext context) {
    */
   public static class CreateResources extends PTransform, Write.Result> {
     private final String fhirStore;
-    private final String type;
     private SerializableFunction ifNoneExistFunction;
     private SerializableFunction formatBodyFunction;
+    private SerializableFunction typeFunction;
     private static final Logger LOG = LoggerFactory.getLogger(CreateResources.class);
 
     /**
      * Instantiates a new Create resources transform.
      *
      * @param fhirStore the fhir store
-     * @param type the type
      */
-    CreateResources(ValueProvider fhirStore, String type) {
+    CreateResources(ValueProvider fhirStore) {
       this.fhirStore = fhirStore.get();
-      this.type = type;
     }
 
     /**
      * Instantiates a new Create resources.
      *
      * @param fhirStore the fhir store
-     * @param type the type
      */
-    CreateResources(String fhirStore, String type) {
+    CreateResources(String fhirStore) {
       this.fhirStore = fhirStore;
-      this.type = type;
     }
 
     /**
@@ -1300,6 +1317,20 @@ public CreateResources withIfNotExistFunction(
       return this;
     }
 
+    /**
+     * This adds a {@link SerializableFunction} that reads an resource string and extracts an
+     * resource type.
+     *
+     * 
    https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/create
+     *
+     * @param typeFunction for extracting type from a resource.
+     * @return the create resources
+     */
+    public CreateResources withTypeFunction(
+        SerializableFunction typeFunction) {
+      this.typeFunction = typeFunction;
+      return this;
+    }
     /**
      * With format body function create resources.
      *
@@ -1314,6 +1345,9 @@ public CreateResources withFormatBodyFunction(
 
     @Override
     public FhirIO.Write.Result expand(PCollection input) {
+      checkArgument(
+          typeFunction != null,
+          "FhirIO.CreateResources should always be called with a " + "withTypeFunction");
       checkArgument(
           formatBodyFunction != null,
           "FhirIO.CreateResources should always be called with a " + "withFromatBodyFunction");
@@ -1327,7 +1361,7 @@ public FhirIO.Write.Result expand(PCollection input) {
           input
               .apply(
                   ParDo.of(
-                      new CreateFn(fhirStore, type, formatBodyFunction, ifNoneExistFunction)))
+                      new CreateFn(fhirStore, typeFunction, formatBodyFunction, ifNoneExistFunction)))
               .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of())));
     }
 
@@ -1337,17 +1371,17 @@ static class CreateFn extends DoFn> {
       private transient HealthcareApiClient client;
       private final ObjectMapper mapper = new ObjectMapper();
       private final String fhirStore;
-      private final String type;
       private SerializableFunction ifNoneExistFunction;
       private SerializableFunction formatBodyFunction;
+      private SerializableFunction typeFunction;
 
       CreateFn(
           String fhirStore,
-          String type,
+          SerializableFunction typeFunction,
           SerializableFunction formatBodyFunction,
           @Nullable SerializableFunction ifNoneExistFunction) {
         this.fhirStore = fhirStore;
-        this.type = type;
+        this.typeFunction = typeFunction;
         this.formatBodyFunction = formatBodyFunction;
         this.ifNoneExistFunction = ifNoneExistFunction;
       }
@@ -1361,6 +1395,7 @@ public void initClient() throws IOException {
       public void create(ProcessContext context) {
         T input = context.element();
         String body = formatBodyFunction.apply(input);
+        String type = typeFunction.apply(input);
         try {
           // Validate that data was set to valid JSON.
           mapper.readTree(input.toString());
@@ -1378,6 +1413,28 @@ public void create(ProcessContext context) {
     }
   }
 
+  /**
+   * Update resources update resources.
+   *
+   * @param  the type parameter
+   * @param fhirStore the fhir store
+   * @return the update resources
+   */
+  public static  UpdateResources update(ValueProvider fhirStore){
+    return new UpdateResources(fhirStore);
+  }
+
+  /**
+   * Update resources update resources.
+   *
+   * @param  the type parameter
+   * @param fhirStore the fhir store
+   * @return the update resources
+   */
+  public static  UpdateResources update(String fhirStore){
+    return new UpdateResources(fhirStore);
+  }
+
   /**
    * {@link PTransform} for Updating FHIR resources resources.
    *
@@ -1488,6 +1545,28 @@ public void update(ProcessContext context) {
     }
   }
 
+  /**
+   * Conditional update conditional update.
+   *
+   * @param  the type parameter
+   * @param fhirStore the fhir store
+   * @return the conditional update
+   */
+  public static  ConditionalUpdate conditionalUpdate(ValueProvider fhirStore){
+   return new ConditionalUpdate(fhirStore);
+  }
+
+  /**
+   * Conditional update conditional update.
+   *
+   * @param  the type parameter
+   * @param fhirStore the fhir store
+   * @return the conditional update
+   */
+  public static  ConditionalUpdate conditionalUpdate(String fhirStore){
+    return new ConditionalUpdate(fhirStore);
+  }
+
   /**
    * {@link PTransform} to perform Conditional updates on the FHIR store.
    *
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java
index 4bbea81cb87e..1c3a795fc2ec 100644
--- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java
@@ -44,8 +44,11 @@
 class FhirIOTestUtil {
   public static final String DEFAULT_TEMP_BUCKET = "temp-storage-for-healthcare-io-tests";
 
+  // TODO read initial resources function.
+  // TODO read update resources function.
+  // TODO spot check resource update utility.
   private static Stream readPrettyBundles(String version) {
-    Path resourceDir = Paths.get("src", "test", "resources", version);
+    Path resourceDir = Paths.get("src", "test", "resources", "transactional_bundles",version);
     String absolutePath = resourceDir.toFile().getAbsolutePath();
     File dir = new File(absolutePath);
     File[] fhirJsons = dir.listFiles();
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java
index e8e06c60493c..8d46186c472b 100644
--- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java
@@ -25,12 +25,17 @@
 import java.security.SecureRandom;
 import java.util.Arrays;
 import java.util.Collection;
+import java.util.HashMap;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import java.util.Map;
 import org.apache.beam.sdk.Pipeline;
 import org.apache.beam.sdk.extensions.gcp.options.GcpOptions;
 import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure;
+import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Write.Result;
 import org.apache.beam.sdk.options.PipelineOptionsFactory;
 import org.apache.beam.sdk.testing.PAssert;
 import org.apache.beam.sdk.testing.TestPipeline;
+import org.apache.beam.sdk.transforms.Count;
 import org.apache.beam.sdk.transforms.Create;
 import org.junit.After;
 import org.junit.AfterClass;
@@ -128,4 +133,64 @@ public void testFhirIO_Import() {
   }
 
   // TODO(jaketf) add IT for conditional create, update, conditional update transforms.
+  @Test
+  public void testFhirIO_CreateResources() {
+    FhirIO.Write.Result writeResult =
+        (Result) pipeline
+            .apply(Create.of(BUNDLES.get(version)))
+            .apply(FhirIO.createResources(options.getFhirStore())
+                .withTypeFunction((String resource) -> {
+                  ObjectMapper mapper = new ObjectMapper();
+                  Map map = mapper.readValue(resource, Map.class);
+                  return map.get("resourceType");
+
+                })
+                .withIfNotExistFunction((String resource) -> {
+                  ObjectMapper mapper = new ObjectMapper();
+                  Map map = mapper.readValue(resource, Map.class);
+                  String id = map.get("id");
+                  return String.format("_id=%s", id);
+                })
+                .withFormatBodyFunction((String x) -> x)
+            );
+
+
+    // TODO have a known number of pre-condition failed case and assert it appears in error queue
+    PAssert.thatSingleton(writeResult.getFailedBodies().apply(Count.globally())).isEqualTo(1L);
+
+    pipeline.run().waitUntilFinish();
+  }
+
+  @Test
+  public void testFhirIO_Update() {
+    // TODO write initial resources to FHIR
+    // use beam to perform updates
+    FhirIO.Write.Result writeResult =
+        (Result) pipeline
+            .apply(Create.of(BUNDLES.get(version)))
+            .apply(FhirIO.update(options.getFhirStore())
+                .withFormatBodyFunction(x -> "{}")
+                .withResourceNameFunction(x -> "name")
+            );
+
+    PAssert.that(writeResult.getFailedBodies()).empty();
+
+    pipeline.run().waitUntilFinish();
+    // TODO spot check update results
+  }
+
+  @Test
+  public void testFhirIO_ConditionalUpdate() {
+    // TODO write initial resources to FHIR
+    FhirIO.Write.Result writeResult =
+        (Result) pipeline
+            .apply(Create.of(BUNDLES.get(version)))
+            .apply(FhirIO.conditionalUpdate(options.getFhirStore())
+                .withTypeFunction(x -> "patient")
+                .withFormatBodyFunction(x -> "{}")
+                .withSearchParametersFunction(x-> new HashMap())
+            );
+    // TODO spot check update results
+    // TODO have a known number of pre-condition failed case and assert it appears in error queue
+  }
 }
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/CarePlan.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/CarePlan.ndjson
new file mode 100644
index 000000000000..a4034d143b89
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/CarePlan.ndjson
@@ -0,0 +1,3 @@
+{"resourceType":"CarePlan","id":"ba15e4c6-414b-4385-8abf-7be2eae77983","text":{"status":"generated","div":"
    Respiratory therapy
    "},"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"status":"completed","context":{"reference":"Encounter/429ca9b0-f562-4845-aff6-0b6fc3aa1085"},"period":{"start":"2015-04-12T14:15:05-07:00","end":"2015-04-19T14:15:05-07:00"},"category":[{"coding":[{"system":"http://snomed.info/sct","code":"53950000","display":"Respiratory therapy"}],"text":"Respiratory therapy"}],"addresses":[{"reference":"Condition/46d525ba-6571-44de-a6b0-e43a3810bc8e"}],"activity":[{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"304510005","display":"Recommendation to avoid exercise"}],"text":"Recommendation to avoid exercise"},"status":"completed","prohibited":false}},{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"371605008","display":"Deep breathing and coughing exercises"}],"text":"Deep breathing and coughing exercises"},"status":"completed","prohibited":false}}]}
+{"resourceType":"CarePlan","id":"c9f29319-842a-4528-8866-b915f558d66b","text":{"status":"generated","div":"
    Fracture care
    "},"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"status":"completed","context":{"reference":"Encounter/0059d564-708d-467b-b8d8-449492ad93c7"},"period":{"start":"2016-10-30T14:15:05-07:00","end":"2016-12-29T13:15:05-08:00"},"category":[{"coding":[{"system":"http://snomed.info/sct","code":"385691007","display":"Fracture care"}],"text":"Fracture care"}],"addresses":[{"reference":"Condition/b1cecfd7-b8b9-4159-98c8-95e7ad63d74a"}],"activity":[{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"183051005","display":"Recommendation to rest"}],"text":"Recommendation to rest"},"status":"completed","prohibited":false}},{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"408580007","display":"Physical activity target light exercise"}],"text":"Physical activity target light exercise"},"status":"completed","prohibited":false}}]}
+{"resourceType":"CarePlan","id":"0b324605-d5b0-4356-a80b-59148979151a","text":{"status":"generated","div":"
    Minor surgery care management (procedure)
    "},"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"status":"completed","context":{"reference":"Encounter/dd792a18-dcd6-4d70-ad52-78a04ab63018"},"period":{"start":"2018-02-09T13:15:05-08:00","end":"2018-02-23T13:15:05-08:00"},"category":[{"coding":[{"system":"http://snomed.info/sct","code":"737471002","display":"Minor surgery care management (procedure)"}],"text":"Minor surgery care management (procedure)"}],"activity":[{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"183051005","display":"Recommendation to rest"}],"text":"Recommendation to rest"},"status":"completed","prohibited":false}},{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"243077000","display":"Recommendation to limit sexual activity"}],"text":"Recommendation to limit sexual activity"},"status":"completed","prohibited":false}}]}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Claim.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Claim.ndjson
new file mode 100644
index 000000000000..49cc9d98c2b9
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Claim.ndjson
@@ -0,0 +1,25 @@
+{"resourceType":"Claim","id":"fd5133df-a283-4ed2-a0a1-600c5f781504","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","prescription":{"reference":"MedicationOrder/759887f5-cdb3-42aa-ba72-403b3c1017ec"},"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"}}
+{"resourceType":"Claim","id":"40f42d0e-2644-4b93-b81e-aa8333f5d107","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","diagnosis":[{"sequence":1,"diagnosis":{"system":"http://snomed.info/sct","code":"43878008","display":"Streptococcal sore throat (disorder)"}}],"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"item":[{"sequence":1,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"185345009","display":"Encounter for symptom"}}]}
+{"resourceType":"Claim","id":"c3d7130b-eab8-472f-86d6-21dd373ad796","type":"institutional","organization":{"reference":"Organization/58fe1815-1e8a-38ed-a91a-17d4ef18c8d8"},"use":"complete","patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"item":[{"sequence":1,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"162673000","display":"General examination of patient (procedure)"}},{"sequence":2,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://hl7.org/fhir/sid/cvx","code":"140","display":"Influenza, seasonal, injectable, preservative free"},"net":{"value":140.52,"system":"urn:iso:std:iso:4217","code":"USD"}},{"sequence":3,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"430193006","display":"Medication Reconciliation (procedure)"},"net":{"value":504.83,"system":"urn:iso:std:iso:4217","code":"USD"}}]}
+{"resourceType":"Claim","id":"f0059888-64fd-4177-b90f-dbb450d95914","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","prescription":{"reference":"MedicationOrder/e1582c1a-e002-40be-8e5e-041d71b32945"},"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"}}
+{"resourceType":"Claim","id":"aea74302-dc46-4032-80b9-dfc41748edf3","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"item":[{"sequence":1,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"698314001","display":"Consultation for treatment"}}]}
+{"resourceType":"Claim","id":"8e1db8cc-ce4c-426c-8421-a9d518a30a73","type":"institutional","organization":{"reference":"Organization/58fe1815-1e8a-38ed-a91a-17d4ef18c8d8"},"use":"complete","patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"item":[{"sequence":1,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"162673000","display":"General examination of patient (procedure)"}},{"sequence":2,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://hl7.org/fhir/sid/cvx","code":"140","display":"Influenza, seasonal, injectable, preservative free"},"net":{"value":140.52,"system":"urn:iso:std:iso:4217","code":"USD"}}]}
+{"resourceType":"Claim","id":"a53e8d15-f6ab-4c5a-b984-c60796304d9c","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","prescription":{"reference":"MedicationOrder/442bf25b-fd87-4bec-9c71-7fff3389f54d"},"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"}}
+{"resourceType":"Claim","id":"7fab04c8-ea33-4cc3-a050-0b8008a50409","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"item":[{"sequence":1,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"698314001","display":"Consultation for treatment"}}]}
+{"resourceType":"Claim","id":"98f46e66-f451-47db-81cc-f77bed1e183c","type":"institutional","organization":{"reference":"Organization/58fe1815-1e8a-38ed-a91a-17d4ef18c8d8"},"use":"complete","patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"item":[{"sequence":1,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"162673000","display":"General examination of patient (procedure)"}},{"sequence":2,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://hl7.org/fhir/sid/cvx","code":"140","display":"Influenza, seasonal, injectable, preservative free"},"net":{"value":140.52,"system":"urn:iso:std:iso:4217","code":"USD"}},{"sequence":3,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://hl7.org/fhir/sid/cvx","code":"113","display":"Td (adult) preservative free"},"net":{"value":140.52,"system":"urn:iso:std:iso:4217","code":"USD"}},{"sequence":4,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://hl7.org/fhir/sid/cvx","code":"43","display":"Hep B, adult"},"net":{"value":140.52,"system":"urn:iso:std:iso:4217","code":"USD"}},{"sequence":5,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://hl7.org/fhir/sid/cvx","code":"114","display":"meningococcal MCV4P"},"net":{"value":140.52,"system":"urn:iso:std:iso:4217","code":"USD"}}]}
+{"resourceType":"Claim","id":"75510ac1-f51c-4fad-a255-711d8d1acfbe","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","prescription":{"reference":"MedicationOrder/2339a360-d66a-4518-848b-f2ebdf0db27e"},"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"}}
+{"resourceType":"Claim","id":"89f97d6a-9511-4cf8-84fe-9c8369af8188","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"item":[{"sequence":1,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"698314001","display":"Consultation for treatment"}}]}
+{"resourceType":"Claim","id":"ea6a35dc-0be4-4be9-90ec-88f58800b35b","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","prescription":{"reference":"MedicationOrder/417abd1f-43e3-446f-8b4e-3b237bc6c1ba"},"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"}}
+{"resourceType":"Claim","id":"966e64bb-385a-4ac0-b97e-4cfa225ecea5","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","diagnosis":[{"sequence":1,"diagnosis":{"system":"http://snomed.info/sct","code":"10509002","display":"Acute bronchitis (disorder)"}}],"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"item":[{"sequence":1,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"185345009","display":"Encounter for symptom"}},{"sequence":3,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"399208008","display":"Plain chest X-ray (procedure)"},"net":{"value":6535.58,"system":"urn:iso:std:iso:4217","code":"USD"}}]}
+{"resourceType":"Claim","id":"f731e722-2f3b-4c90-8488-2595ae8374b6","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"item":[{"sequence":1,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"185349003","display":"Encounter for check up (procedure)"}},{"sequence":2,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://hl7.org/fhir/sid/cvx","code":"140","display":"Influenza, seasonal, injectable, preservative free"},"net":{"value":140.52,"system":"urn:iso:std:iso:4217","code":"USD"}},{"sequence":3,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://hl7.org/fhir/sid/cvx","code":"43","display":"Hep B, adult"},"net":{"value":140.52,"system":"urn:iso:std:iso:4217","code":"USD"}}]}
+{"resourceType":"Claim","id":"0b196692-83fa-4edd-beab-fc1a4e3a31b3","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","prescription":{"reference":"MedicationOrder/fe1a0af0-3bb4-4864-a7f6-8bc91a6f29e6"},"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"}}
+{"resourceType":"Claim","id":"e1b59b3b-65ee-45f0-ae4d-5c69fadd3e94","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"item":[{"sequence":1,"type":{"system":"http://hl7.org/fhir/v3/ActCode","code":"CSINV","display":"clinical service invoice"},"service":{"system":"http://snomed.info/sct","code":"698314001","display":"Consultation for treatment"}}]}
+{"resourceType":"Claim","id":"a975e6b7-b0ee-4df0-b1f3-406da196f899","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","prescription":{"reference":"MedicationOrder/8fcc3aa1-2288-4c60-9670-8c756295d7e1"},"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"}}
+{"resourceType":"Claim","id":"37aa3b3c-0bd6-4756-bdba-a19c17b6f3ff","type":"institutional","organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa"},"use":"complete","prescription":{"reference":"MedicationOrder/7dc37b2f-c065-48fc-a5e4-c0973fe705b7"},"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"}}
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Condition.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Condition.ndjson
new file mode 100644
index 000000000000..03293ca003c5
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Condition.ndjson
@@ -0,0 +1,4 @@
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/DiagnosticReport.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/DiagnosticReport.ndjson
new file mode 100644
index 000000000000..446b6c943cfe
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/DiagnosticReport.ndjson
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+{"resourceType":"DiagnosticReport","id":"202599a0-96e1-40d7-ad50-7759082e833b","status":"final","category":{"coding":[{"system":"http://hl7.org/fhir/ValueSet/diagnostic-service-sections","code":"LAB"}]},"code":{"coding":[{"system":"http://loinc.org","code":"58410-2","display":"Complete blood count (hemogram) panel - Blood by Automated count"}],"text":"Complete blood count (hemogram) panel - Blood by Automated count"},"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"encounter":{"reference":"Encounter/c416f8eb-c3b5-4c45-bfb8-4617e9050442"},"effectiveDateTime":"2014-06-12T14:15:05-07:00","issued":"2014-06-12T14:15:05.225-07:00","performer":{"reference":"Organization/58fe1815-1e8a-38ed-a91a-17d4ef18c8d8"},"result":[{"reference":"Observation/af682f69-afe1-4d95-b2ff-701e99b48057","display":"Platelet mean volume [Entitic volume] in Blood by Automated count"}]}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Encounter.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Encounter.ndjson
new file mode 100644
index 000000000000..53f484883471
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Encounter.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/ImagingStudy.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/ImagingStudy.ndjson
new file mode 100644
index 000000000000..a59b691dd652
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/ImagingStudy.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Immunization.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Immunization.ndjson
new file mode 100644
index 000000000000..fa03bd45f190
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Immunization.ndjson
@@ -0,0 +1,9 @@
+{"resourceType":"Immunization","id":"217e6566-fef3-4cfc-9bc1-b4dda86f4a7d","status":"completed","date":"2010-06-03T14:15:05-07:00","vaccineCode":{"coding":[{"system":"http://hl7.org/fhir/sid/cvx","code":"140","display":"Influenza, seasonal, injectable, preservative free"}],"text":"Influenza, seasonal, injectable, preservative free"},"patient":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"wasNotGiven":false,"reported":false,"encounter":{"reference":"Encounter/2a0b33f5-4f48-468a-b814-16415492c421"}}
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/MedicationOrder.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/MedicationOrder.ndjson
new file mode 100644
index 000000000000..a29d53277cff
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/MedicationOrder.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Observation.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Observation.ndjson
new file mode 100644
index 000000000000..a139a7c21cc7
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Observation.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Organization.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Organization.ndjson
new file mode 100644
index 000000000000..6e8753228fa1
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Organization.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Patient.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Patient.ndjson
new file mode 100644
index 000000000000..d8d4f4a9c389
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Patient.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Practitioner.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Practitioner.ndjson
new file mode 100644
index 000000000000..e40c5c9d1f46
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Practitioner.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Procedure.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Procedure.ndjson
new file mode 100644
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+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/Procedure.ndjson
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+{"resourceType":"Procedure","id":"ef872ffd-e080-4432-bd24-1d41aef41ed7","subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"status":"completed","code":{"coding":[{"system":"http://snomed.info/sct","code":"168594001","display":"Clavicle X-ray"}],"text":"Clavicle X-ray"},"performedPeriod":{"start":"2016-10-30T14:15:05-07:00","end":"2016-10-30T14:45:05-07:00"},"encounter":{"reference":"Encounter/0059d564-708d-467b-b8d8-449492ad93c7"}}
+{"resourceType":"Procedure","id":"61a3a3f6-bcad-49ef-ab79-ea87fab516cc","subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"status":"completed","code":{"coding":[{"system":"http://snomed.info/sct","code":"305428000","display":"Admission to orthopedic department"}],"text":"Admission to orthopedic department"},"reasonReference":{"reference":"Condition/b1cecfd7-b8b9-4159-98c8-95e7ad63d74a"},"performedPeriod":{"start":"2016-10-30T14:15:05-07:00","end":"2016-10-30T15:15:05-07:00"},"encounter":{"reference":"Encounter/0059d564-708d-467b-b8d8-449492ad93c7"}}
+{"resourceType":"Procedure","id":"cdfebd64-8e72-4aec-bd6a-2be27eb41b82","subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"status":"completed","code":{"coding":[{"system":"http://snomed.info/sct","code":"430193006","display":"Medication Reconciliation (procedure)"}],"text":"Medication Reconciliation (procedure)"},"performedPeriod":{"start":"2017-06-15T14:15:05-07:00","end":"2017-06-15T14:30:05-07:00"},"encounter":{"reference":"Encounter/6ca65d01-35b1-4b58-8ee7-d4a6cedd2f5c"}}
+{"resourceType":"Procedure","id":"b34c7fd4-6bb2-4c62-9d3c-98aa4e125251","subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"status":"completed","code":{"coding":[{"system":"http://snomed.info/sct","code":"287664005","display":"Bilateral tubal ligation"}],"text":"Bilateral tubal ligation"},"performedPeriod":{"start":"2018-02-09T13:15:05-08:00","end":"2018-02-09T15:15:05-08:00"},"encounter":{"reference":"Encounter/dd792a18-dcd6-4d70-ad52-78a04ab63018"}}
+{"resourceType":"Procedure","id":"edf461c8-c51f-4161-bc66-7b61e12627af","subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"status":"completed","code":{"coding":[{"system":"http://snomed.info/sct","code":"117015009","display":"Throat culture (procedure)"}],"text":"Throat culture (procedure)"},"reasonReference":{"reference":"Condition/83443d35-4ad0-43f9-9d04-a38fd1a40546"},"performedPeriod":{"start":"2018-12-11T13:15:05-08:00","end":"2018-12-11T13:30:05-08:00"},"encounter":{"reference":"Encounter/bfb92e78-2a6d-4a28-8cac-9511f1ec98ce"}}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/hospitalInformation1589831190233.json b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/hospitalInformation1589831190233.json
new file mode 100644
index 000000000000..9cf9888c287a
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/hospitalInformation1589831190233.json
@@ -0,0 +1,183 @@
+{
+  "resourceType": "Bundle",
+  "type": "collection",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:465de31f-3098-365c-af70-48a071e1f5aa",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "465de31f-3098-365c-af70-48a071e1f5aa",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 27
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "465de31f-3098-365c-af70-48a071e1f5aa"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "METROWEST MEDICAL CENTER",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5083831000"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "115 LINCOLN STREET"
+            ],
+            "city": "FRAMINGHAM",
+            "state": "MA",
+            "postalCode": "01701",
+            "country": "US"
+          }
+        ]
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:58fe1815-1e8a-38ed-a91a-17d4ef18c8d8",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "58fe1815-1e8a-38ed-a91a-17d4ef18c8d8",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 30
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 23
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 5
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 17
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "58fe1815-1e8a-38ed-a91a-17d4ef18c8d8"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "PCP68975",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "508-881-4368"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "259 MAIN ST"
+            ],
+            "city": "ASHLAND",
+            "state": "MA",
+            "postalCode": "01721-2115",
+            "country": "US"
+          }
+        ]
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:d672f853-e2a5-324e-98fa-c6d5f8dfc255",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "d672f853-e2a5-324e-98fa-c6d5f8dfc255",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "d672f853-e2a5-324e-98fa-c6d5f8dfc255"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "WALTHAM URGENT CARE",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-243-5591"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "9 HOPE AVENUE"
+            ],
+            "city": "WALTHAM",
+            "state": "MA",
+            "postalCode": "2453",
+            "country": "US"
+          }
+        ]
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/practitionerInformation1589831190233.json b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/practitionerInformation1589831190233.json
new file mode 100644
index 000000000000..76f865f73c7c
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/practitionerInformation1589831190233.json
@@ -0,0 +1,135 @@
+{
+  "resourceType": "Bundle",
+  "type": "collection",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:c16820ae-2954-32d4-863c-e9ceb741154c",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "c16820ae-2954-32d4-863c-e9ceb741154c",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 27
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "530"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Murphy561"
+          ],
+          "given": [
+            "Mari763"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "115 LINCOLN STREET"
+            ],
+            "city": "FRAMINGHAM",
+            "state": "MA",
+            "postalCode": "01701",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 30
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "35750"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Hilpert278"
+          ],
+          "given": [
+            "Cathryn51"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "259 MAIN ST"
+            ],
+            "city": "ASHLAND",
+            "state": "MA",
+            "postalCode": "01721-2115",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:861aa935-d89f-3b41-861b-b791fa112253",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "861aa935-d89f-3b41-861b-b791fa112253",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "93440"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Reynolds644"
+          ],
+          "given": [
+            "Salena230"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "9 HOPE AVENUE"
+            ],
+            "city": "WALTHAM",
+            "state": "MA",
+            "postalCode": "2453",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/CarePlan.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/CarePlan.ndjson
new file mode 100644
index 000000000000..12ba93cc62a8
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/CarePlan.ndjson
@@ -0,0 +1,3 @@
+{"resourceType":"CarePlan","id":"32841402-d5d8-4615-af90-473bf6f417fa","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-careplan"]},"text":{"status":"generated","div":"
    Care Plan for Respiratory therapy.
    Activities: 
    • Respiratory therapy
    • Respiratory therapy

    Care plan is meant to treat Acute bronchitis (disorder).
    "},"status":"completed","intent":"order","category":[{"coding":[{"system":"http://hl7.org/fhir/us/core/CodeSystem/careplan-category","code":"assess-plan"}]},{"coding":[{"system":"http://snomed.info/sct","code":"53950000","display":"Respiratory therapy"}],"text":"Respiratory therapy"}],"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"encounter":{"reference":"Encounter/12b98110-3df6-40cb-bb70-87ea01d4aa31"},"period":{"start":"2015-04-12T14:15:05-07:00","end":"2015-04-19T14:15:05-07:00"},"careTeam":[{"reference":"CareTeam/111c8459-549e-4a2b-ab70-27f3b2408eac"}],"addresses":[{"reference":"Condition/c8d97153-17c7-4a2b-bafd-052ff8f30eb9"}],"activity":[{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"304510005","display":"Recommendation to avoid exercise"}],"text":"Recommendation to avoid exercise"},"status":"completed","location":{"reference":"Location/e39647c2-31b8-4e0c-b383-0994cd478ca0","display":"METROWEST MEDICAL CENTER"}}},{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"371605008","display":"Deep breathing and coughing exercises"}],"text":"Deep breathing and coughing exercises"},"status":"completed","location":{"reference":"Location/e39647c2-31b8-4e0c-b383-0994cd478ca0","display":"METROWEST MEDICAL CENTER"}}}]}
+{"resourceType":"CarePlan","id":"ac2893f1-9c90-437d-852f-4cc1a0155d39","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-careplan"]},"text":{"status":"generated","div":"
    Care Plan for Fracture care.
    Activities: 
    • Fracture care
    • Fracture care

    Care plan is meant to treat Fracture of clavicle.
    "},"status":"completed","intent":"order","category":[{"coding":[{"system":"http://hl7.org/fhir/us/core/CodeSystem/careplan-category","code":"assess-plan"}]},{"coding":[{"system":"http://snomed.info/sct","code":"385691007","display":"Fracture care"}],"text":"Fracture care"}],"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"encounter":{"reference":"Encounter/e32f7ba3-c22a-4222-8b53-58a3118450f7"},"period":{"start":"2016-10-30T14:15:05-07:00","end":"2016-12-29T13:15:05-08:00"},"careTeam":[{"reference":"CareTeam/31d5cf9a-c745-4087-8042-6a9b9babaef9"}],"addresses":[{"reference":"Condition/115098be-c26e-47d0-9cad-be9df75d7042"}],"activity":[{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"183051005","display":"Recommendation to rest"}],"text":"Recommendation to rest"},"status":"completed","location":{"reference":"Location/e39647c2-31b8-4e0c-b383-0994cd478ca0","display":"METROWEST MEDICAL CENTER"}}},{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"408580007","display":"Physical activity target light exercise"}],"text":"Physical activity target light exercise"},"status":"completed","location":{"reference":"Location/e39647c2-31b8-4e0c-b383-0994cd478ca0","display":"METROWEST MEDICAL CENTER"}}}]}
+{"resourceType":"CarePlan","id":"5a1fb9d1-310b-4fe3-b7c3-6370529400b8","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-careplan"]},"text":{"status":"generated","div":"
    Care Plan for Minor surgery care management (procedure).
    Activities: 
    • Minor surgery care management (procedure)
    • Minor surgery care management (procedure)
    "},"status":"completed","intent":"order","category":[{"coding":[{"system":"http://hl7.org/fhir/us/core/CodeSystem/careplan-category","code":"assess-plan"}]},{"coding":[{"system":"http://snomed.info/sct","code":"737471002","display":"Minor surgery care management (procedure)"}],"text":"Minor surgery care management (procedure)"}],"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"encounter":{"reference":"Encounter/498dc8b8-db3d-4064-87eb-4011786324d5"},"period":{"start":"2018-02-09T13:15:05-08:00","end":"2018-02-23T13:15:05-08:00"},"careTeam":[{"reference":"CareTeam/e1ab345a-81bd-461e-921d-9eae42c47f8a"}],"activity":[{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"183051005","display":"Recommendation to rest"}],"text":"Recommendation to rest"},"status":"completed","location":{"reference":"Location/e39647c2-31b8-4e0c-b383-0994cd478ca0","display":"METROWEST MEDICAL CENTER"}}},{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"243077000","display":"Recommendation to limit sexual activity"}],"text":"Recommendation to limit sexual activity"},"status":"completed","location":{"reference":"Location/e39647c2-31b8-4e0c-b383-0994cd478ca0","display":"METROWEST MEDICAL CENTER"}}}]}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/CareTeam.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/CareTeam.ndjson
new file mode 100644
index 000000000000..1bd6a0f44212
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/CareTeam.ndjson
@@ -0,0 +1,3 @@
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Claim.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Claim.ndjson
new file mode 100644
index 000000000000..05a7d0cf7222
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Claim.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Condition.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Condition.ndjson
new file mode 100644
index 000000000000..138f07decf90
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Condition.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/DiagnosticReport.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/DiagnosticReport.ndjson
new file mode 100644
index 000000000000..7d7861955132
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/DiagnosticReport.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/DocumentReference.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/DocumentReference.ndjson
new file mode 100644
index 000000000000..c6da76c2a773
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/DocumentReference.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Encounter.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Encounter.ndjson
new file mode 100644
index 000000000000..d973abf02d66
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Encounter.ndjson
@@ -0,0 +1,16 @@
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/ExplanationOfBenefit.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/ExplanationOfBenefit.ndjson
new file mode 100644
index 000000000000..6a785b678a13
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/ExplanationOfBenefit.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/ImagingStudy.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/ImagingStudy.ndjson
new file mode 100644
index 000000000000..ca85bc9f5ad0
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/ImagingStudy.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Immunization.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Immunization.ndjson
new file mode 100644
index 000000000000..cf15293f2474
--- /dev/null
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Location.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Location.ndjson
new file mode 100644
index 000000000000..dc8773c211f9
--- /dev/null
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/MedicationRequest.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/MedicationRequest.ndjson
new file mode 100644
index 000000000000..2e45acdbad98
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/MedicationRequest.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Observation.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Observation.ndjson
new file mode 100644
index 000000000000..e81bd862bb17
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Observation.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Organization.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Organization.ndjson
new file mode 100644
index 000000000000..e1036faf02c4
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Organization.ndjson
@@ -0,0 +1,2 @@
+{"resourceType":"Organization","id":"465de31f-3098-365c-af70-48a071e1f5aa","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization"]},"identifier":[{"system":"https://github.com/synthetichealth/synthea","value":"465de31f-3098-365c-af70-48a071e1f5aa"}],"active":true,"type":[{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/organization-type","code":"prov","display":"Healthcare Provider"}],"text":"Healthcare Provider"}],"name":"METROWEST MEDICAL CENTER","telecom":[{"system":"phone","value":"5083831000"}],"address":[{"line":["115 LINCOLN STREET"],"city":"FRAMINGHAM","state":"MA","postalCode":"01701","country":"US"}]}
+{"resourceType":"Organization","id":"58fe1815-1e8a-38ed-a91a-17d4ef18c8d8","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization"]},"identifier":[{"system":"https://github.com/synthetichealth/synthea","value":"58fe1815-1e8a-38ed-a91a-17d4ef18c8d8"}],"active":true,"type":[{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/organization-type","code":"prov","display":"Healthcare Provider"}],"text":"Healthcare Provider"}],"name":"PCP68975","telecom":[{"system":"phone","value":"508-881-4368"}],"address":[{"line":["259 MAIN ST"],"city":"ASHLAND","state":"MA","postalCode":"01721-2115","country":"US"}]}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Patient.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Patient.ndjson
new file mode 100644
index 000000000000..e86812afb434
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Patient.ndjson
@@ -0,0 +1 @@
+{"resourceType":"Patient","id":"1416dec1-f4b1-4b48-b7f4-650e8f67499c","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"]},"text":{"status":"generated","div":"
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Practitioner.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Practitioner.ndjson
new file mode 100644
index 000000000000..1ff54077e908
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Practitioner.ndjson
@@ -0,0 +1,2 @@
+{"resourceType":"Practitioner","id":"c16820ae-2954-32d4-863c-e9ceb741154c","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner"]},"identifier":[{"system":"http://hl7.org/fhir/sid/us-npi","value":"530"}],"active":true,"name":[{"family":"Murphy561","given":["Mari763"],"prefix":["Dr."]}],"telecom":[{"extension":[{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-direct","valueBoolean":true}],"system":"email","value":"Mari763.Murphy561@example.com","use":"work"}],"address":[{"line":["115 LINCOLN STREET"],"city":"FRAMINGHAM","state":"MA","postalCode":"01701","country":"US"}],"gender":"female"}
+{"resourceType":"Practitioner","id":"a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner"]},"identifier":[{"system":"http://hl7.org/fhir/sid/us-npi","value":"35750"}],"active":true,"name":[{"family":"Hilpert278","given":["Cathryn51"],"prefix":["Dr."]}],"telecom":[{"extension":[{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-direct","valueBoolean":true}],"system":"email","value":"Cathryn51.Hilpert278@example.com","use":"work"}],"address":[{"line":["259 MAIN ST"],"city":"ASHLAND","state":"MA","postalCode":"01721-2115","country":"US"}],"gender":"female"}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/PractitionerRole.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/PractitionerRole.ndjson
new file mode 100644
index 000000000000..72bd745ca8d0
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/PractitionerRole.ndjson
@@ -0,0 +1,2 @@
+{"resourceType":"PractitionerRole","id":"47501a3e-8eaa-4432-9b47-750769e4bf56","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole"]},"practitioner":{"reference":"Practitioner/c16820ae-2954-32d4-863c-e9ceb741154c","display":"Dr. Mari763 Murphy561"},"organization":{"reference":"Organization/465de31f-3098-365c-af70-48a071e1f5aa","display":"METROWEST MEDICAL CENTER"},"code":[{"coding":[{"system":"http://nucc.org/provider-taxonomy","code":"208D00000X","display":"General Practice"}],"text":"General Practice"}],"specialty":[{"coding":[{"system":"http://nucc.org/provider-taxonomy","code":"208D00000X","display":"General Practice"}],"text":"General Practice"}],"location":[{"reference":"Location/e39647c2-31b8-4e0c-b383-0994cd478ca0","display":"METROWEST MEDICAL CENTER"}],"telecom":[{"system":"phone","value":"5083831000"}]}
+{"resourceType":"PractitionerRole","id":"af8e91ae-aedf-419e-bd06-cfcf8a1c612f","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole"]},"practitioner":{"reference":"Practitioner/a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8","display":"Dr. Cathryn51 Hilpert278"},"organization":{"reference":"Organization/58fe1815-1e8a-38ed-a91a-17d4ef18c8d8","display":"PCP68975"},"code":[{"coding":[{"system":"http://nucc.org/provider-taxonomy","code":"208D00000X","display":"General Practice"}],"text":"General Practice"}],"specialty":[{"coding":[{"system":"http://nucc.org/provider-taxonomy","code":"208D00000X","display":"General Practice"}],"text":"General Practice"}],"location":[{"reference":"Location/7a41edc1-c724-4bf9-b850-c78f9b1d387d","display":"PCP68975"}],"telecom":[{"system":"phone","value":"508-881-4368"}]}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Procedure.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Procedure.ndjson
new file mode 100644
index 000000000000..6bda489a5287
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Procedure.ndjson
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+{"resourceType":"Procedure","id":"eba3e367-30ea-418d-ae97-e91506dea85f","meta":{"profile":["http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure"]},"status":"completed","code":{"coding":[{"system":"http://snomed.info/sct","code":"430193006","display":"Medication Reconciliation (procedure)"}],"text":"Medication Reconciliation (procedure)"},"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"encounter":{"reference":"Encounter/7c8b9bd7-0172-47af-bd21-6af5b0eacf08"},"performedPeriod":{"start":"2010-06-03T14:15:05-07:00","end":"2010-06-03T14:30:05-07:00"},"location":{"reference":"Location/7a41edc1-c724-4bf9-b850-c78f9b1d387d","display":"PCP68975"}}
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Provenance.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Provenance.ndjson
new file mode 100644
index 000000000000..736f152ede70
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/Provenance.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/hospitalInformation1589831190233.json b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/hospitalInformation1589831190233.json
new file mode 100644
index 000000000000..b80501554861
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/hospitalInformation1589831190233.json
@@ -0,0 +1,318 @@
+{
+  "resourceType": "Bundle",
+  "type": "collection",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:5cd31fbf-76ba-4e8c-84dd-6c72071c98cf",
+      "resource": {
+        "resourceType": "Location",
+        "id": "5cd31fbf-76ba-4e8c-84dd-6c72071c98cf",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-location"
+          ]
+        },
+        "status": "active",
+        "name": "METROWEST MEDICAL CENTER",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5083831000"
+          }
+        ],
+        "address": {
+          "line": [
+            "115 LINCOLN STREET"
+          ],
+          "city": "FRAMINGHAM",
+          "state": "MA",
+          "postalCode": "01701",
+          "country": "US"
+        },
+        "position": {
+          "longitude": -71.436196,
+          "latitude": 42.307905
+        },
+        "managingOrganization": {
+          "reference": "urn:uuid:465de31f-3098-365c-af70-48a071e1f5aa",
+          "display": "METROWEST MEDICAL CENTER"
+        }
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:465de31f-3098-365c-af70-48a071e1f5aa",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "465de31f-3098-365c-af70-48a071e1f5aa",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization"
+          ]
+        },
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 27
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "465de31f-3098-365c-af70-48a071e1f5aa"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "METROWEST MEDICAL CENTER",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5083831000"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "115 LINCOLN STREET"
+            ],
+            "city": "FRAMINGHAM",
+            "state": "MA",
+            "postalCode": "01701",
+            "country": "US"
+          }
+        ]
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:274697c5-2d9d-412f-b825-194f88241aec",
+      "resource": {
+        "resourceType": "Location",
+        "id": "274697c5-2d9d-412f-b825-194f88241aec",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-location"
+          ]
+        },
+        "status": "active",
+        "name": "PCP68975",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "508-881-4368"
+          }
+        ],
+        "address": {
+          "line": [
+            "259 MAIN ST"
+          ],
+          "city": "ASHLAND",
+          "state": "MA",
+          "postalCode": "01721-2115",
+          "country": "US"
+        },
+        "position": {
+          "longitude": -71.473526,
+          "latitude": 42.257754999999996
+        },
+        "managingOrganization": {
+          "reference": "urn:uuid:58fe1815-1e8a-38ed-a91a-17d4ef18c8d8",
+          "display": "PCP68975"
+        }
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:58fe1815-1e8a-38ed-a91a-17d4ef18c8d8",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "58fe1815-1e8a-38ed-a91a-17d4ef18c8d8",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization"
+          ]
+        },
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 30
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 23
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 5
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 17
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "58fe1815-1e8a-38ed-a91a-17d4ef18c8d8"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "PCP68975",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "508-881-4368"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "259 MAIN ST"
+            ],
+            "city": "ASHLAND",
+            "state": "MA",
+            "postalCode": "01721-2115",
+            "country": "US"
+          }
+        ]
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:31352f93-39d4-447d-bb77-8cac27d5c9d0",
+      "resource": {
+        "resourceType": "Location",
+        "id": "31352f93-39d4-447d-bb77-8cac27d5c9d0",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-location"
+          ]
+        },
+        "status": "active",
+        "name": "WALTHAM URGENT CARE",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-243-5591"
+          }
+        ],
+        "address": {
+          "line": [
+            "9 HOPE AVENUE"
+          ],
+          "city": "WALTHAM",
+          "state": "MA",
+          "postalCode": "2453",
+          "country": "US"
+        },
+        "position": {
+          "longitude": -71.2490152,
+          "latitude": 42.3700513
+        },
+        "managingOrganization": {
+          "reference": "urn:uuid:d672f853-e2a5-324e-98fa-c6d5f8dfc255",
+          "display": "WALTHAM URGENT CARE"
+        }
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:d672f853-e2a5-324e-98fa-c6d5f8dfc255",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "d672f853-e2a5-324e-98fa-c6d5f8dfc255",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization"
+          ]
+        },
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "d672f853-e2a5-324e-98fa-c6d5f8dfc255"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "WALTHAM URGENT CARE",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-243-5591"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "9 HOPE AVENUE"
+            ],
+            "city": "WALTHAM",
+            "state": "MA",
+            "postalCode": "2453",
+            "country": "US"
+          }
+        ]
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/practitionerInformation1589831190233.json b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/practitionerInformation1589831190233.json
new file mode 100644
index 000000000000..90fcfcc493a2
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/practitionerInformation1589831190233.json
@@ -0,0 +1,354 @@
+{
+  "resourceType": "Bundle",
+  "type": "collection",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:c16820ae-2954-32d4-863c-e9ceb741154c",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "c16820ae-2954-32d4-863c-e9ceb741154c",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner"
+          ]
+        },
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 27
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "530"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Murphy561",
+            "given": [
+              "Mari763"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-direct",
+                "valueBoolean": true
+              }
+            ],
+            "system": "email",
+            "value": "Mari763.Murphy561@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "115 LINCOLN STREET"
+            ],
+            "city": "FRAMINGHAM",
+            "state": "MA",
+            "postalCode": "01701",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:70dbe417-06dc-4c57-93ce-84209ac38ff5",
+      "resource": {
+        "resourceType": "PractitionerRole",
+        "id": "70dbe417-06dc-4c57-93ce-84209ac38ff5",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole"
+          ]
+        },
+        "practitioner": {
+          "reference": "urn:uuid:c16820ae-2954-32d4-863c-e9ceb741154c",
+          "display": "Dr. Mari763 Murphy561"
+        },
+        "organization": {
+          "reference": "urn:uuid:465de31f-3098-365c-af70-48a071e1f5aa",
+          "display": "METROWEST MEDICAL CENTER"
+        },
+        "code": [
+          {
+            "coding": [
+              {
+                "system": "http://nucc.org/provider-taxonomy",
+                "code": "208D00000X",
+                "display": "General Practice"
+              }
+            ],
+            "text": "General Practice"
+          }
+        ],
+        "specialty": [
+          {
+            "coding": [
+              {
+                "system": "http://nucc.org/provider-taxonomy",
+                "code": "208D00000X",
+                "display": "General Practice"
+              }
+            ],
+            "text": "General Practice"
+          }
+        ],
+        "location": [
+          {
+            "display": "METROWEST MEDICAL CENTER"
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5083831000"
+          }
+        ]
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner"
+          ]
+        },
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 30
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "35750"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Hilpert278",
+            "given": [
+              "Cathryn51"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-direct",
+                "valueBoolean": true
+              }
+            ],
+            "system": "email",
+            "value": "Cathryn51.Hilpert278@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "259 MAIN ST"
+            ],
+            "city": "ASHLAND",
+            "state": "MA",
+            "postalCode": "01721-2115",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:d163bdcf-8294-4320-85b8-86e0680dc34a",
+      "resource": {
+        "resourceType": "PractitionerRole",
+        "id": "d163bdcf-8294-4320-85b8-86e0680dc34a",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole"
+          ]
+        },
+        "practitioner": {
+          "reference": "urn:uuid:a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8",
+          "display": "Dr. Cathryn51 Hilpert278"
+        },
+        "organization": {
+          "reference": "urn:uuid:58fe1815-1e8a-38ed-a91a-17d4ef18c8d8",
+          "display": "PCP68975"
+        },
+        "code": [
+          {
+            "coding": [
+              {
+                "system": "http://nucc.org/provider-taxonomy",
+                "code": "208D00000X",
+                "display": "General Practice"
+              }
+            ],
+            "text": "General Practice"
+          }
+        ],
+        "specialty": [
+          {
+            "coding": [
+              {
+                "system": "http://nucc.org/provider-taxonomy",
+                "code": "208D00000X",
+                "display": "General Practice"
+              }
+            ],
+            "text": "General Practice"
+          }
+        ],
+        "location": [
+          {
+            "display": "PCP68975"
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "508-881-4368"
+          }
+        ]
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:861aa935-d89f-3b41-861b-b791fa112253",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "861aa935-d89f-3b41-861b-b791fa112253",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner"
+          ]
+        },
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "93440"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Reynolds644",
+            "given": [
+              "Salena230"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-direct",
+                "valueBoolean": true
+              }
+            ],
+            "system": "email",
+            "value": "Salena230.Reynolds644@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "9 HOPE AVENUE"
+            ],
+            "city": "WALTHAM",
+            "state": "MA",
+            "postalCode": "2453",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:689adf0e-16fd-4546-9764-69d26ef64777",
+      "resource": {
+        "resourceType": "PractitionerRole",
+        "id": "689adf0e-16fd-4546-9764-69d26ef64777",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole"
+          ]
+        },
+        "practitioner": {
+          "reference": "urn:uuid:861aa935-d89f-3b41-861b-b791fa112253",
+          "display": "Dr. Salena230 Reynolds644"
+        },
+        "organization": {
+          "reference": "urn:uuid:d672f853-e2a5-324e-98fa-c6d5f8dfc255",
+          "display": "WALTHAM URGENT CARE"
+        },
+        "code": [
+          {
+            "coding": [
+              {
+                "system": "http://nucc.org/provider-taxonomy",
+                "code": "208D00000X",
+                "display": "General Practice"
+              }
+            ],
+            "text": "General Practice"
+          }
+        ],
+        "specialty": [
+          {
+            "coding": [
+              {
+                "system": "http://nucc.org/provider-taxonomy",
+                "code": "208D00000X",
+                "display": "General Practice"
+              }
+            ],
+            "text": "General Practice"
+          }
+        ],
+        "location": [
+          {
+            "display": "WALTHAM URGENT CARE"
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-243-5591"
+          }
+        ]
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/CarePlan.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/CarePlan.ndjson
new file mode 100644
index 000000000000..99dec1a97ca0
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/CarePlan.ndjson
@@ -0,0 +1,3 @@
+{"resourceType":"CarePlan","id":"e1162c3b-86cf-4097-a33d-34bb9a93cfb9","status":"completed","intent":"order","category":[{"coding":[{"system":"http://snomed.info/sct","code":"53950000","display":"Respiratory therapy"}],"text":"Respiratory therapy"}],"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"context":{"reference":"Encounter/37cce86a-e35b-4879-b8ed-4f22b10b2f7c"},"period":{"start":"2015-04-12T14:15:05-07:00","end":"2015-04-19T14:15:05-07:00"},"addresses":[{"reference":"Condition/5953e3df-ed6c-4509-8d56-04c745817bd0"}],"activity":[{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"304510005","display":"Recommendation to avoid exercise"}],"text":"Recommendation to avoid exercise"},"status":"completed"}},{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"371605008","display":"Deep breathing and coughing exercises"}],"text":"Deep breathing and coughing exercises"},"status":"completed"}}]}
+{"resourceType":"CarePlan","id":"04330c15-061f-494c-9d2f-4e42eca9e099","status":"completed","intent":"order","category":[{"coding":[{"system":"http://snomed.info/sct","code":"385691007","display":"Fracture care"}],"text":"Fracture care"}],"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"context":{"reference":"Encounter/187a1ecd-b5f5-4566-b39d-ae646062cfbc"},"period":{"start":"2016-10-30T14:15:05-07:00","end":"2016-12-29T13:15:05-08:00"},"addresses":[{"reference":"Condition/0aa16b8a-bce6-4362-8312-879d7ccf29f8"}],"activity":[{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"183051005","display":"Recommendation to rest"}],"text":"Recommendation to rest"},"status":"completed"}},{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"408580007","display":"Physical activity target light exercise"}],"text":"Physical activity target light exercise"},"status":"completed"}}]}
+{"resourceType":"CarePlan","id":"28ffafe4-9be5-4eb5-b663-c22d10c82cf0","status":"completed","intent":"order","category":[{"coding":[{"system":"http://snomed.info/sct","code":"737471002","display":"Minor surgery care management (procedure)"}],"text":"Minor surgery care management (procedure)"}],"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"context":{"reference":"Encounter/89c75588-d3a0-4ff8-8202-665ff4349fa7"},"period":{"start":"2018-02-09T13:15:05-08:00","end":"2018-02-23T13:15:05-08:00"},"activity":[{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"183051005","display":"Recommendation to rest"}],"text":"Recommendation to rest"},"status":"completed"}},{"detail":{"code":{"coding":[{"system":"http://snomed.info/sct","code":"243077000","display":"Recommendation to limit sexual activity"}],"text":"Recommendation to limit sexual activity"},"status":"completed"}}]}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Claim.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Claim.ndjson
new file mode 100644
index 000000000000..7c94153bf3d3
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Claim.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Condition.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Condition.ndjson
new file mode 100644
index 000000000000..ce06594b71d7
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Condition.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/DiagnosticReport.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/DiagnosticReport.ndjson
new file mode 100644
index 000000000000..826daad9fed0
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/DiagnosticReport.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Encounter.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Encounter.ndjson
new file mode 100644
index 000000000000..b0bdae6dc4c0
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Encounter.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/ExplanationOfBenefit.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/ExplanationOfBenefit.ndjson
new file mode 100644
index 000000000000..7a6f130333c9
--- /dev/null
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new file mode 100644
index 000000000000..9e226f86482e
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/ImagingStudy.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Immunization.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Immunization.ndjson
new file mode 100644
index 000000000000..03e078d441ce
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Immunization.ndjson
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/MedicationRequest.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/MedicationRequest.ndjson
new file mode 100644
index 000000000000..718327c2cfcc
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/MedicationRequest.ndjson
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new file mode 100644
index 000000000000..56e2b92c6649
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Organization.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Organization.ndjson
new file mode 100644
index 000000000000..06c5160f19af
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Organization.ndjson
@@ -0,0 +1,2 @@
+{"resourceType":"Organization","id":"465de31f-3098-365c-af70-48a071e1f5aa","identifier":[{"system":"https://github.com/synthetichealth/synthea","value":"465de31f-3098-365c-af70-48a071e1f5aa"}],"type":[{"coding":[{"system":"http://hl7.org/fhir/organization-type","code":"prov","display":"Healthcare Provider"}],"text":"Healthcare Provider"}],"name":"METROWEST MEDICAL CENTER","telecom":[{"system":"phone","value":"5083831000"}],"address":[{"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/geolocation","extension":[{"url":"latitude","valueDecimal":42.307905},{"url":"longitude","valueDecimal":-71.436196}]}],"line":["115 LINCOLN STREET"],"city":"FRAMINGHAM","state":"MA","postalCode":"01701","country":"US"}]}
+{"resourceType":"Organization","id":"58fe1815-1e8a-38ed-a91a-17d4ef18c8d8","identifier":[{"system":"https://github.com/synthetichealth/synthea","value":"58fe1815-1e8a-38ed-a91a-17d4ef18c8d8"}],"type":[{"coding":[{"system":"http://hl7.org/fhir/organization-type","code":"prov","display":"Healthcare Provider"}],"text":"Healthcare Provider"}],"name":"PCP68975","telecom":[{"system":"phone","value":"508-881-4368"}],"address":[{"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/geolocation","extension":[{"url":"latitude","valueDecimal":42.257754999999996},{"url":"longitude","valueDecimal":-71.473526}]}],"line":["259 MAIN ST"],"city":"ASHLAND","state":"MA","postalCode":"01721-2115","country":"US"}]}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Patient.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Patient.ndjson
new file mode 100644
index 000000000000..3243439fb2f8
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Patient.ndjson
@@ -0,0 +1 @@
+{"resourceType":"Patient","id":"1416dec1-f4b1-4b48-b7f4-650e8f67499c","text":{"status":"generated","div":"
    Generated by Synthea.Version identifier: v2.5.0-265-gbd5a00e8\n .   Person seed: 6732543839779682504  Population seed: 1589831189867
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Practitioner.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Practitioner.ndjson
new file mode 100644
index 000000000000..eba7b8c26455
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Practitioner.ndjson
@@ -0,0 +1,2 @@
+{"resourceType":"Practitioner","id":"c16820ae-2954-32d4-863c-e9ceb741154c","identifier":[{"system":"http://hl7.org/fhir/sid/us-npi","value":"530"}],"active":true,"name":[{"family":"Murphy561","given":["Mari763"],"prefix":["Dr."]}],"address":[{"line":["115 LINCOLN STREET"],"city":"FRAMINGHAM","state":"MA","postalCode":"01701","country":"US"}],"gender":"female"}
+{"resourceType":"Practitioner","id":"a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8","identifier":[{"system":"http://hl7.org/fhir/sid/us-npi","value":"35750"}],"active":true,"name":[{"family":"Hilpert278","given":["Cathryn51"],"prefix":["Dr."]}],"address":[{"line":["259 MAIN ST"],"city":"ASHLAND","state":"MA","postalCode":"01721-2115","country":"US"}],"gender":"female"}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Procedure.ndjson b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Procedure.ndjson
new file mode 100644
index 000000000000..3a484c87be00
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/Procedure.ndjson
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+{"resourceType":"Procedure","id":"bbedb163-5b9d-4865-bd9f-d59f7a9c21ad","status":"completed","code":{"coding":[{"system":"http://snomed.info/sct","code":"399208008","display":"Plain chest X-ray (procedure)"}],"text":"Plain chest X-ray (procedure)"},"subject":{"reference":"Patient/1416dec1-f4b1-4b48-b7f4-650e8f67499c"},"context":{"reference":"Encounter/37cce86a-e35b-4879-b8ed-4f22b10b2f7c"},"performedPeriod":{"start":"2015-04-12T14:15:05-07:00","end":"2015-04-12T14:26:05-07:00"},"reasonReference":[{"reference":"Condition/5953e3df-ed6c-4509-8d56-04c745817bd0","display":"Acute bronchitis (disorder)"}]}
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/hospitalInformation1589831190233.json b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/hospitalInformation1589831190233.json
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index 000000000000..dfe338def8e6
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/hospitalInformation1589831190233.json
@@ -0,0 +1,234 @@
+{
+  "resourceType": "Bundle",
+  "type": "collection",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:465de31f-3098-365c-af70-48a071e1f5aa",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "465de31f-3098-365c-af70-48a071e1f5aa",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 27
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "465de31f-3098-365c-af70-48a071e1f5aa"
+          }
+        ],
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://hl7.org/fhir/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "METROWEST MEDICAL CENTER",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5083831000"
+          }
+        ],
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.307905
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.436196
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "115 LINCOLN STREET"
+            ],
+            "city": "FRAMINGHAM",
+            "state": "MA",
+            "postalCode": "01701",
+            "country": "US"
+          }
+        ]
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:58fe1815-1e8a-38ed-a91a-17d4ef18c8d8",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "58fe1815-1e8a-38ed-a91a-17d4ef18c8d8",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 30
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 23
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 5
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 17
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "58fe1815-1e8a-38ed-a91a-17d4ef18c8d8"
+          }
+        ],
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://hl7.org/fhir/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "PCP68975",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "508-881-4368"
+          }
+        ],
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.257754999999996
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.473526
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "259 MAIN ST"
+            ],
+            "city": "ASHLAND",
+            "state": "MA",
+            "postalCode": "01721-2115",
+            "country": "US"
+          }
+        ]
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:d672f853-e2a5-324e-98fa-c6d5f8dfc255",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "d672f853-e2a5-324e-98fa-c6d5f8dfc255",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "d672f853-e2a5-324e-98fa-c6d5f8dfc255"
+          }
+        ],
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://hl7.org/fhir/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "WALTHAM URGENT CARE",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-243-5591"
+          }
+        ],
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.3700513
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.2490152
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "9 HOPE AVENUE"
+            ],
+            "city": "WALTHAM",
+            "state": "MA",
+            "postalCode": "2453",
+            "country": "US"
+          }
+        ]
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/practitionerInformation1589831190233.json b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/practitionerInformation1589831190233.json
new file mode 100644
index 000000000000..9e963d958d03
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/practitionerInformation1589831190233.json
@@ -0,0 +1,135 @@
+{
+  "resourceType": "Bundle",
+  "type": "collection",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:c16820ae-2954-32d4-863c-e9ceb741154c",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "c16820ae-2954-32d4-863c-e9ceb741154c",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 27
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "530"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Murphy561",
+            "given": [
+              "Mari763"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "115 LINCOLN STREET"
+            ],
+            "city": "FRAMINGHAM",
+            "state": "MA",
+            "postalCode": "01701",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 30
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "35750"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Hilpert278",
+            "given": [
+              "Cathryn51"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "259 MAIN ST"
+            ],
+            "city": "ASHLAND",
+            "state": "MA",
+            "postalCode": "01721-2115",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:861aa935-d89f-3b41-861b-b791fa112253",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "861aa935-d89f-3b41-861b-b791fa112253",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "93440"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Reynolds644",
+            "given": [
+              "Salena230"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "9 HOPE AVENUE"
+            ],
+            "city": "WALTHAM",
+            "state": "MA",
+            "postalCode": "2453",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      }
+    }
+  ]
+}

From 35db9f7c4ed9baf7f263bd93f75bbb549d3f09ce Mon Sep 17 00:00:00 2001
From: Esun Kim 
Date: Tue, 19 May 2020 13:26:19 -0700
Subject: [PATCH 018/151] Add grpc-alts and grpc-netty-shaded explicitly

---
 .../main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy  | 2 ++
 sdks/java/io/google-cloud-platform/build.gradle                 | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy b/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy
index ac53a23daf4a..0adb35c5ba20 100644
--- a/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy
+++ b/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy
@@ -481,6 +481,7 @@ class BeamModulePlugin implements Plugin {
         google_oauth_client                         : "com.google.oauth-client:google-oauth-client:$google_oauth_clients_version",
         google_oauth_client_java6                   : "com.google.oauth-client:google-oauth-client-java6:$google_oauth_clients_version",
         grpc_all                                    : "io.grpc:grpc-all:$grpc_version",
+        grpc_alts                                   : "io.grpc:grpc-alts:$grpc_version",
         grpc_auth                                   : "io.grpc:grpc-auth:$grpc_version",
         grpc_core                                   : "io.grpc:grpc-core:$grpc_version",
         grpc_context                                : "io.grpc:grpc-context:$grpc_version",
@@ -489,6 +490,7 @@ class BeamModulePlugin implements Plugin {
         grpc_protobuf                               : "io.grpc:grpc-protobuf:$grpc_version",
         grpc_protobuf_lite                          : "io.grpc:grpc-protobuf-lite:$grpc_version",
         grpc_netty                                  : "io.grpc:grpc-netty:$grpc_version",
+        grpc_netty_shaded                           : "io.grpc:grpc-netty-shaded:$grpc_version",
         grpc_stub                                   : "io.grpc:grpc-stub:$grpc_version",
         guava                                       : "com.google.guava:guava:$guava_version",
         guava_testlib                               : "com.google.guava:guava-testlib:$guava_version",
diff --git a/sdks/java/io/google-cloud-platform/build.gradle b/sdks/java/io/google-cloud-platform/build.gradle
index c6c8e93927a2..e36bac6fa402 100644
--- a/sdks/java/io/google-cloud-platform/build.gradle
+++ b/sdks/java/io/google-cloud-platform/build.gradle
@@ -56,11 +56,13 @@ dependencies {
   compile library.java.google_http_client
   compile library.java.google_http_client_jackson2
   compile library.java.grpc_all
+  compile library.java.grpc_alts
   compile library.java.grpc_auth
   compile library.java.grpc_core
   compile library.java.grpc_context
   compile library.java.grpc_grpclb
   compile library.java.grpc_netty
+  compile library.java.grpc_netty_shaded
   compile library.java.grpc_stub
   compile library.java.grpc_google_cloud_pubsub_v1
   compile library.java.guava

From 3b50369b089a94eb961dcc170bee7b97c0345805 Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Tue, 19 May 2020 17:15:22 -0700
Subject: [PATCH 019/151] [BEAM-10038] Add script to mass-comment Jenkins
 triggers on PR

---
 release/src/main/scripts/mass_comment.py | 141 +++++++++++++++++++++++
 1 file changed, 141 insertions(+)
 create mode 100644 release/src/main/scripts/mass_comment.py

diff --git a/release/src/main/scripts/mass_comment.py b/release/src/main/scripts/mass_comment.py
new file mode 100644
index 000000000000..bd9e26aa3789
--- /dev/null
+++ b/release/src/main/scripts/mass_comment.py
@@ -0,0 +1,141 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+"""Script for mass-commenting Jenkins test triggers on a Beam PR."""
+
+import itertools
+import os
+import socket
+import sys
+import time
+import traceback
+import re
+import requests
+from datetime import datetime
+
+
+COMMENTS_TO_ADD=[
+  "Run Go PostCommit",
+  "Run Java PostCommit",
+  "Run Java PortabilityApi PostCommit",
+  "Run Java Flink PortableValidatesRunner Batch",
+  "Run Java Flink PortableValidatesRunner Streaming",
+  "Run Apex ValidatesRunner",
+  "Run Dataflow ValidatesRunner",
+  "Run Flink ValidatesRunner",
+  "Run Gearpump ValidatesRunner",
+  "Run Dataflow PortabilityApi ValidatesRunner",
+  "Run Samza ValidatesRunner",
+  "Run Spark ValidatesRunner",
+  "Run Python Dataflow ValidatesContainer",
+  "Run Python Dataflow ValidatesRunner",
+  "Run Python 3.5 Flink ValidatesRunner",
+  "Run Python 2 PostCommit",
+  "Run Python 3.5 PostCommit",
+  "Run SQL PostCommit",
+  "Run Go PreCommit",
+  "Run Java PreCommit",
+  "Run Java_Examples_Dataflow PreCommit",
+  "Run JavaPortabilityApi PreCommit",
+  "Run Portable_Python PreCommit",
+  "Run PythonLint PreCommit",
+  "Run Python PreCommit",
+  "Run Python DockerBuild PreCommit"
+]
+
+def executeGHGraphqlQuery(accessToken, query):
+  '''Runs graphql query on GitHub.'''
+  url = 'https://api.github.com/graphql'
+  headers = {'Authorization': 'Bearer %s' % accessToken}
+  r = requests.post(url=url, json={'query': query}, headers=headers)
+  return r.json()
+
+def getSubjectId(accessToken, prNumber):
+  query = '''
+query FindPullRequestID {
+  repository(owner:"apache", name:"beam") {
+    pullRequest(number:%s) {
+      id
+    }
+  }
+}
+''' % prNumber
+  response = executeGHGraphqlQuery(accessToken, query)
+  return response['data']['repository']['pullRequest']['id']
+
+def fetchGHData(accessToken, subjectId, commentBody):
+  '''Fetches GitHub data required for reporting Beam metrics'''
+  query = '''
+mutation AddPullRequestComment {
+  addComment(input:{subjectId:"%s",body: "%s"}) {
+    commentEdge {
+        node {
+        createdAt
+        body
+      }
+    }
+    subject {
+      id
+    }
+  }
+}
+''' % (subjectId, commentBody)
+  return executeGHGraphqlQuery(accessToken, query)
+
+def postComments(accessToken, subjectId):
+  '''
+  Main workhorse method. Fetches data from GitHub and puts it in metrics table.
+  '''
+
+  for commentBody in COMMENTS_TO_ADD:
+    jsonData = fetchGHData(accessToken, subjectId, commentBody)
+  print(jsonData)
+
+def probeGitHubIsUp():
+  '''
+  Returns True if GitHub responds to simple queries. Else returns False.
+  '''
+  sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+  result = sock.connect_ex(('github.com', 443))
+  return True if result == 0 else False
+
+
+################################################################################
+if __name__ == '__main__':
+  '''
+  This script is supposed to be invoked directly.
+  However for testing purposes and to allow importing,
+  wrap work code in module check.
+  '''
+  print("Started.")
+
+
+  if not probeGitHubIsUp():
+    print("GitHub is unavailable, skipping fetching data.")
+    exit();
+
+  print("GitHub is available start fetching data.")
+
+  accessToken = input("Enter your Github access token: ")
+
+  pr = input("Enter the Beam PR number to test (e.g. 11403): ")
+  subjectId = getSubjectId(accessToken, pr)
+
+  postComments(accessToken, subjectId)
+  print("Fetched data.")
+
+  print('Done.')

From 5dda6a86f5a7bd9881d059e28bf6bfe367486822 Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Tue, 19 May 2020 20:26:28 -0400
Subject: [PATCH 020/151] Add mass comment script to release guide.

---
 website/www/site/content/en/contribute/release-guide.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/website/www/site/content/en/contribute/release-guide.md b/website/www/site/content/en/contribute/release-guide.md
index 95c95c2272bb..55ec1d126d9a 100644
--- a/website/www/site/content/en/contribute/release-guide.md
+++ b/website/www/site/content/en/contribute/release-guide.md
@@ -398,7 +398,7 @@ There are 2 ways to perform this verification, either running automation script(
 Jenkins job `beam_Release_Gradle_Build` basically run `./gradlew build -PisRelease`.
 This only verifies that everything builds with unit tests passing.
 
-You can refer to [this script](https://gist.github.com/Ardagan/13e6031e8d1c9ebbd3029bf365c1a517) to mass-comment on PR.
+You can use [mass_comment.py](https://github.com/apache/beam/blob/master/release/src/main/scripts/mass_comment.py) to mass-comment on PR.
 
 #### Verify the build succeeds
 

From c2d6c36e03dffcbfd2387ac19862a4d9cb401494 Mon Sep 17 00:00:00 2001
From: Yichi Zhang 
Date: Tue, 19 May 2020 17:53:16 -0700
Subject: [PATCH 021/151] [BEAM-9603] Add timer family support to
 FnApiDoFnRunner

---
 .../sdk/transforms/reflect/DoFnInvoker.java   |   8 +-
 .../beam/fn/harness/FnApiDoFnRunner.java      | 122 ++++++++++++++----
 2 files changed, 104 insertions(+), 26 deletions(-)

diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/reflect/DoFnInvoker.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/reflect/DoFnInvoker.java
index f8d4a365f8b1..40d2ca9c6332 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/reflect/DoFnInvoker.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/reflect/DoFnInvoker.java
@@ -241,6 +241,10 @@ interface ArgumentProvider {
      */
     TimerMap timerFamily(String tagId);
 
+    /**
+     * Returns the timer id for the current timer of a {@link
+     * org.apache.beam.sdk.transforms.DoFn.TimerFamily}.
+     */
     String timerId(DoFn doFn);
   }
 
@@ -532,8 +536,8 @@ public Timer timer(String timerId) {
     }
 
     @Override
-    public TimerMap timerFamily(String tagId) {
-      return delegate.timerFamily(tagId);
+    public TimerMap timerFamily(String timerFamilyId) {
+      return delegate.timerFamily(timerFamilyId);
     }
 
     @Override
diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java
index 98b3e66ad4f6..7ee066956de6 100644
--- a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java
+++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java
@@ -93,6 +93,7 @@
 import org.apache.beam.sdk.transforms.reflect.DoFnSignature;
 import org.apache.beam.sdk.transforms.reflect.DoFnSignature.StateDeclaration;
 import org.apache.beam.sdk.transforms.reflect.DoFnSignature.TimerDeclaration;
+import org.apache.beam.sdk.transforms.reflect.DoFnSignature.TimerFamilyDeclaration;
 import org.apache.beam.sdk.transforms.reflect.DoFnSignatures;
 import org.apache.beam.sdk.transforms.splittabledofn.RestrictionTracker;
 import org.apache.beam.sdk.transforms.splittabledofn.RestrictionTracker.HasProgress;
@@ -460,14 +461,22 @@ public void accept(WindowedValue input) throws Exception {
       // Extract out relevant TimerFamilySpec information in preparation for execution.
       for (Map.Entry entry :
           parDoPayload.getTimerFamilySpecsMap().entrySet()) {
-        String timerFamilyId = entry.getKey();
-        TimeDomain timeDomain =
-            DoFnSignatures.getTimerSpecOrThrow(
-                    doFnSignature.timerDeclarations().get(timerFamilyId), doFn)
-                .getTimeDomain();
+        String timerIdOrTimerFamilyId = entry.getKey();
+        TimeDomain timeDomain;
+        if (timerIdOrTimerFamilyId.startsWith(TimerFamilyDeclaration.PREFIX)) {
+          timeDomain =
+              DoFnSignatures.getTimerFamilySpecOrThrow(
+                      doFnSignature.timerFamilyDeclarations().get(timerIdOrTimerFamilyId), doFn)
+                  .getTimeDomain();
+        } else {
+          timeDomain =
+              DoFnSignatures.getTimerSpecOrThrow(
+                      doFnSignature.timerDeclarations().get(timerIdOrTimerFamilyId), doFn)
+                  .getTimeDomain();
+        }
         Coder> timerCoder =
             (Coder) rehydratedComponents.getCoder(entry.getValue().getTimerFamilyCoderId());
-        timerFamilyInfosBuilder.put(timerFamilyId, KV.of(timeDomain, timerCoder));
+        timerFamilyInfosBuilder.put(timerIdOrTimerFamilyId, KV.of(timeDomain, timerCoder));
       }
       timerFamilyInfos = timerFamilyInfosBuilder.build();
 
@@ -962,16 +971,25 @@ private HandlesSplits.SplitResult trySplitForElementAndRestriction(
             .build());
   }
 
-  private  void processTimer(String timerId, TimeDomain timeDomain, Timer timer) {
+  private  void processTimer(
+      String timerIdOrTimerFamilyId, TimeDomain timeDomain, Timer timer) {
     currentTimer = timer;
     currentTimeDomain = timeDomain;
     onTimerContext = new OnTimerContext<>(timer.getUserKey());
+    String timerId =
+        timerIdOrTimerFamilyId.startsWith(TimerFamilyDeclaration.PREFIX)
+            ? ""
+            : timerIdOrTimerFamilyId;
+    String timerFamilyId =
+        timerIdOrTimerFamilyId.startsWith(TimerFamilyDeclaration.PREFIX)
+            ? timerIdOrTimerFamilyId
+            : "";
     try {
       Iterator windowIterator =
           (Iterator) timer.getWindows().iterator();
       while (windowIterator.hasNext()) {
         currentWindow = windowIterator.next();
-        doFnInvoker.invokeOnTimer(timerId, "", onTimerContext);
+        doFnInvoker.invokeOnTimer(timerId, timerFamilyId, onTimerContext);
       }
     } finally {
       currentTimer = null;
@@ -1037,16 +1055,15 @@ private class FnApiTimer implements org.apache.beam.sdk.state.Timer {
         BoundedWindow boundedWindow,
         Instant elementTimestampOrTimerHoldTimestamp,
         Instant elementTimestampOrTimerFireTimestamp,
-        PaneInfo paneInfo) {
+        PaneInfo paneInfo,
+        TimeDomain timeDomain) {
       this.timerId = timerId;
       this.userKey = userKey;
       this.dynamicTimerTag = dynamicTimerTag;
       this.elementTimestampOrTimerHoldTimestamp = elementTimestampOrTimerHoldTimestamp;
       this.boundedWindow = boundedWindow;
       this.paneInfo = paneInfo;
-
-      TimerDeclaration timerDeclaration = doFnSignature.timerDeclarations().get(timerId);
-      this.timeDomain = DoFnSignatures.getTimerSpecOrThrow(timerDeclaration, doFn).getTimeDomain();
+      this.timeDomain = timeDomain;
 
       switch (timeDomain) {
         case EVENT_TIME:
@@ -1207,15 +1224,51 @@ private void output(Instant scheduledTime) {
     }
   }
 
-  private static class FnApiTimerMap implements TimerMap {
-    FnApiTimerMap() {}
+  private class FnApiTimerMap implements TimerMap {
+    private final String timerFamilyId;
+    private final K userKey;
+    private final TimeDomain timeDomain;
+    private final Instant elementTimestampOrTimerHoldTimestamp;
+    private final Instant elementTimestampOrTimerFireTimestamp;
+    private final BoundedWindow boundedWindow;
+    private final PaneInfo paneInfo;
+
+    FnApiTimerMap(
+        String timerFamilyId,
+        K userKey,
+        BoundedWindow boundedWindow,
+        Instant elementTimestampOrTimerHoldTimestamp,
+        Instant elementTimestampOrTimerFireTimestamp,
+        PaneInfo paneInfo) {
+      this.timerFamilyId = timerFamilyId;
+      this.userKey = userKey;
+      this.elementTimestampOrTimerHoldTimestamp = elementTimestampOrTimerHoldTimestamp;
+      this.elementTimestampOrTimerFireTimestamp = elementTimestampOrTimerFireTimestamp;
+      this.boundedWindow = boundedWindow;
+      this.paneInfo = paneInfo;
+
+      TimerFamilyDeclaration timerFamilyDeclaration =
+          doFnSignature.timerFamilyDeclarations().get(timerFamilyId);
+      this.timeDomain =
+          DoFnSignatures.getTimerFamilySpecOrThrow(timerFamilyDeclaration, doFn).getTimeDomain();
+    }
 
     @Override
-    public void set(String timerId, Instant absoluteTime) {}
+    public void set(String dynamicTimerTag, Instant absoluteTime) {
+      get(dynamicTimerTag).set(absoluteTime);
+    }
 
     @Override
-    public org.apache.beam.sdk.state.Timer get(String timerId) {
-      return null;
+    public org.apache.beam.sdk.state.Timer get(String dynamicTimerTag) {
+      return new FnApiTimer(
+          timerFamilyId,
+          userKey,
+          dynamicTimerTag,
+          boundedWindow,
+          elementTimestampOrTimerHoldTimestamp,
+          elementTimestampOrTimerFireTimestamp,
+          paneInfo,
+          timeDomain);
     }
   }
 
@@ -1447,6 +1500,9 @@ public org.apache.beam.sdk.state.Timer timer(String timerId) {
       // For the initial timestamps we pass in the current elements timestamp for the hold timestamp
       // and the current element's timestamp which will be used for the fire timestamp if this
       // timer is in the EVENT time domain.
+      TimerDeclaration timerDeclaration = doFnSignature.timerDeclarations().get(timerId);
+      TimeDomain timeDomain =
+          DoFnSignatures.getTimerSpecOrThrow(timerDeclaration, doFn).getTimeDomain();
       return new FnApiTimer(
           timerId,
           ((KV) currentElement.getValue()).getKey(),
@@ -1454,13 +1510,19 @@ public org.apache.beam.sdk.state.Timer timer(String timerId) {
           currentWindow,
           currentElement.getTimestamp(),
           currentElement.getTimestamp(),
-          currentElement.getPane());
+          currentElement.getPane(),
+          timeDomain);
     }
 
     @Override
-    public TimerMap timerFamily(String tagId) {
-      // TODO: implement timerFamily
-      return null;
+    public TimerMap timerFamily(String timerFamilyId) {
+      return new FnApiTimerMap(
+          timerFamilyId,
+          ((KV) currentElement.getValue()).getKey(),
+          currentWindow,
+          currentElement.getTimestamp(),
+          currentElement.getTimestamp(),
+          currentElement.getPane());
     }
 
     @Override
@@ -1689,13 +1751,25 @@ public org.apache.beam.sdk.state.Timer timer(String timerId) {
           currentWindow,
           currentTimer.getHoldTimestamp(),
           currentTimer.getFireTimestamp(),
+          currentTimer.getPane(),
+          currentTimeDomain);
+    }
+
+    @Override
+    public TimerMap timerFamily(String timerFamilyId) {
+      return new FnApiTimerMap(
+          timerFamilyId,
+          currentTimer.getUserKey(),
+          currentWindow,
+          currentTimer.getHoldTimestamp(),
+          currentTimer.getFireTimestamp(),
           currentTimer.getPane());
     }
 
     @Override
-    public TimerMap timerFamily(String tagId) {
-      // TODO: implement timerFamily
-      return super.timerFamily(tagId);
+    public String timerId(DoFn doFn) {
+      // Timer id is aliased to dynamic timer tag in a TimerFamily timer.
+      return currentTimer.getDynamicTimerTag();
     }
 
     @Override

From 48c2c584cf207c68509dc8db0179d97fd0f4ba3c Mon Sep 17 00:00:00 2001
From: "chamikara@google.com" 
Date: Tue, 19 May 2020 22:46:44 -0700
Subject: [PATCH 022/151] Clarifies Dataflow execution environment model

---
 .../apache_beam/runners/dataflow/internal/apiclient.py   | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py b/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
index 06bb26029aeb..8c906bd39715 100644
--- a/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
+++ b/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
@@ -314,8 +314,15 @@ def __init__(
         if container_image_url in already_added_containers:
           # Do not add the pipeline environment again.
 
+          # Currently, Dataflow uses Docker container images to uniquely
+          # identify execution environments. Hence Dataflow executes all
+          # transforms that specifies the same Docker contaienr image in the
+          # same container. Dependencies of all environments that specifies a
+          # given container image will be staged in the container for that
+          # particular container image.
           # TODO(BEAM-9455): loosen this restriction to support multiple
-          # environments with the same container name.
+          # environments with the same container image when Dataflow supports
+          # environment specific artifact provisioning.
           continue
         already_added_containers.append(container_image_url)
 

From 13568c83ac7155000e7f8a1241fa3f02d8acf819 Mon Sep 17 00:00:00 2001
From: Ashwin Ramaswami 
Date: Wed, 20 May 2020 11:59:00 -0400
Subject: [PATCH 023/151] Fix grammar / spelling

---
 website/www/site/static/js/language-switch.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/website/www/site/static/js/language-switch.js b/website/www/site/static/js/language-switch.js
index 57d8f20341c0..7b6cb5942117 100644
--- a/website/www/site/static/js/language-switch.js
+++ b/website/www/site/static/js/language-switch.js
@@ -68,7 +68,7 @@ $(document).ready(function() {
             },
             /**
              * @desc Search next sibling and if it's also a code block, then store
-                    it's type and move onto the next element. It will keep
+                    its type and move on to the next element. It will keep
                     looking until there is no direct code block descendant left.
              * @param object $el - jQuery object, from where to start searching.
              * @param array $lang - list to hold types, found while searching.

From 7bdd52ea42aea939be59d2d38bf543f9b1710550 Mon Sep 17 00:00:00 2001
From: Ashwin Ramaswami 
Date: Wed, 20 May 2020 12:05:12 -0400
Subject: [PATCH 024/151] Remove curly quotes from documentation code samples

---
 .../en/documentation/programming-guide.md     | 88 +++++++++----------
 1 file changed, 44 insertions(+), 44 deletions(-)

diff --git a/website/www/site/content/en/documentation/programming-guide.md b/website/www/site/content/en/documentation/programming-guide.md
index c30578a0ec86..5f18e2ef0202 100644
--- a/website/www/site/content/en/documentation/programming-guide.md
+++ b/website/www/site/content/en/documentation/programming-guide.md
@@ -2362,7 +2362,7 @@ This logical type allows creating an enumeration type consisting of a set of nam
 {{< highlight java >}}
 Schema schema = Schema.builder()
                …
-     .addLogicalTypeField(“color”, EnumerationType.create(“RED”, “GREEN”, “BLUE”))
+     .addLogicalTypeField("color", EnumerationType.create("RED", "GREEN", "BLUE"))
      .build();
 {{< /highlight >}}
 
@@ -2370,15 +2370,15 @@ The value of this field is stored in the row as an INT32 type, however the logic
 you access the enumeration either as a string or a value. For example:
 
 {{< highlight java >}}
-EnumerationType.Value enumValue = enumType.valueOf(“RED”);
+EnumerationType.Value enumValue = enumType.valueOf("RED");
 enumValue.getValue();  // Returns 0, the integer value of the constant.
-enumValue.toString();  // Returns “RED”, the string value of the constant
+enumValue.toString();  // Returns "RED", the string value of the constant
 {{< /highlight >}}
 
 Given a row object with an enumeration field, you can also extract the field as the enumeration value.
 
 {{< highlight java >}}
-EnumerationType.Value enumValue = row.getLogicalTypeValue(“color”, EnumerationType.Value.class);
+EnumerationType.Value enumValue = row.getLogicalTypeValue("color", EnumerationType.Value.class);
 {{< /highlight >}}
 
 Automatic schema inference from Java POJOs and JavaBeans automatically converts Java enums to EnumerationType logical 
@@ -2391,10 +2391,10 @@ OneOfType allows creating a disjoint union type over a set of schema fields. For
 {{< highlight java >}}
 Schema schema = Schema.builder()
                …
-     .addLogicalTypeField(“oneOfField”, 
-        OneOfType.create(Field.of(“intField”, FieldType.INT32),
-                         Field.of(“stringField”, FieldType.STRING),
-                         Field.of(“bytesField”, FieldType.BYTES)))
+     .addLogicalTypeField("oneOfField", 
+        OneOfType.create(Field.of("intField", FieldType.INT32),
+                         Field.of("stringField", FieldType.STRING),
+                         Field.of("bytesField", FieldType.BYTES)))
       .build();
 {{< /highlight >}}
 
@@ -2405,19 +2405,19 @@ logical type however defines a Value object that contains an enumeration value i
 {{< highlight java >}}
 // Returns an enumeration indicating all possible case values for the enum.
 // For the above example, this will be 
-// EnumerationType.create(“intField”, “stringField”, “bytesField”);
+// EnumerationType.create("intField", "stringField", "bytesField");
 EnumerationType oneOfEnum = onOfType.getCaseEnumType();
 
 // Creates an instance of the union with the string field set.
-OneOfType.Value oneOfValue = oneOfType.createValue(“stringField”, “foobar”);
+OneOfType.Value oneOfValue = oneOfType.createValue("stringField", "foobar");
 
 // Handle the oneof
 switch (oneOfValue.getCaseEnumType().toString()) {
-  case “intField”:  
+  case "intField":  
     return processInt(oneOfValue.getValue(Integer.class));
-  case “stringField”:
+  case "stringField":
     return processString(oneOfValue.getValue(String.class));
-  case “bytesField”:
+  case "bytesField":
     return processBytes(oneOfValue.getValue(bytes[].class));
 }
 {{< /highlight >}}
@@ -2565,7 +2565,7 @@ In order to select a field at the top level of a schema, the name of the field i
 the user ids from a `PCollection` of purchases one would write (using the `Select` transform)
 
 {{< highlight java >}}
-purchases.apply(Select.fieldNames(“userId”));
+purchases.apply(Select.fieldNames("userId"));
 {{< /highlight >}}
 
 ##### **Nested fields**
@@ -2574,7 +2574,7 @@ Individual nested fields can be specified using the dot operator. For example, t
  shipping address one would write
 
 {{< highlight java >}}
-purchases.apply(Select.fieldNames(“shippingAddress.postCode”));
+purchases.apply(Select.fieldNames("shippingAddress.postCode"));
 {{< /highlight >}}
 
 ##### **Wildcards**
@@ -2583,7 +2583,7 @@ The * operator can be specified at any nesting level to represent all fields at
 shipping-address fields one would write
 
 {{< highlight java >}}
-purchases.apply(Select.fieldNames(“shippingAddress.*”));
+purchases.apply(Select.fieldNames("shippingAddress.*"));
 {{< /highlight >}}
 
 ##### **Arrays**
@@ -2592,7 +2592,7 @@ An array field, where the array element type is a row, can also have subfields o
 selected, the result is an array of the selected subfield type. For example
 
 {{< highlight java >}}
-purchases.apply(Select.fieldNames(“transactions[].bank”));
+purchases.apply(Select.fieldNames("transactions[].bank"));
 {{< /highlight >}}
 
 Will result in a row containing an array field with element-type string, containing the list of banks for each 
@@ -2631,7 +2631,7 @@ specific keys from the map. For example, given the following schema:
 The following 
 
 {{< highlight java >}}
-purchasesByType.apply(Select.fieldNames(“purchases{}.userId”));
+purchasesByType.apply(Select.fieldNames("purchases{}.userId"));
 {{< /highlight >}}
 
 Will result in a row containing an map field with key-type string and value-type string. The selected map will contain
@@ -2655,7 +2655,7 @@ field as a top-level field. Both top-level and nested fields can be selected. Fo
 could select only the userId and streetAddress fields as follows
 
 {{< highlight java >}}
-purchases.apply(Select.fieldNames(“userId”, shippingAddress.streetAddress”));
+purchases.apply(Select.fieldNames("userId", shippingAddress.streetAddress"));
 {{< /highlight >}}
 
 The resulting `PCollection` will have the following schema
@@ -2683,7 +2683,7 @@ The resulting `PCollection` will have the following schema
 The same is true for wildcard selections. The following
 
 {{< highlight java >}}
-purchases.apply(Select.fieldNames(“userId”, shippingAddress.*”));
+purchases.apply(Select.fieldNames("userId", shippingAddress.*"));
 {{< /highlight >}}
 
 Will result in the following schema
@@ -2729,7 +2729,7 @@ top-level field in the resulting row. This means that if multiple fields are sel
 selected field will appear as its own array field. For example
 
 {{< highlight java >}}
-purchases.apply(Select.fieldNames( “transactions.bank”, transactions.purchaseAmount”));
+purchases.apply(Select.fieldNames( "transactions.bank", transactions.purchaseAmount"));
 {{< /highlight >}}
 
 Will result in the following schema
@@ -2832,7 +2832,7 @@ The simplest usage of `Group` specifies no aggregations, in which case all input
 are grouped together into an `ITERABLE` field. For example
 
 {{< highlight java >}}
-purchases.apply(Group.byFieldNames(“userId”, shippingAddress.streetAddress”));
+purchases.apply(Group.byFieldNames("userId", shippingAddress.streetAddress"));
 {{< /highlight >}}
 
 The output schema of this is:
@@ -2863,9 +2863,9 @@ The names of the key and values fields in the output schema can be controlled us
 builders, as follows:
 
 {{< highlight java >}}
-purchases.apply(Group.byFieldNames(“userId”, shippingAddress.streetAddress”)
-    .withKeyField(“userAndStreet”)
-    .withValueField(“matchingPurchases”));
+purchases.apply(Group.byFieldNames("userId", shippingAddress.streetAddress")
+    .withKeyField("userAndStreet")
+    .withValueField("matchingPurchases"));
 {{< /highlight >}}
 
 It is quite common to apply one or more aggregations to the grouped result. Each aggregation can  specify one or more fields 
@@ -2874,10 +2874,10 @@ following application computes three aggregations grouped by userId, with all ag
 output schema:
 
 {{< highlight java >}}
-purchases.apply(Group.byFieldNames(“userId”)
-    .aggregateField(“itemId”, Count.combineFn(), “numPurchases”)
-    .aggregateField(“costCents”, Sum.ofLongs(), “totalSpendCents”)
-    .aggregateField(“costCents”, Top.largestLongsFn(10), “topPurchases”));
+purchases.apply(Group.byFieldNames("userId")
+    .aggregateField("itemId", Count.combineFn(), "numPurchases")
+    .aggregateField("costCents", Sum.ofLongs(), "totalSpendCents")
+    .aggregateField("costCents", Top.largestLongsFn(10), "topPurchases"));
 {{< /highlight >}}
 
 The result of this aggregation will have the following schema:
@@ -2915,7 +2915,7 @@ and is specified with the `using` keyword:
 PCollection transactions = readTransactions();
 PCollection reviews = readReviews();
 PCollection joined = transactions.apply(
-    Join.innerJoin(reviews).using(“userId”, “productId”));
+    Join.innerJoin(reviews).using("userId", "productId"));
 {{< /highlight >}}
 
 The resulting schema is the following:
@@ -2948,8 +2948,8 @@ Review schema named those fields differently than the Transaction schema, then w
 PCollection joined = transactions.apply(
     Join.innerJoin(reviews).on(
       FieldsEqual
-         .left(“userId”, “productId”)
-         .right(“reviewUserId”, “reviewProductId”)));
+         .left("userId", "productId")
+         .right("reviewUserId", "reviewProductId")));
 {{< /highlight >}}
 
 In addition to inner joins, the Join transform supports full outer joins, left outer joins, and right outer joins.
@@ -2971,8 +2971,8 @@ which all predicates return true will pass the filter. For example the following
 
 {{< highlight java >}}
 purchases.apply(Filter
-    .whereFieldName(“costCents”, c -> c > 100 * 20)
-    .whereFieldName(“shippingAddress.country”, c -> c.equals(“de”));
+    .whereFieldName("costCents", c -> c > 100 * 20)
+    .whereFieldName("shippingAddress.country", c -> c.equals("de"));
 {{< /highlight >}}
 
 Will produce all purchases made from Germany with a purchase price of greater than twenty cents.
@@ -2989,9 +2989,9 @@ For example, the following application
 
 {{< highlight java >}}
 purchases.apply(AddFields.create()
-    .field(“timeOfDaySeconds”, FieldType.INT32)
-    .field(“shippingAddress.deliveryNotes”, FieldType.STRING)
-    .field(“transactions.isFlagged, FieldType.BOOLEAN, false));
+    .field("timeOfDaySeconds", FieldType.INT32)
+    .field("shippingAddress.deliveryNotes", FieldType.STRING)
+    .field("transactions.isFlagged, FieldType.BOOLEAN, false));
 {{< /highlight >}}
 
 Results in a `PCollection` with an expanded schema. All of the rows and fields of the input, but also with the specified 
@@ -3007,7 +3007,7 @@ syntax.
 For example, the following snippet
 
 {{< highlight java >}}
-purchases.apply(DropFields.fields(“userId”, “shippingAddress.streetAddress”));
+purchases.apply(DropFields.fields("userId", "shippingAddress.streetAddress"));
 {{< /highlight >}}
 
 Results in a copy of the input with those two fields and their corresponding values removed.
@@ -3024,8 +3024,8 @@ For example, the following snippet
 
 {{< highlight java >}}
 purchases.apply(RenameFields.create()
-  .rename(“userId”, “userIdentifier”)
-  .rename(“shippingAddress.streetAddress”, “shippingAddress.street”));
+  .rename("userId", "userIdentifier")
+  .rename("shippingAddress.streetAddress", "shippingAddress.street"));
 {{< /highlight >}}
 
 Results in the same set of unmodified input elements, however the schema on the PCollection has been changed to rename 
@@ -3113,7 +3113,7 @@ using the above-described selection expressions, as follows:
 {{< highlight java >}}
 purchases.appy(ParDo.of(new DoFn() {
   @ProcessElement public void process(
-     @FieldAccess(“userId”) String userId, @FieldAccess(“itemId”) long itemId) {
+     @FieldAccess("userId") String userId, @FieldAccess("itemId") long itemId) {
       ...
   }
 }));
@@ -3124,7 +3124,7 @@ You can also select nested fields, as follows.
 {{< highlight java >}}
 purchases.appy(ParDo.of(new DoFn() {
   @ProcessElement public void process(
-    @FieldAccess(“shippingAddress.street”) String street) {
+    @FieldAccess("shippingAddress.street") String street) {
       ...
   }
 }));
@@ -3953,8 +3953,8 @@ It is important to note that if, for example, you specify
 AfterCount(50) and only 32 elements arrive,
 those 32 elements sit around forever. If the 32 elements are important to you,
 consider using [composite triggers](#composite-triggers) to combine multiple
-conditions. This allows you to specify multiple firing conditions such as “fire
-either when I receive 50 elements, or every 1 second”.
+conditions. This allows you to specify multiple firing conditions such as "fire
+either when I receive 50 elements, or every 1 second".
 
 ### 9.4. Setting a trigger {#setting-a-trigger}
 

From 696ebf29c8235c12a3fae3ce11ce2f512fad244a Mon Sep 17 00:00:00 2001
From: "chamikara@google.com" 
Date: Wed, 20 May 2020 09:57:27 -0700
Subject: [PATCH 025/151] Fixes typos.

---
 .../python/apache_beam/runners/dataflow/internal/apiclient.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py b/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
index 8c906bd39715..d0e7911264ed 100644
--- a/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
+++ b/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
@@ -316,8 +316,8 @@ def __init__(
 
           # Currently, Dataflow uses Docker container images to uniquely
           # identify execution environments. Hence Dataflow executes all
-          # transforms that specifies the same Docker contaienr image in the
-          # same container. Dependencies of all environments that specifies a
+          # transforms that specify the same Docker container image in the
+          # same container. Dependencies of all environments that specify a
           # given container image will be staged in the container for that
           # particular container image.
           # TODO(BEAM-9455): loosen this restriction to support multiple

From cdc78211282be7c9b9b794996388b6e0428d3ba9 Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Wed, 20 May 2020 13:17:25 -0400
Subject: [PATCH 026/151] Update test list.

---
 release/src/main/scripts/mass_comment.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/release/src/main/scripts/mass_comment.py b/release/src/main/scripts/mass_comment.py
index bd9e26aa3789..b418aa3c9176 100644
--- a/release/src/main/scripts/mass_comment.py
+++ b/release/src/main/scripts/mass_comment.py
@@ -29,23 +29,26 @@
 
 
 COMMENTS_TO_ADD=[
+  "Run Release Gradle Build",
   "Run Go PostCommit",
   "Run Java PostCommit",
-  "Run Java PortabilityApi PostCommit",
   "Run Java Flink PortableValidatesRunner Batch",
   "Run Java Flink PortableValidatesRunner Streaming",
   "Run Apex ValidatesRunner",
   "Run Dataflow ValidatesRunner",
   "Run Flink ValidatesRunner",
   "Run Gearpump ValidatesRunner",
-  "Run Dataflow PortabilityApi ValidatesRunner",
   "Run Samza ValidatesRunner",
   "Run Spark ValidatesRunner",
+  "Run Java Spark PortableValidatesRunner Batch",
+  "Run Python Spark ValidatesRunner",
   "Run Python Dataflow ValidatesContainer",
   "Run Python Dataflow ValidatesRunner",
   "Run Python 3.5 Flink ValidatesRunner",
   "Run Python 2 PostCommit",
   "Run Python 3.5 PostCommit",
+  "Run Python 3.6 PostCommit",
+  "Run Python 3.7 PostCommit",
   "Run SQL PostCommit",
   "Run Go PreCommit",
   "Run Java PreCommit",

From 0a8d955e49776b872e8fda59cbeb0870afa68784 Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Wed, 20 May 2020 14:23:02 -0400
Subject: [PATCH 027/151] Update verify_release_build.sh to use
 mass_comment.py.

---
 .../src/main/scripts/verify_release_build.sh  | 39 +------------------
 1 file changed, 1 insertion(+), 38 deletions(-)

diff --git a/release/src/main/scripts/verify_release_build.sh b/release/src/main/scripts/verify_release_build.sh
index bc3671f46d93..77c184bc463a 100755
--- a/release/src/main/scripts/verify_release_build.sh
+++ b/release/src/main/scripts/verify_release_build.sh
@@ -40,40 +40,6 @@ BEAM_REPO_URL=https://github.com/apache/beam.git
 RELEASE_BRANCH=release-${RELEASE_VER}
 WORKING_BRANCH=postcommit_validation_pr
 
-JOB_TRIGGER_PHRASES=(
-  # To verify Gradle release build
-  "**Run Release Gradle Build**"
-  # To run all PostCommit jobs
-  "Run Go PostCommit"
-  "Run Java PostCommit"
-  "Run Java PortabilityApi PostCommit"
-  "Run Java Flink PortableValidatesRunner Batch"
-  "Run Java Flink PortableValidatesRunner Streaming"
-  "Run Apex ValidatesRunner"
-  "Run Dataflow ValidatesRunner"
-  "Run Flink ValidatesRunner"
-  "Run Gearpump ValidatesRunner"
-  "Run Dataflow PortabilityApi ValidatesRunner"
-  "Run Samza ValidatesRunner"
-  "Run Spark ValidatesRunner"
-  "Run Python Dataflow ValidatesContainer"
-  "Run Python Dataflow ValidatesRunner"
-  "Run Python 3.5 Flink ValidatesRunner"
-  # Python versions match those in run_rc_validation.sh.
-  "Run Python 2 PostCommit"
-  "Run Python 3.5 PostCommit"
-  "Run SQL PostCommit"
-  "Run Go PreCommit"
-  "Run Java PreCommit"
-  "Run Java_Examples_Dataflow PreCommit"
-  "Run JavaPortabilityApi PreCommit"
-  "Run Portable_Python PreCommit"
-  "Run PythonLint PreCommit"
-  "Run Python PreCommit"
-  "Run Python DockerBuild PreCommit"
-)
-
-
 function clean_up(){
   echo ""
   echo "==================== Final Cleanup ===================="
@@ -164,12 +130,9 @@ if [[ ! -z `which hub` ]]; then
   git commit -m "Changed version.py and gradle.properties to python dev version to create a test PR" --quiet
   git push -f ${GITHUB_USERNAME} --quiet
 
-  trigger_phrases=$(IFS=$'\n'; echo "${JOB_TRIGGER_PHRASES[*]}")
   hub pull-request -b apache:${RELEASE_BRANCH} -h ${GITHUB_USERNAME}:${WORKING_BRANCH} -F- <<<"[DO NOT MERGE] Run all PostCommit and PreCommit Tests against Release Branch
 
-  Please comment as instructions below, one phrase per comment:
-
-  ${trigger_phrases}"
+  You can run many tests automatically using release/src/main/scripts/mass_comment.py."
 
   echo ""
   echo "[NOTE]: Please make sure all test targets have been invoked."

From 84343b06fa63aec081ea2c16b2ec3ebd6baad394 Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Wed, 20 May 2020 14:35:18 -0400
Subject: [PATCH 028/151] Run yapf on mass_comment.py.

---
 release/src/main/scripts/mass_comment.py | 69 ++++++++++++------------
 1 file changed, 36 insertions(+), 33 deletions(-)

diff --git a/release/src/main/scripts/mass_comment.py b/release/src/main/scripts/mass_comment.py
index b418aa3c9176..b0f74896dc22 100644
--- a/release/src/main/scripts/mass_comment.py
+++ b/release/src/main/scripts/mass_comment.py
@@ -27,39 +27,39 @@
 import requests
 from datetime import datetime
 
-
-COMMENTS_TO_ADD=[
-  "Run Release Gradle Build",
-  "Run Go PostCommit",
-  "Run Java PostCommit",
-  "Run Java Flink PortableValidatesRunner Batch",
-  "Run Java Flink PortableValidatesRunner Streaming",
-  "Run Apex ValidatesRunner",
-  "Run Dataflow ValidatesRunner",
-  "Run Flink ValidatesRunner",
-  "Run Gearpump ValidatesRunner",
-  "Run Samza ValidatesRunner",
-  "Run Spark ValidatesRunner",
-  "Run Java Spark PortableValidatesRunner Batch",
-  "Run Python Spark ValidatesRunner",
-  "Run Python Dataflow ValidatesContainer",
-  "Run Python Dataflow ValidatesRunner",
-  "Run Python 3.5 Flink ValidatesRunner",
-  "Run Python 2 PostCommit",
-  "Run Python 3.5 PostCommit",
-  "Run Python 3.6 PostCommit",
-  "Run Python 3.7 PostCommit",
-  "Run SQL PostCommit",
-  "Run Go PreCommit",
-  "Run Java PreCommit",
-  "Run Java_Examples_Dataflow PreCommit",
-  "Run JavaPortabilityApi PreCommit",
-  "Run Portable_Python PreCommit",
-  "Run PythonLint PreCommit",
-  "Run Python PreCommit",
-  "Run Python DockerBuild PreCommit"
+COMMENTS_TO_ADD = [
+    "Run Release Gradle Build",
+    "Run Go PostCommit",
+    "Run Java PostCommit",
+    "Run Java Flink PortableValidatesRunner Batch",
+    "Run Java Flink PortableValidatesRunner Streaming",
+    "Run Apex ValidatesRunner",
+    "Run Dataflow ValidatesRunner",
+    "Run Flink ValidatesRunner",
+    "Run Gearpump ValidatesRunner",
+    "Run Samza ValidatesRunner",
+    "Run Spark ValidatesRunner",
+    "Run Java Spark PortableValidatesRunner Batch",
+    "Run Python Spark ValidatesRunner",
+    "Run Python Dataflow ValidatesContainer",
+    "Run Python Dataflow ValidatesRunner",
+    "Run Python 3.5 Flink ValidatesRunner",
+    "Run Python 2 PostCommit",
+    "Run Python 3.5 PostCommit",
+    "Run Python 3.6 PostCommit",
+    "Run Python 3.7 PostCommit",
+    "Run SQL PostCommit",
+    "Run Go PreCommit",
+    "Run Java PreCommit",
+    "Run Java_Examples_Dataflow PreCommit",
+    "Run JavaPortabilityApi PreCommit",
+    "Run Portable_Python PreCommit",
+    "Run PythonLint PreCommit",
+    "Run Python PreCommit",
+    "Run Python DockerBuild PreCommit"
 ]
 
+
 def executeGHGraphqlQuery(accessToken, query):
   '''Runs graphql query on GitHub.'''
   url = 'https://api.github.com/graphql'
@@ -67,6 +67,7 @@ def executeGHGraphqlQuery(accessToken, query):
   r = requests.post(url=url, json={'query': query}, headers=headers)
   return r.json()
 
+
 def getSubjectId(accessToken, prNumber):
   query = '''
 query FindPullRequestID {
@@ -80,6 +81,7 @@ def getSubjectId(accessToken, prNumber):
   response = executeGHGraphqlQuery(accessToken, query)
   return response['data']['repository']['pullRequest']['id']
 
+
 def fetchGHData(accessToken, subjectId, commentBody):
   '''Fetches GitHub data required for reporting Beam metrics'''
   query = '''
@@ -99,6 +101,7 @@ def fetchGHData(accessToken, subjectId, commentBody):
 ''' % (subjectId, commentBody)
   return executeGHGraphqlQuery(accessToken, query)
 
+
 def postComments(accessToken, subjectId):
   '''
   Main workhorse method. Fetches data from GitHub and puts it in metrics table.
@@ -108,6 +111,7 @@ def postComments(accessToken, subjectId):
     jsonData = fetchGHData(accessToken, subjectId, commentBody)
   print(jsonData)
 
+
 def probeGitHubIsUp():
   '''
   Returns True if GitHub responds to simple queries. Else returns False.
@@ -126,10 +130,9 @@ def probeGitHubIsUp():
   '''
   print("Started.")
 
-
   if not probeGitHubIsUp():
     print("GitHub is unavailable, skipping fetching data.")
-    exit();
+    exit()
 
   print("GitHub is available start fetching data.")
 

From e88362ee2cc56f5c58a11fa4e36edbfabb83eb67 Mon Sep 17 00:00:00 2001
From: Sam Rohde 
Date: Wed, 20 May 2020 11:01:53 -0700
Subject: [PATCH 029/151] Skip checking input determinism for GBKs embedded in
 x-lang transforms. We can assume safely assume that the expansion service
 constructs transforms correctly.

Change-Id: I46d40e40ac33933004836681d06f91c031655f06
---
 .../python/apache_beam/runners/dataflow/dataflow_runner.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py b/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py
index 4c02168cee58..505316d5fdf6 100644
--- a/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py
+++ b/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py
@@ -849,8 +849,15 @@ def _verify_gbk_coders(self, transform, pcoll):
     #
     # TODO(ccy): make Coder inference and checking less specialized and more
     # comprehensive.
+
     parent = pcoll.producer
     if parent:
+      # Skip the check because we can assume that any x-lang transform is
+      # properly formed (the onus is on the expansion service to construct
+      # transforms correctly).
+      if isinstance(parent.transform, RunnerAPIPTransformHolder):
+        return
+
       coder = parent.transform._infer_output_coder()  # pylint: disable=protected-access
     if not coder:
       coder = self._get_coder(pcoll.element_type or typehints.Any, None)

From d5d7c88b2d330f02260cab3b1075509a34181f3a Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Wed, 20 May 2020 14:50:41 -0400
Subject: [PATCH 030/151] Remove irrelevant instruction.

---
 website/www/site/content/en/contribute/release-guide.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/website/www/site/content/en/contribute/release-guide.md b/website/www/site/content/en/contribute/release-guide.md
index 55ec1d126d9a..7e199ae9d5ab 100644
--- a/website/www/site/content/en/contribute/release-guide.md
+++ b/website/www/site/content/en/contribute/release-guide.md
@@ -406,7 +406,6 @@ You can use [mass_comment.py](https://github.com/apache/beam/blob/master/release
   1. Check the build result.
   2. If build failed, scan log will contain all failures.
   3. You should stabilize the release branch until release build succeeded.
-  4. The script will output a set of Jenkins phrases to enter in the created PR.
   
 There are some projects that don't produce the artifacts, e.g. `beam-test-tools`, you may be able to
 ignore failures there.

From 583991565db7b684957c9a97a0ed6bb09593c01f Mon Sep 17 00:00:00 2001
From: Yichi Zhang 
Date: Wed, 20 May 2020 11:56:36 -0700
Subject: [PATCH 031/151] Address comments and add tests

---
 .../beam/fn/harness/FnApiDoFnRunner.java      |  50 ++--
 .../beam/fn/harness/FnApiDoFnRunnerTest.java  | 245 +++++++++++++-----
 2 files changed, 215 insertions(+), 80 deletions(-)

diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java
index 7ee066956de6..ab07ca319ac0 100644
--- a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java
+++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java
@@ -92,7 +92,6 @@
 import org.apache.beam.sdk.transforms.reflect.DoFnInvokers;
 import org.apache.beam.sdk.transforms.reflect.DoFnSignature;
 import org.apache.beam.sdk.transforms.reflect.DoFnSignature.StateDeclaration;
-import org.apache.beam.sdk.transforms.reflect.DoFnSignature.TimerDeclaration;
 import org.apache.beam.sdk.transforms.reflect.DoFnSignature.TimerFamilyDeclaration;
 import org.apache.beam.sdk.transforms.reflect.DoFnSignatures;
 import org.apache.beam.sdk.transforms.splittabledofn.RestrictionTracker;
@@ -461,19 +460,10 @@ public void accept(WindowedValue input) throws Exception {
       // Extract out relevant TimerFamilySpec information in preparation for execution.
       for (Map.Entry entry :
           parDoPayload.getTimerFamilySpecsMap().entrySet()) {
+        // The timer family spec map key is either from timerId of timer declaration or
+        // timerFamilyId from timer family declaration.
         String timerIdOrTimerFamilyId = entry.getKey();
-        TimeDomain timeDomain;
-        if (timerIdOrTimerFamilyId.startsWith(TimerFamilyDeclaration.PREFIX)) {
-          timeDomain =
-              DoFnSignatures.getTimerFamilySpecOrThrow(
-                      doFnSignature.timerFamilyDeclarations().get(timerIdOrTimerFamilyId), doFn)
-                  .getTimeDomain();
-        } else {
-          timeDomain =
-              DoFnSignatures.getTimerSpecOrThrow(
-                      doFnSignature.timerDeclarations().get(timerIdOrTimerFamilyId), doFn)
-                  .getTimeDomain();
-        }
+        TimeDomain timeDomain = translateTimeDomain(entry.getValue().getTimeDomain());
         Coder> timerCoder =
             (Coder) rehydratedComponents.getCoder(entry.getValue().getTimerFamilyCoderId());
         timerFamilyInfosBuilder.put(timerIdOrTimerFamilyId, KV.of(timeDomain, timerCoder));
@@ -976,6 +966,8 @@ private  void processTimer(
     currentTimer = timer;
     currentTimeDomain = timeDomain;
     onTimerContext = new OnTimerContext<>(timer.getUserKey());
+    // The timerIdOrTimerFamilyId contains either a timerId from timer declaration or timerFamilyId
+    // from timer family declaration.
     String timerId =
         timerIdOrTimerFamilyId.startsWith(TimerFamilyDeclaration.PREFIX)
             ? ""
@@ -1057,6 +1049,9 @@ private class FnApiTimer implements org.apache.beam.sdk.state.Timer {
         Instant elementTimestampOrTimerFireTimestamp,
         PaneInfo paneInfo,
         TimeDomain timeDomain) {
+      if (timerId.equals("ts-event") && timeDomain.equals(TimeDomain.PROCESSING_TIME)) {
+        throw new IllegalStateException("illegal");
+      }
       this.timerId = timerId;
       this.userKey = userKey;
       this.dynamicTimerTag = dynamicTimerTag;
@@ -1246,11 +1241,9 @@ private class FnApiTimerMap implements TimerMap {
       this.elementTimestampOrTimerFireTimestamp = elementTimestampOrTimerFireTimestamp;
       this.boundedWindow = boundedWindow;
       this.paneInfo = paneInfo;
-
-      TimerFamilyDeclaration timerFamilyDeclaration =
-          doFnSignature.timerFamilyDeclarations().get(timerFamilyId);
       this.timeDomain =
-          DoFnSignatures.getTimerFamilySpecOrThrow(timerFamilyDeclaration, doFn).getTimeDomain();
+          translateTimeDomain(
+              parDoPayload.getTimerFamilySpecsMap().get(timerFamilyId).getTimeDomain());
     }
 
     @Override
@@ -1500,9 +1493,8 @@ public org.apache.beam.sdk.state.Timer timer(String timerId) {
       // For the initial timestamps we pass in the current elements timestamp for the hold timestamp
       // and the current element's timestamp which will be used for the fire timestamp if this
       // timer is in the EVENT time domain.
-      TimerDeclaration timerDeclaration = doFnSignature.timerDeclarations().get(timerId);
       TimeDomain timeDomain =
-          DoFnSignatures.getTimerSpecOrThrow(timerDeclaration, doFn).getTimeDomain();
+          translateTimeDomain(parDoPayload.getTimerFamilySpecsMap().get(timerId).getTimeDomain());
       return new FnApiTimer(
           timerId,
           ((KV) currentElement.getValue()).getKey(),
@@ -1744,15 +1736,17 @@ public State state(String stateId, boolean alwaysFetched) {
 
     @Override
     public org.apache.beam.sdk.state.Timer timer(String timerId) {
+      TimeDomain timeDomain =
+          translateTimeDomain(parDoPayload.getTimerFamilySpecsMap().get(timerId).getTimeDomain());
       return new FnApiTimer(
           timerId,
           currentTimer.getUserKey(),
-          currentTimer.getDynamicTimerTag(),
+          "",
           currentWindow,
           currentTimer.getHoldTimestamp(),
           currentTimer.getFireTimestamp(),
           currentTimer.getPane(),
-          currentTimeDomain);
+          timeDomain);
     }
 
     @Override
@@ -1782,4 +1776,18 @@ public String getErrorContext() {
       return "FnApiDoFnRunner/OnTimer";
     }
   }
+
+  private TimeDomain translateTimeDomain(
+      org.apache.beam.model.pipeline.v1.RunnerApi.TimeDomain.Enum domain) {
+    switch (domain) {
+      case EVENT_TIME:
+        return TimeDomain.EVENT_TIME;
+      case PROCESSING_TIME:
+        return TimeDomain.PROCESSING_TIME;
+      case SYNCHRONIZED_PROCESSING_TIME:
+        return TimeDomain.SYNCHRONIZED_PROCESSING_TIME;
+      default:
+        throw new IllegalArgumentException("Unknown time domain");
+    }
+  }
 }
diff --git a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java
index 1da967269b32..e763fface9f4 100644
--- a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java
+++ b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java
@@ -94,6 +94,7 @@
 import org.apache.beam.sdk.state.StateSpecs;
 import org.apache.beam.sdk.state.TimeDomain;
 import org.apache.beam.sdk.state.Timer;
+import org.apache.beam.sdk.state.TimerMap;
 import org.apache.beam.sdk.state.TimerSpec;
 import org.apache.beam.sdk.state.TimerSpecs;
 import org.apache.beam.sdk.state.ValueState;
@@ -759,58 +760,6 @@ public void testUsingMetrics() throws Exception {
     assertThat(result, containsInAnyOrder(expected.toArray()));
   }
 
-  private static class TestTimerfulDoFn extends DoFn, String> {
-    @StateId("bag")
-    private final StateSpec> bagStateSpec = StateSpecs.bag(StringUtf8Coder.of());
-
-    @TimerId("event")
-    private final TimerSpec eventTimerSpec = TimerSpecs.timer(TimeDomain.EVENT_TIME);
-
-    @TimerId("processing")
-    private final TimerSpec processingTimerSpec = TimerSpecs.timer(TimeDomain.PROCESSING_TIME);
-
-    @ProcessElement
-    public void processElement(
-        ProcessContext context,
-        @StateId("bag") BagState bagState,
-        @TimerId("event") Timer eventTimeTimer,
-        @TimerId("processing") Timer processingTimeTimer) {
-      context.output("main" + context.element().getKey() + Iterables.toString(bagState.read()));
-      bagState.add(context.element().getValue());
-      eventTimeTimer.withOutputTimestamp(context.timestamp()).set(context.timestamp().plus(1L));
-      processingTimeTimer.offset(Duration.millis(2L));
-      processingTimeTimer.setRelative();
-    }
-
-    @OnTimer("event")
-    public void eventTimer(
-        OnTimerContext context,
-        @StateId("bag") BagState bagState,
-        @TimerId("event") Timer eventTimeTimer,
-        @TimerId("processing") Timer processingTimeTimer) {
-      context.output("event" + Iterables.toString(bagState.read()));
-      bagState.add("event");
-      eventTimeTimer
-          .withOutputTimestamp(context.timestamp())
-          .set(context.fireTimestamp().plus(11L));
-      processingTimeTimer.offset(Duration.millis(12L));
-      processingTimeTimer.setRelative();
-    }
-
-    @OnTimer("processing")
-    public void processingTimer(
-        OnTimerContext context,
-        @StateId("bag") BagState bagState,
-        @TimerId("event") Timer eventTimeTimer,
-        @TimerId("processing") Timer processingTimeTimer) {
-      context.output("processing" + Iterables.toString(bagState.read()));
-      bagState.add("processing");
-      eventTimeTimer.withOutputTimestamp(context.timestamp()).set(context.timestamp().plus(21L));
-      processingTimeTimer.offset(Duration.millis(22L));
-      processingTimeTimer.setRelative();
-    }
-  }
-
   @Test
   public void testTimers() throws Exception {
     dateTimeProvider.setDateTimeFixed(10000L);
@@ -889,6 +838,10 @@ public void testTimers() throws Exception {
     LogicalEndpoint eventTimer = LogicalEndpoint.timer("57L", TEST_TRANSFORM_ID, "ts-event");
     LogicalEndpoint processingTimer =
         LogicalEndpoint.timer("57L", TEST_TRANSFORM_ID, "ts-processing");
+    LogicalEndpoint eventFamilyTimer =
+        LogicalEndpoint.timer("57L", TEST_TRANSFORM_ID, "tfs-event-family");
+    LogicalEndpoint processingFamilyTimer =
+        LogicalEndpoint.timer("57L", TEST_TRANSFORM_ID, "tfs-processing-family");
     // Ensure that bag user state that is initially empty or populated works.
     // Ensure that the key order does not matter when we traverse over KV pairs.
     FnDataReceiver> mainInput =
@@ -909,6 +862,12 @@ public void testTimers() throws Exception {
         processingTimer, timerInGlobalWindow("C", new Instant(1800L), new Instant(2800L)));
     fakeTimerClient.sendTimer(
         processingTimer, timerInGlobalWindow("B", new Instant(1900L), new Instant(2900L)));
+    fakeTimerClient.sendTimer(
+        eventFamilyTimer,
+        timerInGlobalWindow("B", "event-timer2", new Instant(2000L), new Instant(3000L)));
+    fakeTimerClient.sendTimer(
+        processingFamilyTimer,
+        timerInGlobalWindow("Y", "processing-timer2", new Instant(2100L), new Instant(3100L)));
     assertThat(
         mainOutputValues,
         contains(
@@ -921,7 +880,9 @@ public void testTimers() throws Exception {
             timestampedValueInGlobalWindow("event[A0, event]", new Instant(1600L)),
             timestampedValueInGlobalWindow("processing[X0, X1, X2]", new Instant(1700L)),
             timestampedValueInGlobalWindow("processing[C0]", new Instant(1800L)),
-            timestampedValueInGlobalWindow("processing[event]", new Instant(1900L))));
+            timestampedValueInGlobalWindow("processing[event]", new Instant(1900L)),
+            timestampedValueInGlobalWindow("event-family[event, processing]", new Instant(2000L)),
+            timestampedValueInGlobalWindow("processing-family[Y1, Y2]", new Instant(2100L))));
     assertThat(
         fakeTimerClient.getTimers(eventTimer),
         contains(
@@ -934,7 +895,9 @@ public void testTimers() throws Exception {
             timerInGlobalWindow("A", new Instant(1600L), new Instant(2611L)),
             timerInGlobalWindow("X", new Instant(1700L), new Instant(1721L)),
             timerInGlobalWindow("C", new Instant(1800L), new Instant(1821L)),
-            timerInGlobalWindow("B", new Instant(1900L), new Instant(1921L))));
+            timerInGlobalWindow("B", new Instant(1900L), new Instant(1921L)),
+            timerInGlobalWindow("B", new Instant(2000L), new Instant(2031L)),
+            timerInGlobalWindow("Y", new Instant(2100L), new Instant(2141L))));
     assertThat(
         fakeTimerClient.getTimers(processingTimer),
         contains(
@@ -947,19 +910,58 @@ public void testTimers() throws Exception {
             timerInGlobalWindow("A", new Instant(1600L), new Instant(10012L)),
             timerInGlobalWindow("X", new Instant(1700L), new Instant(10022L)),
             timerInGlobalWindow("C", new Instant(1800L), new Instant(10022L)),
-            timerInGlobalWindow("B", new Instant(1900L), new Instant(10022L))));
+            timerInGlobalWindow("B", new Instant(1900L), new Instant(10022L)),
+            timerInGlobalWindow("B", new Instant(2000L), new Instant(10032L)),
+            timerInGlobalWindow("Y", new Instant(2100L), new Instant(10042L))));
+    assertThat(
+        fakeTimerClient.getTimers(eventFamilyTimer),
+        contains(
+            timerInGlobalWindow("X", "event-timer1", new Instant(1000L), new Instant(1003L)),
+            timerInGlobalWindow("Y", "event-timer1", new Instant(1100L), new Instant(1103L)),
+            timerInGlobalWindow("X", "event-timer1", new Instant(1200L), new Instant(1203L)),
+            timerInGlobalWindow("Y", "event-timer1", new Instant(1300L), new Instant(1303L)),
+            timerInGlobalWindow("A", "event-timer1", new Instant(1400L), new Instant(2413L)),
+            timerInGlobalWindow("B", "event-timer1", new Instant(1500L), new Instant(2513L)),
+            timerInGlobalWindow("A", "event-timer1", new Instant(1600L), new Instant(2613L)),
+            timerInGlobalWindow("X", "event-timer1", new Instant(1700L), new Instant(1723L)),
+            timerInGlobalWindow("C", "event-timer1", new Instant(1800L), new Instant(1823L)),
+            timerInGlobalWindow("B", "event-timer1", new Instant(1900L), new Instant(1923L)),
+            timerInGlobalWindow("B", "event-timer1", new Instant(2000L), new Instant(2033L)),
+            timerInGlobalWindow("Y", "event-timer1", new Instant(2100L), new Instant(2143L))));
+    assertThat(
+        fakeTimerClient.getTimers(processingFamilyTimer),
+        contains(
+            timerInGlobalWindow("X", "processing-timer1", new Instant(1000L), new Instant(10004L)),
+            timerInGlobalWindow("Y", "processing-timer1", new Instant(1100L), new Instant(10004L)),
+            timerInGlobalWindow("X", "processing-timer1", new Instant(1200L), new Instant(10004L)),
+            timerInGlobalWindow("Y", "processing-timer1", new Instant(1300L), new Instant(10004L)),
+            timerInGlobalWindow("A", "processing-timer1", new Instant(1400L), new Instant(10014L)),
+            timerInGlobalWindow("B", "processing-timer1", new Instant(1500L), new Instant(10014L)),
+            timerInGlobalWindow("A", "processing-timer1", new Instant(1600L), new Instant(10014L)),
+            timerInGlobalWindow("X", "processing-timer1", new Instant(1700L), new Instant(10024L)),
+            timerInGlobalWindow("C", "processing-timer1", new Instant(1800L), new Instant(10024L)),
+            timerInGlobalWindow("B", "processing-timer1", new Instant(1900L), new Instant(10024L)),
+            timerInGlobalWindow("B", "processing-timer1", new Instant(2000L), new Instant(10034L)),
+            timerInGlobalWindow(
+                "Y", "processing-timer1", new Instant(2100L), new Instant(10044L))));
     mainOutputValues.clear();
 
     assertFalse(fakeTimerClient.isOutboundClosed(eventTimer));
     assertFalse(fakeTimerClient.isOutboundClosed(processingTimer));
+    assertFalse(fakeTimerClient.isOutboundClosed(eventFamilyTimer));
+    assertFalse(fakeTimerClient.isOutboundClosed(processingFamilyTimer));
     fakeTimerClient.closeInbound(eventTimer);
     fakeTimerClient.closeInbound(processingTimer);
+    fakeTimerClient.closeInbound(eventFamilyTimer);
+    fakeTimerClient.closeInbound(processingFamilyTimer);
 
     Iterables.getOnlyElement(finishFunctionRegistry.getFunctions()).run();
     assertThat(mainOutputValues, empty());
 
     assertTrue(fakeTimerClient.isOutboundClosed(eventTimer));
     assertTrue(fakeTimerClient.isOutboundClosed(processingTimer));
+    assertTrue(fakeTimerClient.isOutboundClosed(eventFamilyTimer));
+    assertTrue(fakeTimerClient.isOutboundClosed(processingFamilyTimer));
 
     Iterables.getOnlyElement(teardownFunctions).run();
     assertThat(mainOutputValues, empty());
@@ -967,29 +969,154 @@ public void testTimers() throws Exception {
     assertEquals(
         ImmutableMap.builder()
             .put(bagUserStateKey("bag", "X"), encode("X0", "X1", "X2", "processing"))
-            .put(bagUserStateKey("bag", "Y"), encode("Y1", "Y2"))
+            .put(bagUserStateKey("bag", "Y"), encode("Y1", "Y2", "processing-family"))
             .put(bagUserStateKey("bag", "A"), encode("A0", "event", "event"))
-            .put(bagUserStateKey("bag", "B"), encode("event", "processing"))
+            .put(bagUserStateKey("bag", "B"), encode("event", "processing", "event-family"))
             .put(bagUserStateKey("bag", "C"), encode("C0", "processing"))
             .build(),
         fakeStateClient.getData());
   }
 
+  private  org.apache.beam.runners.core.construction.Timer timerInGlobalWindow(
+      K userKey, Instant holdTimestamp, Instant fireTimestamp) {
+    return timerInGlobalWindow(userKey, "", holdTimestamp, fireTimestamp);
+  }
+
   private  WindowedValue valueInWindow(T value, BoundedWindow window) {
     return WindowedValue.of(value, window.maxTimestamp(), window, PaneInfo.NO_FIRING);
   }
 
   private  org.apache.beam.runners.core.construction.Timer timerInGlobalWindow(
-      K userKey, Instant holdTimestamp, Instant fireTimestamp) {
+      K userKey, String dynamicTimerTag, Instant holdTimestamp, Instant fireTimestamp) {
     return org.apache.beam.runners.core.construction.Timer.of(
         userKey,
-        "",
+        dynamicTimerTag,
         Collections.singletonList(GlobalWindow.INSTANCE),
         fireTimestamp,
         holdTimestamp,
         PaneInfo.NO_FIRING);
   }
 
+  private static class TestTimerfulDoFn extends DoFn, String> {
+    @StateId("bag")
+    private final StateSpec> bagStateSpec = StateSpecs.bag(StringUtf8Coder.of());
+
+    @TimerId("event")
+    private final TimerSpec eventTimerSpec = TimerSpecs.timer(TimeDomain.EVENT_TIME);
+
+    @TimerId("processing")
+    private final TimerSpec processingTimerSpec = TimerSpecs.timer(TimeDomain.PROCESSING_TIME);
+
+    @TimerFamily("event-family")
+    private final TimerSpec eventTimerFamilySpec = TimerSpecs.timerMap(TimeDomain.EVENT_TIME);
+
+    @TimerFamily("processing-family")
+    private final TimerSpec processingTimerFamilySpec =
+        TimerSpecs.timerMap(TimeDomain.PROCESSING_TIME);
+
+    @ProcessElement
+    public void processElement(
+        ProcessContext context,
+        @StateId("bag") BagState bagState,
+        @TimerId("event") Timer eventTimeTimer,
+        @TimerId("processing") Timer processingTimeTimer,
+        @TimerFamily("event-family") TimerMap eventTimerFamily,
+        @TimerFamily("processing-family") TimerMap processingTimerFamily) {
+      context.output("main" + context.element().getKey() + Iterables.toString(bagState.read()));
+      bagState.add(context.element().getValue());
+      eventTimeTimer.withOutputTimestamp(context.timestamp()).set(context.timestamp().plus(1L));
+      processingTimeTimer.offset(Duration.millis(2L));
+      processingTimeTimer.setRelative();
+      eventTimerFamily
+          .get("event-timer1")
+          .withOutputTimestamp(context.timestamp())
+          .set(context.timestamp().plus(3L));
+      processingTimerFamily.get("processing-timer1").offset(Duration.millis(4L)).setRelative();
+    }
+
+    @OnTimer("event")
+    public void eventTimer(
+        OnTimerContext context,
+        @StateId("bag") BagState bagState,
+        @TimerId("event") Timer eventTimeTimer,
+        @TimerId("processing") Timer processingTimeTimer,
+        @TimerFamily("event-family") TimerMap eventTimerFamily,
+        @TimerFamily("processing-family") TimerMap processingTimerFamily) {
+      context.output("event" + Iterables.toString(bagState.read()));
+      bagState.add("event");
+      eventTimeTimer
+          .withOutputTimestamp(context.timestamp())
+          .set(context.fireTimestamp().plus(11L));
+      processingTimeTimer.offset(Duration.millis(12L));
+      processingTimeTimer.setRelative();
+      eventTimerFamily
+          .get("event-timer1")
+          .withOutputTimestamp(context.timestamp())
+          .set(context.fireTimestamp().plus(13L));
+      processingTimerFamily.get("processing-timer1").offset(Duration.millis(14L)).setRelative();
+    }
+
+    @OnTimer("processing")
+    public void processingTimer(
+        OnTimerContext context,
+        @StateId("bag") BagState bagState,
+        @TimerId("event") Timer eventTimeTimer,
+        @TimerId("processing") Timer processingTimeTimer,
+        @TimerFamily("event-family") TimerMap eventTimerFamily,
+        @TimerFamily("processing-family") TimerMap processingTimerFamily) {
+      context.output("processing" + Iterables.toString(bagState.read()));
+      bagState.add("processing");
+      eventTimeTimer.withOutputTimestamp(context.timestamp()).set(context.timestamp().plus(21L));
+      processingTimeTimer.offset(Duration.millis(22L));
+      processingTimeTimer.setRelative();
+      eventTimerFamily
+          .get("event-timer1")
+          .withOutputTimestamp(context.timestamp())
+          .set(context.timestamp().plus(23L));
+      processingTimerFamily.get("processing-timer1").offset(Duration.millis(24L)).setRelative();
+    }
+
+    @OnTimerFamily("event-family")
+    public void eventFamilyOnTimer(
+        OnTimerContext context,
+        @StateId("bag") BagState bagState,
+        @TimerId("event") Timer eventTimeTimer,
+        @TimerId("processing") Timer processingTimeTimer,
+        @TimerFamily("event-family") TimerMap eventTimerFamily,
+        @TimerFamily("processing-family") TimerMap processingTimerFamily) {
+      context.output("event-family" + Iterables.toString(bagState.read()));
+      bagState.add("event-family");
+      eventTimeTimer.withOutputTimestamp(context.timestamp()).set(context.timestamp().plus(31L));
+      processingTimeTimer.offset(Duration.millis(32L));
+      processingTimeTimer.setRelative();
+      eventTimerFamily
+          .get("event-timer1")
+          .withOutputTimestamp(context.timestamp())
+          .set(context.timestamp().plus(33L));
+      processingTimerFamily.get("processing-timer1").offset(Duration.millis(34L)).setRelative();
+    }
+
+    @OnTimerFamily("processing-family")
+    public void processingFamilyOnTimer(
+        OnTimerContext context,
+        @StateId("bag") BagState bagState,
+        @TimerId("event") Timer eventTimeTimer,
+        @TimerId("processing") Timer processingTimeTimer,
+        @TimerFamily("event-family") TimerMap eventTimerFamily,
+        @TimerFamily("processing-family") TimerMap processingTimerFamily) {
+      context.output("processing-family" + Iterables.toString(bagState.read()));
+      bagState.add("processing-family");
+      eventTimeTimer.withOutputTimestamp(context.timestamp()).set(context.timestamp().plus(41L));
+      processingTimeTimer.offset(Duration.millis(42L));
+      processingTimeTimer.setRelative();
+      eventTimerFamily
+          .get("event-timer1")
+          .withOutputTimestamp(context.timestamp())
+          .set(context.timestamp().plus(43L));
+      processingTimerFamily.get("processing-timer1").offset(Duration.millis(44L)).setRelative();
+    }
+  }
+
   /**
    * Produces a multimap side input {@link StateKey} for the test PTransform id in the global
    * window.

From b2fefaf9e02b83942eeb1c7b85c8f765da89a14d Mon Sep 17 00:00:00 2001
From: Damon Douglas 
Date: Wed, 20 May 2020 12:58:41 -0700
Subject: [PATCH 032/151] [BEAM-9679] Add Core Transforms section / GroupByKey
 lesson to the Go SDK katas (#11734)

---
 .../GroupByKey/GroupByKey/cmd/main.go         |  43 +++
 .../GroupByKey/GroupByKey/go.mod              |  26 ++
 .../GroupByKey/GroupByKey/go.sum              | 315 ++++++++++++++++++
 .../GroupByKey/GroupByKey/pkg/task/task.go    |  25 ++
 .../GroupByKey/GroupByKey/task-info.yaml      |  35 ++
 .../GroupByKey/task-remote-info.yaml          |   2 +
 .../GroupByKey/GroupByKey/task.md             |  54 +++
 .../GroupByKey/GroupByKey/test/task_test.go   |  57 ++++
 .../GroupByKey/lesson-info.yaml               |  21 ++
 .../GroupByKey/lesson-remote-info.yaml        |   3 +
 .../Map/ParDo OneToMany/task-remote-info.yaml |   2 +-
 .../Map/ParDo Struct/task-remote-info.yaml    |   2 +-
 .../Map/ParDo/task-remote-info.yaml           |   2 +-
 .../go/Core Transforms/section-info.yaml      |   1 +
 .../Hello Beam/task-remote-info.yaml          |   2 +-
 learning/katas/go/course-remote-info.yaml     |   2 +-
 16 files changed, 587 insertions(+), 5 deletions(-)
 create mode 100644 learning/katas/go/Core Transforms/GroupByKey/GroupByKey/cmd/main.go
 create mode 100644 learning/katas/go/Core Transforms/GroupByKey/GroupByKey/go.mod
 create mode 100644 learning/katas/go/Core Transforms/GroupByKey/GroupByKey/go.sum
 create mode 100644 learning/katas/go/Core Transforms/GroupByKey/GroupByKey/pkg/task/task.go
 create mode 100644 learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task-info.yaml
 create mode 100644 learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task-remote-info.yaml
 create mode 100644 learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task.md
 create mode 100644 learning/katas/go/Core Transforms/GroupByKey/GroupByKey/test/task_test.go
 create mode 100644 learning/katas/go/Core Transforms/GroupByKey/lesson-info.yaml
 create mode 100644 learning/katas/go/Core Transforms/GroupByKey/lesson-remote-info.yaml

diff --git a/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/cmd/main.go b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/cmd/main.go
new file mode 100644
index 000000000000..e2c077867af6
--- /dev/null
+++ b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/cmd/main.go	
@@ -0,0 +1,43 @@
+// Licensed to the Apache Software Foundation (ASF) under one or more
+// contributor license agreements.  See the NOTICE file distributed with
+// this work for additional information regarding copyright ownership.
+// The ASF licenses this file to You under the Apache License, Version 2.0
+// (the "License"); you may not use this file except in compliance with
+// the License.  You may obtain a copy of the License at
+//
+//    http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package main
+
+import (
+	"context"
+	"github.com/apache/beam/sdks/go/pkg/beam"
+	"github.com/apache/beam/sdks/go/pkg/beam/log"
+	"github.com/apache/beam/sdks/go/pkg/beam/x/beamx"
+	"github.com/apache/beam/sdks/go/pkg/beam/x/debug"
+	"groupbykey/pkg/task"
+)
+
+func main() {
+	ctx := context.Background()
+
+	p, s := beam.NewPipelineWithRoot()
+
+	input := beam.Create(s, "apple", "ball", "car", "bear", "cheetah", "ant")
+
+	output := task.ApplyTransform(s, input)
+
+	debug.Print(s, output)
+
+	err := beamx.Run(ctx, p)
+
+	if err != nil {
+		log.Exitf(context.Background(), "Failed to execute job: %v", err)
+	}
+}
diff --git a/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/go.mod b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/go.mod
new file mode 100644
index 000000000000..2cb9df14a34d
--- /dev/null
+++ b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/go.mod	
@@ -0,0 +1,26 @@
+// Licensed to the Apache Software Foundation (ASF) under one or more
+// contributor license agreements.  See the NOTICE file distributed with
+// this work for additional information regarding copyright ownership.
+// The ASF licenses this file to You under the Apache License, Version 2.0
+// (the "License"); you may not use this file except in compliance with
+// the License.  You may obtain a copy of the License at
+//
+//    http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+module groupbykey
+
+go 1.14
+
+require (
+	github.com/apache/beam v2.20.0+incompatible
+	github.com/golang/protobuf v1.4.2 // indirect
+	github.com/google/go-cmp v0.4.1
+	google.golang.org/api v0.24.0 // indirect
+	google.golang.org/grpc v1.29.1 // indirect
+)
diff --git a/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/go.sum b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/go.sum
new file mode 100644
index 000000000000..eb28a28159c5
--- /dev/null
+++ b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/go.sum	
@@ -0,0 +1,315 @@
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+honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
+honnef.co/go/tools v0.0.0-20190106161140-3f1c8253044a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
+honnef.co/go/tools v0.0.0-20190418001031-e561f6794a2a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
+honnef.co/go/tools v0.0.0-20190523083050-ea95bdfd59fc/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
+honnef.co/go/tools v0.0.1-2019.2.3/go.mod h1:a3bituU0lyd329TUQxRnasdCoJDkEUEAqEt0JzvZhAg=
+honnef.co/go/tools v0.0.1-2020.1.3 h1:sXmLre5bzIR6ypkjXCDI3jHPssRhc8KD/Ome589sc3U=
+honnef.co/go/tools v0.0.1-2020.1.3/go.mod h1:X/FiERA/W4tHapMX5mGpAtMSVEeEUOyHaw9vFzvIQ3k=
+rsc.io/binaryregexp v0.2.0/go.mod h1:qTv7/COck+e2FymRvadv62gMdZztPaShugOCi3I+8D8=
+rsc.io/quote/v3 v3.1.0/go.mod h1:yEA65RcK8LyAZtP9Kv3t0HmxON59tX3rD+tICJqUlj0=
+rsc.io/sampler v1.3.0/go.mod h1:T1hPZKmBbMNahiBKFy5HrXp6adAjACjK9JXDnKaTXpA=
diff --git a/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/pkg/task/task.go b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/pkg/task/task.go
new file mode 100644
index 000000000000..1d9ce6d45c6b
--- /dev/null
+++ b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/pkg/task/task.go	
@@ -0,0 +1,25 @@
+// Licensed to the Apache Software Foundation (ASF) under one or more
+// contributor license agreements.  See the NOTICE file distributed with
+// this work for additional information regarding copyright ownership.
+// The ASF licenses this file to You under the Apache License, Version 2.0
+// (the "License"); you may not use this file except in compliance with
+// the License.  You may obtain a copy of the License at
+//
+//    http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package task
+
+import "github.com/apache/beam/sdks/go/pkg/beam"
+
+func ApplyTransform(s beam.Scope, input beam.PCollection) beam.PCollection {
+	kv := beam.ParDo(s, func(element string) (string, string) {
+		return string(element[0]), element
+	}, input)
+	return beam.GroupByKey(s, kv)
+}
diff --git a/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task-info.yaml b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task-info.yaml
new file mode 100644
index 000000000000..b4aebb3cf48c
--- /dev/null
+++ b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task-info.yaml	
@@ -0,0 +1,35 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#  http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
+type: edu
+files:
+- name: test/task_test.go
+  visible: false
+- name: cmd/main.go
+  visible: true
+- name: go.mod
+  visible: false
+- name: pkg/task/task.go
+  visible: true
+  placeholders:
+  - offset: 937
+    length: 138
+    placeholder_text: TODO()
+- name: go.sum
+  visible: false
diff --git a/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task-remote-info.yaml b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task-remote-info.yaml
new file mode 100644
index 000000000000..a766ed47f2b3
--- /dev/null
+++ b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task-remote-info.yaml	
@@ -0,0 +1,2 @@
+id: 1325218
+update_date: Wed, 20 May 2020 06:15:19 UTC
diff --git a/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task.md b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task.md
new file mode 100644
index 000000000000..66ce7c896d0a
--- /dev/null
+++ b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/task.md	
@@ -0,0 +1,54 @@
+
+
+# GroupByKey
+
+GroupByKey is a Beam transform for processing collections of key/value pairs. It’s a parallel
+reduction operation, analogous to the Shuffle phase of a Map/Shuffle/Reduce-style algorithm. The
+input to GroupByKey is a collection of key/value pairs that represents a multimap, where the
+collection contains multiple pairs that have the same key, but different values. Given such a
+collection, you use GroupByKey to collect all of the values associated with each unique key.
+
+**Kata:** Implement a 
+
+beam.GroupByKey transform that groups words by its first letter.
+
+
    
+  Refer to 
+  beam.GroupByKey to solve this problem.
+
    
+
+
    
+  Refer to the Beam Programming Guide
+  
+    "GroupByKey" section for more information.
+
    
+
+
    
+  To return as a KV, you can return two values from your DoFn. The first return value represents the Key, and 
+  the second return value represents the Value.  An example is shown below.
+  
+```
+func doFn(element string) (string, string) {
+    key := string(element[0])
+    value := element
+    return key, value
+}
+``` 
+
    
diff --git a/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/test/task_test.go b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/test/task_test.go
new file mode 100644
index 000000000000..7f9a8827a984
--- /dev/null
+++ b/learning/katas/go/Core Transforms/GroupByKey/GroupByKey/test/task_test.go	
@@ -0,0 +1,57 @@
+// Licensed to the Apache Software Foundation (ASF) under one or more
+// contributor license agreements.  See the NOTICE file distributed with
+// this work for additional information regarding copyright ownership.
+// The ASF licenses this file to You under the Apache License, Version 2.0
+// (the "License"); you may not use this file except in compliance with
+// the License.  You may obtain a copy of the License at
+//
+//    http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package test
+
+import (
+	"github.com/apache/beam/sdks/go/pkg/beam"
+	"github.com/apache/beam/sdks/go/pkg/beam/testing/ptest"
+	"github.com/google/go-cmp/cmp"
+	"groupbykey/pkg/task"
+	"testing"
+)
+
+func TestApplyTransform(t *testing.T) {
+	p, s := beam.NewPipelineWithRoot()
+	tests := []struct {
+		input beam.PCollection
+		want map[string][]string
+	}{
+		{
+			input: beam.Create(s, "apple", "ball", "car", "bear", "cheetah", "ant"),
+			want: map[string][]string{
+				"a": {"apple", "ant"},
+				"b": {"ball", "bear"},
+				"c": {"car", "cheetah"},
+			},
+		},
+	}
+	for _, tt := range tests {
+		got := task.ApplyTransform(s, tt.input)
+		beam.ParDo0(s, func(key string, values func(*string) bool) {
+			var got []string
+			var v string
+			for values(&v) {
+				got = append(got, v)
+			}
+			if !cmp.Equal(got, tt.want[key]) {
+				t.Errorf("ApplyTransform() key = %s, got %v , want %v", key, got, tt.want[key])
+			}
+		}, got)
+		if err := ptest.Run(p); err != nil {
+			t.Error(err)
+		}
+	}
+}
diff --git a/learning/katas/go/Core Transforms/GroupByKey/lesson-info.yaml b/learning/katas/go/Core Transforms/GroupByKey/lesson-info.yaml
new file mode 100644
index 000000000000..5de9eb69f819
--- /dev/null
+++ b/learning/katas/go/Core Transforms/GroupByKey/lesson-info.yaml	
@@ -0,0 +1,21 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#  http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
+content:
+- GroupByKey
diff --git a/learning/katas/go/Core Transforms/GroupByKey/lesson-remote-info.yaml b/learning/katas/go/Core Transforms/GroupByKey/lesson-remote-info.yaml
new file mode 100644
index 000000000000..6391a8192a9c
--- /dev/null
+++ b/learning/katas/go/Core Transforms/GroupByKey/lesson-remote-info.yaml	
@@ -0,0 +1,3 @@
+id: 358048
+update_date: Wed, 20 May 2020 06:15:15 UTC
+unit: 342241
diff --git a/learning/katas/go/Core Transforms/Map/ParDo OneToMany/task-remote-info.yaml b/learning/katas/go/Core Transforms/Map/ParDo OneToMany/task-remote-info.yaml
index 2512ec8b7de9..8e0e17b2c09f 100644
--- a/learning/katas/go/Core Transforms/Map/ParDo OneToMany/task-remote-info.yaml	
+++ b/learning/katas/go/Core Transforms/Map/ParDo OneToMany/task-remote-info.yaml	
@@ -1,2 +1,2 @@
 id: 1289189
-update_date: Tue, 05 May 2020 02:01:57 UTC
+update_date: Wed, 20 May 2020 06:15:28 UTC
diff --git a/learning/katas/go/Core Transforms/Map/ParDo Struct/task-remote-info.yaml b/learning/katas/go/Core Transforms/Map/ParDo Struct/task-remote-info.yaml
index 190348ed6ee7..5ca73c7400f6 100644
--- a/learning/katas/go/Core Transforms/Map/ParDo Struct/task-remote-info.yaml	
+++ b/learning/katas/go/Core Transforms/Map/ParDo Struct/task-remote-info.yaml	
@@ -1,2 +1,2 @@
 id: 1289190
-update_date: Tue, 05 May 2020 02:01:59 UTC
+update_date: Wed, 20 May 2020 06:15:31 UTC
diff --git a/learning/katas/go/Core Transforms/Map/ParDo/task-remote-info.yaml b/learning/katas/go/Core Transforms/Map/ParDo/task-remote-info.yaml
index 72b8745db6fc..c5aaaae2a15f 100644
--- a/learning/katas/go/Core Transforms/Map/ParDo/task-remote-info.yaml	
+++ b/learning/katas/go/Core Transforms/Map/ParDo/task-remote-info.yaml	
@@ -1,2 +1,2 @@
 id: 1289188
-update_date: Tue, 05 May 2020 02:01:55 UTC
+update_date: Wed, 20 May 2020 06:15:25 UTC
diff --git a/learning/katas/go/Core Transforms/section-info.yaml b/learning/katas/go/Core Transforms/section-info.yaml
index 23c69bef45f5..8ea49eb04ce4 100644
--- a/learning/katas/go/Core Transforms/section-info.yaml	
+++ b/learning/katas/go/Core Transforms/section-info.yaml	
@@ -19,3 +19,4 @@
 
 content:
 - Map
+- GroupByKey
diff --git a/learning/katas/go/Introduction/Hello Beam/Hello Beam/task-remote-info.yaml b/learning/katas/go/Introduction/Hello Beam/Hello Beam/task-remote-info.yaml
index bf68a02eca35..46551fb4c9fd 100644
--- a/learning/katas/go/Introduction/Hello Beam/Hello Beam/task-remote-info.yaml	
+++ b/learning/katas/go/Introduction/Hello Beam/Hello Beam/task-remote-info.yaml	
@@ -1,2 +1,2 @@
 id: 1236831
-update_date: Thu, 16 Apr 2020 06:53:05 UTC
+update_date: Wed, 20 May 2020 06:15:22 UTC
diff --git a/learning/katas/go/course-remote-info.yaml b/learning/katas/go/course-remote-info.yaml
index 4252852155fc..2651d8336da7 100644
--- a/learning/katas/go/course-remote-info.yaml
+++ b/learning/katas/go/course-remote-info.yaml
@@ -1,2 +1,2 @@
 id: 70387
-update_date: Fri, 24 Apr 2020 07:39:05 UTC
+update_date: Tue, 05 May 2020 02:02:55 UTC

From 21da8903180e58244f817d956a080d5a8c5e66a8 Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Tue, 19 May 2020 20:22:52 -0400
Subject: [PATCH 033/151] [BEAM-10048] Clean up release guide.

- Remove redundancies between the release guide and build_release_candidate.sh.
- Update website-related instructions for Hugo.
---
 .../main/scripts/build_release_candidate.sh   |  18 +-
 .../content/en/contribute/release-guide.md    | 212 +++---------------
 2 files changed, 36 insertions(+), 194 deletions(-)

diff --git a/release/src/main/scripts/build_release_candidate.sh b/release/src/main/scripts/build_release_candidate.sh
index 36548d530f68..be3d741bb06c 100755
--- a/release/src/main/scripts/build_release_candidate.sh
+++ b/release/src/main/scripts/build_release_candidate.sh
@@ -113,7 +113,7 @@ if [[ $confirmation = "y" ]]; then
   echo "-------------Staging Java Artifacts into Maven---------------"
   gpg --local-user ${SIGNING_KEY} --output /dev/null --sign ~/.bashrc
   ./gradlew publish -Psigning.gnupg.keyName=${SIGNING_KEY} -PisRelease --no-daemon
-  echo "Please review all artifacts in staging URL. e.g. https://repository.apache.org/content/repositories/orgapachebeam-NNNN/"
+  echo "You need to close the staging repository manually on Apache Nexus. See the release guide for instructions."
   rm -rf ~/${LOCAL_CLONE_DIR}
 fi
 
@@ -205,7 +205,7 @@ if [[ $confirmation = "y" ]]; then
   rm -rf ~/${PYTHON_ARTIFACTS_DIR}
 fi
 
-echo "[Current Step]: Stage SDK docker images"
+echo "[Current Step]: Stage docker images"
 echo "Do you want to proceed? [y|N]"
 read confirmation
 if [[ $confirmation = "y" ]]; then
@@ -330,18 +330,6 @@ if [[ $confirmation = "y" ]]; then
 fi
 
 echo "===========Please Review All Items in the Checklist=========="
-echo "1. Maven artifacts deployed to https://repository.apache.org/content/repositories/"
+echo "1. You need to close the staging repository manually on Apache Nexus. See the release guide for instructions."
 echo "2. Source distribution deployed to https://dist.apache.org/repos/dist/dev/beam/${RELEASE}"
 echo "3. Website pull request published the Java API reference manual the Python API reference manual."
-
-echo "==============Things Needed To Be Done Manually=============="
-echo "1.Make sure a pull request is created to update the javadoc and pydoc to the beam-site: "
-echo "  - cd ~/${LOCAL_WEBSITE_UPDATE_DIR}/${LOCAL_WEBSITE_REPO}/${WEBSITE_ROOT_DIR}"
-echo "  - git checkout updates_release_${RELEASE}"
-echo "  - Check if both javadoc/ and pydoc/ exist."
-echo "  - commit your changes"
-echo "2.Create a pull request to update the release in the beam/website:"
-echo "  - An example pull request：https://github.com/apache/beam/pull/9341"
-echo "  - You can find the release note in JIRA: https://issues.apache.org/jira/projects/BEAM?selectedItem=com.atlassian.jira.jira-projects-plugin%3Arelease-page&status=unreleased"
-echo "3.You need to build Python Wheels."
-echo "4.Start the review-and-vote thread on the dev@ mailing list."
diff --git a/website/www/site/content/en/contribute/release-guide.md b/website/www/site/content/en/contribute/release-guide.md
index 95c95c2272bb..3da9fbcc3973 100644
--- a/website/www/site/content/en/contribute/release-guide.md
+++ b/website/www/site/content/en/contribute/release-guide.md
@@ -171,7 +171,6 @@ Configure access to the [Apache Nexus repository](https://repository.apache.org/
             
           
         
-__NOTE__: make sure the XML you end up with matches the structure above.
 
 #### Submit your GPG public key into MIT PGP Public Key Server
 In order to make yourself have right permission to stage java artifacts in Apache Nexus staging repository, 
@@ -583,189 +582,44 @@ For this step, we recommend you using automation script to create a RC, but you
   1. Stage source release into dist.apache.org dev [repo](https://dist.apache.org/repos/dist/dev/beam/).
   1. Stage,sign and hash python binaries into dist.apache.ord dev repo python dir
   1. Stage SDK docker images to [docker hub Apache organization](https://hub.docker.com/search?q=apache%2Fbeam&type=image).
-  1. Create a PR to update beam and beam-site, changes includes:
+  1. Create a PR to update beam-site, changes includes:
      * Copy python doc into beam-site
      * Copy java doc into beam-site
-     * Update release version into [_config.yml](https://github.com/apache/beam/blob/master/website/_config.yml).
      
 #### Tasks you need to do manually
-  1. Add new release into `website/src/get-started/downloads.md`.
-  1. Update last release download links in `website/src/get-started/downloads.md`.
-  1. Update `website/src/.htaccess` to redirect to the new version.
-  1. Build and stage python wheels.
+  1. Verify the script worked.
+      1. Verify that the source and Python binaries are present in [dist.apache.org](https://dist.apache.org/repos/dist/dev/beam).
+      1. Verify Docker images are published. How to find images:
+          1. Visit [https://hub.docker.com/u/apache](https://hub.docker.com/search?q=apache%2Fbeam&type=image)
+          2. Visit each repository and navigate to *tags* tab.
+          3. Verify images are pushed with tags: ${RELEASE}_rc{RC_NUM}
+      1. Verify that third party licenses are included in Docker containers by logging in to the images.
+          - For Python SDK images, there should be around 80 ~ 100 dependencies.
+          Please note that dependencies for the SDKs with different Python versions vary.
+          Need to verify all Python images by replacing `${ver}` with each supported Python version `X.Y`.
+          ```
+          docker run -it --entrypoint=/bin/bash apache/beam_python${ver}_sdk:${RELEASE}_rc{RC_NUM}
+          ls -al /opt/apache/beam/third_party_licenses/ | wc -l
+          ```
+          - For Java SDK images, there should be around 1400 dependencies.
+          ```
+          docker run -it --entrypoint=/bin/bash apache/beam_java_sdk:${RELEASE}_rc{RC_NUM}
+          ls -al /opt/apache/beam/third_party_licenses/ | wc -l
+          ```
   1. Publish staging artifacts
-      1. Go to the staging repo to close the staging repository on [Apache Nexus](https://repository.apache.org/#stagingRepositories). 
+      1. Go to the staging repo to close the staging repository on [Apache Nexus](https://repository.apache.org/#stagingRepositories).
       1. When prompted for a description, enter “Apache Beam, version X, release candidate Y”.
-
-
-### (Alternative) Run all steps manually
-
-#### Build and stage Java artifacts with Gradle
-
-Set up a few environment variables to simplify the commands that follow. These identify the release candidate being built, and the branch where you will stage files. Start with `RC_NUM` equal to `1` and increment it for each candidate.
-
-    RC_NUM=1
-
-Make sure your git config will maintain your account:
-    
-    git config credential.helper store
-
-Use Gradle release plugin to build the release artifacts, and push code and
-release tag to the origin repository (this would be the Apache Beam repo):
-
-    ./gradlew release -Prelease.newVersion=${RELEASE}-SNAPSHOT \
-                  -Prelease.releaseVersion=${RELEASE}-RC${RC_NUM} \
-                  -Prelease.useAutomaticVersion=true --info --no-daemon
-
-Use Gradle publish plugin to stage these artifacts on the Apache Nexus repository, as follows:
-
-    ./gradlew publish -PisRelease --no-parallel --no-daemon
-
-Review all staged artifacts. They should contain all relevant parts for each module, including `pom.xml`, jar, test jar, javadoc, etc. Artifact names should follow [the existing format](https://search.maven.org/#search%7Cga%7C1%7Cg%3A%22org.apache.beam%22) in which artifact name mirrors directory structure, e.g., `beam-sdks-java-io-kafka`. Carefully review any new artifacts.
-
-Close the staging repository on Apache Nexus. When prompted for a description, enter “Apache Beam, version X, release candidate Y”.
-
-#### Stage source release on dist.apache.org
-
-Attention: Only committer has permissions to perform following steps.
-
-Copy the source release to the dev repository of `dist.apache.org`.
-
-1. If you have not already, check out the Beam section of the `dev` repository on `dist.apache.org` via Subversion. In a fresh directory:
-
-        svn co https://dist.apache.org/repos/dist/dev/beam
-
-1. Make a directory for the new release:
-
-        mkdir beam/${RELEASE}
-        cd beam/${RELEASE}
-
-1. Download source zip from GitHub:
-
-        wget https://github.com/apache/beam/archive/release-${RELEASE}.zip \
-            -O apache-beam-${RELEASE}-source-release.zip
-
-1. Create hashes and sign the source distribution:
-
-        gpg --armor --detach-sig apache-beam-${RELEASE}-source-release.zip
-        sha512sum apache-beam-${RELEASE}-source-release.zip > apache-beam-${RELEASE}-source-release.zip.sha512
-
-1. Add and commit all the files.
-
-        svn add beam/${RELEASE}
-        svn commit
-
-1. Verify that files are [present](https://dist.apache.org/repos/dist/dev/beam).
-
-#### Stage python binaries on dist.apache.org
-
-Build python binaries in release branch in sdks/python dir.
-
-    pip install -r build-requirements.txt
-    python setup.py sdist --format=zip
-    cd dist
-    cp apache-beam-${RELEASE}.zip staging/apache-beam-${RELEASE}-python.zip
-    cd staging
-
-Create hashes and sign the binaries
-
-    gpg --armor --detach-sig apache-beam-${RELEASE}-python.zip
-    sha512sum apache-beam-${RELEASE}-python.zip > apache-beam-${RELEASE}-python.zip.sha512
-
-Staging binaries
-
-    svn co https://dist.apache.org/repos/dist/dev/beam
-    cd beam/${RELEASE}
-    svn add *
-    svn commit
-
-Verify that files are [present](https://dist.apache.org/repos/dist/dev/beam).
-
-#### Stage SDK images on hub.docker.com
-* Build Python images and push to DockerHub.
-
-```
-./gradlew :sdks:python:container:buildAll -Pdocker-pull-licenses -Pdocker-tag=${RELEASE}_rc{RC_NUM}
-```
-
-Verify that third party licenses are included by logging in to the images. For Python SDK images, there should be around 80 ~ 100 dependencies. 
-Please note that dependencies for the SDKs with different Python versions vary. 
-Need to verify all Python images by replacing `${ver}` in the following command to `python2.7, python3.5, python3.6, python3.7`.
-
-```
-docker run -it --entrypoint=/bin/bash apache/beam_${ver}_sdk:${RELEASE}_rc{RC_NUM}
-ls -al /opt/apache/beam/third_party_licenses/ | wc -l
-```
-
-After verifying the third party licenses are included correctly, push the images to DockerHub.
-```
-PYTHON_VER=("python2.7" "python3.5" "python3.6" "python3.7")
-for ver in "${PYTHON_VER[@]}"; do
-   docker push apache/beam_${ver}_sdk:${RELEASE}_rc{RC_NUM} &
-done
-``` 
-
-* Build Java images and push to DockerHub.
-
-```
-./gradlew :sdks:java:container:docker -Pdocker-pull-licenses -Pdocker-tag=${RELEASE}_rc{RC_NUM}
-```
-
-Verify that third party licenses are included by logging in to the images. For Java SDK images, there should be around 1400 dependencies. 
-```
-docker run -it --entrypoint=/bin/bash apache/beam_java_sdk:${RELEASE}_rc{RC_NUM}
-ls -al /opt/apache/beam/third_party_licenses/ | wc -l
-```
-
-After verifying the third party licenses are included correctly, push the images to DockerHub.
-```
-docker push apache/beam_java_sdk:${RELEASE}_rc{RC_NUM}
-```
-
-* Build Flink job server images and push to DockerHub.
-
-```
-FLINK_VER=("1.8" "1.9" "1.10")
-for ver in "${FLINK_VER[@]}"; do
-  ./gradlew ":runners:flink:${ver}:job-server-container:dockerPush" -Pdocker-tag="${RELEASE}_rc${RC_NUM}"
-done
-```
-
-* Build Spark job server image and push to DockerHub.
-
-```
-./gradlew ":runners:spark:job-server:container:dockerPush" -Pdocker-tag="${RELEASE}_rc${RC_NUM}"
-```
-
-Clean up images from local
-
-```
-for ver in "${PYTHON_VER[@]}"; do
-   docker rmi -f apache/beam_${ver}_sdk:${RELEASE}_rc{RC_NUM}
-done
-docker rmi -f apache/beam_java_sdk:${RELEASE}_rc{RC_NUM}
-for ver in "${FLINK_VER[@]}"; do
-   docker rmi -f "apache/beam_flink${ver}_job_server:${RELEASE}_rc${RC_NUM}"
-done
-docker rmi -f "apache/beam_spark_job_server:${RELEASE}_rc${RC_NUM}"
-```
-
-How to find images:
-1. Visit [https://hub.docker.com/u/apache](https://hub.docker.com/search?q=apache%2Fbeam&type=image)
-2. Visit each repository and navigate to *tags* tab.
-3. Verify images are pushed with tags: ${RELEASE}_rc{RC_NUM}
-
-### Build and stage python wheels
-
-There is a wrapper repo [beam-wheels](https://github.com/apache/beam-wheels) to help build python wheels.
-
-If you are interested in how it works, please refer to the [structure section](https://github.com/apache/beam-wheels#structure).
-
-Please follow the [user guide](https://github.com/apache/beam-wheels#user-guide) to build python wheels.
-
-Once all python wheels have been staged [dist.apache.org](https://dist.apache.org/repos/dist/dev/beam/),
-please run [./sign_hash_python_wheels.sh](https://github.com/apache/beam/blob/master/release/src/main/scripts/sign_hash_python_wheels.sh) to sign and hash python wheels.
-
+      1. Review all staged artifacts on https://repository.apache.org/content/repositories/orgapachebeam-NNNN/. They should contain all relevant parts for each module, including `pom.xml`, jar, test jar, javadoc, etc. Artifact names should follow [the existing format](https://search.maven.org/#search%7Cga%7C1%7Cg%3A%22org.apache.beam%22) in which artifact name mirrors directory structure, e.g., `beam-sdks-java-io-kafka`. Carefully review any new artifacts.
+  1. Build and stage python wheels.
+      - There is a wrapper repo [beam-wheels](https://github.com/apache/beam-wheels) to help build python wheels.
+      - If you are interested in how it works, please refer to the [structure section](https://github.com/apache/beam-wheels#structure).
+      - Please follow the [user guide](https://github.com/apache/beam-wheels#user-guide) to build python wheels.
+      - Once all python wheels have been staged [dist.apache.org](https://dist.apache.org/repos/dist/dev/beam/),
+      please run [./sign_hash_python_wheels.sh](https://github.com/apache/beam/blob/master/release/src/main/scripts/sign_hash_python_wheels.sh) to sign and hash python wheels.
+  1. Update Beam website ([example](https://github.com/apache/beam/pull/11727))
+      1. Update release version in `website/www/site/config.toml`.
+      1. Add new release in `website/www/site/content/en/get-started/downloads.md`.
+      1. Update `website/www/site/static/.htaccess` to redirect to the new version.
 
 **********
 
@@ -842,7 +696,7 @@ This pull request is against the `apache/beam` repo, on the `master` branch.
 
 ### Blog post
 
-Write a blog post similar to https://beam.apache.org/blog/2019/08/22/beam-2.15.0.html
+Write a blog post similar to [beam-2.20.0.md](https://github.com/apache/beam/blob/master/website/www/site/content/en/blog/beam-2.20.0.md).
 
 - Update `CHANGES.md` by adding a new section for the next release.
 - Copy the changes for the current release from `CHANGES.md` to the blog post and edit as necessary.

From 1404c6a1ab3ca7e9ff3267c7bd28e18472c33e2a Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Wed, 20 May 2020 17:10:21 -0400
Subject: [PATCH 034/151] Remove checklist from build_release_candidate.sh.

It is included in the release guide.
---
 release/src/main/scripts/build_release_candidate.sh | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/release/src/main/scripts/build_release_candidate.sh b/release/src/main/scripts/build_release_candidate.sh
index be3d741bb06c..df5470bc2dec 100755
--- a/release/src/main/scripts/build_release_candidate.sh
+++ b/release/src/main/scripts/build_release_candidate.sh
@@ -328,8 +328,3 @@ if [[ $confirmation = "y" ]]; then
   rm -rf ~/${LOCAL_WEBSITE_UPDATE_DIR}/${LOCAL_JAVA_DOC}
   rm -rf ~/${LOCAL_WEBSITE_UPDATE_DIR}/${LOCAL_PYTHON_DOC}
 fi
-
-echo "===========Please Review All Items in the Checklist=========="
-echo "1. You need to close the staging repository manually on Apache Nexus. See the release guide for instructions."
-echo "2. Source distribution deployed to https://dist.apache.org/repos/dist/dev/beam/${RELEASE}"
-echo "3. Website pull request published the Java API reference manual the Python API reference manual."

From 74a53409a39de1549f9fb33f40b2266ef49f4fdc Mon Sep 17 00:00:00 2001
From: "chamikara@google.com" 
Date: Wed, 20 May 2020 14:27:07 -0700
Subject: [PATCH 035/151] Clarifies text.

---
 .../apache_beam/runners/dataflow/internal/apiclient.py    | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py b/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
index d0e7911264ed..ee1e4720548d 100644
--- a/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
+++ b/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
@@ -316,10 +316,10 @@ def __init__(
 
           # Currently, Dataflow uses Docker container images to uniquely
           # identify execution environments. Hence Dataflow executes all
-          # transforms that specify the same Docker container image in the
-          # same container. Dependencies of all environments that specify a
-          # given container image will be staged in the container for that
-          # particular container image.
+          # transforms that specify the the same Docker container image in a
+          # single container instance. Dependencies of all environments that
+          # specify a given container image will be staged in the container
+          # instance for that particular container image.
           # TODO(BEAM-9455): loosen this restriction to support multiple
           # environments with the same container image when Dataflow supports
           # environment specific artifact provisioning.

From 9818fa823a4ef35840a281503b3402723b5c82fe Mon Sep 17 00:00:00 2001
From: Brian Hulette 
Date: Wed, 20 May 2020 14:59:41 -0700
Subject: [PATCH 036/151] [BEAM-9699] Add test verifying we can use ZetaSQL in
 Python SqlTransform (#11575)

* Add zetasql to SQL expansion service

* Add support for ZetaSQL in Python SqlTransform

plumbs through queryPlannerClassName param

* Move dialect -> planner class resolution to Java

Requires moving ExternalTransform classes to
extensions/sql/expansion-service so we can reference ZetaSQL

* add expansion-service package-info (checkstyle)
---
 .../sql/expansion-service/build.gradle        |  1 +
 .../ExternalSqlTransformRegistrar.java        | 82 +++++++++++++++++++
 .../sql/expansion/package-info.java           | 20 +++++
 .../beam/sdk/extensions/sql/SqlTransform.java | 39 +--------
 sdks/python/apache_beam/transforms/sql.py     |  8 +-
 .../python/apache_beam/transforms/sql_test.py | 10 +++
 6 files changed, 119 insertions(+), 41 deletions(-)
 create mode 100644 sdks/java/extensions/sql/expansion-service/src/main/java/org/apache/beam/sdk/extensions/sql/expansion/ExternalSqlTransformRegistrar.java
 create mode 100644 sdks/java/extensions/sql/expansion-service/src/main/java/org/apache/beam/sdk/extensions/sql/expansion/package-info.java

diff --git a/sdks/java/extensions/sql/expansion-service/build.gradle b/sdks/java/extensions/sql/expansion-service/build.gradle
index 19a32709522b..998d3cae5f2d 100644
--- a/sdks/java/extensions/sql/expansion-service/build.gradle
+++ b/sdks/java/extensions/sql/expansion-service/build.gradle
@@ -30,6 +30,7 @@ ext.summary = """Contains code to run a SQL Expansion Service."""
 
 dependencies {
   compile project(path: ":sdks:java:extensions:sql")
+  compile project(path: ":sdks:java:extensions:sql:zetasql")
   compile project(path: ":sdks:java:expansion-service")
 }
 
diff --git a/sdks/java/extensions/sql/expansion-service/src/main/java/org/apache/beam/sdk/extensions/sql/expansion/ExternalSqlTransformRegistrar.java b/sdks/java/extensions/sql/expansion-service/src/main/java/org/apache/beam/sdk/extensions/sql/expansion/ExternalSqlTransformRegistrar.java
new file mode 100644
index 000000000000..cec0a867bc0d
--- /dev/null
+++ b/sdks/java/extensions/sql/expansion-service/src/main/java/org/apache/beam/sdk/extensions/sql/expansion/ExternalSqlTransformRegistrar.java
@@ -0,0 +1,82 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.extensions.sql.expansion;
+
+import com.google.auto.service.AutoService;
+import java.util.Map;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.expansion.ExternalTransformRegistrar;
+import org.apache.beam.sdk.extensions.sql.SqlTransform;
+import org.apache.beam.sdk.extensions.sql.impl.CalciteQueryPlanner;
+import org.apache.beam.sdk.extensions.sql.impl.QueryPlanner;
+import org.apache.beam.sdk.extensions.sql.zetasql.ZetaSQLQueryPlanner;
+import org.apache.beam.sdk.transforms.ExternalTransformBuilder;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.Row;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+
+@AutoService(ExternalTransformRegistrar.class)
+public class ExternalSqlTransformRegistrar implements ExternalTransformRegistrar {
+  private static final String URN = "beam:external:java:sql:v1";
+  private static final ImmutableMap> DIALECTS =
+      ImmutableMap.>builder()
+          .put("zetasql", ZetaSQLQueryPlanner.class)
+          .put("calcite", CalciteQueryPlanner.class)
+          .build();
+
+  @Override
+  public Map> knownBuilders() {
+    return org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap.of(
+        URN, Builder.class);
+  }
+
+  public static class Configuration {
+    String query;
+    String dialect;
+
+    public void setQuery(String query) {
+      this.query = query;
+    }
+
+    public void setDialect(@Nullable String dialect) {
+      this.dialect = dialect;
+    }
+  }
+
+  private static class Builder
+      implements ExternalTransformBuilder> {
+    @Override
+    public PTransform> buildExternal(Configuration configuration) {
+      SqlTransform transform = SqlTransform.query(configuration.query);
+      if (configuration.dialect != null) {
+        Class queryPlanner =
+            DIALECTS.get(configuration.dialect.toLowerCase());
+        if (queryPlanner == null) {
+          throw new IllegalArgumentException(
+              String.format(
+                  "Received unknown SQL Dialect '%s'. Known dialects: %s",
+                  configuration.dialect, DIALECTS.keySet()));
+        }
+        transform = transform.withQueryPlannerClass(queryPlanner);
+      }
+      return transform;
+    }
+  }
+}
diff --git a/sdks/java/extensions/sql/expansion-service/src/main/java/org/apache/beam/sdk/extensions/sql/expansion/package-info.java b/sdks/java/extensions/sql/expansion-service/src/main/java/org/apache/beam/sdk/extensions/sql/expansion/package-info.java
new file mode 100644
index 000000000000..1dcf3fca9e16
--- /dev/null
+++ b/sdks/java/extensions/sql/expansion-service/src/main/java/org/apache/beam/sdk/extensions/sql/expansion/package-info.java
@@ -0,0 +1,20 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+/** External Transform Registration for Beam SQL. */
+package org.apache.beam.sdk.extensions.sql.expansion;
diff --git a/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/SqlTransform.java b/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/SqlTransform.java
index 496dd6d37f46..12ce337f9685 100644
--- a/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/SqlTransform.java
+++ b/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/SqlTransform.java
@@ -17,7 +17,6 @@
  */
 package org.apache.beam.sdk.extensions.sql;
 
-import com.google.auto.service.AutoService;
 import com.google.auto.value.AutoValue;
 import java.util.Collections;
 import java.util.HashMap;
@@ -25,7 +24,6 @@
 import java.util.Map;
 import javax.annotation.Nullable;
 import org.apache.beam.sdk.annotations.Experimental;
-import org.apache.beam.sdk.expansion.ExternalTransformRegistrar;
 import org.apache.beam.sdk.extensions.sql.impl.BeamSqlEnv;
 import org.apache.beam.sdk.extensions.sql.impl.BeamSqlEnv.BeamSqlEnvBuilder;
 import org.apache.beam.sdk.extensions.sql.impl.BeamSqlPipelineOptions;
@@ -37,7 +35,6 @@
 import org.apache.beam.sdk.extensions.sql.meta.provider.ReadOnlyTableProvider;
 import org.apache.beam.sdk.extensions.sql.meta.provider.TableProvider;
 import org.apache.beam.sdk.transforms.Combine;
-import org.apache.beam.sdk.transforms.ExternalTransformBuilder;
 import org.apache.beam.sdk.transforms.PTransform;
 import org.apache.beam.sdk.transforms.SerializableFunction;
 import org.apache.beam.sdk.values.PCollection;
@@ -273,8 +270,7 @@ static Builder builder() {
   }
 
   @AutoValue.Builder
-  abstract static class Builder
-      implements ExternalTransformBuilder> {
+  abstract static class Builder {
     abstract Builder setQueryString(String queryString);
 
     abstract Builder setQueryParameters(QueryParameters queryParameters);
@@ -292,19 +288,6 @@ abstract static class Builder
     abstract Builder setQueryPlannerClassName(@Nullable String queryPlannerClassName);
 
     abstract SqlTransform build();
-
-    @Override
-    public PTransform> buildExternal(
-        External.Configuration configuration) {
-      return builder()
-          .setQueryString(configuration.query)
-          .setQueryParameters(QueryParameters.ofNone())
-          .setUdafDefinitions(Collections.emptyList())
-          .setUdfDefinitions(Collections.emptyList())
-          .setTableProviderMap(Collections.emptyMap())
-          .setAutoUdfUdafLoad(false)
-          .build();
-    }
   }
 
   @AutoValue
@@ -330,24 +313,4 @@ static UdafDefinition of(String udafName, Combine.CombineFn combineFn) {
       return new AutoValue_SqlTransform_UdafDefinition(udafName, combineFn);
     }
   }
-
-  @AutoService(ExternalTransformRegistrar.class)
-  public static class External implements ExternalTransformRegistrar {
-
-    private static final String URN = "beam:external:java:sql:v1";
-
-    @Override
-    public Map> knownBuilders() {
-      return org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap.of(
-          URN, AutoValue_SqlTransform.Builder.class);
-    }
-
-    public static class Configuration {
-      String query;
-
-      public void setQuery(String query) {
-        this.query = query;
-      }
-    }
-  }
 }
diff --git a/sdks/python/apache_beam/transforms/sql.py b/sdks/python/apache_beam/transforms/sql.py
index 86423761b8b6..ce409d21fd26 100644
--- a/sdks/python/apache_beam/transforms/sql.py
+++ b/sdks/python/apache_beam/transforms/sql.py
@@ -32,7 +32,8 @@
 __all__ = ['SqlTransform']
 
 SqlTransformSchema = typing.NamedTuple(
-    'SqlTransformSchema', [('query', unicode)])
+    'SqlTransformSchema', [('query', unicode),
+                           ('dialect', typing.Optional[unicode])])
 
 
 class SqlTransform(ExternalTransform):
@@ -66,9 +67,10 @@ class SqlTransform(ExternalTransform):
   """
   URN = 'beam:external:java:sql:v1'
 
-  def __init__(self, query):
+  def __init__(self, query, dialect=None):
     super(SqlTransform, self).__init__(
         self.URN,
-        NamedTupleBasedPayloadBuilder(SqlTransformSchema(query=query)),
+        NamedTupleBasedPayloadBuilder(
+            SqlTransformSchema(query=query, dialect=dialect)),
         BeamJarExpansionService(
             ':sdks:java:extensions:sql:expansion-service:shadowJar'))
diff --git a/sdks/python/apache_beam/transforms/sql_test.py b/sdks/python/apache_beam/transforms/sql_test.py
index b8097145def0..d2271bbfd923 100644
--- a/sdks/python/apache_beam/transforms/sql_test.py
+++ b/sdks/python/apache_beam/transforms/sql_test.py
@@ -138,6 +138,16 @@ def test_tagged_join(self):
               ON simple.`int` = enrich.`int`"""))
       assert_that(out, equal_to([(1, "a"), (26, "z"), (1, "a")]))
 
+  def test_zetasql_generate_data(self):
+    with TestPipeline() as p:
+      out = p | SqlTransform(
+          """SELECT
+            CAST(1 AS INT64) AS `int`,
+            CAST('foo' AS STRING) AS `str`,
+            CAST(3.14  AS FLOAT64) AS `flt`""",
+          dialect="zetasql")
+      assert_that(out, equal_to([(1, "foo", 3.14)]))
+
 
 if __name__ == "__main__":
   logging.getLogger().setLevel(logging.INFO)

From 758d821ac64edebf24bc1bba1f7bfa34fd03a2da Mon Sep 17 00:00:00 2001
From: omarismail94 <44980219+omarismail94@users.noreply.github.com>
Date: Wed, 20 May 2020 18:01:15 -0400
Subject: [PATCH 037/151] [BEAM-10037] BeamSqlExample.java fails to build 
 (#11754)

* [BEAM-10037] BeamSqlExample.java fails to build when running ./gradlew command

* [BEAM-10037] Added BeamSQLExample and PojoExample to sqlPreCommit(), and fixed coder in BeamSqlExample

* [BEAM-10037] Reverted first query to c1>1 as opposed to c3. I added c3 for testing and forgot to change it back :)

Co-authored-by: Omar Ismail 
---
 build.gradle                                  |  2 +
 .../sql/example/BeamSqlExample.java           | 56 ++++++++++---------
 2 files changed, 33 insertions(+), 25 deletions(-)

diff --git a/build.gradle b/build.gradle
index ca4b54ea2710..c26a02067da3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -152,6 +152,8 @@ task javaPreCommit() {
 }
 
 task sqlPreCommit() {
+  dependsOn ":sdks:java:extensions:sql:runBasicExample"
+  dependsOn ":sdks:java:extensions:sql:runPojoExample"
   dependsOn ":sdks:java:extensions:sql:build"
   dependsOn ":sdks:java:extensions:sql:buildDependents"
 }
diff --git a/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/example/BeamSqlExample.java b/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/example/BeamSqlExample.java
index 8496a712fef0..9742a3384b33 100644
--- a/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/example/BeamSqlExample.java
+++ b/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/example/BeamSqlExample.java
@@ -45,6 +45,7 @@
  * Beam documentation on how to run pipelines.
  */
 class BeamSqlExample {
+
   public static void main(String[] args) {
     PipelineOptions options = PipelineOptionsFactory.fromArgs(args).create();
     Pipeline p = Pipeline.create(options);
@@ -66,19 +67,21 @@ public static void main(String[] args) {
         inputTable.apply(SqlTransform.query("select c1, c2, c3 from PCOLLECTION where c1 > 1"));
 
     // print the output record of case 1;
-    outputStream.apply(
-        "log_result",
-        MapElements.via(
-            new SimpleFunction() {
-              @Override
-              public Row apply(Row input) {
-                // expect output:
-                //  PCOLLECTION: [3, row, 3.0]
-                //  PCOLLECTION: [2, row, 2.0]
-                System.out.println("PCOLLECTION: " + input.getValues());
-                return input;
-              }
-            }));
+    outputStream
+        .apply(
+            "log_result",
+            MapElements.via(
+                new SimpleFunction() {
+                  @Override
+                  public Row apply(Row input) {
+                    // expect output:
+                    //  PCOLLECTION: [3, row, 3.0]
+                    //  PCOLLECTION: [2, row, 2.0]
+                    System.out.println("PCOLLECTION: " + input.getValues());
+                    return input;
+                  }
+                }))
+        .setRowSchema(type);
 
     // Case 2. run the query with SqlTransform.query over result PCollection of case 1.
     PCollection outputStream2 =
@@ -86,18 +89,21 @@ public Row apply(Row input) {
             .apply(SqlTransform.query("select c2, sum(c3) from CASE1_RESULT group by c2"));
 
     // print the output record of case 2;
-    outputStream2.apply(
-        "log_result",
-        MapElements.via(
-            new SimpleFunction() {
-              @Override
-              public Row apply(Row input) {
-                // expect output:
-                //  CASE1_RESULT: [row, 5.0]
-                System.out.println("CASE1_RESULT: " + input.getValues());
-                return input;
-              }
-            }));
+    outputStream2
+        .apply(
+            "log_result",
+            MapElements.via(
+                new SimpleFunction() {
+                  @Override
+                  public Row apply(Row input) {
+                    // expect output:
+                    //  CASE1_RESULT: [row, 5.0]
+                    System.out.println("CASE1_RESULT: " + input.getValues());
+                    return input;
+                  }
+                }))
+        .setRowSchema(
+            Schema.builder().addStringField("stringField").addDoubleField("doubleField").build());
 
     p.run().waitUntilFinish();
   }

From e1b148bf1f2e735ee082c06e1097fe72bb152365 Mon Sep 17 00:00:00 2001
From: Boyuan Zhang 
Date: Tue, 12 May 2020 20:24:56 -0700
Subject: [PATCH 038/151] Implement GrowableOffsetRangeTracker

---
 .../GrowableOffsetRangeTracker.java           | 143 ++++++++++
 .../splittabledofn/OffsetRangeTracker.java    |  58 +++-
 .../GrowableOffsetRangeTrackerTest.java       | 255 ++++++++++++++++++
 .../OffsetRangeTrackerTest.java               |  43 +++
 4 files changed, 485 insertions(+), 14 deletions(-)
 create mode 100644 sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/splittabledofn/GrowableOffsetRangeTracker.java
 create mode 100644 sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/splittabledofn/GrowableOffsetRangeTrackerTest.java

diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/splittabledofn/GrowableOffsetRangeTracker.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/splittabledofn/GrowableOffsetRangeTracker.java
new file mode 100644
index 000000000000..a74d72b72b3d
--- /dev/null
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/splittabledofn/GrowableOffsetRangeTracker.java
@@ -0,0 +1,143 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.transforms.splittabledofn;
+
+import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkNotNull;
+
+import java.math.BigDecimal;
+import java.math.MathContext;
+import org.apache.beam.sdk.annotations.Experimental;
+import org.apache.beam.sdk.annotations.Experimental.Kind;
+import org.apache.beam.sdk.io.range.OffsetRange;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Suppliers;
+
+/**
+ * An {@link OffsetRangeTracker} for tracking a growable offset range. {@code Long.MAX_VALUE} is
+ * used as the end of the range to indicate infinity.
+ *
+ * 
    An offset range is considered growable when the end offset could grow (or change) during
+ * execution time (e.g., Kafka topic partition offset, appended file, ...).
+ *
+ * 
    The growable range is marked as done by claiming {@code Long.MAX_VALUE}.
+ */
+@Experimental(Kind.SPLITTABLE_DO_FN)
+public class GrowableOffsetRangeTracker extends OffsetRangeTracker {
+  /**
+   * Provides the estimated end offset of the range.
+   *
+   * 
    {@link #estimate} is called to give the end offset when {@link #trySplit} or {@link
+   * #getProgress} is invoked. The end offset is exclusive for the range. The estimated end is not
+   * required to monotonically increase as it will only be taken into consideration when the
+   * estimated end offset is larger than the current position. Returning {@code Long.MAX_VALUE} as
+   * the estimate implies the largest possible position for the range is {@code Long.MAX_VALUE - 1}.
+   * Return {@code Long.MIN_VALUE} if an estimate can not be provided.
+   *
+   * 
    Providing a good estimate is important for an accurate progress signal and will impact
+   * splitting decisions by the runner.
+   *
+   * 
    If {@link #estimate} is expensive to compute, consider wrapping the implementation with
+   * {@link Suppliers#memoizeWithExpiration} or equivalent as an optimization.
+   *
+   * 
    TODO(BEAM-10032): Also consider using {@link RangeEndEstimator} when the range is not ended
+   * with {@code Long.MAX_VALUE}.
+   */
+  @FunctionalInterface
+  public interface RangeEndEstimator {
+    long estimate();
+  }
+
+  private final RangeEndEstimator rangeEndEstimator;
+
+  public GrowableOffsetRangeTracker(long start, RangeEndEstimator rangeEndEstimator) {
+    super(new OffsetRange(start, Long.MAX_VALUE));
+    this.rangeEndEstimator = checkNotNull(rangeEndEstimator);
+  }
+
+  @Override
+  public SplitResult trySplit(double fractionOfRemainder) {
+    // If current tracking range is no longer growable, split it as a normal range.
+    if (range.getTo() != Long.MAX_VALUE || range.getTo() == range.getFrom()) {
+      return super.trySplit(fractionOfRemainder);
+    }
+    // If current range has been done, there is no more space to split.
+    if (lastAttemptedOffset != null && lastAttemptedOffset == Long.MAX_VALUE) {
+      return null;
+    }
+    BigDecimal cur =
+        (lastAttemptedOffset == null)
+            ? BigDecimal.valueOf(range.getFrom()).subtract(BigDecimal.ONE, MathContext.DECIMAL128)
+            : BigDecimal.valueOf(lastAttemptedOffset);
+
+    // Fetch the estimated end offset. If the estimated end is smaller than the next offset, use
+    // the next offset as end.
+    BigDecimal estimateRangeEnd =
+        BigDecimal.valueOf(rangeEndEstimator.estimate())
+            .max(cur.add(BigDecimal.ONE, MathContext.DECIMAL128));
+
+    // Convert to BigDecimal in computation to prevent overflow, which may result in loss of
+    // precision.
+    // split = cur + max(1, (estimateRangeEnd - cur) * fractionOfRemainder)
+    BigDecimal splitPos =
+        cur.add(
+            estimateRangeEnd
+                .subtract(cur, MathContext.DECIMAL128)
+                .multiply(BigDecimal.valueOf(fractionOfRemainder), MathContext.DECIMAL128)
+                .max(BigDecimal.ONE),
+            MathContext.DECIMAL128);
+    long split = splitPos.longValue();
+    if (split > estimateRangeEnd.longValue()) {
+      return null;
+    }
+    OffsetRange res = new OffsetRange(split, range.getTo());
+    this.range = new OffsetRange(range.getFrom(), split);
+    return SplitResult.of(range, res);
+  }
+
+  @Override
+  public Progress getProgress() {
+    // If current tracking range is no longer growable, get progress as a normal range.
+    if (range.getTo() != Long.MAX_VALUE || range.getTo() == range.getFrom()) {
+      return super.getProgress();
+    }
+
+    // Convert to BigDecimal in computation to prevent overflow, which may result in lost of
+    // precision.
+    BigDecimal estimateRangeEnd = BigDecimal.valueOf(rangeEndEstimator.estimate());
+
+    if (lastAttemptedOffset == null) {
+      return Progress.from(
+          0,
+          estimateRangeEnd
+              .subtract(BigDecimal.valueOf(range.getFrom()), MathContext.DECIMAL128)
+              .max(BigDecimal.ZERO)
+              .doubleValue());
+    }
+
+    BigDecimal workRemaining =
+        estimateRangeEnd
+            .subtract(BigDecimal.valueOf(lastAttemptedOffset), MathContext.DECIMAL128)
+            .max(BigDecimal.ZERO);
+    BigDecimal totalWork =
+        estimateRangeEnd
+            .max(BigDecimal.valueOf(lastAttemptedOffset))
+            .subtract(BigDecimal.valueOf(range.getFrom()), MathContext.DECIMAL128);
+    return Progress.from(
+        totalWork.subtract(workRemaining, MathContext.DECIMAL128).doubleValue(),
+        workRemaining.doubleValue());
+  }
+}
diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/splittabledofn/OffsetRangeTracker.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/splittabledofn/OffsetRangeTracker.java
index 2743a1dc56c4..9c7116f5e8c1 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/splittabledofn/OffsetRangeTracker.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/splittabledofn/OffsetRangeTracker.java
@@ -21,6 +21,8 @@
 import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkNotNull;
 import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkState;
 
+import java.math.BigDecimal;
+import java.math.MathContext;
 import javax.annotation.Nullable;
 import org.apache.beam.sdk.annotations.Experimental;
 import org.apache.beam.sdk.annotations.Experimental.Kind;
@@ -31,13 +33,16 @@
 /**
  * A {@link RestrictionTracker} for claiming offsets in an {@link OffsetRange} in a monotonically
  * increasing fashion.
+ *
+ * 
    The smallest offset is {@code Long.MIN_VALUE} and the largest offset is {@code Long.MAX_VALUE
+ * - 1}.
  */
 @Experimental(Kind.SPLITTABLE_DO_FN)
 public class OffsetRangeTracker extends RestrictionTracker
     implements HasProgress {
-  private OffsetRange range;
-  @Nullable private Long lastClaimedOffset = null;
-  @Nullable private Long lastAttemptedOffset = null;
+  protected OffsetRange range;
+  @Nullable protected Long lastClaimedOffset = null;
+  @Nullable protected Long lastAttemptedOffset = null;
 
   public OffsetRangeTracker(OffsetRange range) {
     this.range = checkNotNull(range);
@@ -50,16 +55,27 @@ public OffsetRange currentRestriction() {
 
   @Override
   public SplitResult trySplit(double fractionOfRemainder) {
-    long cur = (lastAttemptedOffset == null) ? range.getFrom() - 1 : lastAttemptedOffset;
-    long splitPos =
-        cur
-            + Math.max(
-                1L, (Double.valueOf((range.getTo() - cur) * fractionOfRemainder)).longValue());
-    if (splitPos >= range.getTo()) {
+    // Convert to BigDecimal in computation to prevent overflow, which may result in loss of
+    // precision.
+    BigDecimal cur =
+        (lastAttemptedOffset == null)
+            ? BigDecimal.valueOf(range.getFrom()).subtract(BigDecimal.ONE, MathContext.DECIMAL128)
+            : BigDecimal.valueOf(lastAttemptedOffset);
+    // split = cur + max(1, (range.getTo() - cur) * fractionOfRemainder)
+    BigDecimal splitPos =
+        cur.add(
+            BigDecimal.valueOf(range.getTo())
+                .subtract(cur, MathContext.DECIMAL128)
+                .multiply(BigDecimal.valueOf(fractionOfRemainder), MathContext.DECIMAL128)
+                .max(BigDecimal.ONE),
+            MathContext.DECIMAL128);
+
+    long split = splitPos.longValue();
+    if (split >= range.getTo()) {
       return null;
     }
-    OffsetRange res = new OffsetRange(splitPos, range.getTo());
-    this.range = new OffsetRange(range.getFrom(), splitPos);
+    OffsetRange res = new OffsetRange(split, range.getTo());
+    this.range = new OffsetRange(range.getFrom(), split);
     return SplitResult.of(range, res);
   }
 
@@ -120,13 +136,27 @@ public String toString() {
   public Progress getProgress() {
     // If we have never attempted an offset, we return the length of the entire range as work
     // remaining.
+    // Convert to BigDecimal in computation to prevent overflow, which may result in loss of
+    // precision.
     if (lastAttemptedOffset == null) {
-      return Progress.from(0, range.getTo() - range.getFrom());
+      return Progress.from(
+          0,
+          BigDecimal.valueOf(range.getTo())
+              .subtract(BigDecimal.valueOf(range.getFrom()), MathContext.DECIMAL128)
+              .doubleValue());
     }
 
     // Compute the amount of work remaining from where we are to where we are attempting to get to
     // with a minimum of zero in case we have claimed beyond the end of the range.
-    long workRemaining = Math.max(range.getTo() - lastAttemptedOffset, 0);
-    return Progress.from(range.getTo() - range.getFrom() - workRemaining, workRemaining);
+    BigDecimal workRemaining =
+        BigDecimal.valueOf(range.getTo())
+            .subtract(BigDecimal.valueOf(lastAttemptedOffset), MathContext.DECIMAL128)
+            .max(BigDecimal.ZERO);
+    BigDecimal totalWork =
+        BigDecimal.valueOf(range.getTo())
+            .subtract(BigDecimal.valueOf(range.getFrom()), MathContext.DECIMAL128);
+    return Progress.from(
+        totalWork.subtract(workRemaining, MathContext.DECIMAL128).doubleValue(),
+        workRemaining.doubleValue());
   }
 }
diff --git a/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/splittabledofn/GrowableOffsetRangeTrackerTest.java b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/splittabledofn/GrowableOffsetRangeTrackerTest.java
new file mode 100644
index 000000000000..17050157d4cc
--- /dev/null
+++ b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/splittabledofn/GrowableOffsetRangeTrackerTest.java
@@ -0,0 +1,255 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.transforms.splittabledofn;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.math.BigDecimal;
+import java.math.MathContext;
+import org.apache.beam.sdk.io.range.OffsetRange;
+import org.apache.beam.sdk.transforms.splittabledofn.RestrictionTracker.Progress;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.ExpectedException;
+import org.junit.runner.RunWith;
+import org.junit.runners.JUnit4;
+
+/** Tests for {@link GrowableOffsetRangeTracker}. */
+@RunWith(JUnit4.class)
+public class GrowableOffsetRangeTrackerTest {
+  private static class SimpleEstimator implements GrowableOffsetRangeTracker.RangeEndEstimator {
+    private long estimateRangeEnd = 0;
+
+    @Override
+    public long estimate() {
+      return estimateRangeEnd;
+    }
+
+    public void setEstimateRangeEnd(long offset) {
+      estimateRangeEnd = offset;
+    }
+  }
+
+  @Rule public final ExpectedException expected = ExpectedException.none();
+
+  @Test
+  public void testIllegalInitialization() throws Exception {
+    expected.expect(NullPointerException.class);
+    GrowableOffsetRangeTracker tracker = new GrowableOffsetRangeTracker(0L, null);
+  }
+
+  @Test
+  public void testTryClaim() throws Exception {
+    GrowableOffsetRangeTracker tracker = new GrowableOffsetRangeTracker(0L, new SimpleEstimator());
+    assertTrue(tracker.tryClaim(10L));
+    assertTrue(tracker.tryClaim(100L));
+    assertFalse(tracker.tryClaim(Long.MAX_VALUE));
+    tracker.checkDone();
+  }
+
+  @Test
+  public void testCheckpointBeforeStart() throws Exception {
+    SimpleEstimator simpleEstimator = new SimpleEstimator();
+    GrowableOffsetRangeTracker tracker = new GrowableOffsetRangeTracker(0L, simpleEstimator);
+    simpleEstimator.setEstimateRangeEnd(10);
+    SplitResult res = tracker.trySplit(0);
+    tracker.checkDone();
+    assertEquals(new OffsetRange(0, 0), res.getPrimary());
+    assertEquals(new OffsetRange(0, 0), tracker.currentRestriction());
+    assertEquals(new OffsetRange(0, Long.MAX_VALUE), res.getResidual());
+  }
+
+  @Test
+  public void testCheckpointJustStarted() throws Exception {
+    SimpleEstimator simpleEstimator = new SimpleEstimator();
+    GrowableOffsetRangeTracker tracker = new GrowableOffsetRangeTracker(0L, simpleEstimator);
+    assertTrue(tracker.tryClaim(5L));
+    simpleEstimator.setEstimateRangeEnd(0L);
+    SplitResult res = tracker.trySplit(0);
+    tracker.checkDone();
+    assertEquals(new OffsetRange(0, 6), res.getPrimary());
+    assertEquals(new OffsetRange(0, 6), tracker.currentRestriction());
+    assertEquals(new OffsetRange(6, Long.MAX_VALUE), res.getResidual());
+
+    tracker = new GrowableOffsetRangeTracker(0L, simpleEstimator);
+    assertTrue(tracker.tryClaim(5L));
+    simpleEstimator.setEstimateRangeEnd(20L);
+    res = tracker.trySplit(0);
+    tracker.checkDone();
+    assertEquals(new OffsetRange(0, 6), res.getPrimary());
+    assertEquals(new OffsetRange(6, Long.MAX_VALUE), res.getResidual());
+  }
+
+  @Test
+  public void testCheckpointAfterAllProcessed() throws Exception {
+    SimpleEstimator simpleEstimator = new SimpleEstimator();
+    GrowableOffsetRangeTracker tracker = new GrowableOffsetRangeTracker(0L, simpleEstimator);
+    assertFalse(tracker.tryClaim(Long.MAX_VALUE));
+    tracker.checkDone();
+    assertNull(tracker.trySplit(0));
+  }
+
+  @Test
+  public void testCheckpointAtEmptyRange() throws Exception {
+    GrowableOffsetRangeTracker tracker =
+        new GrowableOffsetRangeTracker(Long.MAX_VALUE, new SimpleEstimator());
+    tracker.checkDone();
+    assertNull(tracker.trySplit(0));
+  }
+
+  @Test
+  public void testSplit() throws Exception {
+    SimpleEstimator simpleEstimator = new SimpleEstimator();
+    GrowableOffsetRangeTracker tracker = new GrowableOffsetRangeTracker(0L, simpleEstimator);
+    assertTrue(tracker.tryClaim(0L));
+
+    simpleEstimator.setEstimateRangeEnd(16L);
+    // The split of infinite range results in one finite range and one infinite range.
+    SplitResult res = tracker.trySplit(0.5);
+    assertEquals(new OffsetRange(0, 8), res.getPrimary());
+    assertEquals(new OffsetRange(0, 8), tracker.currentRestriction());
+    assertEquals(new OffsetRange(8, Long.MAX_VALUE), res.getResidual());
+
+    // After the first split, the tracker should track a finite range. Estimate offset should not
+    // impact split.
+    simpleEstimator.setEstimateRangeEnd(12L);
+    res = tracker.trySplit(0.5);
+    assertEquals(new OffsetRange(0, 4), res.getPrimary());
+    assertEquals(new OffsetRange(0, 4), tracker.currentRestriction());
+    assertEquals(new OffsetRange(4, 8), res.getResidual());
+    assertFalse(tracker.tryClaim(4L));
+    tracker.checkDone();
+  }
+
+  @Test
+  public void testSplitWithMaxEstimateRangeEnd() throws Exception {
+    SimpleEstimator simpleEstimator = new SimpleEstimator();
+    GrowableOffsetRangeTracker tracker = new GrowableOffsetRangeTracker(0L, simpleEstimator);
+    assertTrue(tracker.tryClaim(1L));
+    simpleEstimator.setEstimateRangeEnd(Long.MAX_VALUE);
+    SplitResult res = tracker.trySplit(0.5);
+    long expectedEnd = 1L + (Long.MAX_VALUE - 1L) / 2;
+    assertEquals(new OffsetRange(0L, expectedEnd), res.getPrimary());
+    assertEquals(new OffsetRange(expectedEnd, Long.MAX_VALUE), res.getResidual());
+  }
+
+  @Test
+  public void testProgressBeforeStart() throws Exception {
+    SimpleEstimator simpleEstimator = new SimpleEstimator();
+    GrowableOffsetRangeTracker tracker = new GrowableOffsetRangeTracker(10L, simpleEstimator);
+    simpleEstimator.setEstimateRangeEnd(20);
+    Progress currentProcess = tracker.getProgress();
+    assertEquals(0, currentProcess.getWorkCompleted(), 0.001);
+    assertEquals(10, currentProcess.getWorkRemaining(), 0.001);
+
+    simpleEstimator.setEstimateRangeEnd(15);
+    currentProcess = tracker.getProgress();
+    assertEquals(0, currentProcess.getWorkCompleted(), 0.001);
+    assertEquals(5, currentProcess.getWorkRemaining(), 0.001);
+
+    simpleEstimator.setEstimateRangeEnd(5);
+    currentProcess = tracker.getProgress();
+    assertEquals(0, currentProcess.getWorkCompleted(), 0.001);
+    assertEquals(0, currentProcess.getWorkRemaining(), 0.001);
+  }
+
+  @Test
+  public void testProgressAfterFinished() throws Exception {
+    SimpleEstimator simpleEstimator = new SimpleEstimator();
+    GrowableOffsetRangeTracker tracker = new GrowableOffsetRangeTracker(10L, simpleEstimator);
+    assertFalse(tracker.tryClaim(Long.MAX_VALUE));
+    tracker.checkDone();
+    simpleEstimator.setEstimateRangeEnd(0L);
+    Progress currentProgress = tracker.getProgress();
+    assertEquals(Long.MAX_VALUE - 10L, currentProgress.getWorkCompleted(), 0.001);
+    assertEquals(0, currentProgress.getWorkRemaining(), 0.001);
+  }
+
+  @Test
+  public void testProgress() throws Exception {
+    long start = 10L;
+    SimpleEstimator simpleEstimator = new SimpleEstimator();
+    GrowableOffsetRangeTracker tracker = new GrowableOffsetRangeTracker(start, simpleEstimator);
+    long cur = 20L;
+    assertTrue(tracker.tryClaim(cur));
+
+    simpleEstimator.setEstimateRangeEnd(5L);
+    Progress currentProgress = tracker.getProgress();
+    assertEquals(cur - start, currentProgress.getWorkCompleted(), 0.001);
+    assertEquals(0, currentProgress.getWorkRemaining(), 0.001);
+
+    simpleEstimator.setEstimateRangeEnd(35L);
+    currentProgress = tracker.getProgress();
+    assertEquals(cur - start, currentProgress.getWorkCompleted(), 0.001);
+    assertEquals(35L - cur, currentProgress.getWorkRemaining(), 0.001);
+
+    simpleEstimator.setEstimateRangeEnd(25L);
+    currentProgress = tracker.getProgress();
+    assertEquals(cur - start, currentProgress.getWorkCompleted(), 0.001);
+    assertEquals(25L - cur, currentProgress.getWorkRemaining(), 0.001);
+
+    simpleEstimator.setEstimateRangeEnd(Long.MAX_VALUE);
+    currentProgress = tracker.getProgress();
+    assertEquals(cur - start, currentProgress.getWorkCompleted(), 0.001);
+    assertEquals(Long.MAX_VALUE - cur, currentProgress.getWorkRemaining(), 0.001);
+  }
+
+  @Test
+  public void testLargeRange() throws Exception {
+    SimpleEstimator simpleEstimator = new SimpleEstimator();
+    GrowableOffsetRangeTracker tracker =
+        new GrowableOffsetRangeTracker(Long.MIN_VALUE, simpleEstimator);
+
+    simpleEstimator.setEstimateRangeEnd(Long.MAX_VALUE);
+    Progress progress = tracker.getProgress();
+    assertEquals(0, progress.getWorkCompleted(), 0.001);
+    assertEquals(
+        BigDecimal.valueOf(Long.MAX_VALUE)
+            .subtract(BigDecimal.valueOf(Long.MIN_VALUE), MathContext.DECIMAL128)
+            .doubleValue(),
+        progress.getWorkRemaining(),
+        0.001);
+
+    simpleEstimator.setEstimateRangeEnd(Long.MIN_VALUE);
+    SplitResult res = tracker.trySplit(0);
+    assertEquals(new OffsetRange(Long.MIN_VALUE, Long.MIN_VALUE), res.getPrimary());
+    assertEquals(new OffsetRange(Long.MIN_VALUE, Long.MAX_VALUE), res.getResidual());
+  }
+
+  @Test
+  public void testSmallRangeWithLargeValue() throws Exception {
+    SimpleEstimator simpleEstimator = new SimpleEstimator();
+    GrowableOffsetRangeTracker tracker =
+        new GrowableOffsetRangeTracker(123456789012345677L, simpleEstimator);
+    assertTrue(tracker.tryClaim(123456789012345677L));
+    simpleEstimator.setEstimateRangeEnd(123456789012345679L);
+    SplitResult res = tracker.trySplit(0.5);
+    assertEquals(new OffsetRange(123456789012345677L, 123456789012345678L), res.getPrimary());
+    assertEquals(new OffsetRange(123456789012345678L, Long.MAX_VALUE), res.getResidual());
+
+    tracker = new GrowableOffsetRangeTracker(123456789012345681L, simpleEstimator);
+    assertTrue(tracker.tryClaim(123456789012345681L));
+    simpleEstimator.setEstimateRangeEnd(123456789012345683L);
+    res = tracker.trySplit(0.5);
+    assertEquals(new OffsetRange(123456789012345681L, 123456789012345682L), res.getPrimary());
+    assertEquals(new OffsetRange(123456789012345682L, Long.MAX_VALUE), res.getResidual());
+  }
+}
diff --git a/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/splittabledofn/OffsetRangeTrackerTest.java b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/splittabledofn/OffsetRangeTrackerTest.java
index 6fdd2549a301..b2c381c58590 100644
--- a/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/splittabledofn/OffsetRangeTrackerTest.java
+++ b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/splittabledofn/OffsetRangeTrackerTest.java
@@ -22,6 +22,8 @@
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 
+import java.math.BigDecimal;
+import java.math.MathContext;
 import org.apache.beam.sdk.io.range.OffsetRange;
 import org.apache.beam.sdk.transforms.splittabledofn.RestrictionTracker.Progress;
 import org.junit.Rule;
@@ -35,6 +37,12 @@
 public class OffsetRangeTrackerTest {
   @Rule public final ExpectedException expected = ExpectedException.none();
 
+  @Test
+  public void testIllegalInitialization() throws Exception {
+    expected.expect(NullPointerException.class);
+    OffsetRangeTracker tracker = new OffsetRangeTracker(null);
+  }
+
   @Test
   public void testTryClaim() throws Exception {
     OffsetRange range = new OffsetRange(100, 200);
@@ -231,4 +239,39 @@ public void testBacklogPartiallyCompleted() {
     assertEquals(50, progress.getWorkCompleted(), 0.001);
     assertEquals(50, progress.getWorkRemaining(), 0.001);
   }
+
+  @Test
+  public void testLargeRange() throws Exception {
+    OffsetRangeTracker tracker =
+        new OffsetRangeTracker(new OffsetRange(Long.MIN_VALUE, Long.MAX_VALUE));
+
+    Progress progress = tracker.getProgress();
+    assertEquals(0, progress.getWorkCompleted(), 0.001);
+    assertEquals(
+        BigDecimal.valueOf(Long.MAX_VALUE)
+            .subtract(BigDecimal.valueOf(Long.MIN_VALUE), MathContext.DECIMAL128)
+            .doubleValue(),
+        progress.getWorkRemaining(),
+        0.001);
+
+    SplitResult res = tracker.trySplit(0);
+    assertEquals(new OffsetRange(Long.MIN_VALUE, Long.MIN_VALUE), res.getPrimary());
+    assertEquals(new OffsetRange(Long.MIN_VALUE, Long.MAX_VALUE), res.getResidual());
+  }
+
+  @Test
+  public void testSmallRangeWithLargeValue() throws Exception {
+    OffsetRangeTracker tracker =
+        new OffsetRangeTracker(new OffsetRange(123456789012345677L, 123456789012345679L));
+    assertTrue(tracker.tryClaim(123456789012345677L));
+    SplitResult res = tracker.trySplit(0.5);
+    assertEquals(new OffsetRange(123456789012345677L, 123456789012345678L), res.getPrimary());
+    assertEquals(new OffsetRange(123456789012345678L, 123456789012345679L), res.getResidual());
+
+    tracker = new OffsetRangeTracker(new OffsetRange(123456789012345681L, 123456789012345683L));
+    assertTrue(tracker.tryClaim(123456789012345681L));
+    res = tracker.trySplit(0.5);
+    assertEquals(new OffsetRange(123456789012345681L, 123456789012345682L), res.getPrimary());
+    assertEquals(new OffsetRange(123456789012345682L, 123456789012345683L), res.getResidual());
+  }
 }

From cf0375689181528d55d5a611d6c6789beced9291 Mon Sep 17 00:00:00 2001
From: Brian Hulette 
Date: Wed, 20 May 2020 16:15:26 -0700
Subject: [PATCH 039/151] [BEAM-9899] Fix some issues around storing schema
 `id` on user types (#11701)

* Change column name to 'id' to expose row_coder error

* Pull out fields as a tuple rather than attribute access

Fixes bug where we read the incorrect value for a field named 'id'

* Ensure user types have a _beam_schema_id set

* Tag types with '_beam_schema_id' rather than 'id' to avoid collisions

* lint

* Revert "Pull out fields as a tuple rather than attribute access"

This reverts commit 3198086a33ba44da92719bc80d989a2ca7b49d38.
---
 sdks/python/apache_beam/transforms/sql_test.py    | 14 +++++++-------
 sdks/python/apache_beam/typehints/schemas.py      | 11 ++++++++---
 sdks/python/apache_beam/typehints/schemas_test.py | 11 +++++++++++
 3 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/sdks/python/apache_beam/transforms/sql_test.py b/sdks/python/apache_beam/transforms/sql_test.py
index d2271bbfd923..918954cb84d7 100644
--- a/sdks/python/apache_beam/transforms/sql_test.py
+++ b/sdks/python/apache_beam/transforms/sql_test.py
@@ -37,10 +37,10 @@
 from apache_beam.transforms.sql import SqlTransform
 
 SimpleRow = typing.NamedTuple(
-    "SimpleRow", [("int", int), ("str", unicode), ("flt", float)])
+    "SimpleRow", [("id", int), ("str", unicode), ("flt", float)])
 coders.registry.register_coder(SimpleRow, coders.RowCoder)
 
-Enrich = typing.NamedTuple("Enrich", [("int", int), ("metadata", unicode)])
+Enrich = typing.NamedTuple("Enrich", [("id", int), ("metadata", unicode)])
 coders.registry.register_coder(Enrich, coders.RowCoder)
 
 
@@ -71,7 +71,7 @@ def test_generate_data(self):
     with TestPipeline() as p:
       out = p | SqlTransform(
           """SELECT
-            CAST(1 AS INT) AS `int`,
+            CAST(1 AS INT) AS `id`,
             CAST('foo' AS VARCHAR) AS `str`,
             CAST(3.14  AS DOUBLE) AS `flt`""")
       assert_that(out, equal_to([(1, "foo", 3.14)]))
@@ -80,7 +80,7 @@ def test_project(self):
     with TestPipeline() as p:
       out = (
           p | beam.Create([SimpleRow(1, "foo", 3.14)])
-          | SqlTransform("SELECT `int`, `flt` FROM PCOLLECTION"))
+          | SqlTransform("SELECT `id`, `flt` FROM PCOLLECTION"))
       assert_that(out, equal_to([(1, 3.14)]))
 
   def test_filter(self):
@@ -109,7 +109,7 @@ def test_agg(self):
               SELECT
                 `str`,
                 COUNT(*) AS `count`,
-                SUM(`int`) AS `sum`,
+                SUM(`id`) AS `sum`,
                 AVG(`flt`) AS `avg`
               FROM PCOLLECTION GROUP BY `str`"""))
       assert_that(out, equal_to([("foo", 3, 3, 2), ("bar", 4, 8, 1.414)]))
@@ -131,11 +131,11 @@ def test_tagged_join(self):
              | SqlTransform(
                  """
               SELECT
-                simple.`int` AS `int`,
+                simple.`id` AS `id`,
                 enrich.metadata AS metadata
               FROM simple
               JOIN enrich
-              ON simple.`int` = enrich.`int`"""))
+              ON simple.`id` = enrich.`id`"""))
       assert_that(out, equal_to([(1, "a"), (26, "z"), (1, "a")]))
 
   def test_zetasql_generate_data(self):
diff --git a/sdks/python/apache_beam/typehints/schemas.py b/sdks/python/apache_beam/typehints/schemas.py
index faff159ed17e..f69f4756deaa 100644
--- a/sdks/python/apache_beam/typehints/schemas.py
+++ b/sdks/python/apache_beam/typehints/schemas.py
@@ -115,12 +115,16 @@ def get_schema_by_id(self, unique_id):
     float: schema_pb2.DOUBLE,
 })
 
+# Name of the attribute added to user types (existing and generated) to store
+# the corresponding schema ID
+_BEAM_SCHEMA_ID = "_beam_schema_id"
+
 
 def typing_to_runner_api(type_):
   if _match_is_named_tuple(type_):
     schema = None
-    if hasattr(type_, 'id'):
-      schema = SCHEMA_REGISTRY.get_schema_by_id(type_.id)
+    if hasattr(type_, _BEAM_SCHEMA_ID):
+      schema = SCHEMA_REGISTRY.get_schema_by_id(getattr(type_, _BEAM_SCHEMA_ID))
     if schema is None:
       fields = [
           schema_pb2.Field(
@@ -129,6 +133,7 @@ def typing_to_runner_api(type_):
       ]
       type_id = str(uuid4())
       schema = schema_pb2.Schema(fields=fields, id=type_id)
+      setattr(type_, _BEAM_SCHEMA_ID, type_id)
       SCHEMA_REGISTRY.add(type_, schema)
 
     return schema_pb2.FieldType(row_type=schema_pb2.RowType(schema=schema))
@@ -199,7 +204,7 @@ def typing_from_runner_api(fieldtype_proto):
           [(field.name, typing_from_runner_api(field.type))
            for field in schema.fields])
 
-      user_type.id = schema.id
+      setattr(user_type, _BEAM_SCHEMA_ID, schema.id)
 
       # Define a reduce function, otherwise these types can't be pickled
       # (See BEAM-9574)
diff --git a/sdks/python/apache_beam/typehints/schemas_test.py b/sdks/python/apache_beam/typehints/schemas_test.py
index 42e7198db4e2..2bf471734019 100644
--- a/sdks/python/apache_beam/typehints/schemas_test.py
+++ b/sdks/python/apache_beam/typehints/schemas_test.py
@@ -37,6 +37,7 @@
 
 from apache_beam.portability.api import schema_pb2
 from apache_beam.typehints.schemas import named_tuple_from_schema
+from apache_beam.typehints.schemas import named_tuple_to_schema
 from apache_beam.typehints.schemas import typing_from_runner_api
 from apache_beam.typehints.schemas import typing_to_runner_api
 
@@ -285,6 +286,16 @@ def test_generated_class_pickle(self):
 
     self.assertEqual(instance, pickle.loads(pickle.dumps(instance)))
 
+  def test_user_type_annotated_with_id_after_conversion(self):
+    MyCuteClass = NamedTuple('MyCuteClass', [
+        ('name', unicode),
+    ])
+    self.assertFalse(hasattr(MyCuteClass, '_beam_schema_id'))
+
+    schema = named_tuple_to_schema(MyCuteClass)
+    self.assertTrue(hasattr(MyCuteClass, '_beam_schema_id'))
+    self.assertEqual(MyCuteClass._beam_schema_id, schema.id)
+
 
 if __name__ == '__main__':
   unittest.main()

From 3c1c757f353073ceb2947f4ad65fe7ecd56b73b6 Mon Sep 17 00:00:00 2001
From: Jacob Ferriero 
Date: Wed, 20 May 2020 17:27:56 -0700
Subject: [PATCH 040/151] Merge pull request #11339 from [BEAM-9468] Fhir io

* add HL7v2IO and FhirIO, test dependency issue

* add to changes

* minor updates

* staging before splitting PRs

* remove FhirIO

* simplify HL7v2IO structure

* add write result

* refactor to HL7v2IO.Read.Result

* add Coders and HL7v2IOTest

* spotless

* encode more of the Message

* fix read result getPipeline

* add adaptive throttler to write

* remove unused import

* improve test readability

* nvm spotless apply didn't like that

* scaffolding of Read integration test

scaffolding of Read integration test

* scaffolding for Write IT

* small integration test

* clean up

* fix integration tests

* add labels to Message coder

* add parsed data coder

* Refactor to use HL7v2Message wrapper class

* Expose schematized data as JSON string to support motivating use case of
HL7v2 -> FHIR via HCLS DataHamonization Mapping Engine.
* The healthcare model Message class has fields
(namely ParsedData and PatientIds) that are difficult to deal with in the Coder
and provide little value for users.

* set scope and user agent

* add schematized data to coder

* refactor list fn to avoid double get, improve tests, extract json from schematized data

* add IT for new ListHL7v2Messages PTransform

* migration to latest beta client library

* beta api migration

* add RunWith

* remove adaptive throttling

* revert AdaptiveThrottler to package private

* Revert "remove FhirIO"

This reverts commit d6967914e10da1bf42815573b567cfff564d71a1.

fhir write

wip

wip fhirio

* remove fhir adaptive throttling

* spotless

* fix javadoc

* wip: tests failing with 400 errors

* prepared integration tests

* staging EOD

* wip

* add HealthcareIOErrorToTableRow convenience transform

* spotless

* wip

* Add convenience function for writing deadletter to bigquery

* Address review feedback

* Fix FetchHL7v2Message javadoc
* Add observedTime to HealthcareIOErrorCoder

* Improve API surface for users

* ephemeral HL7v2 stores in integration tests

* prepare integration tests for apache-beam-testing

* workaround broken executeBundle in client library

* integration tests for FhirIO

* separate ITs for all fhir versions

* r4 working

* remove DLQ in integration test

* DRY up GCS clean up in util

* manage TODO comments

* improve docstring

* improve docs rename tests

* fix docstring typos

* fhirio test

* update google_clients_version to 1.30.9

* fix merge issue w/ duplicate google_oauth_clients_version

* add placeholder for FhirIOReadIT

* parameterize write ITs add scaffolidng for Read IT

* add parameterized FhirIOReadIT

* read project from options

* remove FhirIO.Read experimental tag / warning

* Use Jackson

* complete jackson migration

* spotlessApply

* add TODO to add support for batch API in the future once available

* add reshuffle to increase downstream paralelism

* add setCoder before reshuffle

* add GroupIntoBatches logic to FhirIO.Import to write more resources to files

* add GroupIntoBatches test for uneven batches

* test scoped pubsub topic

* Refactor FhirIO.Import

This commit is the first in a series of explorations of best method
for batching files to a single GCS prefix for fhirStores.import call.

FhirIO.Import now follow the algorithm of:
- Write Bundles of input PCollection to GCS
- GroupByKey (random key to parallelize GroupIntoBatches)
- GroupIntoBatches (of 10,000 files)
- move each batch of files to uniquely named GCS path
- make import calls for each of these GCS paths

* numShards 5->100

* fix auto value issue causing canot find symbol

* Patches for HL7v2IO

* Use TestPipeline in ITs
* Drop schematized data before calling message ingest (should be output only) to help pipelines that read/write from/to two HL7v2 stores
* Make HL7v2MessageCoder constructor public

* use TestPipeline

* block on run

* add sleep to avoid flakiness due to asyncronous HL7v2 indexing

* E2E integration test

* fix merge issue

* reconcile double sleeping

* improve error hanlding

* improve error handling

* fix docs typo

* add latency distribution metrics

* remove unused imports

* ingest only data and labels

* fix comment

* call spliterator directly, use page size 1000

* output elements more eagerly in ListHL72MessageFn

* eagerly emit data from early pages

* Optimization of Listing and Stablization of ITs

* allow HL7v2 Message listing to emit early panes rather than waiting on pagination of all list results
* add EBO on HL7v2 Message listing reaching a certain expected length in ITs to account for async indexing BEAM-9779

* revert unrelated changes

* add back test

* Add constant for HL7v2 indexing timeout minutes

* Add constant for HL7v2 indexing timeout minutes

* fix checkstyle

* implement improvements in BEAM-9831

* use HL7V2_INDEXING_TIMEOUT_MINUTES everywhere

* make HL7v2Message constructor public

* remove dead code

* add TODO for verifying triggering behavior BEAM-9847

* remove inappropriate 'optimizaiton', add status code to HealthcareIOError

* refactor Fhir to use String, add status code for apache http client lib errors

* fix reading

* fix FHIR resource reading to use object mapper

* Clean up based on offline review feedback

* Add SDK version to user agent
* Improve naming of FetchString
* Add value provider support

* Refactors Import to Copy and Clean Up

* Uses copy instead of rename in FhirIO.ImportFn to be more resilient to rescheduling
* adds .of() static methods for all coders
* make FhirIO.Import extend FhirIO.Write and return both body and file failures

* improving coder interface and safety of FhirIO.Import

* check failedBodies empty in FhirIO.WriteIT

* Update sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java

Co-authored-by: Pablo 

* Update sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java

Co-authored-by: Pablo 

* Update sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java

Co-authored-by: Pablo 

* fallback to tempLocation for fhir import temp files

* spotless

* Update sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java

Co-authored-by: Pablo 

* fixing javadoc

* avoid exposing apache http dep in api

* copy test resources for dataflow ITs

* remove preconditions from test util

* fix value provider implementation for FhirIO

* wip

* wip

* Exclude FhirIOReadIT from google-cloud-dataflow-java tests

* spotless

Co-authored-by: Pablo 
---
 .../google-cloud-dataflow-java/build.gradle   |     8 +-
 .../sdk/transforms/GroupIntoBatchesTest.java  |    51 +-
 .../io/google-cloud-platform/build.gradle     |     4 +-
 .../beam/sdk/io/gcp/healthcare/FhirIO.java    |  1176 +
 .../beam/sdk/io/gcp/healthcare/HL7v2IO.java   |    11 +-
 .../io/gcp/healthcare/HL7v2MessageCoder.java  |     6 +-
 .../gcp/healthcare/HealthcareApiClient.java   |    52 +-
 .../io/gcp/healthcare/HealthcareIOError.java  |     9 +-
 .../healthcare/HttpHealthcareApiClient.java   |   216 +-
 .../beam/sdk/io/gcp/pubsub/TestPubsub.java    |     4 +-
 .../sdk/io/gcp/healthcare/FhirIOReadIT.java   |   147 +
 .../sdk/io/gcp/healthcare/FhirIOTest.java     |   112 +
 .../io/gcp/healthcare/FhirIOTestOptions.java  |    46 +
 .../sdk/io/gcp/healthcare/FhirIOTestUtil.java |   127 +
 .../sdk/io/gcp/healthcare/FhirIOWriteIT.java  |   129 +
 .../sdk/io/gcp/healthcare/HL7v2IOReadIT.java  |     4 +-
 .../io/gcp/healthcare/HL7v2IOReadWriteIT.java |     2 +-
 .../sdk/io/gcp/healthcare/HL7v2IOWriteIT.java |     2 +-
 ..._ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json | 14018 +++
 ..._1fd2683f-2a56-47c7-b674-98f2cc8319e7.json | 10877 +++
 ..._4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json | 17399 ++++
 ..._8ed31d3e-7352-4055-89c4-f017db3f594e.json |  9279 ++
 ..._f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json | 10047 ++
 .../hospitalInformation1586309771387.json     |   825 +
 .../practitionerInformation1586309771387.json |   617 +
 ..._d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json | 16391 ++++
 ..._af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json | 31841 ++++++
 ..._a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json | 16971 ++++
 ..._fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json | 80348 ++++++++++++++++
 ..._55a5307d-5f23-49c1-9100-7d5c513abca3.json | 16018 +++
 .../R4/hospitalInformation1586368892823.json  |  1182 +
 .../practitionerInformation1586368892823.json |   978 +
 ..._02a63c07-9fcc-42ba-aec0-9d5399ac4796.json | 16003 +++
 ..._88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json | 15372 +++
 ..._df27a976-5c5e-4b84-ad00-fe32972dce9c.json | 22688 +++++
 ..._136f997d-0a94-4573-97da-a53b5060a612.json | 28126 ++++++
 ..._74779846-85a4-4b26-9da4-414a5fec1aed.json | 18231 ++++
 ..._3024090f-fe14-40a9-8fae-79952d3c95ce.json | 32061 ++++++
 .../hospitalInformation1586298239556.json     |   880 +
 .../practitionerInformation1586298239556.json |   523 +
 40 files changed, 362685 insertions(+), 96 deletions(-)
 create mode 100644 sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOReadIT.java
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTest.java
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestOptions.java
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Ernesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/hospitalInformation1586309771387.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/practitionerInformation1586309771387.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/Emerson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/Seymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/hospitalInformation1586368892823.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/practitionerInformation1586368892823.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Alexander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Basil991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Dannette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/hospitalInformation1586298239556.json
 create mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/practitionerInformation1586298239556.json

diff --git a/runners/google-cloud-dataflow-java/build.gradle b/runners/google-cloud-dataflow-java/build.gradle
index 0f42b9d8a7db..f5f585041707 100644
--- a/runners/google-cloud-dataflow-java/build.gradle
+++ b/runners/google-cloud-dataflow-java/build.gradle
@@ -223,7 +223,12 @@ task validatesRunner {
   dependsOn validatesRunnerLegacyWorkerTest
 }
 
-task googleCloudPlatformLegacyWorkerIntegrationTest(type: Test) {
+task copyGoogleCloudPlatformTestResources(type: Copy){
+  from project(':sdks:java:io:google-cloud-platform').fileTree("src/test/resources")
+  into "$buildDir/resources/test/"
+}
+
+task googleCloudPlatformLegacyWorkerIntegrationTest(type: Test, dependsOn: copyGoogleCloudPlatformTestResources) {
   group = "Verification"
   dependsOn ":runners:google-cloud-dataflow-java:worker:legacy-worker:shadowJar"
   systemProperty "beamTestPipelineOptions", JsonOutput.toJson([
@@ -239,6 +244,7 @@ task googleCloudPlatformLegacyWorkerIntegrationTest(type: Test) {
   exclude '**/BigQueryIOReadIT.class'
   exclude '**/BigQueryIOStorageReadTableRowIT.class'
   exclude '**/PubsubReadIT.class'
+  exclude '**/FhirIOReadIT.class'
   maxParallelForks 4
   classpath = configurations.googleCloudPlatformIntegrationTest
   testClassesDirs = files(project(":sdks:java:io:google-cloud-platform").sourceSets.test.output.classesDirs)
diff --git a/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/GroupIntoBatchesTest.java b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/GroupIntoBatchesTest.java
index dab99e659a3a..ab49ec0bbcd3 100644
--- a/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/GroupIntoBatchesTest.java
+++ b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/GroupIntoBatchesTest.java
@@ -54,13 +54,14 @@
 @RunWith(JUnit4.class)
 public class GroupIntoBatchesTest implements Serializable {
   private static final int BATCH_SIZE = 5;
-  private static final long NUM_ELEMENTS = 10;
+  private static final long EVEN_NUM_ELEMENTS = 10;
+  private static final long ODD_NUM_ELEMENTS = 11;
   private static final int ALLOWED_LATENESS = 0;
   private static final Logger LOG = LoggerFactory.getLogger(GroupIntoBatchesTest.class);
   @Rule public transient TestPipeline pipeline = TestPipeline.create();
-  private transient ArrayList> data = createTestData();
+  private transient ArrayList> data = createTestData(EVEN_NUM_ELEMENTS);
 
-  private static ArrayList> createTestData() {
+  private static ArrayList> createTestData(long numElements) {
     String[] scientists = {
       "Einstein",
       "Darwin",
@@ -74,7 +75,7 @@ private static ArrayList> createTestData() {
       "Maxwell"
     };
     ArrayList> data = new ArrayList<>();
-    for (int i = 0; i < NUM_ELEMENTS; i++) {
+    for (int i = 0; i < numElements; i++) {
       int index = i % scientists.length;
       KV element = KV.of("key", scientists[index]);
       data.add(element);
@@ -111,7 +112,45 @@ public Void apply(Iterable>> input) {
               }
             });
     PAssert.thatSingleton("Incorrect collection size", collection.apply("Count", Count.globally()))
-        .isEqualTo(NUM_ELEMENTS / BATCH_SIZE);
+        .isEqualTo(EVEN_NUM_ELEMENTS / BATCH_SIZE);
+    pipeline.run();
+  }
+
+  /** test behavior when the number of input elements is not evenly divisible by batch size. */
+  @Test
+  @Category({NeedsRunner.class, UsesTimersInParDo.class, UsesStatefulParDo.class})
+  public void testWithUnevenBatches() {
+    PCollection>> collection =
+        pipeline
+            .apply("Input data", Create.of(createTestData(ODD_NUM_ELEMENTS)))
+            .apply(GroupIntoBatches.ofSize(BATCH_SIZE))
+            // set output coder
+            .setCoder(KvCoder.of(StringUtf8Coder.of(), IterableCoder.of(StringUtf8Coder.of())));
+    PAssert.that("Incorrect batch size in one or more elements", collection)
+        .satisfies(
+            new SerializableFunction>>, Void>() {
+
+              private boolean checkBatchSizes(Iterable>> listToCheck) {
+                for (KV> element : listToCheck) {
+                  // number of elements should be less than or equal to BATCH_SIZE
+                  if (Iterables.size(element.getValue()) > BATCH_SIZE) {
+                    return false;
+                  }
+                }
+                return true;
+              }
+
+              @Override
+              public Void apply(Iterable>> input) {
+                assertTrue(checkBatchSizes(input));
+                return null;
+              }
+            });
+    PAssert.thatSingleton("Incorrect collection size", collection.apply("Count", Count.globally()))
+        .isEqualTo(
+            // round up division for positive numbers
+            // https://math.stackexchange.com/questions/2591316/proof-for-integer-division-algorithm-that-rounds-up.
+            (ODD_NUM_ELEMENTS + BATCH_SIZE - 1) / BATCH_SIZE);
     pipeline.run();
   }
 
@@ -142,7 +181,7 @@ public void testInStreamingMode() {
         streamBuilder
             .advanceWatermarkTo(startInstant.plus(Duration.standardSeconds(windowDuration - 1)))
             .advanceWatermarkTo(startInstant.plus(Duration.standardSeconds(windowDuration + 1)))
-            .advanceWatermarkTo(startInstant.plus(Duration.standardSeconds(NUM_ELEMENTS)))
+            .advanceWatermarkTo(startInstant.plus(Duration.standardSeconds(EVEN_NUM_ELEMENTS)))
             .advanceWatermarkToInfinity();
 
     PCollection> inputCollection =
diff --git a/sdks/java/io/google-cloud-platform/build.gradle b/sdks/java/io/google-cloud-platform/build.gradle
index c6c8e93927a2..442479563f69 100644
--- a/sdks/java/io/google-cloud-platform/build.gradle
+++ b/sdks/java/io/google-cloud-platform/build.gradle
@@ -92,10 +92,11 @@ dependencies {
   testRuntimeOnly library.java.slf4j_jdk14
 }
 
+
 /**
  * These are integration tests with the real Pubsub service and the DirectRunner.
  */
-task integrationTest(type: Test) {
+task integrationTest(type: Test, dependsOn: processTestResources) {
   group = "Verification"
   def gcpProject = project.findProperty('gcpProject') ?: 'apache-beam-testing'
   def gcpTempRoot = project.findProperty('gcpTempRoot') ?: 'gs://temp-storage-for-end-to-end-tests'
@@ -117,6 +118,7 @@ task integrationTest(type: Test) {
   maxParallelForks 4
   classpath = sourceSets.test.runtimeClasspath
   testClassesDirs = sourceSets.test.output.classesDirs
+
   useJUnit {
     excludeCategories "org.apache.beam.sdk.testing.UsesKms"
   }
diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
new file mode 100644
index 000000000000..13b696edd74f
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
@@ -0,0 +1,1176 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkState;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.api.services.healthcare.v1beta1.model.HttpBody;
+import com.google.api.services.healthcare.v1beta1.model.Operation;
+import com.google.auto.value.AutoValue;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.WritableByteChannel;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.concurrent.ThreadLocalRandom;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.IterableCoder;
+import org.apache.beam.sdk.coders.KvCoder;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import org.apache.beam.sdk.coders.TextualIntegerCoder;
+import org.apache.beam.sdk.coders.VoidCoder;
+import org.apache.beam.sdk.io.FileIO;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.EmptyMatchTreatment;
+import org.apache.beam.sdk.io.fs.MatchResult.Metadata;
+import org.apache.beam.sdk.io.fs.MoveOptions.StandardMoveOptions;
+import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
+import org.apache.beam.sdk.io.fs.ResourceId;
+import org.apache.beam.sdk.io.fs.ResourceIdCoder;
+import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO;
+import org.apache.beam.sdk.metrics.Counter;
+import org.apache.beam.sdk.metrics.Metrics;
+import org.apache.beam.sdk.options.ValueProvider;
+import org.apache.beam.sdk.options.ValueProvider.StaticValueProvider;
+import org.apache.beam.sdk.transforms.Create;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.GroupIntoBatches;
+import org.apache.beam.sdk.transforms.MapElements;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.transforms.Wait;
+import org.apache.beam.sdk.transforms.WithKeys;
+import org.apache.beam.sdk.transforms.windowing.BoundedWindow;
+import org.apache.beam.sdk.values.KV;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollection.IsBounded;
+import org.apache.beam.sdk.values.PCollectionTuple;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.sdk.values.PValue;
+import org.apache.beam.sdk.values.TupleTag;
+import org.apache.beam.sdk.values.TupleTagList;
+import org.apache.beam.sdk.values.TypeDescriptors;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Throwables;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.codehaus.jackson.JsonProcessingException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * {@link FhirIO} provides an API for reading and writing resources to Google Cloud Healthcare Fhir API.
+ * 
+ *
+ * 
    Reading
    
+ *
+ * 
    FHIR resources can be read with {@link FhirIO.Read}, which supports use cases where you have a
+ * ${@link PCollection} of message IDS. This is appropriate for reading the Fhir notifications from
+ * a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases where you have a manually
+ * prepared list of messages that you need to process (e.g. in a text file read with {@link
+ * org.apache.beam.sdk.io.TextIO}*) .
+ *
+ * 
    Fetch Resource contents from Fhir Store based on the {@link PCollection} of message ID strings
+ * {@link FhirIO.Read.Result} where one can call {@link Read.Result#getResources()} to retrieve a
+ * {@link PCollection} containing the successfully fetched {@link String}s and/or {@link
+ * FhirIO.Read.Result#getFailedReads()}* to retrieve a {@link PCollection} of {@link
+ * HealthcareIOError}* containing the resource ID that could not be fetched and the exception as a
+ * {@link HealthcareIOError}, this can be used to write to the dead letter storage system of your
+ * choosing. This error handling is mainly to transparently surface errors where the upstream {@link
+ * PCollection}* contains IDs that are not valid or are not reachable due to permissions issues.
+ *
+ * 
    Writing
    
+ *
+ * 
    Write Resources can be written to FHIR with two different methods: Import or Execute Bundle.
+ *
+ * 
    Execute Bundle This is best for use cases where you are writing to a non-empty FHIR store with
+ * other clients or otherwise need referential integrity (e.g. A Streaming HL7v2 to FHIR ETL
+ * pipeline).
+ *
+ * 
    Import This is best for use cases where you are populating an empty FHIR store with no other
+ * clients. It is faster than the execute bundles method but does not respect referential integrity
+ * and the resources are not written transactionally (e.g. a historicaly backfill on a new FHIR
+ * store) This requires each resource to contain a client provided ID. It is important that when
+ * using import you give the appropriate permissions to the Google Cloud Healthcare Service Agent.
+ *
+ * @see https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/executeBundle>
+ * @see https://cloud.google.com/healthcare/docs/how-tos/permissions-healthcare-api-gcp-products#fhir_store_cloud_storage_permissions>
+ * @see https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores/import>
+ *     A {@link PCollection} of {@link String} can be ingested into an Fhir store using {@link
+ *     FhirIO.Write#fhirStoresImport(String, String, String, FhirIO.Import.ContentStructure)} This
+ *     will return a {@link FhirIO.Write.Result} on which you can call {@link
+ *     FhirIO.Write.Result#getFailedBodies()} to retrieve a {@link PCollection} of {@link
+ *     HealthcareIOError} containing the {@link String} that failed to be ingested and the
+ *     exception.
+ *     
    Example
+ *     
    {@code
+ * Pipeline pipeline = ...
+ *
+ * // Tail the FHIR store by retrieving resources based on Pub/Sub notifications.
+ * FhirIO.Read.Result readResult = p
+ *   .apply("Read FHIR notifications",
+ *     PubsubIO.readStrings().fromSubscription(options.getNotificationSubscription()))
+ *   .apply(FhirIO.readResources());
+ *
+ * // happily retrived messages
+ * PCollection resources = readResult.getResources();
+ * // message IDs that couldn't be retrieved + error context
+ * PCollection> failedReads = readResult.getFailedReads();
+ *
+ * failedReads.apply("Write Message IDs / Stacktrace for Failed Reads to BigQuery",
+ *     BigQueryIO
+ *         .write()
+ *         .to(option.getBQFhirExecuteBundlesDeadLetterTable())
+ *         .withFormatFunction(new HealthcareIOErrorToTableRow()));
+ *
+ * output = resources.apply("Happy path transformations", ...);
+ * FhirIO.Write.Result writeResult =
+ *     output.apply("Execute FHIR Bundles", FhirIO.executeBundles(options.getExistingFhirStore()));
+ *
+ * PCollection> failedBundles = writeResult.getFailedInsertsWithErr();
+ *
+ * failedBundles.apply("Write failed bundles to BigQuery",
+ *     BigQueryIO
+ *         .write()
+ *         .to(option.getBQFhirExecuteBundlesDeadLetterTable())
+ *         .withFormatFunction(new HealthcareIOErrorToTableRow()));
+ *
+ * // Alternatively you could use import for high throughput to a new store.
+ * FhirIO.Write.Result writeResult =
+ *     output.apply("Import FHIR Resources", FhirIO.executeBundles(options.getNewFhirStore()));
+ * }***
+ * 
    
+ */
+public class FhirIO {
+
+  /**
+   * Read resources from a PCollection of resource IDs (e.g. when subscribing the pubsub
+   * notifications)
+   *
+   * @return the read
+   * @see Read
+   */
+  public static Read readResources() {
+    return new Read();
+  }
+
+  /**
+   * Import resources. Intended for use on empty FHIR stores
+   *
+   * @param fhirStore the fhir store
+   * @param tempDir the temp dir
+   * @param deadLetterDir the dead letter dir
+   * @param contentStructure the content structure
+   * @return the import
+   * @see Import
+   */
+  public static Import importResources(
+      String fhirStore,
+      String tempDir,
+      String deadLetterDir,
+      @Nullable FhirIO.Import.ContentStructure contentStructure) {
+    return new Import(fhirStore, tempDir, deadLetterDir, contentStructure);
+  }
+
+  /**
+   * Import resources. Intended for use on empty FHIR stores
+   *
+   * @param fhirStore the fhir store
+   * @param tempDir the temp dir
+   * @param deadLetterDir the dead letter dir
+   * @param contentStructure the content structure
+   * @return the import
+   * @see Import
+   */
+  public static Import importResources(
+      ValueProvider fhirStore,
+      ValueProvider tempDir,
+      ValueProvider deadLetterDir,
+      @Nullable FhirIO.Import.ContentStructure contentStructure) {
+    return new Import(fhirStore, tempDir, deadLetterDir, contentStructure);
+  }
+
+  /** The type Read. */
+  public static class Read extends PTransform, FhirIO.Read.Result> {
+    private static final Logger LOG = LoggerFactory.getLogger(Read.class);
+
+    /** Instantiates a new Read. */
+    public Read() {}
+
+    /** The type Result. */
+    public static class Result implements POutput, PInput {
+      private PCollection resources;
+
+      private PCollection> failedReads;
+      /** The Pct. */
+      PCollectionTuple pct;
+
+      /**
+       * Create FhirIO.Read.Result form PCollectionTuple with OUT and DEAD_LETTER tags.
+       *
+       * @param pct the pct
+       * @return the read result
+       * @throws IllegalArgumentException the illegal argument exception
+       */
+      static FhirIO.Read.Result of(PCollectionTuple pct) throws IllegalArgumentException {
+        if (pct.getAll()
+            .keySet()
+            .containsAll((Collection) TupleTagList.of(OUT).and(DEAD_LETTER))) {
+          return new FhirIO.Read.Result(pct);
+        } else {
+          throw new IllegalArgumentException(
+              "The PCollection tuple must have the FhirIO.Read.OUT "
+                  + "and FhirIO.Read.DEAD_LETTER tuple tags");
+        }
+      }
+
+      private Result(PCollectionTuple pct) {
+        this.pct = pct;
+        this.resources = pct.get(OUT);
+        this.failedReads =
+            pct.get(DEAD_LETTER).setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()));
+      }
+
+      /**
+       * Gets failed reads.
+       *
+       * @return the failed reads
+       */
+      public PCollection> getFailedReads() {
+        return failedReads;
+      }
+
+      /**
+       * Gets resources.
+       *
+       * @return the resources
+       */
+      public PCollection getResources() {
+        return resources;
+      }
+
+      @Override
+      public Pipeline getPipeline() {
+        return this.pct.getPipeline();
+      }
+
+      @Override
+      public Map, PValue> expand() {
+        return ImmutableMap.of(OUT, resources);
+      }
+
+      @Override
+      public void finishSpecifyingOutput(
+          String transformName, PInput input, PTransform transform) {}
+    }
+
+    /** The tag for the main output of Fhir Messages. */
+    public static final TupleTag OUT = new TupleTag() {};
+    /** The tag for the deadletter output of Fhir Messages. */
+    public static final TupleTag> DEAD_LETTER =
+        new TupleTag>() {};
+
+    @Override
+    public FhirIO.Read.Result expand(PCollection input) {
+      return input.apply("Fetch Fhir messages", new FetchResourceJsonString());
+    }
+
+    /**
+     * DoFn to fetch a resource from an Google Cloud Healthcare FHIR store based on resourceID
+     *
+     * 
    This DoFn consumes a {@link PCollection} of notifications {@link String}s from the FHIR
+     * store, and fetches the actual {@link String} object based on the id in the notification and
+     * will output a {@link PCollectionTuple} which contains the output and dead-letter {@link
+     * PCollection}*.
+     *
+     * 
    The {@link PCollectionTuple} output will contain the following {@link PCollection}:
+     *
+     * 
      
+     *   
    • {@link FhirIO.Read#OUT} - Contains all {@link PCollection} records successfully read
+     *       from the Fhir store.
+     *   
    • {@link FhirIO.Read#DEAD_LETTER} - Contains all {@link PCollection} of {@link
+     *       HealthcareIOError}* of message IDs which failed to be fetched from the Fhir store, with
+     *       error message and stacktrace.
+     * 
    
+     */
+    static class FetchResourceJsonString
+        extends PTransform, FhirIO.Read.Result> {
+
+      /** Instantiates a new Fetch Fhir message DoFn. */
+      public FetchResourceJsonString() {}
+
+      @Override
+      public FhirIO.Read.Result expand(PCollection resourceIds) {
+        return new FhirIO.Read.Result(
+            resourceIds.apply(
+                ParDo.of(new ReadResourceFn())
+                    .withOutputTags(FhirIO.Read.OUT, TupleTagList.of(FhirIO.Read.DEAD_LETTER))));
+      }
+
+      /** DoFn for fetching messages from the Fhir store with error handling. */
+      static class ReadResourceFn extends DoFn {
+
+        private Counter failedMessageGets =
+            Metrics.counter(ReadResourceFn.class, "failed-message-reads");
+        private static final Logger LOG = LoggerFactory.getLogger(ReadResourceFn.class);
+        private final Counter successfulStringGets =
+            Metrics.counter(ReadResourceFn.class, "successful-hl7v2-message-gets");
+        private HealthcareApiClient client;
+        private ObjectMapper mapper;
+
+        /** Instantiates a new Hl 7 v 2 message get fn. */
+        ReadResourceFn() {}
+
+        /**
+         * Instantiate healthcare client.
+         *
+         * @throws IOException the io exception
+         */
+        @Setup
+        public void instantiateHealthcareClient() throws IOException {
+          this.client = new HttpHealthcareApiClient();
+          this.mapper = new ObjectMapper();
+        }
+
+        /**
+         * Process element.
+         *
+         * @param context the context
+         */
+        @ProcessElement
+        public void processElement(ProcessContext context) {
+          String resourceId = context.element();
+          try {
+            context.output(fetchResource(this.client, resourceId));
+          } catch (Exception e) {
+            failedMessageGets.inc();
+            LOG.warn(
+                String.format(
+                    "Error fetching Fhir message with ID %s writing to Dead Letter "
+                        + "Queue. Cause: %s Stack Trace: %s",
+                    resourceId, e.getMessage(), Throwables.getStackTraceAsString(e)));
+            context.output(FhirIO.Read.DEAD_LETTER, HealthcareIOError.of(resourceId, e));
+          }
+        }
+
+        private String fetchResource(HealthcareApiClient client, String resourceId)
+            throws IOException, IllegalArgumentException {
+          long startTime = System.currentTimeMillis();
+
+          HttpBody resource = client.readFhirResource(resourceId);
+
+          if (resource == null) {
+            throw new IOException(String.format("GET request for %s returned null", resourceId));
+          }
+          this.successfulStringGets.inc();
+          return mapper.writeValueAsString(resource);
+        }
+      }
+    }
+  }
+
+  /** The type Write. */
+  @AutoValue
+  public abstract static class Write extends PTransform, Write.Result> {
+
+    /** The tag for the failed writes to FHIR store`. */
+    public static final TupleTag> FAILED_BODY =
+        new TupleTag>() {};
+    /** The tag for the files that failed to FHIR store`. */
+    public static final TupleTag> FAILED_FILES =
+        new TupleTag>() {};
+    /** The tag for temp files for import to FHIR store`. */
+    public static final TupleTag TEMP_FILES = new TupleTag() {};
+
+    /** The enum Write method. */
+    public enum WriteMethod {
+      /**
+       * Execute Bundle Method executes a batch of requests as a single transaction @see .
+       */
+      EXECUTE_BUNDLE,
+      /**
+       * Import Method bulk imports resources from GCS. This is ideal for initial loads to empty
+       * FHIR stores. .
+       */
+      IMPORT
+    }
+
+    /** The type Result. */
+    public static class Result implements POutput {
+      private final Pipeline pipeline;
+      private final PCollection> failedBodies;
+      private final PCollection> failedFiles;
+
+      /**
+       * Creates a {@link FhirIO.Write.Result} in the given {@link Pipeline}. @param pipeline the
+       * pipeline
+       *
+       * @param failedBodies the failed inserts
+       * @return the result
+       */
+      static Result in(Pipeline pipeline, PCollection> failedBodies) {
+        return new Result(pipeline, failedBodies, null);
+      }
+
+      static Result in(
+          Pipeline pipeline,
+          PCollection> failedBodies,
+          PCollection> failedFiles) {
+        return new Result(pipeline, failedBodies, failedFiles);
+      }
+
+      /**
+       * Gets failed bodies with err.
+       *
+       * @return the failed inserts with err
+       */
+      public PCollection> getFailedBodies() {
+        return this.failedBodies;
+      }
+
+      /**
+       * Gets failed file imports with err.
+       *
+       * @return the failed GCS uri with err
+       */
+      public PCollection> getFailedFiles() {
+        return this.failedFiles;
+      }
+
+      @Override
+      public Pipeline getPipeline() {
+        return this.pipeline;
+      }
+
+      @Override
+      public Map, PValue> expand() {
+        return ImmutableMap.of(Write.FAILED_BODY, failedBodies, Write.FAILED_FILES, failedFiles);
+      }
+
+      @Override
+      public void finishSpecifyingOutput(
+          String transformName, PInput input, PTransform transform) {}
+
+      private Result(
+          Pipeline pipeline,
+          PCollection> failedBodies,
+          @Nullable PCollection> failedFiles) {
+        this.pipeline = pipeline;
+        this.failedBodies = failedBodies;
+        if (failedFiles == null) {
+          failedFiles =
+              (PCollection>)
+                  pipeline.apply(Create.empty(HealthcareIOErrorCoder.of(StringUtf8Coder.of())));
+        }
+        this.failedFiles = failedFiles;
+      }
+    }
+
+    /**
+     * Gets Fhir store.
+     *
+     * @return the Fhir store
+     */
+    abstract ValueProvider getFhirStore();
+
+    /**
+     * Gets write method.
+     *
+     * @return the write method
+     */
+    abstract WriteMethod getWriteMethod();
+
+    /**
+     * Gets content structure.
+     *
+     * @return the content structure
+     */
+    abstract Optional getContentStructure();
+
+    /**
+     * Gets import gcs temp path.
+     *
+     * @return the import gcs temp path
+     */
+    abstract Optional> getImportGcsTempPath();
+
+    /**
+     * Gets import gcs dead letter path.
+     *
+     * @return the import gcs dead letter path
+     */
+    abstract Optional> getImportGcsDeadLetterPath();
+
+    /** The type Builder. */
+    @AutoValue.Builder
+    abstract static class Builder {
+
+      /**
+       * Sets Fhir store.
+       *
+       * @param fhirStore the Fhir store
+       * @return the Fhir store
+       */
+      abstract Builder setFhirStore(ValueProvider fhirStore);
+
+      /**
+       * Sets write method.
+       *
+       * @param writeMethod the write method
+       * @return the write method
+       */
+      abstract Builder setWriteMethod(WriteMethod writeMethod);
+
+      /**
+       * Sets content structure.
+       *
+       * @param contentStructure the content structure
+       * @return the content structure
+       */
+      abstract Builder setContentStructure(FhirIO.Import.ContentStructure contentStructure);
+
+      /**
+       * Sets import gcs temp path.
+       *
+       * @param gcsTempPath the gcs temp path
+       * @return the import gcs temp path
+       */
+      abstract Builder setImportGcsTempPath(ValueProvider gcsTempPath);
+
+      /**
+       * Sets import gcs dead letter path.
+       *
+       * @param gcsDeadLetterPath the gcs dead letter path
+       * @return the import gcs dead letter path
+       */
+      abstract Builder setImportGcsDeadLetterPath(ValueProvider gcsDeadLetterPath);
+
+      /**
+       * Build write.
+       *
+       * @return the write
+       */
+      abstract Write build();
+    }
+
+    private static Write.Builder write(String fhirStore) {
+      return new AutoValue_FhirIO_Write.Builder().setFhirStore(StaticValueProvider.of(fhirStore));
+    }
+
+    /**
+     * Create Method creates a single FHIR resource. @see 
+     *
+     * @param fhirStore the hl 7 v 2 store
+     * @param gcsTempPath the gcs temp path
+     * @param gcsDeadLetterPath the gcs dead letter path
+     * @param contentStructure the content structure
+     * @return the write
+     */
+    public static Write fhirStoresImport(
+        String fhirStore,
+        String gcsTempPath,
+        String gcsDeadLetterPath,
+        @Nullable FhirIO.Import.ContentStructure contentStructure) {
+      return new AutoValue_FhirIO_Write.Builder()
+          .setFhirStore(StaticValueProvider.of(fhirStore))
+          .setWriteMethod(Write.WriteMethod.IMPORT)
+          .setContentStructure(contentStructure)
+          .setImportGcsTempPath(StaticValueProvider.of(gcsTempPath))
+          .setImportGcsDeadLetterPath(StaticValueProvider.of(gcsDeadLetterPath))
+          .build();
+    }
+
+    public static Write fhirStoresImport(
+        String fhirStore,
+        String gcsDeadLetterPath,
+        @Nullable FhirIO.Import.ContentStructure contentStructure) {
+      return new AutoValue_FhirIO_Write.Builder()
+          .setFhirStore(StaticValueProvider.of(fhirStore))
+          .setWriteMethod(Write.WriteMethod.IMPORT)
+          .setContentStructure(contentStructure)
+          .setImportGcsDeadLetterPath(StaticValueProvider.of(gcsDeadLetterPath))
+          .build();
+    }
+
+    public static Write fhirStoresImport(
+        ValueProvider fhirStore,
+        ValueProvider gcsTempPath,
+        ValueProvider gcsDeadLetterPath,
+        @Nullable FhirIO.Import.ContentStructure contentStructure) {
+      return new AutoValue_FhirIO_Write.Builder()
+          .setFhirStore(fhirStore)
+          .setWriteMethod(Write.WriteMethod.IMPORT)
+          .setContentStructure(contentStructure)
+          .setImportGcsTempPath(gcsTempPath)
+          .setImportGcsDeadLetterPath(gcsDeadLetterPath)
+          .build();
+    }
+
+    /**
+     * Execute Bundle Method executes a batch of requests as a single transaction @see .
+     *
+     * @param fhirStore the hl 7 v 2 store
+     * @return the write
+     */
+    public static Write executeBundles(String fhirStore) {
+      return new AutoValue_FhirIO_Write.Builder()
+          .setFhirStore(StaticValueProvider.of(fhirStore))
+          .setWriteMethod(WriteMethod.EXECUTE_BUNDLE)
+          .build();
+    }
+
+    /**
+     * Execute bundles write.
+     *
+     * @param fhirStore the fhir store
+     * @return the write
+     */
+    public static Write executeBundles(ValueProvider fhirStore) {
+      return new AutoValue_FhirIO_Write.Builder()
+          .setFhirStore(fhirStore)
+          .setWriteMethod(WriteMethod.EXECUTE_BUNDLE)
+          .build();
+    }
+
+    private static final Logger LOG = LoggerFactory.getLogger(Write.class);
+
+    @Override
+    public Result expand(PCollection input) {
+      PCollection> failedBundles;
+      PCollection> failedImports;
+      switch (this.getWriteMethod()) {
+        case IMPORT:
+          LOG.warn(
+              "Make sure the Cloud Healthcare Service Agent has permissions when using import:"
+                  + " https://cloud.google.com/healthcare/docs/how-tos/permissions-healthcare-api-gcp-products#fhir_store_cloud_storage_permissions");
+          ValueProvider deadPath =
+              getImportGcsDeadLetterPath().orElseThrow(IllegalArgumentException::new);
+          FhirIO.Import.ContentStructure contentStructure =
+              getContentStructure().orElseThrow(IllegalArgumentException::new);
+          ValueProvider tempPath =
+              getImportGcsTempPath()
+                  .orElse(
+                      StaticValueProvider.of(input.getPipeline().getOptions().getTempLocation()));
+
+          return input.apply(new Import(getFhirStore(), tempPath, deadPath, contentStructure));
+        case EXECUTE_BUNDLE:
+        default:
+          failedBundles =
+              input
+                  .apply(
+                      "Execute FHIR Bundles",
+                      ParDo.of(new ExecuteBundles.ExecuteBundlesFn(this.getFhirStore())))
+                  .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()));
+      }
+      return Result.in(input.getPipeline(), failedBundles);
+    }
+  }
+
+  /**
+   * Writes each bundle of elements to a new-line delimited JSON file on GCS and issues a
+   * fhirStores.import Request for that file. This is intended for batch use only to facilitate
+   * large backfills to empty FHIR stores and should not be used with unbounded PCollections. If
+   * your use case is streaming checkout using {@link ExecuteBundles} to more safely execute bundles
+   * as transactions which is safer practice for a use on a "live" FHIR store.
+   */
+  public static class Import extends Write {
+
+    private final ValueProvider fhirStore;
+    private final ValueProvider deadLetterGcsPath;
+    private final ContentStructure contentStructure;
+    private static final int DEFAULT_FILES_PER_BATCH = 10000;
+    private static final Logger LOG = LoggerFactory.getLogger(Import.class);
+    private ValueProvider tempGcsPath;
+
+    /*
+     * Instantiates a new Import.
+     *
+     * @param fhirStore the fhir store
+     * @param tempGcsPath the temp gcs path
+     * @param deadLetterGcsPath the dead letter gcs path
+     * @param contentStructure the content structure
+     */
+    Import(
+        ValueProvider fhirStore,
+        ValueProvider tempGcsPath,
+        ValueProvider deadLetterGcsPath,
+        @Nullable ContentStructure contentStructure) {
+      this.fhirStore = fhirStore;
+      this.tempGcsPath = tempGcsPath;
+      this.deadLetterGcsPath = deadLetterGcsPath;
+      if (contentStructure == null) {
+        this.contentStructure = ContentStructure.CONTENT_STRUCTURE_UNSPECIFIED;
+      } else {
+        this.contentStructure = contentStructure;
+      }
+    }
+
+    Import(
+        ValueProvider fhirStore,
+        ValueProvider deadLetterGcsPath,
+        @Nullable ContentStructure contentStructure) {
+      this.fhirStore = fhirStore;
+      this.deadLetterGcsPath = deadLetterGcsPath;
+      if (contentStructure == null) {
+        this.contentStructure = ContentStructure.CONTENT_STRUCTURE_UNSPECIFIED;
+      } else {
+        this.contentStructure = contentStructure;
+      }
+    }
+    /**
+     * Instantiates a new Import.
+     *
+     * @param fhirStore the fhir store
+     * @param tempGcsPath the temp gcs path
+     * @param deadLetterGcsPath the dead letter gcs path
+     * @param contentStructure the content structure
+     */
+    Import(
+        String fhirStore,
+        String tempGcsPath,
+        String deadLetterGcsPath,
+        @Nullable ContentStructure contentStructure) {
+      this.fhirStore = StaticValueProvider.of(fhirStore);
+      this.tempGcsPath = StaticValueProvider.of(tempGcsPath);
+      this.deadLetterGcsPath = StaticValueProvider.of(deadLetterGcsPath);
+      if (contentStructure == null) {
+        this.contentStructure = ContentStructure.CONTENT_STRUCTURE_UNSPECIFIED;
+      } else {
+        this.contentStructure = contentStructure;
+      }
+    }
+
+    @Override
+    ValueProvider getFhirStore() {
+      return fhirStore;
+    }
+
+    @Override
+    WriteMethod getWriteMethod() {
+      return WriteMethod.IMPORT;
+    }
+
+    @Override
+    Optional getContentStructure() {
+      return Optional.of(contentStructure);
+    }
+
+    @Override
+    Optional> getImportGcsTempPath() {
+      return Optional.of(tempGcsPath);
+    }
+
+    @Override
+    Optional> getImportGcsDeadLetterPath() {
+      return Optional.of(deadLetterGcsPath);
+    }
+
+    @Override
+    public Write.Result expand(PCollection input) {
+      checkState(
+          input.isBounded() == IsBounded.BOUNDED,
+          "FhirIO.Import should only be used on unbounded PCollections as it is"
+              + "intended for batch use only.");
+
+      // fall back on pipeline's temp location.
+      ValueProvider tempPath =
+          getImportGcsTempPath()
+              .orElse(StaticValueProvider.of(input.getPipeline().getOptions().getTempLocation()));
+
+      // Write bundles of String to GCS
+      PCollectionTuple writeTmpFileResults =
+          input.apply(
+              "Write nd json to GCS",
+              ParDo.of(new WriteBundlesToFilesFn(fhirStore, tempPath, deadLetterGcsPath))
+                  .withOutputTags(Write.TEMP_FILES, TupleTagList.of(Write.FAILED_BODY)));
+
+      PCollection> failedBodies =
+          writeTmpFileResults
+              .get(Write.FAILED_BODY)
+              .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()));
+      int numShards = 100;
+      PCollection> failedFiles =
+          writeTmpFileResults
+              .get(Write.TEMP_FILES)
+              .apply(
+                  "Shard files", // to paralelize group into batches
+                  WithKeys.of(elm -> ThreadLocalRandom.current().nextInt(0, numShards)))
+              .setCoder(KvCoder.of(TextualIntegerCoder.of(), ResourceIdCoder.of()))
+              .apply("Assemble File Batches", GroupIntoBatches.ofSize(DEFAULT_FILES_PER_BATCH))
+              .setCoder(
+                  KvCoder.of(TextualIntegerCoder.of(), IterableCoder.of(ResourceIdCoder.of())))
+              .apply(
+                  "Import Batches",
+                  ParDo.of(new ImportFn(fhirStore, tempPath, deadLetterGcsPath, contentStructure)))
+              .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()));
+
+      input
+          .getPipeline()
+          .apply("Instantiate Temp Path", Create.ofProvider(tempPath, StringUtf8Coder.of()))
+          .apply(
+              "Resolve SubDirs",
+              MapElements.into(TypeDescriptors.strings())
+                  .via((String path) -> path.endsWith("/") ? path + "*" : path + "/*"))
+          .apply("Wait On File Writing", Wait.on(failedBodies))
+          .apply("Wait On FHIR Importing", Wait.on(failedFiles))
+          .apply(
+              "Match tempGcsPath",
+              FileIO.matchAll().withEmptyMatchTreatment(EmptyMatchTreatment.ALLOW))
+          .apply(
+              "Delete tempGcsPath",
+              ParDo.of(
+                  new DoFn() {
+                    @ProcessElement
+                    public void delete(@Element Metadata path, ProcessContext context) {
+                      String tempPath =
+                          getImportGcsTempPath()
+                              .orElse(
+                                  StaticValueProvider.of(
+                                      context.getPipelineOptions().getTempLocation()))
+                              .get();
+                      // Wait til window closes for failedBodies and failedFiles to ensure we are
+                      // done processing
+                      // anything under tempGcsPath because it has been successfully imported to
+                      // FHIR store or
+                      // copies have been moved to the dead letter path.
+                      // Clean up all of tempGcsPath. This will handle removing phantom temporary
+                      // objects from
+                      // failed / rescheduled ImportFn::importBatch.
+                      try {
+                        FileSystems.delete(
+                            Collections.singleton(path.resourceId()),
+                            StandardMoveOptions.IGNORE_MISSING_FILES);
+                      } catch (IOException e) {
+                        LOG.error("error cleaning up tempGcsDir: %s", e);
+                      }
+                    }
+                  }))
+          .setCoder(VoidCoder.of());
+
+      return Write.Result.in(input.getPipeline(), failedBodies, failedFiles);
+    }
+
+    /** The Write bundles to new line delimited json files. */
+    static class WriteBundlesToFilesFn extends DoFn {
+
+      private final ValueProvider fhirStore;
+      private final ValueProvider tempGcsPath;
+      private final ValueProvider deadLetterGcsPath;
+      private ObjectMapper mapper;
+      private ResourceId resourceId;
+      private WritableByteChannel ndJsonChannel;
+      private BoundedWindow window;
+
+      private transient HealthcareApiClient client;
+      private static final Logger LOG = LoggerFactory.getLogger(WriteBundlesToFilesFn.class);
+
+      WriteBundlesToFilesFn(
+          ValueProvider fhirStore,
+          ValueProvider tempGcsPath,
+          ValueProvider deadLetterGcsPath) {
+        this.fhirStore = fhirStore;
+        this.tempGcsPath = tempGcsPath;
+        this.deadLetterGcsPath = deadLetterGcsPath;
+      }
+
+      /**
+       * Instantiates a new Import fn.
+       *
+       * @param fhirStore the fhir store
+       * @param tempGcsPath the temp gcs path
+       * @param deadLetterGcsPath the dead letter gcs path
+       */
+      WriteBundlesToFilesFn(String fhirStore, String tempGcsPath, String deadLetterGcsPath) {
+        this.fhirStore = StaticValueProvider.of(fhirStore);
+        this.tempGcsPath = StaticValueProvider.of(tempGcsPath);
+        this.deadLetterGcsPath = StaticValueProvider.of(deadLetterGcsPath);
+      }
+
+      /**
+       * Init client.
+       *
+       * @throws IOException the io exception
+       */
+      @Setup
+      public void initClient() throws IOException {
+        this.client = new HttpHealthcareApiClient();
+      }
+
+      /**
+       * Init batch.
+       *
+       * @throws IOException the io exception
+       */
+      @StartBundle
+      public void initFile() throws IOException {
+        // Write each bundle to newline delimited JSON file.
+        String filename = String.format("fhirImportBatch-%s.ndjson", UUID.randomUUID().toString());
+        ResourceId tempDir = FileSystems.matchNewResource(this.tempGcsPath.get(), true);
+        this.resourceId = tempDir.resolve(filename, StandardResolveOptions.RESOLVE_FILE);
+        this.ndJsonChannel = FileSystems.create(resourceId, "application/ld+json");
+        if (mapper == null) {
+          this.mapper = new ObjectMapper();
+        }
+      }
+
+      /**
+       * Add to batch.
+       *
+       * @param context the context
+       * @throws IOException the io exception
+       */
+      @ProcessElement
+      public void addToFile(ProcessContext context, BoundedWindow window) throws IOException {
+        this.window = window;
+        String httpBody = context.element();
+        try {
+          // This will error if not valid JSON an convert Pretty JSON to raw JSON.
+          Object data = this.mapper.readValue(httpBody, Object.class);
+          String ndJson = this.mapper.writeValueAsString(data) + "\n";
+          this.ndJsonChannel.write(ByteBuffer.wrap(ndJson.getBytes(StandardCharsets.UTF_8)));
+        } catch (JsonProcessingException e) {
+          String resource =
+              String.format(
+                  "Failed to parse payload: %s as json at: %s : %s."
+                      + "Dropping message from batch import.",
+                  httpBody.toString(), e.getLocation().getCharOffset(), e.getMessage());
+          LOG.warn(resource);
+          context.output(
+              Write.FAILED_BODY, HealthcareIOError.of(httpBody, new IOException(resource)));
+        }
+      }
+
+      /**
+       * Close file.
+       *
+       * @param context the context
+       * @throws IOException the io exception
+       */
+      @FinishBundle
+      public void closeFile(FinishBundleContext context) throws IOException {
+        // Write the file with all elements in this bundle to GCS.
+        ndJsonChannel.close();
+        context.output(resourceId, window.maxTimestamp(), window);
+      }
+    }
+
+    /** Import batches of new line delimited json files to FHIR Store. */
+    static class ImportFn
+        extends DoFn>, HealthcareIOError> {
+
+      private static final Logger LOG = LoggerFactory.getLogger(ImportFn.class);
+      private final ValueProvider tempGcsPath;
+      private final ValueProvider deadLetterGcsPath;
+      private ResourceId tempDir;
+      private final ContentStructure contentStructure;
+      private HealthcareApiClient client;
+      private final ValueProvider fhirStore;
+
+      ImportFn(
+          ValueProvider fhirStore,
+          ValueProvider tempGcsPath,
+          ValueProvider deadLetterGcsPath,
+          @Nullable ContentStructure contentStructure) {
+        this.fhirStore = fhirStore;
+        this.tempGcsPath = tempGcsPath;
+        this.deadLetterGcsPath = deadLetterGcsPath;
+        if (contentStructure == null) {
+          this.contentStructure = ContentStructure.CONTENT_STRUCTURE_UNSPECIFIED;
+        } else {
+          this.contentStructure = contentStructure;
+        }
+      }
+
+      @Setup
+      public void init() throws IOException {
+        tempDir =
+            FileSystems.matchNewResource(tempGcsPath.get(), true)
+                .resolve(
+                    String.format("tmp-%s", UUID.randomUUID().toString()),
+                    StandardResolveOptions.RESOLVE_DIRECTORY);
+        client = new HttpHealthcareApiClient();
+      }
+
+      /**
+       * Move files to a temporary subdir (to provide common prefix) to execute import with single
+       * GCS URI.
+       */
+      @ProcessElement
+      public void importBatch(
+          @Element KV> element,
+          OutputReceiver> output)
+          throws IOException {
+        Iterable batch = element.getValue();
+        List tempDestinations = new ArrayList<>();
+        List deadLetterDestinations = new ArrayList<>();
+        assert batch != null;
+        for (ResourceId file : batch) {
+          tempDestinations.add(
+              tempDir.resolve(file.getFilename(), StandardResolveOptions.RESOLVE_FILE));
+          deadLetterDestinations.add(
+              FileSystems.matchNewResource(deadLetterGcsPath.get(), true)
+                  .resolve(file.getFilename(), StandardResolveOptions.RESOLVE_FILE));
+        }
+        FileSystems.copy(ImmutableList.copyOf(batch), tempDestinations);
+        ResourceId importUri = tempDir.resolve("*", StandardResolveOptions.RESOLVE_FILE);
+        try {
+          // Blocking fhirStores.import request.
+          assert contentStructure != null;
+          Operation operation =
+              client.importFhirResource(
+                  fhirStore.get(), importUri.toString(), contentStructure.name());
+          client.pollOperation(operation, 500L);
+          // Clean up temp files on GCS as they we successfully imported to FHIR store and no longer
+          // needed.
+          FileSystems.delete(tempDestinations);
+        } catch (IOException | InterruptedException e) {
+          ResourceId deadLetterResourceId =
+              FileSystems.matchNewResource(deadLetterGcsPath.get(), true);
+          LOG.warn(
+              String.format(
+                  "Failed to import %s with error: %s. Moving to deadletter path %s",
+                  importUri.toString(), e.getMessage(), deadLetterResourceId.toString()));
+          FileSystems.rename(tempDestinations, deadLetterDestinations);
+          output.output(HealthcareIOError.of(importUri.toString(), e));
+        } finally {
+          // If we've reached this point files have either been successfully import to FHIR store
+          // or moved to Dead Letter Queue.
+          // Clean up original files for this batch on GCS.
+          FileSystems.delete(ImmutableList.copyOf(batch));
+        }
+      }
+    }
+
+    /** The enum Content structure. */
+    public enum ContentStructure {
+      /** If the content structure is not specified, the default value BUNDLE will be used. */
+      CONTENT_STRUCTURE_UNSPECIFIED,
+      /**
+       * The source file contains one or more lines of newline-delimited JSON (ndjson). Each line is
+       * a bundle, which contains one or more resources. Set the bundle type to history to import
+       * resource versions.
+       */
+      BUNDLE,
+      /**
+       * The source file contains one or more lines of newline-delimited JSON (ndjson). Each line is
+       * a single resource.
+       */
+      RESOURCE,
+      /** The entire file is one JSON bundle. The JSON can span multiple lines. */
+      BUNDLE_PRETTY,
+      /** The entire file is one JSON resource. The JSON can span multiple lines. */
+      RESOURCE_PRETTY
+    }
+  }
+
+  /** The type Execute bundles. */
+  public static class ExecuteBundles extends PTransform, Write.Result> {
+    private final ValueProvider fhirStore;
+
+    /**
+     * Instantiates a new Execute bundles.
+     *
+     * @param fhirStore the fhir store
+     */
+    ExecuteBundles(ValueProvider fhirStore) {
+      this.fhirStore = fhirStore;
+    }
+
+    /**
+     * Instantiates a new Execute bundles.
+     *
+     * @param fhirStore the fhir store
+     */
+    ExecuteBundles(String fhirStore) {
+      this.fhirStore = StaticValueProvider.of(fhirStore);
+    }
+
+    @Override
+    public FhirIO.Write.Result expand(PCollection input) {
+      return Write.Result.in(
+          input.getPipeline(),
+          input
+              .apply(ParDo.of(new ExecuteBundlesFn(fhirStore)))
+              .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of())));
+    }
+
+    /** The type Write Fhir fn. */
+    static class ExecuteBundlesFn extends DoFn> {
+
+      private Counter failedBundles = Metrics.counter(ExecuteBundlesFn.class, "failed-bundles");
+      private transient HealthcareApiClient client;
+      private final ObjectMapper mapper = new ObjectMapper();
+      /** The Fhir store. */
+      private final ValueProvider fhirStore;
+
+      /**
+       * Instantiates a new Write Fhir fn.
+       *
+       * @param fhirStore the Fhir store
+       */
+      ExecuteBundlesFn(ValueProvider fhirStore) {
+        this.fhirStore = fhirStore;
+      }
+
+      /**
+       * Initialize healthcare client.
+       *
+       * @throws IOException the io exception
+       */
+      @Setup
+      public void initClient() throws IOException {
+        this.client = new HttpHealthcareApiClient();
+      }
+
+      /**
+       * Execute Bundles.
+       *
+       * @param context the context
+       */
+      @ProcessElement
+      public void executeBundles(ProcessContext context) {
+        String body = context.element();
+        try {
+          // Validate that data was set to valid JSON.
+          mapper.readTree(body);
+          client.executeFhirBundle(fhirStore.get(), body);
+        } catch (IOException | HealthcareHttpException e) {
+          failedBundles.inc();
+          context.output(HealthcareIOError.of(body, e));
+        }
+      }
+    }
+  }
+}
diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IO.java
index 05f002ac2fc0..8167036bda56 100644
--- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IO.java
+++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IO.java
@@ -27,6 +27,7 @@
 import java.util.Map;
 import javax.annotation.Nullable;
 import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.CoderRegistry;
 import org.apache.beam.sdk.coders.ListCoder;
 import org.apache.beam.sdk.coders.StringUtf8Coder;
 import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO;
@@ -323,6 +324,8 @@ public void finishSpecifyingOutput(
 
     @Override
     public Result expand(PCollection input) {
+      CoderRegistry coderRegistry = input.getPipeline().getCoderRegistry();
+      coderRegistry.registerCoderForClass(HL7v2Message.class, HL7v2MessageCoder.of());
       return input.apply("Fetch HL7v2 messages", new FetchHL7v2Message());
     }
 
@@ -352,6 +355,8 @@ public FetchHL7v2Message() {}
 
       @Override
       public Result expand(PCollection msgIds) {
+        CoderRegistry coderRegistry = msgIds.getPipeline().getCoderRegistry();
+        coderRegistry.registerCoderForClass(HL7v2Message.class, HL7v2MessageCoder.of());
         return new Result(
             msgIds.apply(
                 ParDo.of(new FetchHL7v2Message.HL7v2MessageGetFn())
@@ -470,6 +475,8 @@ public ListHL7v2Messages withInitialSplitDuration(Duration initialSplitDuration)
 
     @Override
     public PCollection expand(PBegin input) {
+      CoderRegistry coderRegistry = input.getPipeline().getCoderRegistry();
+      coderRegistry.registerCoderForClass(HL7v2Message.class, HL7v2MessageCoder.of());
       return input
           .apply(Create.ofProvider(this.hl7v2Stores, ListCoder.of(StringUtf8Coder.of())))
           .apply(FlatMapElements.into(TypeDescriptors.strings()).via((x) -> x))
@@ -625,6 +632,8 @@ public abstract static class Write extends PTransform,
 
     @Override
     public Result expand(PCollection messages) {
+      CoderRegistry coderRegistry = messages.getPipeline().getCoderRegistry();
+      coderRegistry.registerCoderForClass(HL7v2Message.class, HL7v2MessageCoder.of());
       return messages.apply(new WriteHL7v2(this.getHL7v2Store(), this.getWriteMethod()));
     }
 
@@ -728,7 +737,7 @@ public Write.Result expand(PCollection input) {
       PCollection> failedInserts =
           input
               .apply(ParDo.of(new WriteHL7v2Fn(hl7v2Store, writeMethod)))
-              .setCoder(new HealthcareIOErrorCoder<>(new HL7v2MessageCoder()));
+              .setCoder(HealthcareIOErrorCoder.of(HL7v2MessageCoder.of()));
       return Write.Result.in(input.getPipeline(), failedInserts);
     }
 
diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2MessageCoder.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2MessageCoder.java
index a2402b8d5433..d1af961531ed 100644
--- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2MessageCoder.java
+++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2MessageCoder.java
@@ -29,11 +29,15 @@
 import org.apache.beam.sdk.coders.StringUtf8Coder;
 
 public class HL7v2MessageCoder extends CustomCoder {
+  HL7v2MessageCoder() {}
+
   public static HL7v2MessageCoder of() {
     return new HL7v2MessageCoder();
   }
 
-  public HL7v2MessageCoder() {}
+  public static HL7v2MessageCoder of(Class clazz) {
+    return new HL7v2MessageCoder();
+  }
 
   private static final NullableCoder STRING_CODER = NullableCoder.of(StringUtf8Coder.of());
   private static final NullableCoder> MAP_CODER =
diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java
index afb57cd44d95..f504235a78b5 100644
--- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java
+++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java
@@ -18,15 +18,17 @@
 package org.apache.beam.sdk.io.gcp.healthcare;
 
 import com.google.api.services.healthcare.v1beta1.model.Empty;
+import com.google.api.services.healthcare.v1beta1.model.FhirStore;
 import com.google.api.services.healthcare.v1beta1.model.Hl7V2Store;
 import com.google.api.services.healthcare.v1beta1.model.HttpBody;
 import com.google.api.services.healthcare.v1beta1.model.IngestMessageResponse;
 import com.google.api.services.healthcare.v1beta1.model.ListMessagesResponse;
 import com.google.api.services.healthcare.v1beta1.model.Message;
-import com.google.api.services.healthcare.v1beta1.model.SearchResourcesRequest;
+import com.google.api.services.healthcare.v1beta1.model.Operation;
 import java.io.IOException;
 import java.text.ParseException;
 import javax.annotation.Nullable;
+import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException;
 import org.joda.time.Instant;
 
 /** Defines a client that talks to the Cloud Healthcare API. */
@@ -130,26 +132,11 @@ ListMessagesResponse makeHL7v2ListRequest(
    */
   Message createHL7v2Message(String hl7v2Store, Message msg) throws IOException;
 
-  /**
-   * Create fhir resource http body.
-   *
-   * @param fhirStore the fhir store
-   * @param type the type
-   * @param body the body
-   * @return the http body
-   * @throws IOException the io exception
-   */
-  HttpBody createFhirResource(String fhirStore, String type, HttpBody body) throws IOException;
+  Operation importFhirResource(
+      String fhirStore, String gcsSourcePath, @Nullable String contentStructure) throws IOException;
 
-  /**
-   * Fhir search http body.
-   *
-   * @param fhirStore the fhir store
-   * @param query the query
-   * @return the http body
-   * @throws IOException the io exception
-   */
-  HttpBody fhirSearch(String fhirStore, SearchResourcesRequest query) throws IOException;
+  Operation pollOperation(Operation operation, Long sleepMs)
+      throws InterruptedException, IOException;
 
   /**
    * Execute fhir bundle http body.
@@ -159,27 +146,17 @@ ListMessagesResponse makeHL7v2ListRequest(
    * @return the http body
    * @throws IOException the io exception
    */
-  HttpBody executeFhirBundle(String fhirStore, HttpBody bundle) throws IOException;
-
-  /**
-   * List fhir resource for patient http body.
-   *
-   * @param fhirStore the fhir store
-   * @param patient the patient
-   * @return the http body
-   * @throws IOException the io exception
-   */
-  HttpBody listFHIRResourceForPatient(String fhirStore, String patient) throws IOException;
+  HttpBody executeFhirBundle(String fhirStore, String bundle)
+      throws IOException, HealthcareHttpException;
 
   /**
    * Read fhir resource http body.
    *
-   * @param fhirStore the fhir store
-   * @param resource the resource
+   * @param resourceId the resource
    * @return the http body
    * @throws IOException the io exception
    */
-  HttpBody readFHIRResource(String fhirStore, String resource) throws IOException;
+  HttpBody readFhirResource(String resourceId) throws IOException;
 
   /**
    * Create hl 7 v 2 store hl 7 v 2 store.
@@ -191,6 +168,11 @@ ListMessagesResponse makeHL7v2ListRequest(
    */
   Hl7V2Store createHL7v2Store(String dataset, String name) throws IOException;
 
+  FhirStore createFhirStore(String dataset, String name, String version, String pubsubTopic)
+      throws IOException;
+
+  FhirStore createFhirStore(String dataset, String name, String version) throws IOException;
+
   /**
    * Delete hl 7 v 2 store empty.
    *
@@ -199,4 +181,6 @@ ListMessagesResponse makeHL7v2ListRequest(
    * @throws IOException the io exception
    */
   Empty deleteHL7v2Store(String store) throws IOException;
+
+  Empty deleteFhirStore(String store) throws IOException;
 }
diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareIOError.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareIOError.java
index 97f94f8ccf5b..a97cde9ce1b1 100644
--- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareIOError.java
+++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareIOError.java
@@ -19,10 +19,13 @@
 
 import com.google.api.client.googleapis.json.GoogleJsonResponseException;
 import javax.annotation.Nullable;
+import org.apache.beam.sdk.coders.DefaultCoder;
+import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Throwables;
 import org.joda.time.Instant;
 
 /** Class for capturing errors on IO operations on Google Cloud Healthcare APIs resources. */
+@DefaultCoder(HealthcareIOErrorCoder.class)
 public class HealthcareIOError {
   private T dataResource;
   private String errorMessage;
@@ -39,7 +42,9 @@ public class HealthcareIOError {
     this.dataResource = dataResource;
     this.errorMessage = errorMessage;
     this.stackTrace = stackTrace;
-    this.statusCode = statusCode;
+    if (statusCode != null) {
+      this.statusCode = statusCode;
+    }
     if (observedTime != null) {
       this.observedTime = observedTime;
     } else {
@@ -74,6 +79,8 @@ static  HealthcareIOError of(T dataResource, Exception error) {
 
     if (error instanceof com.google.api.client.googleapis.json.GoogleJsonResponseException) {
       statusCode = ((GoogleJsonResponseException) error).getStatusCode();
+    } else if (error instanceof HealthcareHttpException) {
+      statusCode = ((HealthcareHttpException) error).getStatusCode();
     }
     return new HealthcareIOError<>(dataResource, msg, stackTrace, null, statusCode);
   }
diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java
index 46cb95b98790..653e9a855d68 100644
--- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java
+++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java
@@ -28,17 +28,23 @@
 import com.google.api.services.healthcare.v1beta1.CloudHealthcareScopes;
 import com.google.api.services.healthcare.v1beta1.model.CreateMessageRequest;
 import com.google.api.services.healthcare.v1beta1.model.Empty;
+import com.google.api.services.healthcare.v1beta1.model.FhirStore;
+import com.google.api.services.healthcare.v1beta1.model.GoogleCloudHealthcareV1beta1FhirRestGcsSource;
 import com.google.api.services.healthcare.v1beta1.model.Hl7V2Store;
 import com.google.api.services.healthcare.v1beta1.model.HttpBody;
+import com.google.api.services.healthcare.v1beta1.model.ImportResourcesRequest;
 import com.google.api.services.healthcare.v1beta1.model.IngestMessageRequest;
 import com.google.api.services.healthcare.v1beta1.model.IngestMessageResponse;
 import com.google.api.services.healthcare.v1beta1.model.ListMessagesResponse;
 import com.google.api.services.healthcare.v1beta1.model.Message;
-import com.google.api.services.healthcare.v1beta1.model.SearchResourcesRequest;
+import com.google.api.services.healthcare.v1beta1.model.NotificationConfig;
+import com.google.api.services.healthcare.v1beta1.model.Operation;
+import com.google.api.services.storage.StorageScopes;
 import com.google.auth.oauth2.GoogleCredentials;
 import java.io.IOException;
 import java.io.Serializable;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.Iterator;
@@ -48,7 +54,19 @@
 import java.util.stream.Collectors;
 import javax.annotation.Nullable;
 import org.apache.beam.sdk.extensions.gcp.util.RetryHttpRequestInitializer;
+import org.apache.beam.sdk.util.ReleaseInfo;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Strings;
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpUriRequest;
+import org.apache.http.client.methods.RequestBuilder;
+import org.apache.http.client.utils.URIBuilder;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.client.DefaultHttpRequestRetryHandler;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.http.util.EntityUtils;
 import org.joda.time.Instant;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -58,10 +76,19 @@
  * mainly to encapsulate the unserializable dependencies, since most generated classes are not
  * serializable in the HTTP client.
  */
-public class HttpHealthcareApiClient implements HealthcareApiClient, Serializable {
-
-  private transient CloudHealthcare client;
+public class HttpHealthcareApiClient implements HealthcareApiClient, Serializable {
+  private static final String USER_AGENT =
+      String.format(
+          "apache-beam-io-google-cloud-platform-healthcare/%s",
+          ReleaseInfo.getReleaseInfo().getSdkVersion());
+  private static final String FHIRSTORE_HEADER_CONTENT_TYPE = "application/fhir+json";
+  private static final String FHIRSTORE_HEADER_ACCEPT = "application/fhir+json; charset=utf-8";
+  private static final String FHIRSTORE_HEADER_ACCEPT_CHARSET = "utf-8";
   private static final Logger LOG = LoggerFactory.getLogger(HttpHealthcareApiClient.class);
+  private transient CloudHealthcare client;
+  private transient HttpClient httpClient;
+  private transient GoogleCredentials credentials;
+
   /**
    * Instantiates a new Http healthcare api client.
    *
@@ -79,6 +106,7 @@ public HttpHealthcareApiClient() throws IOException {
    */
   public HttpHealthcareApiClient(CloudHealthcare client) throws IOException {
     this.client = client;
+    this.httpClient = HttpClients.createDefault();
     initClient();
   }
 
@@ -99,11 +127,45 @@ public Hl7V2Store createHL7v2Store(String dataset, String name) throws IOExcepti
         .execute();
   }
 
+  @Override
+  public FhirStore createFhirStore(String dataset, String name, String version) throws IOException {
+    return createFhirStore(dataset, name, version, null);
+  }
+
+  @Override
+  public FhirStore createFhirStore(
+      String dataset, String name, String version, @Nullable String pubsubTopic)
+      throws IOException {
+    FhirStore store = new FhirStore();
+
+    store.setVersion(version);
+    store.setDisableReferentialIntegrity(true);
+    store.setEnableUpdateCreate(true);
+    if (pubsubTopic != null) {
+      NotificationConfig notificationConfig = new NotificationConfig();
+      notificationConfig.setPubsubTopic(pubsubTopic);
+      store.setNotificationConfig(notificationConfig);
+    }
+    return client
+        .projects()
+        .locations()
+        .datasets()
+        .fhirStores()
+        .create(dataset, store)
+        .setFhirStoreId(name)
+        .execute();
+  }
+
   @Override
   public Empty deleteHL7v2Store(String name) throws IOException {
     return client.projects().locations().datasets().hl7V2Stores().delete(name).execute();
   }
 
+  @Override
+  public Empty deleteFhirStore(String name) throws IOException {
+    return client.projects().locations().datasets().fhirStores().delete(name).execute();
+  }
+
   @Override
   public Instant getEarliestHL7v2SendTime(String hl7v2Store, @Nullable String filter)
       throws IOException {
@@ -288,18 +350,6 @@ public IngestMessageResponse ingestHL7v2Message(String hl7v2Store, Message msg)
         .execute();
   }
 
-  @Override
-  public HttpBody fhirSearch(String fhirStore, SearchResourcesRequest query) throws IOException {
-    return client
-        .projects()
-        .locations()
-        .datasets()
-        .fhirStores()
-        .fhir()
-        .search(fhirStore, query)
-        .execute();
-  }
-
   @Override
   public Message createHL7v2Message(String hl7v2Store, Message msg) throws IOException {
     CreateMessageRequest createMessageRequest = new CreateMessageRequest();
@@ -315,48 +365,120 @@ public Message createHL7v2Message(String hl7v2Store, Message msg) throws IOExcep
   }
 
   @Override
-  public HttpBody createFhirResource(String fhirStore, String type, HttpBody body)
+  public Operation importFhirResource(
+      String fhirStore, String gcsSourcePath, @Nullable String contentStructure)
       throws IOException {
+    GoogleCloudHealthcareV1beta1FhirRestGcsSource gcsSrc =
+        new GoogleCloudHealthcareV1beta1FhirRestGcsSource();
+
+    gcsSrc.setUri(gcsSourcePath);
+    ImportResourcesRequest importRequest = new ImportResourcesRequest();
+    importRequest.setGcsSource(gcsSrc).setContentStructure(contentStructure);
     return client
         .projects()
         .locations()
         .datasets()
         .fhirStores()
-        .fhir()
-        .create(fhirStore, type, body)
+        .healthcareImport(fhirStore, importRequest)
         .execute();
   }
 
   @Override
-  public HttpBody executeFhirBundle(String fhirStore, HttpBody bundle) throws IOException {
-    return client
-        .projects()
-        .locations()
-        .datasets()
-        .fhirStores()
-        .fhir()
-        .executeBundle(fhirStore, bundle)
-        .execute();
+  public Operation pollOperation(Operation operation, Long sleepMs)
+      throws InterruptedException, IOException {
+    LOG.debug(String.format("started opertation %s. polling until complete.", operation.getName()));
+    while (operation.getDone() == null || !operation.getDone()) {
+      // Update the status of the operation with another request.
+      Thread.sleep(sleepMs); // Pause between requests.
+      operation =
+          client.projects().locations().datasets().operations().get(operation.getName()).execute();
+    }
+    return operation;
   }
 
   @Override
-  public HttpBody listFHIRResourceForPatient(String fhirStore, String patient) throws IOException {
-    return client
-        .projects()
-        .locations()
-        .datasets()
-        .fhirStores()
-        .fhir()
-        .patientEverything(patient)
-        .execute();
+  public HttpBody executeFhirBundle(String fhirStore, String bundle)
+      throws IOException, HealthcareHttpException {
+    if (httpClient == null || client == null) {
+      initClient();
+    }
+
+    credentials.refreshIfExpired();
+    StringEntity requestEntity = new StringEntity(bundle, ContentType.APPLICATION_JSON);
+    URI uri;
+    try {
+      uri =
+          new URIBuilder(client.getRootUrl() + "v1beta1/" + fhirStore + "/fhir")
+              .setParameter("access_token", credentials.getAccessToken().getTokenValue())
+              .build();
+    } catch (URISyntaxException e) {
+      LOG.error("URL error when making executeBundle request to FHIR API. " + e.getMessage());
+      throw new IllegalArgumentException(e);
+    }
+
+    HttpUriRequest request =
+        RequestBuilder.post()
+            .setUri(uri)
+            .setEntity(requestEntity)
+            .addHeader("User-Agent", USER_AGENT)
+            .addHeader("Content-Type", FHIRSTORE_HEADER_CONTENT_TYPE)
+            .addHeader("Accept-Charset", FHIRSTORE_HEADER_ACCEPT_CHARSET)
+            .addHeader("Accept", FHIRSTORE_HEADER_ACCEPT)
+            .build();
+
+    HttpResponse response = httpClient.execute(request);
+    HttpEntity responseEntity = response.getEntity();
+    String content = EntityUtils.toString(responseEntity);
+    // Check 2XX code.
+    if (!(response.getStatusLine().getStatusCode() / 100 == 2)) {
+      throw HealthcareHttpException.of(response);
+    }
+    HttpBody responseModel = new HttpBody();
+    responseModel.setData(content);
+    return responseModel;
+  }
+
+  /**
+   * Wraps {@link HttpResponse} in an exception with a statusCode field for use with {@link
+   * HealthcareIOError}.
+   */
+  public static class HealthcareHttpException extends Exception {
+    private final Integer statusCode;
+
+    HealthcareHttpException(HttpResponse response, String message) {
+      super(message);
+      this.statusCode = response.getStatusLine().getStatusCode();
+      if (statusCode / 100 == 2) {
+        throw new IllegalArgumentException(
+            String.format(
+                "2xx codes should not be exceptions. Got status code: %s with body: %s",
+                statusCode, message));
+      }
+    }
+
+    /**
+     * Create Exception of {@link HttpResponse}.
+     *
+     * @param response the HTTP response
+     * @return the healthcare http exception
+     * @throws IOException the io exception
+     */
+    static HealthcareHttpException of(HttpResponse response) throws IOException {
+      return new HealthcareHttpException(response, EntityUtils.toString(response.getEntity()));
+    }
+
+    Integer getStatusCode() {
+      return statusCode;
+    }
   }
 
   @Override
-  public HttpBody readFHIRResource(String fhirStore, String resource) throws IOException {
-    return client.projects().locations().datasets().fhirStores().fhir().read(resource).execute();
+  public HttpBody readFhirResource(String resourceId) throws IOException {
+    return client.projects().locations().datasets().fhirStores().fhir().read(resourceId).execute();
   }
 
-  private static class AuthenticatedRetryInitializer extends RetryHttpRequestInitializer {
+  public static class AuthenticatedRetryInitializer extends RetryHttpRequestInitializer {
+
     GoogleCredentials credentials;
 
     public AuthenticatedRetryInitializer(GoogleCredentials credentials) {
@@ -367,11 +489,11 @@ public AuthenticatedRetryInitializer(GoogleCredentials credentials) {
     @Override
     public void initialize(HttpRequest request) throws IOException {
       super.initialize(request);
+      HttpHeaders requestHeaders = request.getHeaders();
+      requestHeaders.setUserAgent(USER_AGENT);
       if (!credentials.hasRequestMetadata()) {
         return;
       }
-      HttpHeaders requestHeaders = request.getHeaders();
-      requestHeaders.setUserAgent("apache-beam-hl7v2-io");
       URI uri = null;
       if (request.getUrl() != null) {
         uri = request.getUrl().toURI();
@@ -389,19 +511,21 @@ public void initialize(HttpRequest request) throws IOException {
   }
 
   private void initClient() throws IOException {
+
+    credentials = GoogleCredentials.getApplicationDefault();
     // Create a HttpRequestInitializer, which will provide a baseline configuration to all requests.
-    // HttpRequestInitializer requestInitializer = new RetryHttpRequestInitializer();
-    // GoogleCredentials credentials = GoogleCredentials.getApplicationDefault();
     HttpRequestInitializer requestInitializer =
         new AuthenticatedRetryInitializer(
-            GoogleCredentials.getApplicationDefault()
-                .createScoped(CloudHealthcareScopes.CLOUD_PLATFORM));
+            credentials.createScoped(
+                CloudHealthcareScopes.CLOUD_PLATFORM, StorageScopes.CLOUD_PLATFORM_READ_ONLY));
 
     client =
         new CloudHealthcare.Builder(
                 new NetHttpTransport(), new JacksonFactory(), requestInitializer)
             .setApplicationName("apache-beam-hl7v2-io")
             .build();
+    httpClient =
+        HttpClients.custom().setRetryHandler(new DefaultHttpRequestRetryHandler(10, false)).build();
   }
 
   public static class HL7v2MessagePages implements Iterable> {
diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/pubsub/TestPubsub.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/pubsub/TestPubsub.java
index 4ea0b7b62ab9..24b764f04af5 100644
--- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/pubsub/TestPubsub.java
+++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/pubsub/TestPubsub.java
@@ -162,7 +162,9 @@ static String createTopicName(Description description, String name) throws IOExc
     }
 
     if (description.getMethodName() != null) {
-      topicName.append(description.getMethodName()).append("-");
+      // Remove braces (which are illegal in pubsub naming restrictions) in dynamic method names
+      // when using parameterized tests.
+      topicName.append(description.getMethodName().replaceAll("[\\[\\]]", "")).append("-");
     }
 
     DATETIME_FORMAT.printTo(topicName, Instant.now());
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOReadIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOReadIT.java
new file mode 100644
index 000000000000..71499bf98eb4
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOReadIT.java
@@ -0,0 +1,147 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import static org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.HEALTHCARE_DATASET_TEMPLATE;
+
+import java.io.IOException;
+import java.security.SecureRandom;
+import java.util.Arrays;
+import java.util.Collection;
+import org.apache.beam.runners.direct.DirectOptions;
+import org.apache.beam.sdk.PipelineResult;
+import org.apache.beam.sdk.extensions.gcp.options.GcpOptions;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubClient;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubClient.SubscriptionPath;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubClient.TopicPath;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubGrpcClient;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO;
+import org.apache.beam.sdk.io.gcp.pubsub.TestPubsubOptions;
+import org.apache.beam.sdk.io.gcp.pubsub.TestPubsubSignal;
+import org.apache.beam.sdk.testing.TestPipeline;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Supplier;
+import org.joda.time.Duration;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+@RunWith(Parameterized.class)
+public class FhirIOReadIT {
+
+  @Parameters(name = "{0}")
+  public static Collection versions() {
+    return Arrays.asList("DSTU2", "STU3", "R4");
+  }
+
+  @Rule public transient TestPubsubSignal signal = TestPubsubSignal.create();
+  @Rule public transient TestPipeline pipeline = TestPipeline.create();
+
+  private final String fhirStoreName;
+  private final String pubsubTopic;
+  private final String pubsubSubscription;
+  private final String project;
+  private transient HealthcareApiClient client;
+  private String healthcareDataset;
+  private PubsubClient pubsub;
+  private TestPubsubOptions pipelineOptions;
+
+  public String version;
+
+  public FhirIOReadIT(String version) {
+    this.version = version;
+    long testTime = System.currentTimeMillis();
+    this.fhirStoreName =
+        "FHIR_store_" + version + "_write_it_" + testTime + "_" + (new SecureRandom().nextInt(32));
+    this.project = TestPipeline.testingPipelineOptions().as(GcpOptions.class).getProject();
+    this.pubsubTopic =
+        "projects/"
+            + project
+            + "/topics/FhirIO-IT-"
+            + version
+            + "-notifications-"
+            + testTime
+            + "-"
+            + (new SecureRandom().nextInt(32));
+    this.pubsubSubscription = pubsubTopic.replaceAll("topic", "subscription");
+    pipelineOptions = TestPipeline.testingPipelineOptions().as(TestPubsubOptions.class);
+  }
+
+  @Before
+  public void setup() throws Exception {
+    healthcareDataset = String.format(HEALTHCARE_DATASET_TEMPLATE, project);
+    if (client == null) {
+      this.client = new HttpHealthcareApiClient();
+    }
+    pubsub = PubsubGrpcClient.FACTORY.newClient(null, null, pipelineOptions);
+    TopicPath topicPath = PubsubClient.topicPathFromPath(pubsubTopic);
+    pubsub.createTopic(topicPath);
+    SubscriptionPath subscriptionPath = PubsubClient.subscriptionPathFromPath(pubsubSubscription);
+    pubsub.createSubscription(topicPath, subscriptionPath, 60);
+    client.createFhirStore(healthcareDataset, fhirStoreName, version, pubsubTopic);
+
+    // Execute bundles to trigger FHIR notificiations to input topic
+    FhirIOTestUtil.executeFhirBundles(
+        client,
+        healthcareDataset + "/fhirStores/" + fhirStoreName,
+        FhirIOTestUtil.BUNDLES.get(version));
+  }
+
+  @After
+  public void deleteFHIRtore() throws IOException {
+    HealthcareApiClient client = new HttpHealthcareApiClient();
+    client.deleteFhirStore(healthcareDataset + "/fhirStores/" + fhirStoreName);
+    TopicPath topicPath = PubsubClient.topicPathFromPath(pubsubTopic);
+    SubscriptionPath subscriptionPath = PubsubClient.subscriptionPathFromPath(pubsubSubscription);
+    pubsub.deleteSubscription(subscriptionPath);
+    pubsub.deleteTopic(topicPath);
+    pubsub.close();
+  }
+
+  @Test
+  public void testFhirIORead() throws Exception {
+    pipeline.getOptions().as(DirectOptions.class).setBlockOnRun(false);
+
+    FhirIO.Read.Result result =
+        pipeline
+            .apply(PubsubIO.readStrings().fromSubscription(pubsubSubscription))
+            .apply(FhirIO.readResources());
+
+    PCollection resources = result.getResources();
+    resources.apply(
+        "waitForAnyMessage", signal.signalSuccessWhen(resources.getCoder(), anyResources -> true));
+    // wait for any resource
+
+    Supplier start = signal.waitForStart(Duration.standardMinutes(5));
+    pipeline.apply(signal.signalStart());
+    PipelineResult job = pipeline.run();
+    start.get();
+    signal.waitForSuccess(Duration.standardSeconds(30));
+
+    // A runner may not support cancel
+    try {
+      job.cancel();
+    } catch (UnsupportedOperationException exc) {
+      // noop
+    }
+  }
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTest.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTest.java
new file mode 100644
index 000000000000..976c55fcb76c
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTest.java
@@ -0,0 +1,112 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import org.apache.beam.sdk.testing.PAssert;
+import org.apache.beam.sdk.testing.TestPipeline;
+import org.apache.beam.sdk.transforms.Count;
+import org.apache.beam.sdk.transforms.Create;
+import org.apache.beam.sdk.transforms.MapElements;
+import org.apache.beam.sdk.values.KV;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.TypeDescriptors;
+import org.junit.Assert;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.JUnit4;
+
+@RunWith(JUnit4.class)
+public class FhirIOTest {
+  @Rule public final transient TestPipeline pipeline = TestPipeline.create();
+
+  @Test
+  public void test_FhirIO_failedReads() {
+    List badMessageIDs = Arrays.asList("foo", "bar");
+    FhirIO.Read.Result readResult =
+        pipeline.apply(Create.of(badMessageIDs)).apply(FhirIO.readResources());
+
+    PCollection> failed = readResult.getFailedReads();
+
+    PCollection resources = readResult.getResources();
+
+    PCollection failedMsgIds =
+        failed.apply(
+            MapElements.into(TypeDescriptors.strings()).via(HealthcareIOError::getDataResource));
+
+    PAssert.that(failedMsgIds).containsInAnyOrder(badMessageIDs);
+    PAssert.that(resources).empty();
+    pipeline.run();
+  }
+
+  @Test
+  public void test_FhirIO_failedWrites() {
+    String badBundle = "bad";
+    List emptyMessages = Collections.singletonList(badBundle);
+
+    PCollection fhirBundles = pipeline.apply(Create.of(emptyMessages));
+
+    FhirIO.Write.Result writeResult =
+        fhirBundles.apply(
+            FhirIO.Write.executeBundles(
+                "projects/foo/locations/us-central1/datasets/bar/hl7V2Stores/baz"));
+
+    PCollection> failedInserts = writeResult.getFailedBodies();
+
+    PAssert.thatSingleton(failedInserts)
+        .satisfies(
+            (HealthcareIOError err) -> {
+              Assert.assertEquals("bad", err.getDataResource());
+              return null;
+            });
+    PCollection numFailedInserts = failedInserts.apply(Count.globally());
+
+    PAssert.thatSingleton(numFailedInserts).isEqualTo(1L);
+
+    pipeline.run();
+  }
+
+  private static final long NUM_ELEMENTS = 11;
+  private static final long BATCH_SIZE = 5;
+
+  private static ArrayList> createTestData() {
+    String[] scientists = {
+      "Einstein",
+      "Darwin",
+      "Copernicus",
+      "Pasteur",
+      "Curie",
+      "Faraday",
+      "Newton",
+      "Bohr",
+      "Galilei",
+      "Maxwell"
+    };
+    ArrayList> data = new ArrayList<>();
+    for (int i = 0; i < NUM_ELEMENTS; i++) {
+      int index = i % scientists.length;
+      KV element = KV.of("key", scientists[index]);
+      data.add(element);
+    }
+    return data;
+  }
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestOptions.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestOptions.java
new file mode 100644
index 000000000000..33da786c0e4f
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestOptions.java
@@ -0,0 +1,46 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.DEFAULT_TEMP_BUCKET;
+
+import org.apache.beam.sdk.options.Default;
+import org.apache.beam.sdk.options.Description;
+import org.apache.beam.sdk.options.Validation.Required;
+import org.apache.beam.sdk.testing.TestPipelineOptions;
+
+public interface FhirIOTestOptions extends TestPipelineOptions {
+
+  @Description(
+      "FHIR store should match the pattern: projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/HL7V2_STORE_ID")
+  @Required
+  String getFhirStore();
+
+  void setFhirStore(String value);
+
+  @Description("GCS temp path for import should be of the form gs://bucket/path/")
+  @Default.String("gs://" + DEFAULT_TEMP_BUCKET + "/FhirIOWriteIT/temp/")
+  String getGcsTempPath();
+
+  void setGcsTempPath(String value);
+
+  @Description("GCS dead letter path for import should be of the form gs://bucket/path/")
+  String getGcsDeadLetterPath();
+
+  void setGcsDeadLetterPath(String value);
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java
new file mode 100644
index 000000000000..c893f59f744b
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java
@@ -0,0 +1,127 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import com.google.api.client.http.HttpHeaders;
+import com.google.api.client.http.HttpRequestInitializer;
+import com.google.api.client.http.javanet.NetHttpTransport;
+import com.google.api.client.json.jackson2.JacksonFactory;
+import com.google.api.services.storage.Storage;
+import com.google.api.services.storage.model.StorageObject;
+import com.google.auth.oauth2.GoogleCredentials;
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException;
+
+class FhirIOTestUtil {
+  public static final String DEFAULT_TEMP_BUCKET = "temp-storage-for-healthcare-io-tests";
+
+  private static Stream readPrettyBundles(String version) {
+    ClassLoader classLoader = FhirIOTestUtil.class.getClassLoader();
+    Path resourceDir = Paths.get("build", "resources", "test", version);
+    String absolutePath = resourceDir.toFile().getAbsolutePath();
+    File dir = new File(absolutePath);
+    File[] fhirJsons = dir.listFiles();
+    return Arrays.stream(fhirJsons)
+        .map(File::toPath)
+        .map(
+            (Path path) -> {
+              try {
+                return Files.readAllBytes(path);
+              } catch (IOException e) {
+                throw new RuntimeException(e);
+              }
+            })
+        .map(String::new);
+  }
+
+  // Could generate more messages at scale using a tool like
+  // https://synthetichealth.github.io/synthea/ if necessary chose not to avoid the dependency.
+  static final List DSTU2_PRETTY_BUNDLES =
+      readPrettyBundles("DSTU2").collect(Collectors.toList());
+  static final List STU3_PRETTY_BUNDLES =
+      readPrettyBundles("STU3").collect(Collectors.toList());
+  static final List R4_PRETTY_BUNDLES =
+      readPrettyBundles("R4").collect(Collectors.toList());
+
+  static final Map> BUNDLES;
+
+  static {
+    Map> m = new HashMap<>();
+    m.put("DSTU2", DSTU2_PRETTY_BUNDLES);
+    m.put("STU3", STU3_PRETTY_BUNDLES);
+    m.put("R4", R4_PRETTY_BUNDLES);
+    BUNDLES = Collections.unmodifiableMap(m);
+  }
+
+  /** Populate the test resources into the FHIR store and returns a list of resource IDs. */
+  static void executeFhirBundles(HealthcareApiClient client, String fhirStore, List bundles)
+      throws IOException, HealthcareHttpException {
+    for (String bundle : bundles) {
+      client.executeFhirBundle(fhirStore, bundle);
+    }
+  }
+
+  public static void tearDownTempBucket() throws IOException {
+
+    GoogleCredentials credentials = GoogleCredentials.getApplicationDefault();
+    HttpRequestInitializer requestInitializer =
+        request -> {
+          HttpHeaders requestHeaders = request.getHeaders();
+          if (!credentials.hasRequestMetadata()) {
+            return;
+          }
+          URI uri = null;
+          if (request.getUrl() != null) {
+            uri = request.getUrl().toURI();
+          }
+          Map> credentialHeaders = credentials.getRequestMetadata(uri);
+          if (credentialHeaders == null) {
+            return;
+          }
+          for (Map.Entry> entry : credentialHeaders.entrySet()) {
+            String headerName = entry.getKey();
+            List requestValues = new ArrayList<>(entry.getValue());
+            requestHeaders.put(headerName, requestValues);
+          }
+          request.setConnectTimeout(60000); // 1 minute connect timeout
+          request.setReadTimeout(60000); // 1 minute read timeout
+        };
+    Storage storage =
+        new Storage.Builder(new NetHttpTransport(), new JacksonFactory(), requestInitializer)
+            .build();
+    List blobs = storage.objects().list(DEFAULT_TEMP_BUCKET).execute().getItems();
+    if (blobs != null) {
+      for (StorageObject blob : blobs) {
+        storage.objects().delete(DEFAULT_TEMP_BUCKET, blob.getId());
+      }
+    }
+  }
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java
new file mode 100644
index 000000000000..24677ca3fb56
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java
@@ -0,0 +1,129 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.BUNDLES;
+import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.DEFAULT_TEMP_BUCKET;
+import static org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.HEALTHCARE_DATASET_TEMPLATE;
+
+import java.io.IOException;
+import java.security.SecureRandom;
+import java.util.Arrays;
+import java.util.Collection;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.extensions.gcp.options.GcpOptions;
+import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure;
+import org.apache.beam.sdk.options.PipelineOptionsFactory;
+import org.apache.beam.sdk.testing.PAssert;
+import org.apache.beam.sdk.testing.TestPipeline;
+import org.apache.beam.sdk.transforms.Create;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+@RunWith(Parameterized.class)
+public class FhirIOWriteIT {
+
+  @Parameters(name = "{0}")
+  public static Collection versions() {
+    return Arrays.asList("DSTU2", "STU3", "R4");
+  }
+
+  private final String fhirStoreName;
+  private FhirIOTestOptions options;
+  private transient HealthcareApiClient client;
+  private String healthcareDataset;
+  private long testTime = System.currentTimeMillis();
+
+  public String version;
+
+  @Rule public transient TestPipeline pipeline = TestPipeline.create();
+
+  public FhirIOWriteIT(String version) {
+    this.version = version;
+    this.fhirStoreName =
+        "FHIR_store_" + version + "_write_it_" + testTime + "_" + (new SecureRandom().nextInt(32));
+  }
+
+  @Before
+  public void setup() throws Exception {
+    if (client == null) {
+      client = new HttpHealthcareApiClient();
+    }
+    PipelineOptionsFactory.register(FhirIOTestOptions.class);
+    String project = TestPipeline.testingPipelineOptions().as(GcpOptions.class).getProject();
+    healthcareDataset = String.format(HEALTHCARE_DATASET_TEMPLATE, project);
+    options = TestPipeline.testingPipelineOptions().as(FhirIOTestOptions.class);
+    options.setGcsTempPath(
+        String.format("gs://%s/FhirIOWrite%sIT/%s/temp/", DEFAULT_TEMP_BUCKET, version, testTime));
+    options.setGcsDeadLetterPath(
+        String.format(
+            "gs://%s/FhirIOWrite%sIT/%s/deadletter/", DEFAULT_TEMP_BUCKET, version, testTime));
+    options.setFhirStore(healthcareDataset + "/fhirStores/" + fhirStoreName);
+    HealthcareApiClient client = new HttpHealthcareApiClient();
+    client.createFhirStore(healthcareDataset, fhirStoreName, version);
+  }
+
+  @After
+  public void teardownFhirStore() throws IOException {
+    HealthcareApiClient client = new HttpHealthcareApiClient();
+    client.deleteFhirStore(healthcareDataset + "/fhirStores/" + fhirStoreName);
+    // clean up GCS objects if any.
+  }
+
+  @AfterClass
+  public static void teardownBucket() throws IOException {
+    FhirIOTestUtil.tearDownTempBucket();
+  }
+
+  @Test
+  public void testFhirIO_ExecuteBundle() throws IOException {
+    FhirIO.Write.Result writeResult =
+        pipeline
+            .apply(Create.of(BUNDLES.get(version)))
+            .apply(FhirIO.Write.executeBundles(options.getFhirStore()));
+
+    PAssert.that(writeResult.getFailedBodies()).empty();
+
+    pipeline.run().waitUntilFinish();
+  }
+
+  @Test
+  public void testFhirIO_Import() {
+    Pipeline pipeline = Pipeline.create(options);
+    options.setTempLocation("gs://temp-storage-for-healthcare-io-tests");
+    FhirIO.Write.Result result =
+        pipeline
+            .apply(Create.of(BUNDLES.get(version)))
+            .apply(
+                FhirIO.Write.fhirStoresImport(
+                    options.getFhirStore(),
+                    options.getGcsDeadLetterPath(),
+                    ContentStructure.BUNDLE));
+
+    PAssert.that(result.getFailedBodies()).empty();
+    PAssert.that(result.getFailedFiles()).empty();
+
+    pipeline.run().waitUntilFinish();
+  }
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadIT.java
index 94f6ed6086ea..d3769b8fa3db 100644
--- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadIT.java
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadIT.java
@@ -92,7 +92,7 @@ public void testHL7v2IO_ListHL7v2Messages() throws Exception {
     PCollection result =
         pipeline.apply(HL7v2IO.read(healthcareDataset + "/hl7V2Stores/" + HL7V2_STORE_NAME));
     PCollection numReadMessages =
-        result.setCoder(new HL7v2MessageCoder()).apply(Count.globally());
+        result.setCoder(HL7v2MessageCoder.of()).apply(Count.globally());
     PAssert.thatSingleton(numReadMessages).isEqualTo((long) MESSAGES.size());
 
     PAssert.that(result)
@@ -119,7 +119,7 @@ public void testHL7v2IO_ListHL7v2Messages_filtered() throws Exception {
             HL7v2IO.readWithFilter(
                 healthcareDataset + "/hl7V2Stores/" + HL7V2_STORE_NAME, adtFilter));
     PCollection numReadMessages =
-        result.setCoder(new HL7v2MessageCoder()).apply(Count.globally());
+        result.setCoder(HL7v2MessageCoder.of()).apply(Count.globally());
     PAssert.thatSingleton(numReadMessages).isEqualTo(NUM_ADT);
 
     PAssert.that(result)
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadWriteIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadWriteIT.java
index eaffc536ca8b..8a4566bffc26 100644
--- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadWriteIT.java
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadWriteIT.java
@@ -101,7 +101,7 @@ public void testHL7v2IOE2E() throws Exception {
             .apply(HL7v2IO.getAll());
 
     PCollection numReadMessages =
-        readResult.getMessages().setCoder(new HL7v2MessageCoder()).apply(Count.globally());
+        readResult.getMessages().setCoder(HL7v2MessageCoder.of()).apply(Count.globally());
     PAssert.thatSingleton(numReadMessages).isEqualTo((long) MESSAGES.size());
     PAssert.that(readResult.getFailedReads()).empty();
 
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOWriteIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOWriteIT.java
index f52d60744367..88a09e539c21 100644
--- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOWriteIT.java
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOWriteIT.java
@@ -82,7 +82,7 @@ public void tearDown() throws Exception {
   public void testHL7v2IOWrite() throws Exception {
     HL7v2IO.Write.Result result =
         pipeline
-            .apply(Create.of(MESSAGES).withCoder(new HL7v2MessageCoder()))
+            .apply(Create.of(MESSAGES).withCoder(HL7v2MessageCoder.of()))
             .apply(HL7v2IO.ingestMessages(healthcareDataset + "/hl7V2Stores/" + HL7V2_STORE_NAME));
 
     PAssert.that(result.getFailedInsertsWithErr()).empty();
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json
new file mode 100644
index 000000000000..677f4a31ef9e
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json
@@ -0,0 +1,14018 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:ed7a9f5c-37ea-4767-95ba-a6783e9500b3",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "ed7a9f5c-37ea-4767-95ba-a6783e9500b3",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: 3529060201889641636  Population seed: 1586309754086
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/us-core-race",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v3/Race",
+                  "code": "2106-3",
+                  "display": "White"
+                }
+              ],
+              "text": "White"
+            }
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/us-core-ethnicity",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v3/Ethnicity",
+                  "code": "2186-5",
+                  "display": "Not Hispanic or Latino"
+                }
+              ],
+              "text": "Not Hispanic or Latino"
+            }
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Shantay950 Collier206"
+          },
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
+            "valueCode": "F"
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
+            "valueAddress": {
+              "city": "Quincy",
+              "state": "Massachusetts",
+              "country": "US"
+            }
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
+            "valueDecimal": 2.756674276028057
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
+            "valueDecimal": 63.24332572397194
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "ed7a9f5c-37ea-4767-95ba-a6783e9500b3"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v2/0203",
+                  "code": "MR"
+                }
+              ]
+            },
+            "system": "http://hospital.smarthealthit.org",
+            "value": "ed7a9f5c-37ea-4767-95ba-a6783e9500b3"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/identifier-type",
+                  "code": "SB"
+                }
+              ]
+            },
+            "system": "http://hl7.org/fhir/sid/us-ssn",
+            "value": "999-91-5467"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v2/0203",
+                  "code": "DL"
+                }
+              ]
+            },
+            "system": "urn:oid:2.16.840.1.113883.4.3.25",
+            "value": "S99971576"
+          }
+        ],
+        "name": [
+          {
+            "use": "official",
+            "family": [
+              "Krajcik437"
+            ],
+            "given": [
+              "Amelia635"
+            ],
+            "prefix": [
+              "Mrs."
+            ]
+          },
+          {
+            "use": "maiden",
+            "family": [
+              "Hoeger474"
+            ],
+            "given": [
+              "Amelia635"
+            ],
+            "prefix": [
+              "Mrs."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "555-617-5450",
+            "use": "home"
+          }
+        ],
+        "gender": "female",
+        "birthDate": "1953-09-25",
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 41.56777541317302
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -70.99411465843632
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "1056 Stark Trace Suite 42"
+            ],
+            "city": "Dartmouth",
+            "state": "Massachusetts",
+            "country": "US"
+          }
+        ],
+        "maritalStatus": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/v3/MaritalStatus",
+              "code": "M"
+            }
+          ]
+        },
+        "multipleBirthBoolean": false,
+        "communication": [
+          {
+            "language": {
+              "coding": [
+                {
+                  "system": "urn:ietf:bcp:47",
+                  "code": "en-US",
+                  "display": "English"
+                }
+              ],
+              "text": "English"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Patient"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f9914571-32b8-36d3-a422-4cdce9fbb86c",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "f9914571-32b8-36d3-a422-4cdce9fbb86c",
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "f9914571-32b8-36d3-a422-4cdce9fbb86c"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "INDEPENDENCE EYE ASSOCIATES, PC",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "508-985-6600"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "365 FAUNCE CORNER RD"
+            ],
+            "city": "DARTMOUTH",
+            "state": "MA",
+            "postalCode": "02747-6230",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:7e727355-643f-3e2b-b89f-f5076660354b",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "7e727355-643f-3e2b-b89f-f5076660354b",
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "61860"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Salazar800"
+          ],
+          "given": [
+            "Rodrigo242"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "365 FAUNCE CORNER RD"
+            ],
+            "city": "DARTMOUTH",
+            "state": "MA",
+            "postalCode": "02747-6230",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:0f99c02d-1199-4d87-8459-123025910c55",
+      "resource": {
+        "resourceType": "Encounter",
+        "id": "0f99c02d-1199-4d87-8459-123025910c55",
+        "status": "finished",
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "162673000",
+                "display": "General examination of patient (procedure)"
+              }
+            ],
+            "text": "General examination of patient (procedure)"
+          }
+        ],
+        "patient": {
+          "reference": "urn:uuid:ed7a9f5c-37ea-4767-95ba-a6783e9500b3"
+        },
+        "participant": [
+          {
+            "individual": {
+              "reference": "urn:uuid:7e727355-643f-3e2b-b89f-f5076660354b"
+            }
+          }
+        ],
+        "period": {
+          "start": "1993-10-01T19:52:39-07:00",
+          "end": "1993-10-01T20:07:39-07:00"
+        },
+        "serviceProvider": {
+          "reference": "urn:uuid:f9914571-32b8-36d3-a422-4cdce9fbb86c"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Encounter"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:3eaf24a3-0c67-4505-a02e-fcc09a4093a3",
+      "resource": {
+        "resourceType": "Condition",
+        "id": "3eaf24a3-0c67-4505-a02e-fcc09a4093a3",
+        "patient": {
+          "reference": "urn:uuid:ed7a9f5c-37ea-4767-95ba-a6783e9500b3"
+        },
+        "encounter": {
+          "reference": "urn:uuid:0f99c02d-1199-4d87-8459-123025910c55"
+        },
+        "dateRecorded": "1993-10-01",
+        "code": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "15777000",
+              "display": "Prediabetes"
+            }
+          ],
+          "text": "Prediabetes"
+        },
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/condition-category",
+              "code": "diagnosis"
+            }
+          ]
+        },
+        "clinicalStatus": "active",
+        "verificationStatus": "confirmed",
+        "onsetDateTime": "1993-10-01T19:52:39-07:00"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Condition"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:0319b3fc-3373-42f6-9b08-6ee695e640b0",
+      "resource": {
+        "resourceType": "CarePlan",
+        "id": "0319b3fc-3373-42f6-9b08-6ee695e640b0",
+        "text": {
+          "status": "generated",
+          "div": "
    Diabetes self management plan
    "
+        },
+        "subject": {
+          "reference": "urn:uuid:ed7a9f5c-37ea-4767-95ba-a6783e9500b3"
+        },
+        "status": "active",
+        "context": {
+          "reference": "urn:uuid:0f99c02d-1199-4d87-8459-123025910c55"
+        },
+        "period": {
+          "start": "1993-10-01T19:52:39-07:00"
+        },
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "698360004",
+                "display": "Diabetes self management plan"
+              }
+            ],
+            "text": "Diabetes self management plan"
+          }
+        ],
+        "addresses": [
+          {
+            "reference": "urn:uuid:3eaf24a3-0c67-4505-a02e-fcc09a4093a3"
+          }
+        ],
+        "activity": [
+          {
+            "detail": {
+              "code": {
+                "coding": [
+                  {
+                    "system": "http://snomed.info/sct",
+                    "code": "160670007",
+                    "display": "Diabetic diet"
+                  }
+                ],
+                "text": "Diabetic diet"
+              },
+              "status": "in-progress",
+              "prohibited": false
+            }
+          },
+          {
+            "detail": {
+              "code": {
+                "coding": [
+                  {
+                    "system": "http://snomed.info/sct",
+                    "code": "229065009",
+                    "display": "Exercise therapy"
+                  }
+                ],
+                "text": "Exercise therapy"
+              },
+              "status": "in-progress",
+              "prohibited": false
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "CarePlan"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:fa8baaad-a3ec-4e4a-9cd3-483bb9283cdb",
+      "resource": {
+        "resourceType": "Claim",
+        "id": "fa8baaad-a3ec-4e4a-9cd3-483bb9283cdb",
+        "type": "institutional",
+        "organization": {
+          "reference": "urn:uuid:f9914571-32b8-36d3-a422-4cdce9fbb86c"
+        },
+        "use": "complete",
+        "diagnosis": [
+          {
+            "sequence": 1,
+            "diagnosis": {
+              "system": "http://snomed.info/sct",
+              "code": "15777000",
+              "display": "Prediabetes"
+            }
+          }
+        ],
+        "patient": {
+          "reference": "urn:uuid:ed7a9f5c-37ea-4767-95ba-a6783e9500b3"
+        },
+        "item": [
+          {
+            "sequence": 1,
+            "type": {
+              "system": "http://hl7.org/fhir/v3/ActCode",
+              "code": "CSINV",
+              "display": "clinical service invoice"
+            },
+            "service": {
+              "system": "http://snomed.info/sct",
+              "code": "162673000",
+              "display": "General examination of patient (procedure)"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Claim"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:ecc51621-0af3-3b35-ac3e-8b1e34022e92",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "ecc51621-0af3-3b35-ac3e-8b1e34022e92",
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "ecc51621-0af3-3b35-ac3e-8b1e34022e92"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "SAINT ANNE'S HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5086745600"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "795 MIDDLE STREET"
+            ],
+            "city": "FALL RIVER",
+            "state": "MA",
+            "postalCode": "02721",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:38a05f68-cc3b-33b6-993e-1d2bb2696c3d",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "38a05f68-cc3b-33b6-993e-1d2bb2696c3d",
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "100"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Padberg411"
+          ],
+          "given": [
+            "Ligia986"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "795 MIDDLE STREET"
+            ],
+            "city": "FALL RIVER",
+            "state": "MA",
+            "postalCode": "02721",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:29a7628c-9d6d-400a-a495-c6714208d248",
+      "resource": {
+        "resourceType": "Encounter",
+        "id": "29a7628c-9d6d-400a-a495-c6714208d248",
+        "status": "finished",
+        "class": "ambulatory",
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "424441002",
+                "display": "Prenatal initial visit"
+              }
+            ],
+            "text": "Prenatal initial visit"
+          }
+        ],
+        "patient": {
+          "reference": "urn:uuid:ed7a9f5c-37ea-4767-95ba-a6783e9500b3"
+        },
+        "participant": [
+          {
+            "individual": {
+              "reference": "urn:uuid:38a05f68-cc3b-33b6-993e-1d2bb2696c3d"
+            }
+          }
+        ],
+        "period": {
+          "start": "1997-11-21T18:52:39-08:00",
+          "end": "1997-11-21T19:37:39-08:00"
+        },
+        "reason": [
+          {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "72892002",
+                "display": "Normal pregnancy"
+              }
+            ]
+          }
+        ],
+        "serviceProvider": {
+          "reference": "urn:uuid:ecc51621-0af3-3b35-ac3e-8b1e34022e92"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Encounter"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:7e78b2fa-5f76-4547-b107-93e9bff9a3fd",
+      "resource": {
+        "resourceType": "Condition",
+        "id": "7e78b2fa-5f76-4547-b107-93e9bff9a3fd",
+        "patient": {
+          "reference": "urn:uuid:ed7a9f5c-37ea-4767-95ba-a6783e9500b3"
+        },
+        "encounter": {
+          "reference": "urn:uuid:29a7628c-9d6d-400a-a495-c6714208d248"
+        },
+        "dateRecorded": "1997-11-21",
+        "code": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "19169002",
+              "display": "Miscarriage in first trimester"
+            }
+          ],
+          "text": "Miscarriage in first trimester"
+        },
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/condition-category",
+              "code": "diagnosis"
+            }
+          ]
+        },
+        "clinicalStatus": "active",
+        "verificationStatus": "confirmed",
+        "onsetDateTime": "1997-11-21T18:52:39-08:00"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Condition"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f56d5dc9-3ad3-4b81-9dd3-6b9adcdafeb0",
+      "resource": {
+        "resourceType": "Claim",
+        "id": "f56d5dc9-3ad3-4b81-9dd3-6b9adcdafeb0",
+        "type": "institutional",
+        "organization": {
+          "reference": "urn:uuid:ecc51621-0af3-3b35-ac3e-8b1e34022e92"
+        },
+        "use": "complete",
+        "diagnosis": [
+          {
+            "sequence": 1,
+            "diagnosis": {
+              "system": "http://snomed.info/sct",
+              "code": "19169002",
+              "display": "Miscarriage in first trimester"
+            }
+          }
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+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json
new file mode 100644
index 000000000000..0acb308d86d3
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json
@@ -0,0 +1,10877 @@
+{
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+        "text": {
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    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: 481861502406456147  Population seed: 1586309754086
    "
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+                  "system": "http://hl7.org/fhir/v3/Race",
+                  "code": "2106-3",
+                  "display": "White"
+                }
+              ],
+              "text": "White"
+            }
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/us-core-ethnicity",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v3/Ethnicity",
+                  "code": "2186-5",
+                  "display": "Not Hispanic or Latino"
+                }
+              ],
+              "text": "Not Hispanic or Latino"
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+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Dann525 Davis923"
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+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
+            "valueCode": "F"
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+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
+            "valueAddress": {
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+              "state": "Massachusetts",
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+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
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+            "value": "999-31-6576"
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+        "birthDate": "1975-07-18",
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+        "url": "Patient"
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+              "display": "Healthcare Provider"
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+        "name": "NORTH SHORE MEDICAL CENTER -",
+        "telecom": [
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+            "value": "9787411215"
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+            "state": "MA",
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+            "country": "US"
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Ernesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Ernesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json
new file mode 100644
index 000000000000..ac94ea8d8adc
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Ernesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json
@@ -0,0 +1,17399 @@
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diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json
new file mode 100644
index 000000000000..67e63f747028
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json
@@ -0,0 +1,9279 @@
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+              "display": "Tobacco smoking status NHIS"
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+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json
new file mode 100644
index 000000000000..3a6ae7a6d914
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json
@@ -0,0 +1,10047 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "f04ef974-6d6f-4e1c-804f-cd4d62aabb4f",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: -7196695550560093073  Population seed: 1586309754086
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/us-core-race",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v3/Race",
+                  "code": "2106-3",
+                  "display": "White"
+                }
+              ],
+              "text": "White"
+            }
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/us-core-ethnicity",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v3/Ethnicity",
+                  "code": "2186-5",
+                  "display": "Not Hispanic or Latino"
+                }
+              ],
+              "text": "Not Hispanic or Latino"
+            }
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+              "display": "Urea Nitrogen"
+            }
+          ],
+          "text": "Urea Nitrogen"
+        },
+        "subject": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        },
+        "effectiveDateTime": "2018-07-09T15:14:32-07:00",
+        "issued": "2018-07-09T15:14:32.480-07:00",
+        "valueQuantity": {
+          "value": 19.420,
+          "unit": "mg/dL",
+          "system": "http://unitsofmeasure.org",
+          "code": "mg/dL"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:cec03bed-4729-4d42-8010-467d80929cec",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "cec03bed-4729-4d42-8010-467d80929cec",
+        "status": "final",
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/observation-category",
+              "code": "laboratory",
+              "display": "laboratory"
+            }
+          ],
+          "text": "laboratory"
+        },
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "38483-4",
+              "display": "Creatinine"
+            }
+          ],
+          "text": "Creatinine"
+        },
+        "subject": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        },
+        "effectiveDateTime": "2018-07-09T15:14:32-07:00",
+        "issued": "2018-07-09T15:14:32.480-07:00",
+        "valueQuantity": {
+          "value": 1.1200,
+          "unit": "mg/dL",
+          "system": "http://unitsofmeasure.org",
+          "code": "mg/dL"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:695c8154-110e-462a-ab0d-f536809ed44e",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "695c8154-110e-462a-ab0d-f536809ed44e",
+        "status": "final",
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/observation-category",
+              "code": "laboratory",
+              "display": "laboratory"
+            }
+          ],
+          "text": "laboratory"
+        },
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "49765-1",
+              "display": "Calcium"
+            }
+          ],
+          "text": "Calcium"
+        },
+        "subject": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        },
+        "effectiveDateTime": "2018-07-09T15:14:32-07:00",
+        "issued": "2018-07-09T15:14:32.480-07:00",
+        "valueQuantity": {
+          "value": 8.6900,
+          "unit": "mg/dL",
+          "system": "http://unitsofmeasure.org",
+          "code": "mg/dL"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:25dca154-f59e-4a62-ab3d-5f0b0e8fc915",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "25dca154-f59e-4a62-ab3d-5f0b0e8fc915",
+        "status": "final",
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/observation-category",
+              "code": "laboratory",
+              "display": "laboratory"
+            }
+          ],
+          "text": "laboratory"
+        },
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "2947-0",
+              "display": "Sodium"
+            }
+          ],
+          "text": "Sodium"
+        },
+        "subject": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        },
+        "effectiveDateTime": "2018-07-09T15:14:32-07:00",
+        "issued": "2018-07-09T15:14:32.480-07:00",
+        "valueQuantity": {
+          "value": 141.33,
+          "unit": "mmol/L",
+          "system": "http://unitsofmeasure.org",
+          "code": "mmol/L"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:215a790f-9080-4fb9-b950-35ba6fc36a41",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "215a790f-9080-4fb9-b950-35ba6fc36a41",
+        "status": "final",
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/observation-category",
+              "code": "laboratory",
+              "display": "laboratory"
+            }
+          ],
+          "text": "laboratory"
+        },
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "6298-4",
+              "display": "Potassium"
+            }
+          ],
+          "text": "Potassium"
+        },
+        "subject": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        },
+        "effectiveDateTime": "2018-07-09T15:14:32-07:00",
+        "issued": "2018-07-09T15:14:32.480-07:00",
+        "valueQuantity": {
+          "value": 5.1800,
+          "unit": "mmol/L",
+          "system": "http://unitsofmeasure.org",
+          "code": "mmol/L"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:17248f47-1630-4e44-9d77-122d8cb37da5",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "17248f47-1630-4e44-9d77-122d8cb37da5",
+        "status": "final",
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/observation-category",
+              "code": "laboratory",
+              "display": "laboratory"
+            }
+          ],
+          "text": "laboratory"
+        },
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "2069-3",
+              "display": "Chloride"
+            }
+          ],
+          "text": "Chloride"
+        },
+        "subject": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        },
+        "effectiveDateTime": "2018-07-09T15:14:32-07:00",
+        "issued": "2018-07-09T15:14:32.480-07:00",
+        "valueQuantity": {
+          "value": 109.62,
+          "unit": "mmol/L",
+          "system": "http://unitsofmeasure.org",
+          "code": "mmol/L"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f4fb0f1c-0600-4912-8cb3-ca4091597c49",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "f4fb0f1c-0600-4912-8cb3-ca4091597c49",
+        "status": "final",
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/observation-category",
+              "code": "laboratory",
+              "display": "laboratory"
+            }
+          ],
+          "text": "laboratory"
+        },
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "20565-8",
+              "display": "Carbon Dioxide"
+            }
+          ],
+          "text": "Carbon Dioxide"
+        },
+        "subject": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        },
+        "effectiveDateTime": "2018-07-09T15:14:32-07:00",
+        "issued": "2018-07-09T15:14:32.480-07:00",
+        "valueQuantity": {
+          "value": 27.860,
+          "unit": "mmol/L",
+          "system": "http://unitsofmeasure.org",
+          "code": "mmol/L"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:562fc911-423f-46f4-ae18-c56071403825",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "562fc911-423f-46f4-ae18-c56071403825",
+        "status": "final",
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/observation-category",
+              "code": "survey",
+              "display": "survey"
+            }
+          ],
+          "text": "survey"
+        },
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "72166-2",
+              "display": "Tobacco smoking status NHIS"
+            }
+          ],
+          "text": "Tobacco smoking status NHIS"
+        },
+        "subject": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        },
+        "effectiveDateTime": "2018-07-09T15:14:32-07:00",
+        "issued": "2018-07-09T15:14:32.480-07:00",
+        "valueCodeableConcept": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "266919005",
+              "display": "Never smoker"
+            }
+          ],
+          "text": "Never smoker"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:948cc9ea-644e-4430-aa6b-bce7df6983dc",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "948cc9ea-644e-4430-aa6b-bce7df6983dc",
+        "status": "final",
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/observation-category",
+              "code": "laboratory",
+              "display": "laboratory"
+            }
+          ],
+          "text": "laboratory"
+        },
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "4548-4",
+              "display": "Hemoglobin A1c/Hemoglobin.total in Blood"
+            }
+          ],
+          "text": "Hemoglobin A1c/Hemoglobin.total in Blood"
+        },
+        "subject": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        },
+        "effectiveDateTime": "2018-07-09T15:14:32-07:00",
+        "issued": "2018-07-09T15:14:32.480-07:00",
+        "valueQuantity": {
+          "value": 5.9600,
+          "unit": "%",
+          "system": "http://unitsofmeasure.org",
+          "code": "%"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:ba7baf02-d772-4d35-9308-cdbe2c9a3190",
+      "resource": {
+        "resourceType": "Immunization",
+        "id": "ba7baf02-d772-4d35-9308-cdbe2c9a3190",
+        "status": "completed",
+        "date": "2018-07-09T15:14:32-07:00",
+        "vaccineCode": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/sid/cvx",
+              "code": "140",
+              "display": "Influenza, seasonal, injectable, preservative free"
+            }
+          ],
+          "text": "Influenza, seasonal, injectable, preservative free"
+        },
+        "patient": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "wasNotGiven": false,
+        "reported": false,
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Immunization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:badb5f6a-073f-4ad6-b0c2-4a733cc40c89",
+      "resource": {
+        "resourceType": "DiagnosticReport",
+        "id": "badb5f6a-073f-4ad6-b0c2-4a733cc40c89",
+        "status": "final",
+        "category": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/ValueSet/diagnostic-service-sections",
+              "code": "LAB"
+            }
+          ]
+        },
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "51990-0",
+              "display": "Basic Metabolic Panel"
+            }
+          ],
+          "text": "Basic Metabolic Panel"
+        },
+        "subject": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "encounter": {
+          "reference": "urn:uuid:9029c1c3-3e90-430f-84d3-2710961f1a5f"
+        },
+        "effectiveDateTime": "2018-07-09T15:14:32-07:00",
+        "issued": "2018-07-09T15:14:32.480-07:00",
+        "performer": {
+          "reference": "urn:uuid:1f5f3cb7-ad8d-3c50-a15d-470d2a723b84"
+        },
+        "result": [
+          {
+            "reference": "urn:uuid:f4fb0f1c-0600-4912-8cb3-ca4091597c49",
+            "display": "Carbon Dioxide"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "DiagnosticReport"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:6c348dfd-8fe1-4f8e-95f7-6e30e73369ee",
+      "resource": {
+        "resourceType": "Claim",
+        "id": "6c348dfd-8fe1-4f8e-95f7-6e30e73369ee",
+        "type": "institutional",
+        "organization": {
+          "reference": "urn:uuid:1f5f3cb7-ad8d-3c50-a15d-470d2a723b84"
+        },
+        "use": "complete",
+        "patient": {
+          "reference": "urn:uuid:f04ef974-6d6f-4e1c-804f-cd4d62aabb4f"
+        },
+        "item": [
+          {
+            "sequence": 1,
+            "type": {
+              "system": "http://hl7.org/fhir/v3/ActCode",
+              "code": "CSINV",
+              "display": "clinical service invoice"
+            },
+            "service": {
+              "system": "http://snomed.info/sct",
+              "code": "162673000",
+              "display": "General examination of patient (procedure)"
+            }
+          },
+          {
+            "sequence": 2,
+            "type": {
+              "system": "http://hl7.org/fhir/v3/ActCode",
+              "code": "CSINV",
+              "display": "clinical service invoice"
+            },
+            "service": {
+              "system": "http://hl7.org/fhir/sid/cvx",
+              "code": "140",
+              "display": "Influenza, seasonal, injectable, preservative free"
+            },
+            "net": {
+              "value": 140.52,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Claim"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/hospitalInformation1586309771387.json b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/hospitalInformation1586309771387.json
new file mode 100644
index 000000000000..4b9fdcc72d56
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/hospitalInformation1586309771387.json
@@ -0,0 +1,825 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:49318f80-bd8b-3fc7-a096-ac43088b0c12",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "49318f80-bd8b-3fc7-a096-ac43088b0c12",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 21
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "49318f80-bd8b-3fc7-a096-ac43088b0c12"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "COOLEY DICKINSON HOSPITAL INC,THE",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "4135822000"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "30 LOCUST STREET"
+            ],
+            "city": "NORTHAMPTON",
+            "state": "MA",
+            "postalCode": "01060",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:ecc51621-0af3-3b35-ac3e-8b1e34022e92",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "ecc51621-0af3-3b35-ac3e-8b1e34022e92",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 145
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "ecc51621-0af3-3b35-ac3e-8b1e34022e92"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "SAINT ANNE'S HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5086745600"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "795 MIDDLE STREET"
+            ],
+            "city": "FALL RIVER",
+            "state": "MA",
+            "postalCode": "02721",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:08bcda9c-f8c8-3244-82d4-fc306a7a55d3",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "08bcda9c-f8c8-3244-82d4-fc306a7a55d3",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
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+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
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+            "valueInteger": 0
+          }
+        ],
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+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "08bcda9c-f8c8-3244-82d4-fc306a7a55d3"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "BOSTON MEDICAL CENTER CORPORATION-",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "6176388000"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "1 BOSTON MEDICAL CENTER PLACE"
+            ],
+            "city": "BOSTON",
+            "state": "MA",
+            "postalCode": "02118",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:4861d01f-019c-3dac-a153-8334e50919f9",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "4861d01f-019c-3dac-a153-8334e50919f9",
+        "extension": [
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+          {
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+            "valueInteger": 0
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+            "value": "4861d01f-019c-3dac-a153-8334e50919f9"
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+        ],
+        "type": {
+          "coding": [
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+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "NORTH SHORE MEDICAL CENTER -",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "9787411215"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "81 HIGHLAND AVENUE"
+            ],
+            "city": "SALEM",
+            "state": "MA",
+            "postalCode": "01970",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f4e7709c-02f6-37ca-aeea-8247d74e88e7",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "f4e7709c-02f6-37ca-aeea-8247d74e88e7",
+        "extension": [
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+          {
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+          },
+          {
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+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "f4e7709c-02f6-37ca-aeea-8247d74e88e7"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "WINCHESTER HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "7817299000"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "41 HIGHLAND AVENUE"
+            ],
+            "city": "WINCHESTER",
+            "state": "MA",
+            "postalCode": "01890",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:b7175ab4-bde5-3848-891b-579bccb77c7c",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "b7175ab4-bde5-3848-891b-579bccb77c7c",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "b7175ab4-bde5-3848-891b-579bccb77c7c"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "TUFTS MEDICAL CENTER",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "6176365000"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "800 WASHINGTON STREET"
+            ],
+            "city": "BOSTON",
+            "state": "MA",
+            "postalCode": "02111",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:1f5f3cb7-ad8d-3c50-a15d-470d2a723b84",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "1f5f3cb7-ad8d-3c50-a15d-470d2a723b84",
+        "extension": [
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+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 39
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 32
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 22
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 12
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "1f5f3cb7-ad8d-3c50-a15d-470d2a723b84"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "PCP15859",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "413-387-2118"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "92 MAIN ST"
+            ],
+            "city": "FLORENCE",
+            "state": "MA",
+            "postalCode": "01062-1460",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:245f252c-be87-3017-8a0b-a04448a97219",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "245f252c-be87-3017-8a0b-a04448a97219",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 48
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 264
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 19
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 27
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "245f252c-be87-3017-8a0b-a04448a97219"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "PCP45531",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-230-9940"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "661 MASSACHUSETTS AVE"
+            ],
+            "city": "ARLINGTON",
+            "state": "MA",
+            "postalCode": "02476-5001",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f9914571-32b8-36d3-a422-4cdce9fbb86c",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "f9914571-32b8-36d3-a422-4cdce9fbb86c",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 56
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 415
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 45
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 27
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "f9914571-32b8-36d3-a422-4cdce9fbb86c"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "INDEPENDENCE EYE ASSOCIATES, PC",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "508-985-6600"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "365 FAUNCE CORNER RD"
+            ],
+            "city": "DARTMOUTH",
+            "state": "MA",
+            "postalCode": "02747-6230",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:70d8b93b-cc76-3c8b-8929-5aea213ecc86",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "70d8b93b-cc76-3c8b-8929-5aea213ecc86",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 18
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 11
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 2
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 113
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "70d8b93b-cc76-3c8b-8929-5aea213ecc86"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "BROOKLINE DERMATOLOGY ASSOCIATES, PC",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-608-1575"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "1208 B VFW PKWY"
+            ],
+            "city": "WEST ROXBURY",
+            "state": "MA",
+            "postalCode": "02132-4350",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:cab5722d-8856-3fc3-9a04-d3fe34d3e41e",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "cab5722d-8856-3fc3-9a04-d3fe34d3e41e",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 37
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 280
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 13
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 22
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "cab5722d-8856-3fc3-9a04-d3fe34d3e41e"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "COMMONWEALTH RADIOLOGY ASSOCIATES, INC",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "978-741-1200"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "81 HIGHLAND AVE"
+            ],
+            "city": "SALEM",
+            "state": "MA",
+            "postalCode": "01970-2714",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:a76bda1d-f42d-3046-b8c6-021f3db0a086",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "a76bda1d-f42d-3046-b8c6-021f3db0a086",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "a76bda1d-f42d-3046-b8c6-021f3db0a086"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "WALK IN AND PRIMARY CARE",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "781-894-8200"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "808 MAIN STREET"
+            ],
+            "city": "WALTHAM",
+            "state": "MA",
+            "postalCode": "2451",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f7a6cc79-3075-3124-9f62-6fe562440b1d",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "f7a6cc79-3075-3124-9f62-6fe562440b1d",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "f7a6cc79-3075-3124-9f62-6fe562440b1d"
+          }
+        ],
+        "type": {
+          "coding": [
+            {
+              "system": "Healthcare Provider",
+              "code": "prov",
+              "display": "Healthcare Provider"
+            }
+          ],
+          "text": "Healthcare Provider"
+        },
+        "name": "HAWTHORN MEDICAL URGENT CARE CENTER",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "508-961-0861"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "237 STATE ROAD"
+            ],
+            "city": "NORTH DARTMOUTH",
+            "state": "MA",
+            "postalCode": "2747",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/practitionerInformation1586309771387.json b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/practitionerInformation1586309771387.json
new file mode 100644
index 000000000000..59d8bb2107c0
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/practitionerInformation1586309771387.json
@@ -0,0 +1,617 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:c1a3f738-c767-30ab-951c-5c60f3c569c7",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "c1a3f738-c767-30ab-951c-5c60f3c569c7",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 21
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "60"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Hermiston71"
+          ],
+          "given": [
+            "Andrea7"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "30 LOCUST STREET"
+            ],
+            "city": "NORTHAMPTON",
+            "state": "MA",
+            "postalCode": "01060",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:38a05f68-cc3b-33b6-993e-1d2bb2696c3d",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "38a05f68-cc3b-33b6-993e-1d2bb2696c3d",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 145
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "100"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Padberg411"
+          ],
+          "given": [
+            "Ligia986"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "795 MIDDLE STREET"
+            ],
+            "city": "FALL RIVER",
+            "state": "MA",
+            "postalCode": "02721",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:64d6ff1b-ef19-3680-80ea-aa6bcbc550bd",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "64d6ff1b-ef19-3680-80ea-aa6bcbc550bd",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "140"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Kuvalis369"
+          ],
+          "given": [
+            "Maricruz991"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "1 BOSTON MEDICAL CENTER PLACE"
+            ],
+            "city": "BOSTON",
+            "state": "MA",
+            "postalCode": "02118",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:b102f703-9e8c-37a2-8eea-08b67c680a1e",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "b102f703-9e8c-37a2-8eea-08b67c680a1e",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 119
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "160"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Roob72"
+          ],
+          "given": [
+            "Isobel140"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "81 HIGHLAND AVENUE"
+            ],
+            "city": "SALEM",
+            "state": "MA",
+            "postalCode": "01970",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:a0153fac-7137-30d8-bb5a-0cb7af968203",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "a0153fac-7137-30d8-bb5a-0cb7af968203",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 113
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "430"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Carroll471"
+          ],
+          "given": [
+            "Emmitt44"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "41 HIGHLAND AVENUE"
+            ],
+            "city": "WINCHESTER",
+            "state": "MA",
+            "postalCode": "01890",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:002862dc-5ff1-380e-82ad-a3cf9c436044",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "002862dc-5ff1-380e-82ad-a3cf9c436044",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "470"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Orn563"
+          ],
+          "given": [
+            "Serina556"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "800 WASHINGTON STREET"
+            ],
+            "city": "BOSTON",
+            "state": "MA",
+            "postalCode": "02111",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:6d5162ad-3294-398e-9eb4-7021465d4bcd",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "6d5162ad-3294-398e-9eb4-7021465d4bcd",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 39
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "10930"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Pfeffer420"
+          ],
+          "given": [
+            "Darryl392"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "92 MAIN ST"
+            ],
+            "city": "FLORENCE",
+            "state": "MA",
+            "postalCode": "01062-1460",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:8e9a1427-af53-3468-9d67-db3b9191c240",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "8e9a1427-af53-3468-9d67-db3b9191c240",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 48
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "28020"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Waters156"
+          ],
+          "given": [
+            "Damien170"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "661 MASSACHUSETTS AVE"
+            ],
+            "city": "ARLINGTON",
+            "state": "MA",
+            "postalCode": "02476-5001",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:7e727355-643f-3e2b-b89f-f5076660354b",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "7e727355-643f-3e2b-b89f-f5076660354b",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 56
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "61860"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Salazar800"
+          ],
+          "given": [
+            "Rodrigo242"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "365 FAUNCE CORNER RD"
+            ],
+            "city": "DARTMOUTH",
+            "state": "MA",
+            "postalCode": "02747-6230",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:2d307854-d23a-337c-8215-e37f84fdc26e",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "2d307854-d23a-337c-8215-e37f84fdc26e",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 18
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "66350"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Eichmann909"
+          ],
+          "given": [
+            "Marylou497"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "1208 B VFW PKWY"
+            ],
+            "city": "WEST ROXBURY",
+            "state": "MA",
+            "postalCode": "02132-4350",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f4f50d8e-b084-3bc2-a787-30f3a29983fc",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "f4f50d8e-b084-3bc2-a787-30f3a29983fc",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 37
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "78430"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Keeling57"
+          ],
+          "given": [
+            "Johana303"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "81 HIGHLAND AVE"
+            ],
+            "city": "SALEM",
+            "state": "MA",
+            "postalCode": "01970-2714",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:2b592db4-9f8b-3284-bac5-60dc80ccce4c",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "2b592db4-9f8b-3284-bac5-60dc80ccce4c",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "93270"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Padberg411"
+          ],
+          "given": [
+            "Ligia986"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "808 MAIN STREET"
+            ],
+            "city": "WALTHAM",
+            "state": "MA",
+            "postalCode": "2451",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:d4b02c0c-6cc4-31dd-bc8a-817f786b043a",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "d4b02c0c-6cc4-31dd-bc8a-817f786b043a",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "93530"
+          }
+        ],
+        "active": true,
+        "name": {
+          "family": [
+            "Doyle959"
+          ],
+          "given": [
+            "Willis868"
+          ],
+          "prefix": [
+            "Dr."
+          ]
+        },
+        "address": [
+          {
+            "line": [
+              "237 STATE ROAD"
+            ],
+            "city": "NORTH DARTMOUTH",
+            "state": "MA",
+            "postalCode": "2747",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/Emerson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json b/sdks/java/io/google-cloud-platform/src/test/resources/R4/Emerson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json
new file mode 100644
index 000000000000..3bedbb9b820d
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/R4/Emerson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json
@@ -0,0 +1,16391 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: -6045139225077477987  Population seed: 1586368870505
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Pura348 Grant908"
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace",
+            "valueAddress": {
+              "city": "Boston",
+              "state": "Massachusetts",
+              "country": "US"
+            }
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
+            "valueDecimal": 1.3903699305216464
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
+            "valueDecimal": 50.60963006947836
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "MR",
+                  "display": "Medical Record Number"
+                }
+              ],
+              "text": "Medical Record Number"
+            },
+            "system": "http://hospital.smarthealthit.org",
+            "value": "d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "SS",
+                  "display": "Social Security Number"
+                }
+              ],
+              "text": "Social Security Number"
+            },
+            "system": "http://hl7.org/fhir/sid/us-ssn",
+            "value": "999-80-1133"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "DL",
+                  "display": "Driver's License"
+                }
+              ],
+              "text": "Driver's License"
+            },
+            "system": "urn:oid:2.16.840.1.113883.4.3.25",
+            "value": "S99981444"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "PPN",
+                  "display": "Passport Number"
+                }
+              ],
+              "text": "Passport Number"
+            },
+            "system": "http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber",
+            "value": "X32551053X"
+          }
+        ],
+        "name": [
+          {
+            "use": "official",
+            "family": "Prohaska837",
+            "given": [
+              "Emerson869"
+            ],
+            "prefix": [
+              "Mr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "555-300-9464",
+            "use": "home"
+          }
+        ],
+        "gender": "male",
+        "birthDate": "1968-01-01",
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.582871446661336
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.29215663584894
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "113 Toy Mews Unit 67"
+            ],
+            "city": "Billerica",
+            "state": "Massachusetts",
+            "country": "US"
+          }
+        ],
+        "maritalStatus": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus",
+              "code": "M",
+              "display": "M"
+            }
+          ],
+          "text": "M"
+        },
+        "multipleBirthBoolean": false,
+        "communication": [
+          {
+            "language": {
+              "coding": [
+                {
+                  "system": "urn:ietf:bcp:47",
+                  "code": "en-US",
+                  "display": "English"
+                }
+              ],
+              "text": "English"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Patient"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:b0e04623-b02c-3f8b-92ea-943fc4db60da",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "b0e04623-b02c-3f8b-92ea-943fc4db60da",
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "b0e04623-b02c-3f8b-92ea-943fc4db60da"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "LOWELL GENERAL HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "9789376000"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "295 VARNUM AVENUE"
+            ],
+            "city": "LOWELL",
+            "state": "MA",
+            "postalCode": "01854",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:57adca03-a2e1-3753-bcc5-e6ef86bbb821",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "57adca03-a2e1-3753-bcc5-e6ef86bbb821",
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999759"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Tillman293",
+            "given": [
+              "Franklin857"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Franklin857.Tillman293@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "295 VARNUM AVENUE"
+            ],
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+            }
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+          {
+            "sequence": 3,
+            "procedureSequence": [
+              1
+            ],
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "430193006",
+                  "display": "Medication Reconciliation (procedure)"
+                }
+              ],
+              "text": "Medication Reconciliation (procedure)"
+            },
+            "net": {
+              "value": 991.58,
+              "currency": "USD"
+            }
+          }
+        ],
+        "total": {
+          "value": 129.16,
+          "currency": "USD"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Claim"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:bbe8a13e-8315-4a7f-b51e-bd4884fd1d38",
+      "resource": {
+        "resourceType": "ExplanationOfBenefit",
+        "id": "bbe8a13e-8315-4a7f-b51e-bd4884fd1d38",
+        "contained": [
+          {
+            "resourceType": "ServiceRequest",
+            "id": "referral",
+            "status": "completed",
+            "intent": "order",
+            "subject": {
+              "reference": "urn:uuid:d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6"
+            },
+            "requester": {
+              "reference": "urn:uuid:0d5ab589-1d26-346a-b8db-e425d2e139e7"
+            },
+            "performer": [
+              {
+                "reference": "urn:uuid:0d5ab589-1d26-346a-b8db-e425d2e139e7"
+              }
+            ]
+          },
+          {
+            "resourceType": "Coverage",
+            "id": "coverage",
+            "status": "active",
+            "type": {
+              "text": "Cigna Health"
+            },
+            "beneficiary": {
+              "reference": "urn:uuid:d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6"
+            },
+            "payor": [
+              {
+                "display": "Cigna Health"
+              }
+            ]
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://bluebutton.cms.gov/resources/variables/clm_id",
+            "value": "a0c609cd-ca62-45d8-8051-54c4316c4a8a"
+          },
+          {
+            "system": "https://bluebutton.cms.gov/resources/identifier/claim-group",
+            "value": "99999999999"
+          }
+        ],
+        "status": "active",
+        "type": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/claim-type",
+              "code": "institutional"
+            }
+          ]
+        },
+        "use": "claim",
+        "patient": {
+          "reference": "urn:uuid:d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6"
+        },
+        "billablePeriod": {
+          "start": "2020-01-13T04:51:42-08:00",
+          "end": "2021-01-13T04:51:42-08:00"
+        },
+        "created": "2020-01-13T04:51:42-08:00",
+        "insurer": {
+          "display": "Cigna Health"
+        },
+        "provider": {
+          "reference": "urn:uuid:0d5ab589-1d26-346a-b8db-e425d2e139e7"
+        },
+        "referral": {
+          "reference": "#referral"
+        },
+        "claim": {
+          "reference": "urn:uuid:a0c609cd-ca62-45d8-8051-54c4316c4a8a"
+        },
+        "outcome": "complete",
+        "careTeam": [
+          {
+            "sequence": 1,
+            "provider": {
+              "reference": "urn:uuid:0d5ab589-1d26-346a-b8db-e425d2e139e7"
+            },
+            "role": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/claimcareteamrole",
+                  "code": "primary",
+                  "display": "Primary Care Practitioner"
+                }
+              ]
+            }
+          }
+        ],
+        "insurance": [
+          {
+            "focal": true,
+            "coverage": {
+              "reference": "#coverage",
+              "display": "Cigna Health"
+            }
+          }
+        ],
+        "item": [
+          {
+            "sequence": 1,
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "162673000",
+                  "display": "General examination of patient (procedure)"
+                }
+              ],
+              "text": "General examination of patient (procedure)"
+            },
+            "servicedPeriod": {
+              "start": "2020-01-13T04:21:42-08:00",
+              "end": "2020-01-13T04:51:42-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "19",
+                  "display": "Off Campus-Outpatient Hospital"
+                }
+              ]
+            },
+            "encounter": [
+              {
+                "reference": "urn:uuid:c9dd0522-d214-44e6-84a4-30e2751f1896"
+              }
+            ]
+          },
+          {
+            "sequence": 2,
+            "informationSequence": [
+              1
+            ],
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/sid/cvx",
+                  "code": "140",
+                  "display": "Influenza, seasonal, injectable, preservative free"
+                }
+              ],
+              "text": "Influenza, seasonal, injectable, preservative free"
+            },
+            "servicedPeriod": {
+              "start": "2020-01-13T04:21:42-08:00",
+              "end": "2020-01-13T04:51:42-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "19",
+                  "display": "Off Campus-Outpatient Hospital"
+                }
+              ]
+            },
+            "net": {
+              "value": 140.52,
+              "currency": "USD"
+            },
+            "adjudication": [
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 28.104000000000003,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 112.41600000000001,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          },
+          {
+            "sequence": 3,
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "430193006",
+                  "display": "Medication Reconciliation (procedure)"
+                }
+              ],
+              "text": "Medication Reconciliation (procedure)"
+            },
+            "servicedPeriod": {
+              "start": "2020-01-13T04:21:42-08:00",
+              "end": "2020-01-13T04:51:42-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "19",
+                  "display": "Off Campus-Outpatient Hospital"
+                }
+              ]
+            },
+            "net": {
+              "value": 991.58,
+              "currency": "USD"
+            },
+            "adjudication": [
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 198.31600000000003,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 793.2640000000001,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 991.58,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 991.58,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        ],
+        "total": [
+          {
+            "category": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/adjudication",
+                  "code": "submitted",
+                  "display": "Submitted Amount"
+                }
+              ],
+              "text": "Submitted Amount"
+            },
+            "amount": {
+              "value": 129.16,
+              "currency": "USD"
+            }
+          }
+        ],
+        "payment": {
+          "amount": {
+            "value": 905.6800000000002,
+            "currency": "USD"
+          }
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json b/sdks/java/io/google-cloud-platform/src/test/resources/R4/Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json
new file mode 100644
index 000000000000..901fdf2e3177
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/R4/Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json
@@ -0,0 +1,31841 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: -7730420515391289066  Population seed: 1586368870505
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Magnolia736 Weber641"
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace",
+            "valueAddress": {
+              "city": "Concord",
+              "state": "Massachusetts",
+              "country": "US"
+            }
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
+            "valueDecimal": 5.141867221161322
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
+            "valueDecimal": 53.85813277883868
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "MR",
+                  "display": "Medical Record Number"
+                }
+              ],
+              "text": "Medical Record Number"
+            },
+            "system": "http://hospital.smarthealthit.org",
+            "value": "af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "SS",
+                  "display": "Social Security Number"
+                }
+              ],
+              "text": "Social Security Number"
+            },
+            "system": "http://hl7.org/fhir/sid/us-ssn",
+            "value": "999-30-3400"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "DL",
+                  "display": "Driver's License"
+                }
+              ],
+              "text": "Driver's License"
+            },
+            "system": "urn:oid:2.16.840.1.113883.4.3.25",
+            "value": "S99966155"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "PPN",
+                  "display": "Passport Number"
+                }
+              ],
+              "text": "Passport Number"
+            },
+            "system": "http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber",
+            "value": "X73794696X"
+          }
+        ],
+        "name": [
+          {
+            "use": "official",
+            "family": "Marvin195",
+            "given": [
+              "Lorette239"
+            ],
+            "prefix": [
+              "Mrs."
+            ]
+          },
+          {
+            "use": "maiden",
+            "family": "Zemlak964",
+            "given": [
+              "Lorette239"
+            ],
+            "prefix": [
+              "Mrs."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "555-259-1705",
+            "use": "home"
+          }
+        ],
+        "gender": "female",
+        "birthDate": "1960-10-02",
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.378055340679865
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.01059430318017
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "755 Von Mission"
+            ],
+            "city": "Boston",
+            "state": "Massachusetts",
+            "postalCode": "02113",
+            "country": "US"
+          }
+        ],
+        "maritalStatus": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus",
+              "code": "M",
+              "display": "M"
+            }
+          ],
+          "text": "M"
+        },
+        "multipleBirthBoolean": false,
+        "communication": [
+          {
+            "language": {
+              "coding": [
+                {
+                  "system": "urn:ietf:bcp:47",
+                  "code": "en-US",
+                  "display": "English"
+                }
+              ],
+              "text": "English"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Patient"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:76a80350-916e-3fc9-8fed-2c8c4b36c42f",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "76a80350-916e-3fc9-8fed-2c8c4b36c42f",
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "76a80350-916e-3fc9-8fed-2c8c4b36c42f"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "NORTH SUFFOLK MENTAL HEALTH ASSOCIATION, INC.",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-912-7900"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "301 BROADWAY"
+            ],
+            "city": "CHELSEA",
+            "state": "MA",
+            "postalCode": "02150-2807",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:0390078a-1894-335b-9136-5f518ee1dbb6",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "0390078a-1894-335b-9136-5f518ee1dbb6",
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999931799"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Koelpin146",
+            "given": [
+              "Cheryle584"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Cheryle584.Koelpin146@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "301 BROADWAY"
+            ],
+            "city": "CHELSEA",
+            "state": "MA",
+            "postalCode": "02150-2807",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f2ae7ab9-8abe-424a-a52b-72d3603542b7",
+      "resource": {
+        "resourceType": "Encounter",
+        "id": "f2ae7ab9-8abe-424a-a52b-72d3603542b7",
+        "status": "finished",
+        "class": {
+          "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+          "code": "AMB"
+        },
+        "type": [
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+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 28.104000000000003,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 112.41600000000001,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "currency": "USD"
+                }
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+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          },
+          {
+            "sequence": 3,
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "127783003",
+                  "display": "Spirometry (procedure)"
+                }
+              ],
+              "text": "Spirometry (procedure)"
+            },
+            "servicedPeriod": {
+              "start": "2020-01-26T22:43:39-08:00",
+              "end": "2020-01-26T23:13:39-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "19",
+                  "display": "Off Campus-Outpatient Hospital"
+                }
+              ]
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+            "net": {
+              "value": 14224.84,
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 2844.9680000000003,
+                  "currency": "USD"
+                }
+              },
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 11379.872000000001,
+                  "currency": "USD"
+                }
+              },
+              {
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+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 14224.84,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 14224.84,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        ],
+        "total": [
+          {
+            "category": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/adjudication",
+                  "code": "submitted",
+                  "display": "Submitted Amount"
+                }
+              ],
+              "text": "Submitted Amount"
+            },
+            "amount": {
+              "value": 129.16,
+              "currency": "USD"
+            }
+          }
+        ],
+        "payment": {
+          "amount": {
+            "value": 11492.288,
+            "currency": "USD"
+          }
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json b/sdks/java/io/google-cloud-platform/src/test/resources/R4/Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json
new file mode 100644
index 000000000000..a3a593a48dea
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/R4/Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json
@@ -0,0 +1,16971 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:a5e08ef9-fd71-4273-a53a-d5f5df7926f4",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "a5e08ef9-fd71-4273-a53a-d5f5df7926f4",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: -7883787131534806314  Population seed: 1586368870505
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Cinthia596 Thompson596"
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace",
+            "valueAddress": {
+              "city": "Quincy",
+              "state": "Massachusetts",
+              "country": "US"
+            }
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
+            "valueDecimal": 0.0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
+            "valueDecimal": 16.0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "a5e08ef9-fd71-4273-a53a-d5f5df7926f4"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "MR",
+                  "display": "Medical Record Number"
+                }
+              ],
+              "text": "Medical Record Number"
+            },
+            "system": "http://hospital.smarthealthit.org",
+            "value": "a5e08ef9-fd71-4273-a53a-d5f5df7926f4"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "SS",
+                  "display": "Social Security Number"
+                }
+              ],
+              "text": "Social Security Number"
+            },
+            "system": "http://hl7.org/fhir/sid/us-ssn",
+            "value": "999-52-7917"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "DL",
+                  "display": "Driver's License"
+                }
+              ],
+              "text": "Driver's License"
+            },
+            "system": "urn:oid:2.16.840.1.113883.4.3.25",
+            "value": "S99926136"
+          }
+        ],
+        "name": [
+          {
+            "use": "official",
+            "family": "Cole117",
+            "given": [
+              "Norberto865"
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "555-257-6498",
+            "use": "home"
+          }
+        ],
+        "gender": "male",
+        "birthDate": "2003-12-29",
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 41.64238723329318
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.16534881278795
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "436 Rogahn Alley"
+            ],
+            "city": "Fall River",
+            "state": "Massachusetts",
+            "postalCode": "02747",
+            "country": "US"
+          }
+        ],
+        "maritalStatus": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus",
+              "code": "S",
+              "display": "Never Married"
+            }
+          ],
+          "text": "Never Married"
+        },
+        "multipleBirthBoolean": false,
+        "communication": [
+          {
+            "language": {
+              "coding": [
+                {
+                  "system": "urn:ietf:bcp:47",
+                  "code": "en-US",
+                  "display": "English"
+                }
+              ],
+              "text": "English"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Patient"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:75bdb2ec-cbd0-35af-b0fe-18b111890b67",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "75bdb2ec-cbd0-35af-b0fe-18b111890b67",
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "75bdb2ec-cbd0-35af-b0fe-18b111890b67"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "PCP235727",
+        "address": [
+          {
+            "line": [
+              "67 SLADES FERRY BLVD"
+            ],
+            "city": "SOMERSET",
+            "state": "MA",
+            "postalCode": "02726",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:b5c349b9-6f37-31da-a6a0-4c9e00e11ad8",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "b5c349b9-6f37-31da-a6a0-4c9e00e11ad8",
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999931859"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Mante251",
+            "given": [
+              "Bertie593"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Bertie593.Mante251@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "67 SLADES FERRY BLVD"
+            ],
+            "city": "SOMERSET",
+            "state": "MA",
+            "postalCode": "02726",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:3c8db206-734b-4a90-a8bd-c091a117dc86",
+      "resource": {
+        "resourceType": "Encounter",
+        "id": "3c8db206-734b-4a90-a8bd-c091a117dc86",
+        "status": "finished",
+        "class": {
+          "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+          "code": "AMB"
+        },
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "410620009",
+                "display": "Well child visit (procedure)"
+              }
+            ],
+            "text": "Well child visit (procedure)"
+          }
+        ],
+        "subject": {
+          "reference": "urn:uuid:a5e08ef9-fd71-4273-a53a-d5f5df7926f4",
+          "display": "Norberto865 Cole117"
+        },
+        "participant": [
+          {
+            "type": [
+              {
+                "coding": [
+                  {
+                    "system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
+                    "code": "PPRF",
+                    "display": "primary performer"
+                  }
+                ],
+                "text": "primary performer"
+              }
+            ],
+            "period": {
+              "start": "2010-12-20T08:41:37-08:00",
+              "end": "2010-12-20T08:56:37-08:00"
+            },
+            "individual": {
+              "reference": "urn:uuid:b5c349b9-6f37-31da-a6a0-4c9e00e11ad8",
+              "display": "Dr. Bertie593 Mante251"
+            }
+          }
+        ],
+        "period": {
+          "start": "2010-12-20T08:41:37-08:00",
+          "end": "2010-12-20T08:56:37-08:00"
+        },
+        "serviceProvider": {
+          "reference": "urn:uuid:75bdb2ec-cbd0-35af-b0fe-18b111890b67",
+          "display": "PCP235727"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Encounter"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:23a2b208-2135-4a6c-885c-e246549a3f8d",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "23a2b208-2135-4a6c-885c-e246549a3f8d",
+        "status": "final",
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/observation-category",
+                "code": "vital-signs",
+                "display": "vital-signs"
+              }
+            ]
+          }
+        ],
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "8302-2",
+              "display": "Body Height"
+            }
+          ],
+          "text": "Body Height"
+        },
+        "subject": {
+          "reference": "urn:uuid:a5e08ef9-fd71-4273-a53a-d5f5df7926f4"
+        },
+        "encounter": {
+          "reference": "urn:uuid:3c8db206-734b-4a90-a8bd-c091a117dc86"
+        },
+        "effectiveDateTime": "2010-12-20T08:41:37-08:00",
+        "issued": "2010-12-20T08:41:37.844-08:00",
+        "valueQuantity": {
+          "value": 119.1,
+          "unit": "cm",
+          "system": "http://unitsofmeasure.org",
+          "code": "cm"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:e88cac97-70b3-4ec2-bcf4-a1c493d4cdc3",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "e88cac97-70b3-4ec2-bcf4-a1c493d4cdc3",
+        "status": "final",
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/observation-category",
+                "code": "vital-signs",
+                "display": "vital-signs"
+              }
+            ]
+          }
+        ],
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "72514-3",
+              "display": "Pain severity - 0-10 verbal numeric rating [Score] - Reported"
+            }
+          ],
+          "text": "Pain severity - 0-10 verbal numeric rating [Score] - Reported"
+        },
+        "subject": {
+          "reference": "urn:uuid:a5e08ef9-fd71-4273-a53a-d5f5df7926f4"
+        },
+        "encounter": {
+          "reference": "urn:uuid:3c8db206-734b-4a90-a8bd-c091a117dc86"
+        },
+        "effectiveDateTime": "2010-12-20T08:41:37-08:00",
+        "issued": "2010-12-20T08:41:37.844-08:00",
+        "valueQuantity": {
+          "value": 3,
+          "unit": "{score}",
+          "system": "http://unitsofmeasure.org",
+          "code": "{score}"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:3125fbf8-307d-43a9-bb38-409595e448cc",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "3125fbf8-307d-43a9-bb38-409595e448cc",
+        "status": "final",
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/observation-category",
+                "code": "vital-signs",
+                "display": "vital-signs"
+              }
+            ]
+          }
+        ],
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "29463-7",
+              "display": "Body Weight"
+            }
+          ],
+          "text": "Body Weight"
+        },
+        "subject": {
+          "reference": "urn:uuid:a5e08ef9-fd71-4273-a53a-d5f5df7926f4"
+        },
+        "encounter": {
+          "reference": "urn:uuid:3c8db206-734b-4a90-a8bd-c091a117dc86"
+        },
+        "effectiveDateTime": "2010-12-20T08:41:37-08:00",
+        "issued": "2010-12-20T08:41:37.844-08:00",
+        "valueQuantity": {
+          "value": 26.9,
+          "unit": "kg",
+          "system": "http://unitsofmeasure.org",
+          "code": "kg"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:35d44b26-697d-4eb0-b661-44a50a369a16",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "35d44b26-697d-4eb0-b661-44a50a369a16",
+        "status": "final",
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/observation-category",
+                "code": "vital-signs",
+                "display": "vital-signs"
+              }
+            ]
+          }
+        ],
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "39156-5",
+              "display": "Body Mass Index"
+            }
+          ],
+          "text": "Body Mass Index"
+        },
+        "subject": {
+          "reference": "urn:uuid:a5e08ef9-fd71-4273-a53a-d5f5df7926f4"
+        },
+        "encounter": {
+          "reference": "urn:uuid:3c8db206-734b-4a90-a8bd-c091a117dc86"
+        },
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+                "display": "Healthcare Provider"
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+            "text": "Healthcare Provider"
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+        "name": "TRU MEDICAL WALK IN CENTER",
+        "telecom": [
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+            "system": "phone",
+            "value": "508-675-1522"
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+        "address": [
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+            "line": [
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+            "postalCode": "2721",
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+            "family": "Eichmann909",
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+              "Dr."
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+          "reference": "urn:uuid:a5e08ef9-fd71-4273-a53a-d5f5df7926f4"
+        },
+        "billablePeriod": {
+          "start": "2020-02-10T09:11:37-08:00",
+          "end": "2021-02-10T09:11:37-08:00"
+        },
+        "created": "2020-02-10T09:11:37-08:00",
+        "insurer": {
+          "display": "Humana"
+        },
+        "provider": {
+          "reference": "urn:uuid:b5c349b9-6f37-31da-a6a0-4c9e00e11ad8"
+        },
+        "referral": {
+          "reference": "#referral"
+        },
+        "claim": {
+          "reference": "urn:uuid:faa1c861-d568-4d37-a9be-e14f02aabbe5"
+        },
+        "outcome": "complete",
+        "careTeam": [
+          {
+            "sequence": 1,
+            "provider": {
+              "reference": "urn:uuid:b5c349b9-6f37-31da-a6a0-4c9e00e11ad8"
+            },
+            "role": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/claimcareteamrole",
+                  "code": "primary",
+                  "display": "Primary Care Practitioner"
+                }
+              ]
+            }
+          }
+        ],
+        "insurance": [
+          {
+            "focal": true,
+            "coverage": {
+              "reference": "#coverage",
+              "display": "Humana"
+            }
+          }
+        ],
+        "item": [
+          {
+            "sequence": 1,
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "410620009",
+                  "display": "Well child visit (procedure)"
+                }
+              ],
+              "text": "Well child visit (procedure)"
+            },
+            "servicedPeriod": {
+              "start": "2020-02-10T08:41:37-08:00",
+              "end": "2020-02-10T09:11:37-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "19",
+                  "display": "Off Campus-Outpatient Hospital"
+                }
+              ]
+            },
+            "encounter": [
+              {
+                "reference": "urn:uuid:1187f024-a959-4ab6-87b5-8ffe5af07b48"
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+            "informationSequence": [
+              1
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+            "category": {
+              "coding": [
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+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/sid/cvx",
+                  "code": "140",
+                  "display": "Influenza, seasonal, injectable, preservative free"
+                }
+              ],
+              "text": "Influenza, seasonal, injectable, preservative free"
+            },
+            "servicedPeriod": {
+              "start": "2020-02-10T08:41:37-08:00",
+              "end": "2020-02-10T09:11:37-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "19",
+                  "display": "Off Campus-Outpatient Hospital"
+                }
+              ]
+            },
+            "net": {
+              "value": 140.52,
+              "currency": "USD"
+            },
+            "adjudication": [
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+                "category": {
+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 28.104000000000003,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 112.41600000000001,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          },
+          {
+            "sequence": 3,
+            "informationSequence": [
+              2
+            ],
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/sid/cvx",
+                  "code": "114",
+                  "display": "meningococcal MCV4P"
+                }
+              ],
+              "text": "meningococcal MCV4P"
+            },
+            "servicedPeriod": {
+              "start": "2020-02-10T08:41:37-08:00",
+              "end": "2020-02-10T09:11:37-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "19",
+                  "display": "Off Campus-Outpatient Hospital"
+                }
+              ]
+            },
+            "net": {
+              "value": 140.52,
+              "currency": "USD"
+            },
+            "adjudication": [
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 28.104000000000003,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 112.41600000000001,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          },
+          {
+            "sequence": 4,
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "430193006",
+                  "display": "Medication Reconciliation (procedure)"
+                }
+              ],
+              "text": "Medication Reconciliation (procedure)"
+            },
+            "servicedPeriod": {
+              "start": "2020-02-10T08:41:37-08:00",
+              "end": "2020-02-10T09:11:37-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "19",
+                  "display": "Off Campus-Outpatient Hospital"
+                }
+              ]
+            },
+            "net": {
+              "value": 730.56,
+              "currency": "USD"
+            },
+            "adjudication": [
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 146.112,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 584.448,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 730.56,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 730.56,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        ],
+        "total": [
+          {
+            "category": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/adjudication",
+                  "code": "submitted",
+                  "display": "Submitted Amount"
+                }
+              ],
+              "text": "Submitted Amount"
+            },
+            "amount": {
+              "value": 129.16,
+              "currency": "USD"
+            }
+          }
+        ],
+        "payment": {
+          "amount": {
+            "value": 809.28,
+            "currency": "USD"
+          }
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json b/sdks/java/io/google-cloud-platform/src/test/resources/R4/Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json
new file mode 100644
index 000000000000..833a083e3d58
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/R4/Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json
@@ -0,0 +1,80348 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:fcf2f472-77ac-47d7-9c9a-a6702bd2bb80",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "fcf2f472-77ac-47d7-9c9a-a6702bd2bb80",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: -8362707934077662551  Population seed: 1586368870505
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Clelia416 Schmitt836"
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace",
+            "valueAddress": {
+              "city": "Fall River",
+              "state": "Massachusetts",
+              "country": "US"
+            }
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
+            "valueDecimal": 2.806179064509155
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
+            "valueDecimal": 70.19382093549085
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "fcf2f472-77ac-47d7-9c9a-a6702bd2bb80"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "MR",
+                  "display": "Medical Record Number"
+                }
+              ],
+              "text": "Medical Record Number"
+            },
+            "system": "http://hospital.smarthealthit.org",
+            "value": "fcf2f472-77ac-47d7-9c9a-a6702bd2bb80"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "SS",
+                  "display": "Social Security Number"
+                }
+              ],
+              "text": "Social Security Number"
+            },
+            "system": "http://hl7.org/fhir/sid/us-ssn",
+            "value": "999-23-6926"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "DL",
+                  "display": "Driver's License"
+                }
+              ],
+              "text": "Driver's License"
+            },
+            "system": "urn:oid:2.16.840.1.113883.4.3.25",
+            "value": "S99931018"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "PPN",
+                  "display": "Passport Number"
+                }
+              ],
+              "text": "Passport Number"
+            },
+            "system": "http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber",
+            "value": "X38526821X"
+          }
+        ],
+        "name": [
+          {
+            "use": "official",
+            "family": "DuBuque211",
+            "given": [
+              "Robbyn526"
+            ],
+            "prefix": [
+              "Mrs."
+            ]
+          },
+          {
+            "use": "maiden",
+            "family": "Herzog843",
+            "given": [
+              "Robbyn526"
+            ],
+            "prefix": [
+              "Mrs."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "555-953-9961",
+            "use": "home"
+          }
+        ],
+        "gender": "female",
+        "birthDate": "1946-12-09",
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 41.7460901626166
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -70.7291724846944
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "149 Conroy Corner Unit 5"
+            ],
+            "city": "Wareham",
+            "state": "Massachusetts",
+            "country": "US"
+          }
+        ],
+        "maritalStatus": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus",
+              "code": "M",
+              "display": "M"
+            }
+          ],
+          "text": "M"
+        },
+        "multipleBirthBoolean": false,
+        "communication": [
+          {
+            "language": {
+              "coding": [
+                {
+                  "system": "urn:ietf:bcp:47",
+                  "code": "en-US",
+                  "display": "English"
+                }
+              ],
+              "text": "English"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Patient"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:e9e2998f-97d3-3f88-8ee8-82660c5ddfce",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "e9e2998f-97d3-3f88-8ee8-82660c5ddfce",
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "e9e2998f-97d3-3f88-8ee8-82660c5ddfce"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "PCP128586",
+        "address": [
+          {
+            "line": [
+              "2360 CRANBERRY HWY"
+            ],
+            "city": "W WAREHAM",
+            "state": "MA",
+            "postalCode": "02576-1208",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:cf99bf43-51e5-3bab-8623-211cd48f66dc",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "cf99bf43-51e5-3bab-8623-211cd48f66dc",
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999951739"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "DuBuque211",
+            "given": [
+              "Carlyn477"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Carlyn477.DuBuque211@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "2360 CRANBERRY HWY"
+            ],
+            "city": "W WAREHAM",
+            "state": "MA",
+            "postalCode": "02576-1208",
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+                    "display": "Healthcare services (qualifier value)"
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+                ],
+                "text": "Healthcare services (qualifier value)"
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    Activities: 
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    • Lifestyle education regarding hypertension
    • Lifestyle education regarding hypertension
    • Lifestyle education regarding hypertension

    Care plan is meant to treat Hypertension.
    "
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+                    "display": "Counseling about alcohol consumption"
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+              }
+            }
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+                "coding": [
+                  {
+                    "system": "http://snomed.info/sct",
+                    "code": "225323000",
+                    "display": "Smoking cessation education"
+                  }
+                ],
+                "text": "Smoking cessation education"
+              },
+              "status": "in-progress",
+              "location": {
+                "display": "PCP128586"
+              }
+            }
+          }
+        ]
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+          "reference": "urn:uuid:fcf2f472-77ac-47d7-9c9a-a6702bd2bb80",
+          "display": "Robbyn526 DuBuque211"
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+            "focal": true,
+            "coverage": {
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+        ],
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+            "productOrService": {
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+                  "system": "http://snomed.info/sct",
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+                  "display": "General examination of patient (procedure)"
+                }
+              ],
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+            },
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+            ],
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+              "text": "Hypertension"
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+          "currency": "USD"
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+            "id": "coverage",
+            "status": "active",
+            "type": {
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+            "beneficiary": {
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+              }
+            ]
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+            "system": "https://bluebutton.cms.gov/resources/variables/clm_id",
+            "value": "ff4fe9f1-2aef-499b-a72b-809b0d83f747"
+          },
+          {
+            "system": "https://bluebutton.cms.gov/resources/identifier/claim-group",
+            "value": "99999999999"
+          }
+        ],
+        "status": "active",
+        "type": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/claim-type",
+              "code": "institutional"
+            }
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+        },
+        "use": "claim",
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+          "reference": "urn:uuid:fcf2f472-77ac-47d7-9c9a-a6702bd2bb80"
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+          "end": "1966-02-01T04:45:51-08:00"
+        },
+        "created": "1965-02-01T04:45:51-08:00",
+        "insurer": {
+          "display": "Anthem"
+        },
+        "provider": {
+          "reference": "urn:uuid:cf99bf43-51e5-3bab-8623-211cd48f66dc"
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+        "referral": {
+          "reference": "#referral"
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+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/claimcareteamrole",
+                  "code": "primary",
+                  "display": "Primary Care Practitioner"
+                }
+              ]
+            }
+          }
+        ],
+        "diagnosis": [
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+            "diagnosisReference": {
+              "reference": "urn:uuid:023eafd5-a008-4f7e-b974-8e2a25e9e3ad"
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+            "type": [
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+                "coding": [
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+                    "system": "http://terminology.hl7.org/CodeSystem/ex-diagnosistype",
+                    "code": "principal"
+                  }
+                ]
+              }
+            ]
+          }
+        ],
+        "insurance": [
+          {
+            "focal": true,
+            "coverage": {
+              "reference": "#coverage",
+              "display": "Anthem"
+            }
+          }
+        ],
+        "item": [
+          {
+            "sequence": 1,
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "162673000",
+                  "display": "General examination of patient (procedure)"
+                }
+              ],
+              "text": "General examination of patient (procedure)"
+            },
+            "servicedPeriod": {
+              "start": "1965-02-01T04:15:51-08:00",
+              "end": "1965-02-01T04:45:51-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "19",
+                  "display": "Off Campus-Outpatient Hospital"
+                }
+              ]
+            },
+            "encounter": [
+              {
+                "reference": "urn:uuid:24d07440-757c-4b8a-9df9-c8bf9e70a6d3"
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+            "diagnosisSequence": [
+              1
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+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "59621000",
+                  "display": "Hypertension"
+                }
+              ],
+              "text": "Hypertension"
+            },
+            "servicedPeriod": {
+              "start": "1965-02-01T04:15:51-08:00",
+              "end": "1965-02-01T04:45:51-08:00"
+            },
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+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "19",
+                  "display": "Off Campus-Outpatient Hospital"
+                }
+              ]
+            }
+          }
+        ],
+        "total": [
+          {
+            "category": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/adjudication",
+                  "code": "submitted",
+                  "display": "Submitted Amount"
+                }
+              ],
+              "text": "Submitted Amount"
+            },
+            "amount": {
+              "value": 129.16,
+              "currency": "USD"
+            }
+          }
+        ],
+        "payment": {
+          "amount": {
+            "value": 0.0,
+            "currency": "USD"
+          }
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:ef6ab57c-ed94-3dbe-9861-812d515918b3",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "ef6ab57c-ed94-3dbe-9861-812d515918b3",
+        "identifier": [
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+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "ef6ab57c-ed94-3dbe-9861-812d515918b3"
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+        "active": true,
+        "type": [
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+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "CAPE COD HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5087711800"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "88 LEWIS BAY ROAD"
+            ],
+            "city": "HYANNIS",
+            "state": "MA",
+            "postalCode": "02601",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:fb3b949e-e3cb-3069-b280-521ac0512d2e",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "fb3b949e-e3cb-3069-b280-521ac0512d2e",
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999949"
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+        "active": true,
+        "name": [
+          {
+            "family": "Kautzer186",
+            "given": [
+              "Heath320"
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+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Heath320.Kautzer186@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "88 LEWIS BAY ROAD"
+            ],
+            "city": "HYANNIS",
+            "state": "MA",
+            "postalCode": "02601",
+            "country": "US"
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+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
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+                  "code": "312681000",
+                  "display": "Bone density scan (procedure)"
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+          "currency": "USD"
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+            ]
+          },
+          {
+            "resourceType": "Coverage",
+            "id": "coverage",
+            "status": "active",
+            "type": {
+              "text": "Medicare"
+            },
+            "beneficiary": {
+              "reference": "urn:uuid:fcf2f472-77ac-47d7-9c9a-a6702bd2bb80"
+            },
+            "payor": [
+              {
+                "display": "Medicare"
+              }
+            ]
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://bluebutton.cms.gov/resources/variables/clm_id",
+            "value": "5d7891b9-ce88-4018-b029-1734949ed66a"
+          },
+          {
+            "system": "https://bluebutton.cms.gov/resources/identifier/claim-group",
+            "value": "99999999999"
+          }
+        ],
+        "status": "active",
+        "type": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/claim-type",
+              "code": "institutional"
+            }
+          ]
+        },
+        "use": "claim",
+        "patient": {
+          "reference": "urn:uuid:fcf2f472-77ac-47d7-9c9a-a6702bd2bb80"
+        },
+        "billablePeriod": {
+          "start": "2019-12-05T04:51:51-08:00",
+          "end": "2020-12-05T04:51:51-08:00"
+        },
+        "created": "2019-12-05T04:51:51-08:00",
+        "insurer": {
+          "display": "Medicare"
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+        "provider": {
+          "reference": "urn:uuid:fb3b949e-e3cb-3069-b280-521ac0512d2e"
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+          "reference": "#referral"
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+          "reference": "urn:uuid:5d7891b9-ce88-4018-b029-1734949ed66a"
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+                  "system": "http://terminology.hl7.org/CodeSystem/claimcareteamrole",
+                  "code": "primary",
+                  "display": "Primary Care Practitioner"
+                }
+              ]
+            }
+          }
+        ],
+        "insurance": [
+          {
+            "focal": true,
+            "coverage": {
+              "reference": "#coverage",
+              "display": "Medicare"
+            }
+          }
+        ],
+        "item": [
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+            "category": {
+              "coding": [
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+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "185389009",
+                  "display": "Follow-up visit (procedure)"
+                }
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+              "text": "Follow-up visit (procedure)"
+            },
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+              "end": "2019-12-05T04:51:51-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
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+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "21",
+                  "display": "Inpatient Hospital"
+                }
+              ]
+            },
+            "encounter": [
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+                "reference": "urn:uuid:e7ea7228-a522-422b-92f4-1f1481846608"
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+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "312681000",
+                  "display": "Bone density scan (procedure)"
+                }
+              ],
+              "text": "Bone density scan (procedure)"
+            },
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+              "start": "2019-12-05T04:15:51-08:00",
+              "end": "2019-12-05T04:51:51-08:00"
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+                  "display": "Inpatient Hospital"
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+              "currency": "USD"
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+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 2697.6360000000004,
+                  "currency": "USD"
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+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 10790.544000000002,
+                  "currency": "USD"
+                }
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 13488.18,
+                  "currency": "USD"
+                }
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+              {
+                "category": {
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 13488.18,
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        ],
+        "total": [
+          {
+            "category": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/adjudication",
+                  "code": "submitted",
+                  "display": "Submitted Amount"
+                }
+              ],
+              "text": "Submitted Amount"
+            },
+            "amount": {
+              "value": 129.16,
+              "currency": "USD"
+            }
+          }
+        ],
+        "payment": {
+          "amount": {
+            "value": 10790.544000000002,
+            "currency": "USD"
+          }
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/Seymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json b/sdks/java/io/google-cloud-platform/src/test/resources/R4/Seymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json
new file mode 100644
index 000000000000..c4e42e861091
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/R4/Seymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json
@@ -0,0 +1,16018 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:55a5307d-5f23-49c1-9100-7d5c513abca3",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "55a5307d-5f23-49c1-9100-7d5c513abca3",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: -792204183018886300  Population seed: 1586368870505
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Lan153 Dicki44"
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace",
+            "valueAddress": {
+              "city": "Cologne",
+              "state": "North Rhine-Westphalia",
+              "country": "DE"
+            }
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
+            "valueDecimal": 0.1534940636791636
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
+            "valueDecimal": 51.84650593632084
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "55a5307d-5f23-49c1-9100-7d5c513abca3"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "MR",
+                  "display": "Medical Record Number"
+                }
+              ],
+              "text": "Medical Record Number"
+            },
+            "system": "http://hospital.smarthealthit.org",
+            "value": "55a5307d-5f23-49c1-9100-7d5c513abca3"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "SS",
+                  "display": "Social Security Number"
+                }
+              ],
+              "text": "Social Security Number"
+            },
+            "system": "http://hl7.org/fhir/sid/us-ssn",
+            "value": "999-65-3064"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "DL",
+                  "display": "Driver's License"
+                }
+              ],
+              "text": "Driver's License"
+            },
+            "system": "urn:oid:2.16.840.1.113883.4.3.25",
+            "value": "S99982974"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                  "code": "PPN",
+                  "display": "Passport Number"
+                }
+              ],
+              "text": "Passport Number"
+            },
+            "system": "http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber",
+            "value": "X56290648X"
+          }
+        ],
+        "name": [
+          {
+            "use": "official",
+            "family": "Shanahan202",
+            "given": [
+              "Seymour882"
+            ],
+            "prefix": [
+              "Mr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "555-865-2965",
+            "use": "home"
+          }
+        ],
+        "gender": "male",
+        "birthDate": "1967-05-14",
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.38437875197168
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.06923432925981
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "713 Hansen Promenade"
+            ],
+            "city": "Everett",
+            "state": "Massachusetts",
+            "postalCode": "02149",
+            "country": "US"
+          }
+        ],
+        "maritalStatus": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus",
+              "code": "M",
+              "display": "M"
+            }
+          ],
+          "text": "M"
+        },
+        "multipleBirthBoolean": false,
+        "communication": [
+          {
+            "language": {
+              "coding": [
+                {
+                  "system": "urn:ietf:bcp:47",
+                  "code": "de-DE",
+                  "display": "German (Germany)"
+                }
+              ],
+              "text": "German (Germany)"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Patient"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:69176529-fd1f-3b3f-abce-a0a3626769eb",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "69176529-fd1f-3b3f-abce-a0a3626769eb",
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "69176529-fd1f-3b3f-abce-a0a3626769eb"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "MOUNT AUBURN HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "6174923500"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "330 MOUNT AUBURN STREET"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:eabb178d-5fde-3f2a-b2b0-84b601205578",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "eabb178d-5fde-3f2a-b2b0-84b601205578",
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999989"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Streich926",
+            "given": [
+              "Ja391"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Ja391.Streich926@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "330 MOUNT AUBURN STREET"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:b85dd21a-4193-44a8-bcc5-f53d16278ede",
+      "resource": {
+        "resourceType": "Encounter",
+        "id": "b85dd21a-4193-44a8-bcc5-f53d16278ede",
+        "status": "finished",
+        "class": {
+          "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+          "code": "AMB"
+        },
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "185345009",
+                "display": "Encounter for symptom"
+              }
+            ],
+            "text": "Encounter for symptom"
+          }
+        ],
+        "subject": {
+          "reference": "urn:uuid:55a5307d-5f23-49c1-9100-7d5c513abca3",
+          "display": "Mr. Seymour882 Shanahan202"
+        },
+        "participant": [
+          {
+            "type": [
+              {
+                "coding": [
+                  {
+                    "system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
+                    "code": "PPRF",
+                    "display": "primary performer"
+                  }
+                ],
+                "text": "primary performer"
+              }
+            ],
+            "period": {
+              "start": "1970-02-28T16:32:38-08:00",
+              "end": "1970-02-28T17:04:38-08:00"
+            },
+            "individual": {
+              "reference": "urn:uuid:eabb178d-5fde-3f2a-b2b0-84b601205578",
+              "display": "Dr. Ja391 Streich926"
+            }
+          }
+        ],
+        "period": {
+          "start": "1970-02-28T16:32:38-08:00",
+          "end": "1970-02-28T17:04:38-08:00"
+        },
+        "reasonCode": [
+          {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "10509002",
+                "display": "Acute bronchitis (disorder)"
+              }
+            ]
+          }
+        ],
+        "serviceProvider": {
+          "reference": "urn:uuid:69176529-fd1f-3b3f-abce-a0a3626769eb",
+          "display": "MOUNT AUBURN HOSPITAL"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Encounter"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:21af527f-28ce-41d2-ac17-ba4af06c18a0",
+      "resource": {
+        "resourceType": "CareTeam",
+        "id": "21af527f-28ce-41d2-ac17-ba4af06c18a0",
+        "status": "inactive",
+        "subject": {
+          "reference": "urn:uuid:55a5307d-5f23-49c1-9100-7d5c513abca3"
+        },
+        "encounter": {
+          "reference": "urn:uuid:b85dd21a-4193-44a8-bcc5-f53d16278ede"
+        },
+        "period": {
+          "start": "1970-02-28T16:32:38-08:00",
+          "end": "1970-04-19T16:32:38-08:00"
+        },
+        "participant": [
+          {
+            "role": [
+              {
+                "coding": [
+                  {
+                    "system": "http://snomed.info/sct",
+                    "code": "116153009",
+                    "display": "Patient"
+                  }
+                ],
+                "text": "Patient"
+              }
+            ],
+            "member": {
+              "reference": "urn:uuid:55a5307d-5f23-49c1-9100-7d5c513abca3",
+              "display": "Mr. Seymour882 Shanahan202"
+            }
+          },
+          {
+            "role": [
+              {
+                "coding": [
+                  {
+                    "system": "http://snomed.info/sct",
+                    "code": "223366009",
+                    "display": "Healthcare professional (occupation)"
+                  }
+                ],
+                "text": "Healthcare professional (occupation)"
+              }
+            ],
+            "member": {
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+        "id": "d11b0238-af92-47c0-b1c7-a1fee525262c",
+        "contained": [
+          {
+            "resourceType": "ServiceRequest",
+            "id": "referral",
+            "status": "completed",
+            "intent": "order",
+            "subject": {
+              "reference": "urn:uuid:55a5307d-5f23-49c1-9100-7d5c513abca3"
+            },
+            "requester": {
+              "reference": "urn:uuid:eabb178d-5fde-3f2a-b2b0-84b601205578"
+            },
+            "performer": [
+              {
+                "reference": "urn:uuid:eabb178d-5fde-3f2a-b2b0-84b601205578"
+              }
+            ]
+          },
+          {
+            "resourceType": "Coverage",
+            "id": "coverage",
+            "status": "active",
+            "type": {
+              "text": "NO_INSURANCE"
+            },
+            "beneficiary": {
+              "reference": "urn:uuid:55a5307d-5f23-49c1-9100-7d5c513abca3"
+            },
+            "payor": [
+              {
+                "display": "NO_INSURANCE"
+              }
+            ]
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://bluebutton.cms.gov/resources/variables/clm_id",
+            "value": "b8b07ad6-eae4-4e45-b82b-a30d4836203c"
+          },
+          {
+            "system": "https://bluebutton.cms.gov/resources/identifier/claim-group",
+            "value": "99999999999"
+          }
+        ],
+        "status": "active",
+        "type": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/claim-type",
+              "code": "institutional"
+            }
+          ]
+        },
+        "use": "claim",
+        "patient": {
+          "reference": "urn:uuid:55a5307d-5f23-49c1-9100-7d5c513abca3"
+        },
+        "billablePeriod": {
+          "start": "2020-03-22T17:47:38-07:00",
+          "end": "2021-03-22T17:47:38-07:00"
+        },
+        "created": "2020-03-22T17:47:38-07:00",
+        "insurer": {
+          "display": "NO_INSURANCE"
+        },
+        "provider": {
+          "reference": "urn:uuid:eabb178d-5fde-3f2a-b2b0-84b601205578"
+        },
+        "referral": {
+          "reference": "#referral"
+        },
+        "claim": {
+          "reference": "urn:uuid:b8b07ad6-eae4-4e45-b82b-a30d4836203c"
+        },
+        "outcome": "complete",
+        "careTeam": [
+          {
+            "sequence": 1,
+            "provider": {
+              "reference": "urn:uuid:eabb178d-5fde-3f2a-b2b0-84b601205578"
+            },
+            "role": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/claimcareteamrole",
+                  "code": "primary",
+                  "display": "Primary Care Practitioner"
+                }
+              ]
+            }
+          }
+        ],
+        "insurance": [
+          {
+            "focal": true,
+            "coverage": {
+              "reference": "#coverage",
+              "display": "NO_INSURANCE"
+            }
+          }
+        ],
+        "item": [
+          {
+            "sequence": 1,
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://snomed.info/sct",
+                  "code": "185349003",
+                  "display": "Encounter for check up (procedure)"
+                }
+              ],
+              "text": "Encounter for check up (procedure)"
+            },
+            "servicedPeriod": {
+              "start": "2020-03-22T17:32:38-07:00",
+              "end": "2020-03-22T17:47:38-07:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "21",
+                  "display": "Inpatient Hospital"
+                }
+              ]
+            },
+            "encounter": [
+              {
+                "reference": "urn:uuid:59e9b993-6536-4a29-94b4-06b0ac1c47d0"
+              }
+            ]
+          },
+          {
+            "sequence": 2,
+            "informationSequence": [
+              1
+            ],
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "productOrService": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/sid/cvx",
+                  "code": "140",
+                  "display": "Influenza, seasonal, injectable, preservative free"
+                }
+              ],
+              "text": "Influenza, seasonal, injectable, preservative free"
+            },
+            "servicedPeriod": {
+              "start": "2020-03-22T17:32:38-07:00",
+              "end": "2020-03-22T17:47:38-07:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace",
+                  "code": "21",
+                  "display": "Inpatient Hospital"
+                }
+              ]
+            },
+            "net": {
+              "value": 140.52,
+              "currency": "USD"
+            },
+            "adjudication": [
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 28.104000000000003,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 112.41600000000001,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "currency": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        ],
+        "total": [
+          {
+            "category": {
+              "coding": [
+                {
+                  "system": "http://terminology.hl7.org/CodeSystem/adjudication",
+                  "code": "submitted",
+                  "display": "Submitted Amount"
+                }
+              ],
+              "text": "Submitted Amount"
+            },
+            "amount": {
+              "value": 129.16,
+              "currency": "USD"
+            }
+          }
+        ],
+        "payment": {
+          "amount": {
+            "value": 112.41600000000001,
+            "currency": "USD"
+          }
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/hospitalInformation1586368892823.json b/sdks/java/io/google-cloud-platform/src/test/resources/R4/hospitalInformation1586368892823.json
new file mode 100644
index 000000000000..0584f07f2676
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/R4/hospitalInformation1586368892823.json
@@ -0,0 +1,1182 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:69176529-fd1f-3b3f-abce-a0a3626769eb",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "69176529-fd1f-3b3f-abce-a0a3626769eb",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 20
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "69176529-fd1f-3b3f-abce-a0a3626769eb"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "MOUNT AUBURN HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "6174923500"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "330 MOUNT AUBURN STREET"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:e002090d-4e92-300e-b41e-7d1f21dee4c6",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "e002090d-4e92-300e-b41e-7d1f21dee4c6",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 4
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "e002090d-4e92-300e-b41e-7d1f21dee4c6"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "CAMBRIDGE HEALTH ALLIANCE",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "6176652300"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "1493 CAMBRIDGE STREET"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:ef6ab57c-ed94-3dbe-9861-812d515918b3",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "ef6ab57c-ed94-3dbe-9861-812d515918b3",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 199
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "ef6ab57c-ed94-3dbe-9861-812d515918b3"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "CAPE COD HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5087711800"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "88 LEWIS BAY ROAD"
+            ],
+            "city": "HYANNIS",
+            "state": "MA",
+            "postalCode": "02601",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:b0e04623-b02c-3f8b-92ea-943fc4db60da",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "b0e04623-b02c-3f8b-92ea-943fc4db60da",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 38
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "b0e04623-b02c-3f8b-92ea-943fc4db60da"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "LOWELL GENERAL HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "9789376000"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "295 VARNUM AVENUE"
+            ],
+            "city": "LOWELL",
+            "state": "MA",
+            "postalCode": "01854",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:d78e84ec-30aa-3bba-a33a-f29a3a454662",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "d78e84ec-30aa-3bba-a33a-f29a3a454662",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 10
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "d78e84ec-30aa-3bba-a33a-f29a3a454662"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "MASSACHUSETTS GENERAL HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "6177262000"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "55 FRUIT STREET"
+            ],
+            "city": "BOSTON",
+            "state": "MA",
+            "postalCode": "02114",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:23834663-ed53-3da9-b330-d6e1ecb8428e",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "23834663-ed53-3da9-b330-d6e1ecb8428e",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 12
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "23834663-ed53-3da9-b330-d6e1ecb8428e"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "SOUTHCOAST HOSPITAL GROUP, INC",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5086793131"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "363 HIGHLAND AVENUE"
+            ],
+            "city": "FALL RIVER",
+            "state": "MA",
+            "postalCode": "02720",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:44bef9d3-91c2-3005-93e0-ccf436348ff0",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "44bef9d3-91c2-3005-93e0-ccf436348ff0",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 29
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "44bef9d3-91c2-3005-93e0-ccf436348ff0"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "MASSACHUSETTS EYE AND EAR INFIRMARY -",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "6175237900"
+          }
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+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "BRIGHAM AND WOMEN'S FAULKNER HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "6179837000"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "1153 CENTRE STREET"
+            ],
+            "city": "BOSTON",
+            "state": "MA",
+            "postalCode": "02130",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
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+        "url": "Organization"
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+    },
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+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "SHRINERS' HOSPITAL FOR CHILDREN - BOSTON, THE",
+        "telecom": [
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+            "system": "phone",
+            "value": "6177223000"
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+        ],
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+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "NEW ENGLAND ORAL SURGERY ASSOCIATES LLC",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "978-667-8600"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "2 ANDOVER RD"
+            ],
+            "city": "BILLERICA",
+            "state": "MA",
+            "postalCode": "01821-1916",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:7f7c08c8-1c39-3b26-bd34-5122a003dd91",
+      "resource": {
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+          },
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+          }
+        ],
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+            "value": "7f7c08c8-1c39-3b26-bd34-5122a003dd91"
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+        "type": [
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+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "PCP83180",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-389-6951"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "107 FERRY ST"
+            ],
+            "city": "EVERETT",
+            "state": "MA",
+            "postalCode": "02149-4940",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:e9e2998f-97d3-3f88-8ee8-82660c5ddfce",
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+            "value": "e9e2998f-97d3-3f88-8ee8-82660c5ddfce"
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+        "type": [
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+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "PCP128586",
+        "address": [
+          {
+            "line": [
+              "2360 CRANBERRY HWY"
+            ],
+            "city": "W WAREHAM",
+            "state": "MA",
+            "postalCode": "02576-1208",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:75bdb2ec-cbd0-35af-b0fe-18b111890b67",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "75bdb2ec-cbd0-35af-b0fe-18b111890b67",
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+          },
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+            "valueInteger": 4
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 8
+          }
+        ],
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+            "value": "75bdb2ec-cbd0-35af-b0fe-18b111890b67"
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+        ],
+        "active": true,
+        "type": [
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+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "PCP235727",
+        "address": [
+          {
+            "line": [
+              "67 SLADES FERRY BLVD"
+            ],
+            "city": "SOMERSET",
+            "state": "MA",
+            "postalCode": "02726",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:76a80350-916e-3fc9-8fed-2c8c4b36c42f",
+      "resource": {
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+        "id": "76a80350-916e-3fc9-8fed-2c8c4b36c42f",
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+          },
+          {
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+            "valueInteger": 321
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 48
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 55
+          }
+        ],
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+            "value": "76a80350-916e-3fc9-8fed-2c8c4b36c42f"
+          }
+        ],
+        "active": true,
+        "type": [
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+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "NORTH SUFFOLK MENTAL HEALTH ASSOCIATION, INC.",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-912-7900"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "301 BROADWAY"
+            ],
+            "city": "CHELSEA",
+            "state": "MA",
+            "postalCode": "02150-2807",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:4feb5860-8c43-34ea-b2c8-84ff7ca8740b",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "4feb5860-8c43-34ea-b2c8-84ff7ca8740b",
+        "extension": [
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+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
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+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "4feb5860-8c43-34ea-b2c8-84ff7ca8740b"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "TRU MEDICAL WALK IN CENTER",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "508-675-1522"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "528 NEWTON STREET"
+            ],
+            "city": "FALL RIVER",
+            "state": "MA",
+            "postalCode": "2721",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:7116c200-6663-3503-8314-1ee16845e5d3",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "7116c200-6663-3503-8314-1ee16845e5d3",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "7116c200-6663-3503-8314-1ee16845e5d3"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "SAINTS WALK-IN MEDICAL CENTER - URGENT CARE AND OCCUPATIONAL HEALTH",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "978-458-6868"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "85 PARKHURST ROAD"
+            ],
+            "city": "CHELMSFORD",
+            "state": "MA",
+            "postalCode": "1824",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:3265f387-6c51-32ee-8f6d-b2a89caa34d5",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "3265f387-6c51-32ee-8f6d-b2a89caa34d5",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "3265f387-6c51-32ee-8f6d-b2a89caa34d5"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "CHELSEA MGH HEALTH CENTER MEDICAL WALK IN",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-884-8300"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "151 EVERETT AVENUE"
+            ],
+            "city": "CHELSEA",
+            "state": "MA",
+            "postalCode": "2150",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:0f7f97f6-693c-3de9-8190-85feaf4632e2",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "0f7f97f6-693c-3de9-8190-85feaf4632e2",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "0f7f97f6-693c-3de9-8190-85feaf4632e2"
+          }
+        ],
+        "active": true,
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "CONCENTRA URGENT CARE - EAST BOSTON",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-568-6500"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "1 HARBORSIDE DRIVE"
+            ],
+            "city": "EAST BOSTON",
+            "state": "MA",
+            "postalCode": "2128",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/R4/practitionerInformation1586368892823.json b/sdks/java/io/google-cloud-platform/src/test/resources/R4/practitionerInformation1586368892823.json
new file mode 100644
index 000000000000..c2d6b7250129
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/R4/practitionerInformation1586368892823.json
@@ -0,0 +1,978 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:eabb178d-5fde-3f2a-b2b0-84b601205578",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "eabb178d-5fde-3f2a-b2b0-84b601205578",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 20
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999989"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Streich926",
+            "given": [
+              "Ja391"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Ja391.Streich926@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "330 MOUNT AUBURN STREET"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:e4e8b8e3-604e-3bca-978b-afcfa63491d0",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "e4e8b8e3-604e-3bca-978b-afcfa63491d0",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 4
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999959"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Harvey63",
+            "given": [
+              "Alla648"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Alla648.Harvey63@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "1493 CAMBRIDGE STREET"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:fb3b949e-e3cb-3069-b280-521ac0512d2e",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "fb3b949e-e3cb-3069-b280-521ac0512d2e",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 199
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999949"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Kautzer186",
+            "given": [
+              "Heath320"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Heath320.Kautzer186@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "88 LEWIS BAY ROAD"
+            ],
+            "city": "HYANNIS",
+            "state": "MA",
+            "postalCode": "02601",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:57adca03-a2e1-3753-bcc5-e6ef86bbb821",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "57adca03-a2e1-3753-bcc5-e6ef86bbb821",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 38
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999759"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Tillman293",
+            "given": [
+              "Franklin857"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Franklin857.Tillman293@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "295 VARNUM AVENUE"
+            ],
+            "city": "LOWELL",
+            "state": "MA",
+            "postalCode": "01854",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:7b0a96ca-9d87-3146-96e7-ef4e67128176",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "7b0a96ca-9d87-3146-96e7-ef4e67128176",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 10
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999719"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Oberbrunner298",
+            "given": [
+              "Herlinda751"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Herlinda751.Oberbrunner298@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "55 FRUIT STREET"
+            ],
+            "city": "BOSTON",
+            "state": "MA",
+            "postalCode": "02114",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f411d1de-1d0c-365f-8a71-8d225cb962af",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "f411d1de-1d0c-365f-8a71-8d225cb962af",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 12
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999699"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Brakus656",
+            "given": [
+              "Gillian484"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Gillian484.Brakus656@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "363 HIGHLAND AVENUE"
+            ],
+            "city": "FALL RIVER",
+            "state": "MA",
+            "postalCode": "02720",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:fbdf1eef-68c6-378d-90ac-b746ba9bd7ad",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "fbdf1eef-68c6-378d-90ac-b746ba9bd7ad",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 29
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999689"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Mayert710",
+            "given": [
+              "Dovie983"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Dovie983.Mayert710@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "243 CHARLES STREET"
+            ],
+            "city": "BOSTON",
+            "state": "MA",
+            "postalCode": "02114",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:3a576225-3a87-3704-a672-e1c8bc03389f",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "3a576225-3a87-3704-a672-e1c8bc03389f",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 79
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999519"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Howell947",
+            "given": [
+              "Max124"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Max124.Howell947@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "1153 CENTRE STREET"
+            ],
+            "city": "BOSTON",
+            "state": "MA",
+            "postalCode": "02130",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:4c2aa782-3c72-3d1c-be80-70a3bae80c38",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "4c2aa782-3c72-3d1c-be80-70a3bae80c38",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999999379"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Graham902",
+            "given": [
+              "Spencer878"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Spencer878.Graham902@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "51 BLOSSOM STREET"
+            ],
+            "city": "BOSTON",
+            "state": "MA",
+            "postalCode": "02114",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:0d5ab589-1d26-346a-b8db-e425d2e139e7",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "0d5ab589-1d26-346a-b8db-e425d2e139e7",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 42
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999969899"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Gerlach374",
+            "given": [
+              "Lillia547"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Lillia547.Gerlach374@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "2 ANDOVER RD"
+            ],
+            "city": "BILLERICA",
+            "state": "MA",
+            "postalCode": "01821-1916",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:12810b32-78af-32f0-b85c-8177e3f2e2e2",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "12810b32-78af-32f0-b85c-8177e3f2e2e2",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 42
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999959759"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Goldner995",
+            "given": [
+              "Doretta917"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Doretta917.Goldner995@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "107 FERRY ST"
+            ],
+            "city": "EVERETT",
+            "state": "MA",
+            "postalCode": "02149-4940",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:cf99bf43-51e5-3bab-8623-211cd48f66dc",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "cf99bf43-51e5-3bab-8623-211cd48f66dc",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 81
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999951739"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "DuBuque211",
+            "given": [
+              "Carlyn477"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Carlyn477.DuBuque211@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "2360 CRANBERRY HWY"
+            ],
+            "city": "W WAREHAM",
+            "state": "MA",
+            "postalCode": "02576-1208",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:b5c349b9-6f37-31da-a6a0-4c9e00e11ad8",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "b5c349b9-6f37-31da-a6a0-4c9e00e11ad8",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 25
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999931859"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Mante251",
+            "given": [
+              "Bertie593"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Bertie593.Mante251@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "67 SLADES FERRY BLVD"
+            ],
+            "city": "SOMERSET",
+            "state": "MA",
+            "postalCode": "02726",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:0390078a-1894-335b-9136-5f518ee1dbb6",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "0390078a-1894-335b-9136-5f518ee1dbb6",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 54
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999931799"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Koelpin146",
+            "given": [
+              "Cheryle584"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Cheryle584.Koelpin146@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "301 BROADWAY"
+            ],
+            "city": "CHELSEA",
+            "state": "MA",
+            "postalCode": "02150-2807",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:21a54030-cce5-3104-a773-9eb9bd60830b",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "21a54030-cce5-3104-a773-9eb9bd60830b",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 1
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999906799"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Eichmann909",
+            "given": [
+              "Wanetta360"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Wanetta360.Eichmann909@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "528 NEWTON STREET"
+            ],
+            "city": "FALL RIVER",
+            "state": "MA",
+            "postalCode": "2721",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:389e216f-1825-347e-b23b-630d2f37b195",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "389e216f-1825-347e-b23b-630d2f37b195",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999906719"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Watsica258",
+            "given": [
+              "Gidget756"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Gidget756.Watsica258@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "85 PARKHURST ROAD"
+            ],
+            "city": "CHELMSFORD",
+            "state": "MA",
+            "postalCode": "1824",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:fe82a096-86b9-344b-b405-bd24b6ad4715",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "fe82a096-86b9-344b-b405-bd24b6ad4715",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999906709"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Hoppe518",
+            "given": [
+              "Devin82"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Devin82.Hoppe518@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "151 EVERETT AVENUE"
+            ],
+            "city": "CHELSEA",
+            "state": "MA",
+            "postalCode": "2150",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:1296d3c9-02e0-34a2-86e1-0e185a8f92d6",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "1296d3c9-02e0-34a2-86e1-0e185a8f92d6",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "9999906459"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Ankunding277",
+            "given": [
+              "Elton404"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "email",
+            "value": "Elton404.Ankunding277@example.com",
+            "use": "work"
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "1 HARBORSIDE DRIVE"
+            ],
+            "city": "EAST BOSTON",
+            "state": "MA",
+            "postalCode": "2128",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Alexander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Alexander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json
new file mode 100644
index 000000000000..986c874a86e7
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Alexander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json
@@ -0,0 +1,16003 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:02a63c07-9fcc-42ba-aec0-9d5399ac4796",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "02a63c07-9fcc-42ba-aec0-9d5399ac4796",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: 4798728652809701405  Population seed: 1586298193823
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+            "extension": [
+              {
+                "url": "ombCategory",
+                "valueCoding": {
+                  "system": "urn:oid:2.16.840.1.113883.6.238",
+                  "code": "2054-5",
+                  "display": "Black or African American"
+                }
+              },
+              {
+                "url": "text",
+                "valueString": "Black or African American"
+              }
+            ]
+          },
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+            "extension": [
+              {
+                "url": "ombCategory",
+                "valueCoding": {
+                  "system": "urn:oid:2.16.840.1.113883.6.238",
+                  "code": "2186-5",
+                  "display": "Not Hispanic or Latino"
+                }
+              },
+              {
+                "url": "text",
+                "valueString": "Not Hispanic or Latino"
+              }
+            ]
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Mina319 Langworth352"
+          },
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
+            "valueCode": "M"
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
+            "valueAddress": {
+              "city": "Winchester",
+              "state": "Massachusetts",
+              "country": "US"
+            }
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
+            "valueDecimal": 0.0805149386188746
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
+            "valueDecimal": 0.9194850613811254
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "02a63c07-9fcc-42ba-aec0-9d5399ac4796"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v2/0203",
+                  "code": "MR",
+                  "display": "Medical Record Number"
+                }
+              ],
+              "text": "Medical Record Number"
+            },
+            "system": "http://hospital.smarthealthit.org",
+            "value": "02a63c07-9fcc-42ba-aec0-9d5399ac4796"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/identifier-type",
+                  "code": "SB",
+                  "display": "Social Security Number"
+                }
+              ],
+              "text": "Social Security Number"
+            },
+            "system": "http://hl7.org/fhir/sid/us-ssn",
+            "value": "999-16-7591"
+          }
+        ],
+        "name": [
+          {
+            "use": "official",
+            "family": "Romaguera67",
+            "given": [
+              "Alexander630"
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "555-213-6346",
+            "use": "home"
+          }
+        ],
+        "gender": "male",
+        "birthDate": "2018-07-02",
+        "deceasedDateTime": "2020-04-13T06:13:10-07:00",
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.35034978194894
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.11270110210596
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "639 Rogahn Grove"
+            ],
+            "city": "Cambridge",
+            "state": "Massachusetts",
+            "postalCode": "02138",
+            "country": "US"
+          }
+        ],
+        "maritalStatus": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/v3/MaritalStatus",
+              "code": "S",
+              "display": "Never Married"
+            }
+          ],
+          "text": "Never Married"
+        },
+        "multipleBirthBoolean": false,
+        "communication": [
+          {
+            "language": {
+              "coding": [
+                {
+                  "system": "urn:ietf:bcp:47",
+                  "code": "en-US",
+                  "display": "English"
+                }
+              ],
+              "text": "English"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Patient"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:aced4ce4-957a-3d86-b20a-302d12f949a5",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "aced4ce4-957a-3d86-b20a-302d12f949a5",
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "aced4ce4-957a-3d86-b20a-302d12f949a5"
+          }
+        ],
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://hl7.org/fhir/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "LONGFELLOW PRIMARY CARE, PC",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-492-4545"
+          }
+        ],
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.376043
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.11868
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "625 MOUNT AUBURN ST"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138-4518",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:29e6e246-9052-309c-a47f-c2e5bc60c886",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "29e6e246-9052-309c-a47f-c2e5bc60c886",
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "24070"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Waelchi213",
+            "given": [
+              "Cristopher265"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "625 MOUNT AUBURN ST"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138-4518",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:7ad16f28-8d6f-4b2d-a0f2-34ada4ef4492",
+      "resource": {
+        "resourceType": "Encounter",
+        "id": "7ad16f28-8d6f-4b2d-a0f2-34ada4ef4492",
+        "status": "finished",
+        "class": {
+          "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+          "code": "AMB"
+        },
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "410620009",
+                "display": "Well child visit (procedure)"
+              }
+            ],
+            "text": "Well child visit (procedure)"
+          }
+        ],
+        "subject": {
+          "reference": "urn:uuid:02a63c07-9fcc-42ba-aec0-9d5399ac4796"
+        },
+        "participant": [
+          {
+            "individual": {
+              "reference": "urn:uuid:29e6e246-9052-309c-a47f-c2e5bc60c886"
+            }
+          }
+        ],
+        "period": {
+          "start": "2018-07-02T06:13:10-07:00",
+          "end": "2018-07-02T06:28:10-07:00"
+        },
+        "serviceProvider": {
+          "reference": "urn:uuid:aced4ce4-957a-3d86-b20a-302d12f949a5"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Encounter"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:fd976131-d3fc-459a-a942-2cbde9b4ded2",
+      "resource": {
+        "resourceType": "Immunization",
+        "id": "fd976131-d3fc-459a-a942-2cbde9b4ded2",
+        "status": "completed",
+        "notGiven": false,
+        "vaccineCode": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/sid/cvx",
+              "code": "08",
+              "display": "Hep B, adolescent or pediatric"
+            }
+          ],
+          "text": "Hep B, adolescent or pediatric"
+        },
+        "patient": {
+          "reference": "urn:uuid:02a63c07-9fcc-42ba-aec0-9d5399ac4796"
+        },
+        "encounter": {
+          "reference": "urn:uuid:7ad16f28-8d6f-4b2d-a0f2-34ada4ef4492"
+        },
+        "date": "2018-07-02T06:13:10-07:00",
+        "primarySource": true
+      },
+      "request": {
+        "method": "POST",
+        "url": "Immunization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:ac6048bf-c392-489e-a72c-fb2b13c1c181",
+      "resource": {
+        "resourceType": "Claim",
+        "id": "ac6048bf-c392-489e-a72c-fb2b13c1c181",
+        "status": "active",
+        "use": "complete",
+        "patient": {
+          "reference": "urn:uuid:02a63c07-9fcc-42ba-aec0-9d5399ac4796"
+        },
+        "billablePeriod": {
+          "start": "2018-07-02T06:13:10-07:00",
+          "end": "2018-07-02T06:28:10-07:00"
+        },
+        "organization": {
+          "reference": "urn:uuid:aced4ce4-957a-3d86-b20a-302d12f949a5"
+        },
+        "information": [
+          {
+            "sequence": 1,
+            "category": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/claiminformationcategory",
+                  "code": "info"
+                }
+              ]
+            },
+            "valueReference": {
+              "reference": "urn:uuid:fd976131-d3fc-459a-a942-2cbde9b4ded2"
+            }
+          }
+        ],
+        "item": [
+          {
+            "sequence": 1,
+            "encounter": [
+              {
+                "reference": "urn:uuid:7ad16f28-8d6f-4b2d-a0f2-34ada4ef4492"
+              }
+            ]
+          },
+          {
+            "sequence": 2,
+            "informationLinkId": [
+              1
+            ],
+            "net": {
+              "value": 140.52,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          }
+        ],
+        "total": {
+          "value": 129.16,
+          "system": "urn:iso:std:iso:4217",
+          "code": "USD"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Claim"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:750f8437-b065-4c2b-bb4b-05b8b1a90ed8",
+      "resource": {
+        "resourceType": "ExplanationOfBenefit",
+        "id": "750f8437-b065-4c2b-bb4b-05b8b1a90ed8",
+        "meta": {
+          "profile": [
+            "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-claim"
+          ]
+        },
+        "contained": [
+          {
+            "resourceType": "Coverage",
+            "id": "coverage",
+            "type": {
+              "text": "Cigna Health"
+            }
+          }
+        ],
+        "extension": [
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-nch-profnl-cmpnt-chrg-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-nch-bene-ptb-ddctbl-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-nch-bene-ptb-coinsrnc-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-clm-op-prvdr-pmt-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-clm-op-bene-pmt-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-nch-bene-blood-ddctbl-lblty-am-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-clm-mdcr-non-pmt-rsn-cd-extension",
+            "valueCoding": {
+              "system": "https://bluebutton.cms.gov/assets/ig/CodeSystem-clm-mdcr-non-pmt-rsn-cd",
+              "code": "N",
+              "display": "All other reasons for non-payment"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-prpayamt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-fi-num-extension",
+            "valueIdentifier": {
+              "system": "https://bluebutton.cms.gov/assets/ig/CodeSystem-fi-num",
+              "value": "002000"
+            }
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://bluebutton.cms.gov/resources/variables/clm_id",
+            "value": "ac6048bf-c392-489e-a72c-fb2b13c1c181"
+          },
+          {
+            "system": "https://bluebutton.cms.gov/resources/identifier/claim-group",
+            "value": "99999999999"
+          }
+        ],
+        "status": "active",
+        "type": {
+          "coding": [
+            {
+              "system": "https://bluebutton.cms.gov/resources/variables/nch_clm_type_cd",
+              "code": "71",
+              "display": "Local carrier non-durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) claim"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/codesystem/eob-type",
+              "code": "CARRIER",
+              "display": "EOB Type"
+            },
+            {
+              "system": "http://hl7.org/fhir/ex-claimtype",
+              "code": "professional",
+              "display": "Claim Type"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/variables/nch_near_line_rec_ident_cd",
+              "code": "O",
+              "display": "Part B physician/supplier claim record (processed by local carriers; can include DMEPOS services)"
+            }
+          ]
+        },
+        "patient": {
+          "reference": "urn:uuid:02a63c07-9fcc-42ba-aec0-9d5399ac4796"
+        },
+        "billablePeriod": {
+          "extension": [
+            {
+              "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-claim-query-cd-extension",
+              "valueCoding": {
+                "system": "https://bluebutton.cms.gov/assets/ig/ValueSet-claim-query-cd",
+                "code": "3",
+                "display": "Final Bill"
+              }
+            }
+          ],
+          "start": "2018-07-02T06:28:10-07:00",
+          "end": "2019-07-02T06:28:10-07:00"
+        },
+        "provider": {
+          "identifier": {
+            "value": "29e6e246-9052-309c-a47f-c2e5bc60c886"
+          }
+        },
+        "organization": {
+          "identifier": {
+            "value": "aced4ce4-957a-3d86-b20a-302d12f949a5"
+          }
+        },
+        "careTeam": [
+          {
+            "sequence": 1,
+            "provider": {
+              "identifier": {
+                "system": "http://hl7.org/fhir/sid/us-npi",
+                "value": "99999999"
+              }
+            },
+            "role": {
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+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 671.73,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 671.73,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
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+              },
+              {
+                "category": {
+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        ],
+        "totalCost": {
+          "value": 129.16,
+          "system": "urn:iso:std:iso:4217",
+          "code": "USD"
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+            "value": 649.8000000000001,
+            "system": "urn:iso:std:iso:4217",
+            "code": "USD"
+          }
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:b1110ba5-b66d-48bd-98ca-b2cc28ad6eb3",
+      "resource": {
+        "resourceType": "Encounter",
+        "id": "b1110ba5-b66d-48bd-98ca-b2cc28ad6eb3",
+        "status": "finished",
+        "class": {
+          "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+          "code": "AMB"
+        },
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "308646001",
+                "display": "Death Certification"
+              }
+            ],
+            "text": "Death Certification"
+          }
+        ],
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+          "reference": "urn:uuid:02a63c07-9fcc-42ba-aec0-9d5399ac4796"
+        },
+        "participant": [
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+              "reference": "urn:uuid:29e6e246-9052-309c-a47f-c2e5bc60c886"
+            }
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+        ],
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+          "end": "2020-04-13T06:28:10-07:00"
+        },
+        "serviceProvider": {
+          "reference": "urn:uuid:aced4ce4-957a-3d86-b20a-302d12f949a5"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Encounter"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:4a076392-7755-4007-bd4e-516b124cceb5",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "4a076392-7755-4007-bd4e-516b124cceb5",
+        "status": "final",
+        "category": [
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+            "coding": [
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+                "system": "http://hl7.org/fhir/observation-category",
+                "code": "exam",
+                "display": "exam"
+              }
+            ]
+          }
+        ],
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "69453-9",
+              "display": "Cause of Death [US Standard Certificate of Death]"
+            }
+          ],
+          "text": "Cause of Death [US Standard Certificate of Death]"
+        },
+        "subject": {
+          "reference": "urn:uuid:02a63c07-9fcc-42ba-aec0-9d5399ac4796"
+        },
+        "context": {
+          "reference": "urn:uuid:b1110ba5-b66d-48bd-98ca-b2cc28ad6eb3"
+        },
+        "effectiveDateTime": "2020-04-13T06:13:10-07:00",
+        "issued": "2020-04-13T06:13:10.107-07:00",
+        "valueCodeableConcept": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "95281009",
+              "display": "Sudden Cardiac Death"
+            }
+          ],
+          "text": "Sudden Cardiac Death"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:cef6a500-0ea0-41fe-8606-bf3221180ba7",
+      "resource": {
+        "resourceType": "DiagnosticReport",
+        "id": "cef6a500-0ea0-41fe-8606-bf3221180ba7",
+        "status": "final",
+        "code": {
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+              "system": "http://loinc.org",
+              "code": "69409-1",
+              "display": "U.S. standard certificate of death - 2003 revision"
+            }
+          ],
+          "text": "U.S. standard certificate of death - 2003 revision"
+        },
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+          "reference": "urn:uuid:02a63c07-9fcc-42ba-aec0-9d5399ac4796"
+        },
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+          "reference": "urn:uuid:b1110ba5-b66d-48bd-98ca-b2cc28ad6eb3"
+        },
+        "effectiveDateTime": "2020-04-13T06:13:10-07:00",
+        "issued": "2020-04-13T06:13:10.107-07:00",
+        "result": [
+          {
+            "reference": "urn:uuid:4a076392-7755-4007-bd4e-516b124cceb5",
+            "display": "Cause of Death [US Standard Certificate of Death]"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "DiagnosticReport"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:100daf7c-469d-40e7-b263-184f2f44d223",
+      "resource": {
+        "resourceType": "Claim",
+        "id": "100daf7c-469d-40e7-b263-184f2f44d223",
+        "status": "active",
+        "use": "complete",
+        "patient": {
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+        "billablePeriod": {
+          "start": "2020-04-13T06:13:10-07:00",
+          "end": "2020-04-13T06:28:10-07:00"
+        },
+        "organization": {
+          "reference": "urn:uuid:aced4ce4-957a-3d86-b20a-302d12f949a5"
+        },
+        "item": [
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+            "sequence": 1,
+            "encounter": [
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+                "reference": "urn:uuid:b1110ba5-b66d-48bd-98ca-b2cc28ad6eb3"
+              }
+            ]
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+        ],
+        "total": {
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+          "system": "urn:iso:std:iso:4217",
+          "code": "USD"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Claim"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:0c772652-8ab7-4e11-a049-a86d04c2bbb5",
+      "resource": {
+        "resourceType": "ExplanationOfBenefit",
+        "id": "0c772652-8ab7-4e11-a049-a86d04c2bbb5",
+        "meta": {
+          "profile": [
+            "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-claim"
+          ]
+        },
+        "contained": [
+          {
+            "resourceType": "Coverage",
+            "id": "coverage",
+            "type": {
+              "text": "Cigna Health"
+            }
+          }
+        ],
+        "extension": [
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-nch-profnl-cmpnt-chrg-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-nch-bene-ptb-ddctbl-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-nch-bene-ptb-coinsrnc-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-clm-op-prvdr-pmt-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-clm-op-bene-pmt-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-nch-bene-blood-ddctbl-lblty-am-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-clm-mdcr-non-pmt-rsn-cd-extension",
+            "valueCoding": {
+              "system": "https://bluebutton.cms.gov/assets/ig/CodeSystem-clm-mdcr-non-pmt-rsn-cd",
+              "code": "N",
+              "display": "All other reasons for non-payment"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-prpayamt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-fi-num-extension",
+            "valueIdentifier": {
+              "system": "https://bluebutton.cms.gov/assets/ig/CodeSystem-fi-num",
+              "value": "002000"
+            }
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://bluebutton.cms.gov/resources/variables/clm_id",
+            "value": "100daf7c-469d-40e7-b263-184f2f44d223"
+          },
+          {
+            "system": "https://bluebutton.cms.gov/resources/identifier/claim-group",
+            "value": "99999999999"
+          }
+        ],
+        "status": "active",
+        "type": {
+          "coding": [
+            {
+              "system": "https://bluebutton.cms.gov/resources/variables/nch_clm_type_cd",
+              "code": "71",
+              "display": "Local carrier non-durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) claim"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/codesystem/eob-type",
+              "code": "CARRIER",
+              "display": "EOB Type"
+            },
+            {
+              "system": "http://hl7.org/fhir/ex-claimtype",
+              "code": "professional",
+              "display": "Claim Type"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/variables/nch_near_line_rec_ident_cd",
+              "code": "O",
+              "display": "Part B physician/supplier claim record (processed by local carriers; can include DMEPOS services)"
+            }
+          ]
+        },
+        "patient": {
+          "reference": "urn:uuid:02a63c07-9fcc-42ba-aec0-9d5399ac4796"
+        },
+        "billablePeriod": {
+          "extension": [
+            {
+              "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-claim-query-cd-extension",
+              "valueCoding": {
+                "system": "https://bluebutton.cms.gov/assets/ig/ValueSet-claim-query-cd",
+                "code": "3",
+                "display": "Final Bill"
+              }
+            }
+          ],
+          "start": "2020-04-13T06:28:10-07:00",
+          "end": "2021-04-13T06:28:10-07:00"
+        },
+        "provider": {
+          "identifier": {
+            "value": "29e6e246-9052-309c-a47f-c2e5bc60c886"
+          }
+        },
+        "organization": {
+          "identifier": {
+            "value": "aced4ce4-957a-3d86-b20a-302d12f949a5"
+          }
+        },
+        "careTeam": [
+          {
+            "sequence": 1,
+            "provider": {
+              "identifier": {
+                "system": "http://hl7.org/fhir/sid/us-npi",
+                "value": "99999999"
+              }
+            },
+            "role": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/claimcareteamrole",
+                  "code": "primary",
+                  "display": "Primary Care Practitioner"
+                }
+              ]
+            }
+          }
+        ],
+        "insurance": {
+          "coverage": {
+            "reference": "#coverage"
+          }
+        },
+        "item": [
+          {
+            "extension": [
+              {
+                "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-rev-cntr-ndc-qty-extension",
+                "valueQuantity": {
+                  "value": 0
+                }
+              }
+            ],
+            "sequence": 1,
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_place_of_srvc_cd",
+                  "code": "22",
+                  "display": "Outpatient Hospital"
+                }
+              ]
+            }
+          }
+        ],
+        "totalCost": {
+          "value": 129.16,
+          "system": "urn:iso:std:iso:4217",
+          "code": "USD"
+        },
+        "payment": {
+          "amount": {
+            "value": 0.0,
+            "system": "urn:iso:std:iso:4217",
+            "code": "USD"
+          }
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Basil991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Basil991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json
new file mode 100644
index 000000000000..1bf7f49aa84b
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Basil991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json
@@ -0,0 +1,15372 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:88fb71f7-d445-4e5b-8af2-962e8f8e5fb6",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "88fb71f7-d445-4e5b-8af2-962e8f8e5fb6",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: -3160153991630561462  Population seed: 1586298193823
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+            "extension": [
+              {
+                "url": "ombCategory",
+                "valueCoding": {
+                  "system": "urn:oid:2.16.840.1.113883.6.238",
+                  "code": "2054-5",
+                  "display": "Black or African American"
+                }
+              },
+              {
+                "url": "text",
+                "valueString": "Black or African American"
+              }
+            ]
+          },
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+            "extension": [
+              {
+                "url": "ombCategory",
+                "valueCoding": {
+                  "system": "urn:oid:2.16.840.1.113883.6.238",
+                  "code": "2186-5",
+                  "display": "Not Hispanic or Latino"
+                }
+              },
+              {
+                "url": "text",
+                "valueString": "Not Hispanic or Latino"
+              }
+            ]
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Asia282 Crona259"
+          },
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
+            "valueCode": "M"
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
+            "valueAddress": {
+              "city": "Wellesley",
+              "state": "Massachusetts",
+              "country": "US"
+            }
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
+            "valueDecimal": 0.0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
+            "valueDecimal": 1.0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "88fb71f7-d445-4e5b-8af2-962e8f8e5fb6"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v2/0203",
+                  "code": "MR",
+                  "display": "Medical Record Number"
+                }
+              ],
+              "text": "Medical Record Number"
+            },
+            "system": "http://hospital.smarthealthit.org",
+            "value": "88fb71f7-d445-4e5b-8af2-962e8f8e5fb6"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/identifier-type",
+                  "code": "SB",
+                  "display": "Social Security Number"
+                }
+              ],
+              "text": "Social Security Number"
+            },
+            "system": "http://hl7.org/fhir/sid/us-ssn",
+            "value": "999-12-5406"
+          }
+        ],
+        "name": [
+          {
+            "use": "official",
+            "family": "Pfannerstill264",
+            "given": [
+              "Basil991"
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "555-373-9418",
+            "use": "home"
+          }
+        ],
+        "gender": "male",
+        "birthDate": "2018-07-02",
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.40406475290831
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.12753835800636
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "720 Hickle Light Apt 14"
+            ],
+            "city": "Cambridge",
+            "state": "Massachusetts",
+            "postalCode": "02472",
+            "country": "US"
+          }
+        ],
+        "maritalStatus": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/v3/MaritalStatus",
+              "code": "S",
+              "display": "Never Married"
+            }
+          ],
+          "text": "Never Married"
+        },
+        "multipleBirthBoolean": false,
+        "communication": [
+          {
+            "language": {
+              "coding": [
+                {
+                  "system": "urn:ietf:bcp:47",
+                  "code": "en-US",
+                  "display": "English"
+                }
+              ],
+              "text": "English"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Patient"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:83284578-12e5-3582-bfe1-7807e3f7a212",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "83284578-12e5-3582-bfe1-7807e3f7a212",
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "83284578-12e5-3582-bfe1-7807e3f7a212"
+          }
+        ],
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://hl7.org/fhir/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "PCP297713",
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.423844
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -71.10923100000001
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "0 GOVERNORS AVE"
+            ],
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+            "sequence": 2,
+            "diagnosisLinkId": [
+              1
+            ]
+          }
+        ],
+        "total": {
+          "value": 129.16,
+          "system": "urn:iso:std:iso:4217",
+          "code": "USD"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Claim"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:c0afc820-908b-4b15-a534-d05e037ca605",
+      "resource": {
+        "resourceType": "ExplanationOfBenefit",
+        "id": "c0afc820-908b-4b15-a534-d05e037ca605",
+        "contained": [
+          {
+            "resourceType": "ReferralRequest",
+            "id": "1",
+            "status": "completed",
+            "intent": "order",
+            "subject": {
+              "reference": "urn:uuid:88fb71f7-d445-4e5b-8af2-962e8f8e5fb6"
+            },
+            "requester": {
+              "agent": {
+                "identifier": {
+                  "system": "http://hl7.org/fhir/sid/us-npi",
+                  "value": "99999999"
+                }
+              }
+            },
+            "recipient": [
+              {
+                "identifier": {
+                  "system": "http://hl7.org/fhir/sid/us-npi",
+                  "value": "99999999"
+                }
+              }
+            ]
+          },
+          {
+            "resourceType": "Coverage",
+            "id": "coverage",
+            "type": {
+              "text": "NO_INSURANCE"
+            }
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://bluebutton.cms.gov/resources/variables/clm_id",
+            "value": "e322a7e0-7755-4420-8d76-e956d8ef64bb"
+          },
+          {
+            "system": "https://bluebutton.cms.gov/resources/identifier/claim-group",
+            "value": "99999999999"
+          }
+        ],
+        "status": "active",
+        "type": {
+          "coding": [
+            {
+              "system": "https://bluebutton.cms.gov/resources/variables/nch_clm_type_cd",
+              "code": "71",
+              "display": "Local carrier non-durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) claim"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/codesystem/eob-type",
+              "code": "CARRIER",
+              "display": "EOB Type"
+            },
+            {
+              "system": "http://hl7.org/fhir/ex-claimtype",
+              "code": "professional",
+              "display": "Claim Type"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/variables/nch_near_line_rec_ident_cd",
+              "code": "O",
+              "display": "Part B physician/supplier claim record (processed by local carriers; can include DMEPOS services)"
+            }
+          ]
+        },
+        "patient": {
+          "reference": "urn:uuid:88fb71f7-d445-4e5b-8af2-962e8f8e5fb6"
+        },
+        "billablePeriod": {
+          "start": "2019-12-24T05:28:10-08:00",
+          "end": "2020-12-24T05:28:10-08:00"
+        },
+        "created": "2019-12-24T05:28:10-08:00",
+        "provider": {
+          "identifier": {
+            "value": "339a8b0f-de8f-3168-bfe3-89f8b4614840"
+          }
+        },
+        "organization": {
+          "identifier": {
+            "value": "69176529-fd1f-3b3f-abce-a0a3626769eb"
+          }
+        },
+        "referral": {
+          "reference": "#1"
+        },
+        "claim": {
+          "reference": "urn:uuid:e322a7e0-7755-4420-8d76-e956d8ef64bb"
+        },
+        "careTeam": [
+          {
+            "sequence": 1,
+            "provider": {
+              "identifier": {
+                "system": "http://hl7.org/fhir/sid/us-npi",
+                "value": "99999999"
+              }
+            },
+            "role": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/claimcareteamrole",
+                  "code": "primary",
+                  "display": "Primary Care Practitioner"
+                }
+              ]
+            }
+          }
+        ],
+        "diagnosis": [
+          {
+            "extension": [
+              {
+                "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-inpatient-clm-poa-ind-sw1-extension",
+                "valueCoding": {
+                  "system": "https://bluebutton.cms.gov/assets/ig/CodeSystem-clm-poa-ind-sw1",
+                  "code": "Y",
+                  "display": "Diagnosis present at time of admission"
+                }
+              }
+            ],
+            "sequence": 1,
+            "diagnosisReference": {
+              "reference": "urn:uuid:b2631fd3-7099-4f20-b63b-9f6ecc79dec7"
+            },
+            "type": [
+              {
+                "coding": [
+                  {
+                    "system": "https://bluebutton.cms.gov/resources/codesystem/diagnosis-type",
+                    "code": "principal"
+                  }
+                ]
+              }
+            ]
+          }
+        ],
+        "insurance": {
+          "coverage": {
+            "reference": "#coverage"
+          }
+        },
+        "item": [
+          {
+            "sequence": 1,
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "servicedPeriod": {
+              "start": "2019-12-24T05:13:10-08:00",
+              "end": "2019-12-24T05:28:10-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_place_of_srvc_cd",
+                  "code": "21",
+                  "display": "Inpatient Hospital"
+                }
+              ]
+            },
+            "encounter": [
+              {
+                "reference": "urn:uuid:835db05f-836f-4323-bb98-3f330070e494"
+              }
+            ]
+          },
+          {
+            "sequence": 2,
+            "diagnosisLinkId": [
+              1
+            ],
+            "category": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd",
+                  "code": "1",
+                  "display": "Medical care"
+                }
+              ]
+            },
+            "servicedPeriod": {
+              "start": "2019-12-24T05:13:10-08:00",
+              "end": "2019-12-24T05:28:10-08:00"
+            },
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_place_of_srvc_cd",
+                  "code": "21",
+                  "display": "Inpatient Hospital"
+                }
+              ]
+            }
+          }
+        ],
+        "totalCost": {
+          "value": 129.16,
+          "system": "urn:iso:std:iso:4217",
+          "code": "USD"
+        },
+        "payment": {
+          "amount": {
+            "value": 0.0,
+            "system": "urn:iso:std:iso:4217",
+            "code": "USD"
+          }
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json
new file mode 100644
index 000000000000..1f4a6a88e235
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json
@@ -0,0 +1,22688 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:df27a976-5c5e-4b84-ad00-fe32972dce9c",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "df27a976-5c5e-4b84-ad00-fe32972dce9c",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: -4106806494818543385  Population seed: 1586298193823
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+            "extension": [
+              {
+                "url": "ombCategory",
+                "valueCoding": {
+                  "system": "urn:oid:2.16.840.1.113883.6.238",
+                  "code": "2106-3",
+                  "display": "White"
+                }
+              },
+              {
+                "url": "text",
+                "valueString": "White"
+              }
+            ]
+          },
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+            "extension": [
+              {
+                "url": "ombCategory",
+                "valueCoding": {
+                  "system": "urn:oid:2.16.840.1.113883.6.238",
+                  "code": "2186-5",
+                  "display": "Not Hispanic or Latino"
+                }
+              },
+              {
+                "url": "text",
+                "valueString": "Not Hispanic or Latino"
+              }
+            ]
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Babette571 Dooley940"
+          },
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
+            "valueCode": "F"
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
+            "valueAddress": {
+              "city": "Needham",
+              "state": "Massachusetts",
+              "country": "US"
+            }
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
+            "valueDecimal": 0.003367159185079892
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
+            "valueDecimal": 5.99663284081492
+          }
+        ],
+        "identifier": [
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+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "df27a976-5c5e-4b84-ad00-fe32972dce9c"
+          },
+          {
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+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v2/0203",
+                  "code": "MR",
+                  "display": "Medical Record Number"
+                }
+              ],
+              "text": "Medical Record Number"
+            },
+            "system": "http://hospital.smarthealthit.org",
+            "value": "df27a976-5c5e-4b84-ad00-fe32972dce9c"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/identifier-type",
+                  "code": "SB",
+                  "display": "Social Security Number"
+                }
+              ],
+              "text": "Social Security Number"
+            },
+            "system": "http://hl7.org/fhir/sid/us-ssn",
+            "value": "999-61-1293"
+          }
+        ],
+        "name": [
+          {
+            "use": "official",
+            "family": "Lang846",
+            "given": [
+              "Cris921"
+            ]
+          }
+        ],
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "555-281-6453",
+            "use": "home"
+          }
+        ],
+        "gender": "female",
+        "birthDate": "2013-11-29",
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.09755452320718
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -70.83495946935349
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "1082 Vandervort Avenue Apt 70"
+            ],
+            "city": "Hanover",
+            "state": "Massachusetts",
+            "country": "US"
+          }
+        ],
+        "maritalStatus": {
+          "coding": [
+            {
+              "system": "http://hl7.org/fhir/v3/MaritalStatus",
+              "code": "S",
+              "display": "Never Married"
+            }
+          ],
+          "text": "Never Married"
+        },
+        "multipleBirthBoolean": false,
+        "communication": [
+          {
+            "language": {
+              "coding": [
+                {
+                  "system": "urn:ietf:bcp:47",
+                  "code": "en-US",
+                  "display": "English"
+                }
+              ],
+              "text": "English"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Patient"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:97066a41-4fd5-3d4e-b382-a978fb20a5d5",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "97066a41-4fd5-3d4e-b382-a978fb20a5d5",
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "97066a41-4fd5-3d4e-b382-a978fb20a5d5"
+          }
+        ],
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://hl7.org/fhir/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "PCP33234",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "781-829-9300"
+          }
+        ],
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.122956
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -70.85631
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "198 COLUMBIA RD"
+            ],
+            "city": "HANOVER",
+            "state": "MA",
+            "postalCode": "02339-2380",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f9f09686-21e4-3b27-ba68-9b7313d9a553",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "f9f09686-21e4-3b27-ba68-9b7313d9a553",
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "22570"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Homenick806",
+            "given": [
+              "Evan94"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "198 COLUMBIA RD"
+            ],
+            "city": "HANOVER",
+            "state": "MA",
+            "postalCode": "02339-2380",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:de64ec54-276c-4287-b6c1-3584fee7f8b0",
+      "resource": {
+        "resourceType": "Encounter",
+        "id": "de64ec54-276c-4287-b6c1-3584fee7f8b0",
+        "status": "finished",
+        "class": {
+          "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+          "code": "AMB"
+        },
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "410620009",
+                "display": "Well child visit (procedure)"
+              }
+            ],
+            "text": "Well child visit (procedure)"
+          }
+        ],
+        "subject": {
+          "reference": "urn:uuid:df27a976-5c5e-4b84-ad00-fe32972dce9c"
+        },
+        "participant": [
+          {
+            "individual": {
+              "reference": "urn:uuid:f9f09686-21e4-3b27-ba68-9b7313d9a553"
+            }
+          }
+        ],
+        "period": {
+          "start": "2013-11-29T15:21:32-08:00",
+          "end": "2013-11-29T15:51:32-08:00"
+        },
+        "serviceProvider": {
+          "reference": "urn:uuid:97066a41-4fd5-3d4e-b382-a978fb20a5d5"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Encounter"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:1c1addf3-8cd7-4541-bf69-fce5e21f5346",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "1c1addf3-8cd7-4541-bf69-fce5e21f5346",
+        "status": "final",
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://hl7.org/fhir/observation-category",
+                "code": "vital-signs",
+                "display": "vital-signs"
+              }
+            ]
+          }
+        ],
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "8302-2",
+              "display": "Body Height"
+            }
+          ],
+          "text": "Body Height"
+        },
+        "subject": {
+          "reference": "urn:uuid:df27a976-5c5e-4b84-ad00-fe32972dce9c"
+        },
+        "context": {
+          "reference": "urn:uuid:de64ec54-276c-4287-b6c1-3584fee7f8b0"
+        },
+        "effectiveDateTime": "2013-11-29T15:21:32-08:00",
+        "issued": "2013-11-29T15:21:32.447-08:00",
+        "valueQuantity": {
+          "value": 49.600,
+          "unit": "cm",
+          "system": "http://unitsofmeasure.org",
+          "code": "cm"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:bb059a3a-5c99-48ba-b620-ba10f8f98816",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "bb059a3a-5c99-48ba-b620-ba10f8f98816",
+        "status": "final",
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://hl7.org/fhir/observation-category",
+                "code": "vital-signs",
+                "display": "vital-signs"
+              }
+            ]
+          }
+        ],
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "72514-3",
+              "display": "Pain severity - 0-10 verbal numeric rating [Score] - Reported"
+            }
+          ],
+          "text": "Pain severity - 0-10 verbal numeric rating [Score] - Reported"
+        },
+        "subject": {
+          "reference": "urn:uuid:df27a976-5c5e-4b84-ad00-fe32972dce9c"
+        },
+        "context": {
+          "reference": "urn:uuid:de64ec54-276c-4287-b6c1-3584fee7f8b0"
+        },
+        "effectiveDateTime": "2013-11-29T15:21:32-08:00",
+        "issued": "2013-11-29T15:21:32.447-08:00",
+        "valueQuantity": {
+          "value": 1,
+          "unit": "{score}",
+          "system": "http://unitsofmeasure.org",
+          "code": "{score}"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:0ef19301-2656-4de6-bc0b-40543e493be5",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "0ef19301-2656-4de6-bc0b-40543e493be5",
+        "status": "final",
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://hl7.org/fhir/observation-category",
+                "code": "vital-signs",
+                "display": "vital-signs"
+              }
+            ]
+          }
+        ],
+        "code": {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "29463-7",
+              "display": "Body Weight"
+            }
+          ],
+          "text": "Body Weight"
+        },
+        "subject": {
+          "reference": "urn:uuid:df27a976-5c5e-4b84-ad00-fe32972dce9c"
+        },
+        "context": {
+          "reference": "urn:uuid:de64ec54-276c-4287-b6c1-3584fee7f8b0"
+        },
+        "effectiveDateTime": "2013-11-29T15:21:32-08:00",
+        "issued": "2013-11-29T15:21:32.447-08:00",
+        "valueQuantity": {
+          "value": 3.2000,
+          "unit": "kg",
+          "system": "http://unitsofmeasure.org",
+          "code": "kg"
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "Observation"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:9a0ddc69-b028-4339-b4a3-a1d4894e774e",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "9a0ddc69-b028-4339-b4a3-a1d4894e774e",
+        "status": "final",
+        "category": [
+          {
+            "coding": [
+              {
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+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json
new file mode 100644
index 000000000000..65e224b7d394
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json
@@ -0,0 +1,28126 @@
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+              "display": "Head Occipital-frontal circumference"
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+              "system": "https://bluebutton.cms.gov/resources/variables/nch_clm_type_cd",
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+              "display": "Local carrier non-durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) claim"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/codesystem/eob-type",
+              "code": "CARRIER",
+              "display": "EOB Type"
+            },
+            {
+              "system": "http://hl7.org/fhir/ex-claimtype",
+              "code": "professional",
+              "display": "Claim Type"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/variables/nch_near_line_rec_ident_cd",
+              "code": "O",
+              "display": "Part B physician/supplier claim record (processed by local carriers; can include DMEPOS services)"
+            }
+          ]
+        },
+        "patient": {
+          "reference": "urn:uuid:136f997d-0a94-4573-97da-a53b5060a612"
+        },
+        "billablePeriod": {
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+              "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-claim-query-cd-extension",
+              "valueCoding": {
+                "system": "https://bluebutton.cms.gov/assets/ig/ValueSet-claim-query-cd",
+                "code": "3",
+                "display": "Final Bill"
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+            }
+          ],
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+          "end": "2017-12-14T20:20:11-08:00"
+        },
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+                "value": "99999999"
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+                  "system": "http://hl7.org/fhir/claimcareteamrole",
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+                  "display": "Primary Care Practitioner"
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+              ]
+            }
+          }
+        ],
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+        "status": "final",
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+                "display": "vital-signs"
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+        ],
+        "code": {
+          "coding": [
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+              "system": "http://loinc.org",
+              "code": "8302-2",
+              "display": "Body Height"
+            }
+          ],
+          "text": "Body Height"
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+        "subject": {
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+            "valueMoney": {
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+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
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+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-nch-bene-blood-ddctbl-lblty-am-extension",
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+              "system": "urn:iso:std:iso:4217",
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+          },
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+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-clm-mdcr-non-pmt-rsn-cd-extension",
+            "valueCoding": {
+              "system": "https://bluebutton.cms.gov/assets/ig/CodeSystem-clm-mdcr-non-pmt-rsn-cd",
+              "code": "N",
+              "display": "All other reasons for non-payment"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-prpayamt-extension",
+            "valueMoney": {
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+              "system": "urn:iso:std:iso:4217",
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+          },
+          {
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+            "valueIdentifier": {
+              "system": "https://bluebutton.cms.gov/assets/ig/CodeSystem-fi-num",
+              "value": "002000"
+            }
+          }
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+            "value": "337b8fa6-bdbd-4019-9aff-068fab01cdd2"
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+            "value": "99999999999"
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+              "code": "71",
+              "display": "Local carrier non-durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) claim"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/codesystem/eob-type",
+              "code": "CARRIER",
+              "display": "EOB Type"
+            },
+            {
+              "system": "http://hl7.org/fhir/ex-claimtype",
+              "code": "professional",
+              "display": "Claim Type"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/variables/nch_near_line_rec_ident_cd",
+              "code": "O",
+              "display": "Part B physician/supplier claim record (processed by local carriers; can include DMEPOS services)"
+            }
+          ]
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+              "valueCoding": {
+                "system": "https://bluebutton.cms.gov/assets/ig/ValueSet-claim-query-cd",
+                "code": "3",
+                "display": "Final Bill"
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+                      "display": "Line Beneficiary Coinsurance Amount"
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+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
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+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
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+                  "system": "urn:iso:std:iso:4217",
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+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
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+                  "system": "urn:iso:std:iso:4217",
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
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+                }
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+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Dannette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Dannette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json
new file mode 100644
index 000000000000..47d9b906b987
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Dannette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json
@@ -0,0 +1,18231 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:74779846-85a4-4b26-9da4-414a5fec1aed",
+      "resource": {
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+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-clm-op-prvdr-pmt-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-clm-op-bene-pmt-amt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-nch-bene-blood-ddctbl-lblty-am-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-clm-mdcr-non-pmt-rsn-cd-extension",
+            "valueCoding": {
+              "system": "https://bluebutton.cms.gov/assets/ig/CodeSystem-clm-mdcr-non-pmt-rsn-cd",
+              "code": "N",
+              "display": "All other reasons for non-payment"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-prpayamt-extension",
+            "valueMoney": {
+              "value": 0.0,
+              "system": "urn:iso:std:iso:4217",
+              "code": "USD"
+            }
+          },
+          {
+            "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-fi-num-extension",
+            "valueIdentifier": {
+              "system": "https://bluebutton.cms.gov/assets/ig/CodeSystem-fi-num",
+              "value": "002000"
+            }
+          }
+        ],
+        "identifier": [
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+            "system": "https://bluebutton.cms.gov/resources/variables/clm_id",
+            "value": "7fbe2cfb-5891-41d9-bbd0-575b81fb2291"
+          },
+          {
+            "system": "https://bluebutton.cms.gov/resources/identifier/claim-group",
+            "value": "99999999999"
+          }
+        ],
+        "status": "active",
+        "type": {
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+              "system": "https://bluebutton.cms.gov/resources/variables/nch_clm_type_cd",
+              "code": "71",
+              "display": "Local carrier non-durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) claim"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/codesystem/eob-type",
+              "code": "CARRIER",
+              "display": "EOB Type"
+            },
+            {
+              "system": "http://hl7.org/fhir/ex-claimtype",
+              "code": "professional",
+              "display": "Claim Type"
+            },
+            {
+              "system": "https://bluebutton.cms.gov/resources/variables/nch_near_line_rec_ident_cd",
+              "code": "O",
+              "display": "Part B physician/supplier claim record (processed by local carriers; can include DMEPOS services)"
+            }
+          ]
+        },
+        "patient": {
+          "reference": "urn:uuid:74779846-85a4-4b26-9da4-414a5fec1aed"
+        },
+        "billablePeriod": {
+          "extension": [
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+              "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-claim-query-cd-extension",
+              "valueCoding": {
+                "system": "https://bluebutton.cms.gov/assets/ig/ValueSet-claim-query-cd",
+                "code": "3",
+                "display": "Final Bill"
+              }
+            }
+          ],
+          "start": "2019-05-16T23:56:28-07:00",
+          "end": "2020-05-16T23:56:28-07:00"
+        },
+        "provider": {
+          "identifier": {
+            "value": "3dde31b6-dbc2-394b-b2af-a3167d1f6841"
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+        "organization": {
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+            "value": "7bdd7bd6-d521-3b19-81b6-ce2ed80d9e74"
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+                "system": "http://hl7.org/fhir/sid/us-npi",
+                "value": "99999999"
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+            "role": {
+              "coding": [
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+                  "system": "http://hl7.org/fhir/claimcareteamrole",
+                  "code": "primary",
+                  "display": "Primary Care Practitioner"
+                }
+              ]
+            }
+          }
+        ],
+        "insurance": {
+          "coverage": {
+            "reference": "#coverage"
+          }
+        },
+        "item": [
+          {
+            "extension": [
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+                "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-rev-cntr-ndc-qty-extension",
+                "valueQuantity": {
+                  "value": 0
+                }
+              }
+            ],
+            "sequence": 1,
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_place_of_srvc_cd",
+                  "code": "22",
+                  "display": "Outpatient Hospital"
+                }
+              ]
+            }
+          },
+          {
+            "extension": [
+              {
+                "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-rev-cntr-ndc-qty-extension",
+                "valueQuantity": {
+                  "value": 0
+                }
+              }
+            ],
+            "sequence": 2,
+            "locationCodeableConcept": {
+              "coding": [
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+                  "system": "https://bluebutton.cms.gov/resources/variables/line_place_of_srvc_cd",
+                  "code": "22",
+                  "display": "Outpatient Hospital"
+                }
+              ]
+            },
+            "adjudication": [
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+                "category": {
+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 28.104000000000003,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 112.41600000000001,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
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+                "category": {
+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
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+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          },
+          {
+            "extension": [
+              {
+                "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-rev-cntr-ndc-qty-extension",
+                "valueQuantity": {
+                  "value": 0
+                }
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+            ],
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+            "locationCodeableConcept": {
+              "coding": [
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+                  "system": "https://bluebutton.cms.gov/resources/variables/line_place_of_srvc_cd",
+                  "code": "22",
+                  "display": "Outpatient Hospital"
+                }
+              ]
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+            "adjudication": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
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+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
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+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
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+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          },
+          {
+            "extension": [
+              {
+                "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-rev-cntr-ndc-qty-extension",
+                "valueQuantity": {
+                  "value": 0
+                }
+              }
+            ],
+            "sequence": 4,
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_place_of_srvc_cd",
+                  "code": "22",
+                  "display": "Outpatient Hospital"
+                }
+              ]
+            },
+            "adjudication": [
+              {
+                "category": {
+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
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+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
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+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
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+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
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+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
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+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
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+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
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+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          },
+          {
+            "extension": [
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+                "url": "https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton-outpatient-rev-cntr-ndc-qty-extension",
+                "valueQuantity": {
+                  "value": 0
+                }
+              }
+            ],
+            "sequence": 5,
+            "locationCodeableConcept": {
+              "coding": [
+                {
+                  "system": "https://bluebutton.cms.gov/resources/variables/line_place_of_srvc_cd",
+                  "code": "22",
+                  "display": "Outpatient Hospital"
+                }
+              ]
+            },
+            "adjudication": [
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+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_coinsrnc_amt",
+                      "display": "Line Beneficiary Coinsurance Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 28.104000000000003,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
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+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prvdr_pmt_amt",
+                      "display": "Line Provider Payment Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 112.41600000000001,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_sbmtd_chrg_amt",
+                      "display": "Line Submitted Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_alowd_chrg_amt",
+                      "display": "Line Allowed Charge Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 140.52,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_bene_ptb_ddctbl_amt",
+                      "display": "Line Beneficiary Part B Deductible Amount"
+                    }
+                  ]
+                },
+                "amount": {
+                  "value": 0,
+                  "system": "urn:iso:std:iso:4217",
+                  "code": "USD"
+                }
+              },
+              {
+                "category": {
+                  "coding": [
+                    {
+                      "system": "https://bluebutton.cms.gov/resources/codesystem/adjudication",
+                      "code": "https://bluebutton.cms.gov/resources/variables/line_prcsg_ind_cd",
+                      "display": "Line Processing Indicator Code"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        ],
+        "totalCost": {
+          "value": 129.16,
+          "system": "urn:iso:std:iso:4217",
+          "code": "USD"
+        },
+        "payment": {
+          "amount": {
+            "value": 449.66400000000004,
+            "system": "urn:iso:std:iso:4217",
+            "code": "USD"
+          }
+        }
+      },
+      "request": {
+        "method": "POST",
+        "url": "ExplanationOfBenefit"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json
new file mode 100644
index 000000000000..ae6d3327430c
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json
@@ -0,0 +1,32061 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:3024090f-fe14-40a9-8fae-79952d3c95ce",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "3024090f-fe14-40a9-8fae-79952d3c95ce",
+        "text": {
+          "status": "generated",
+          "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n .   Person seed: 8703012480265391650  Population seed: 1586298193823
    "
+        },
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+            "extension": [
+              {
+                "url": "ombCategory",
+                "valueCoding": {
+                  "system": "urn:oid:2.16.840.1.113883.6.238",
+                  "code": "2106-3",
+                  "display": "White"
+                }
+              },
+              {
+                "url": "text",
+                "valueString": "White"
+              }
+            ]
+          },
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+            "extension": [
+              {
+                "url": "ombCategory",
+                "valueCoding": {
+                  "system": "urn:oid:2.16.840.1.113883.6.238",
+                  "code": "2186-5",
+                  "display": "Not Hispanic or Latino"
+                }
+              },
+              {
+                "url": "text",
+                "valueString": "Not Hispanic or Latino"
+              }
+            ]
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
+            "valueString": "Mary779 Green467"
+          },
+          {
+            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
+            "valueCode": "F"
+          },
+          {
+            "url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
+            "valueAddress": {
+              "city": "Danvers",
+              "state": "Massachusetts",
+              "country": "US"
+            }
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years",
+            "valueDecimal": 0.0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years",
+            "valueDecimal": 25.0
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "3024090f-fe14-40a9-8fae-79952d3c95ce"
+          },
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v2/0203",
+                  "code": "MR",
+                  "display": "Medical Record Number"
+                }
+              ],
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+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/hospitalInformation1586298239556.json b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/hospitalInformation1586298239556.json
new file mode 100644
index 000000000000..02eefcfa77eb
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/hospitalInformation1586298239556.json
@@ -0,0 +1,880 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
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+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 0
+          },
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+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 0
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 0
+          }
+        ],
+        "identifier": [
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+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "69176529-fd1f-3b3f-abce-a0a3626769eb"
+          }
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+        "type": [
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+                "system": "http://hl7.org/fhir/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
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+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "MOUNT AUBURN HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "6174923500"
+          }
+        ],
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+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
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+                    "valueDecimal": 42.375967
+                  },
+                  {
+                    "url": "longitude",
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+            "line": [
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+            "country": "US"
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+                "display": "Healthcare Provider"
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+            "text": "Healthcare Provider"
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+        "name": "CAMBRIDGE HEALTH ALLIANCE",
+        "telecom": [
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+            "system": "phone",
+            "value": "6176652300"
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+        ],
+        "address": [
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+                "extension": [
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+            "value": "5844ad77-f653-3c2b-b7dd-e97576ab3b03"
+          }
+        ],
+        "type": [
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+                "system": "http://hl7.org/fhir/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "BAYSTATE WING HOSPITAL AND MEDICAL CENTERS",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "4132837651"
+          }
+        ],
+        "address": [
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+            "extension": [
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+            "state": "MA",
+            "postalCode": "01069",
+            "country": "US"
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+        ]
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+            "value": "c44f361c-2efb-3050-8f97-0354a12e2920"
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+        ],
+        "type": [
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+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "SIGNATURE HEALTHCARE BROCKTON HOSPITAL",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5089417000"
+          }
+        ],
+        "address": [
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+            "extension": [
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+            "line": [
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+      },
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+          {
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+            "value": "226098a2-6a40-3588-b5bb-db56c3a30a04"
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+        ],
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+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
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+        ],
+        "name": "GOOD SAMARITAN MEDICAL CENTER",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "5084273000"
+          }
+        ],
+        "address": [
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+            "line": [
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+            "postalCode": "02301",
+            "country": "US"
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+        ],
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+        "telecom": [
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+            "value": "781-829-9300"
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+            "value": "aced4ce4-957a-3d86-b20a-302d12f949a5"
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+            ],
+            "text": "Healthcare Provider"
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+        ],
+        "name": "LONGFELLOW PRIMARY CARE, PC",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "617-492-4545"
+          }
+        ],
+        "address": [
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+            "postalCode": "02138-4518",
+            "country": "US"
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+        "name": "PCP297713",
+        "address": [
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+            "state": "MA",
+            "postalCode": "02155-3084",
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+            "value": "7bdd7bd6-d521-3b19-81b6-ce2ed80d9e74"
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+            ],
+            "text": "Healthcare Provider"
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+        ],
+        "name": "SIGNATURE HEALTHCARE MEDICAL GROUP INC",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "781-878-1700"
+          }
+        ],
+        "address": [
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+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.119966999999995
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -70.957211
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "360 BROCKTON AVE"
+            ],
+            "city": "ABINGTON",
+            "state": "MA",
+            "postalCode": "02351-2186",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:883860d6-0862-3a47-a18f-7256563c53f4",
+      "resource": {
+        "resourceType": "Organization",
+        "id": "883860d6-0862-3a47-a18f-7256563c53f4",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 34
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension",
+            "valueInteger": 50
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension",
+            "valueInteger": 5
+          },
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension",
+            "valueInteger": 29
+          }
+        ],
+        "identifier": [
+          {
+            "system": "https://github.com/synthetichealth/synthea",
+            "value": "883860d6-0862-3a47-a18f-7256563c53f4"
+          }
+        ],
+        "type": [
+          {
+            "coding": [
+              {
+                "system": "http://hl7.org/fhir/organization-type",
+                "code": "prov",
+                "display": "Healthcare Provider"
+              }
+            ],
+            "text": "Healthcare Provider"
+          }
+        ],
+        "name": "HARRINGTON PHYSICIAN SERVICES INC",
+        "telecom": [
+          {
+            "system": "phone",
+            "value": "413-245-0966"
+          }
+        ],
+        "address": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
+                "extension": [
+                  {
+                    "url": "latitude",
+                    "valueDecimal": 42.128176
+                  },
+                  {
+                    "url": "longitude",
+                    "valueDecimal": -72.205352
+                  }
+                ]
+              }
+            ],
+            "line": [
+              "255 E OLD STURBRIDGE RD"
+            ],
+            "city": "BRIMFIELD",
+            "state": "MA",
+            "postalCode": "01010-9647",
+            "country": "US"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization"
+      }
+    }
+  ]
+}
diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/STU3/practitionerInformation1586298239556.json b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/practitionerInformation1586298239556.json
new file mode 100644
index 000000000000..32853f75bf0c
--- /dev/null
+++ b/sdks/java/io/google-cloud-platform/src/test/resources/STU3/practitionerInformation1586298239556.json
@@ -0,0 +1,523 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:339a8b0f-de8f-3168-bfe3-89f8b4614840",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "339a8b0f-de8f-3168-bfe3-89f8b4614840",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 11
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "10"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Jenkins714",
+            "given": [
+              "Lara964"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "330 MOUNT AUBURN STREET"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:6a3782fa-7d6e-302f-bec5-695563b123a8",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "6a3782fa-7d6e-302f-bec5-695563b123a8",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 9
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "40"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Gibson10",
+            "given": [
+              "Loretta235"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "1493 CAMBRIDGE STREET"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:42f9935b-696e-37c9-8261-2a8c72d02dc9",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "42f9935b-696e-37c9-8261-2a8c72d02dc9",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 46
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "130"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Abernathy524",
+            "given": [
+              "Kirby843"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "40 WRIGHT STREET"
+            ],
+            "city": "PALMER",
+            "state": "MA",
+            "postalCode": "01069",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:d08d5908-40a4-3571-8c54-0cc029c8277f",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "d08d5908-40a4-3571-8c54-0cc029c8277f",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 2
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "200"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Padberg411",
+            "given": [
+              "Nila48"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "680 CENTER STREET"
+            ],
+            "city": "BROCKTON",
+            "state": "MA",
+            "postalCode": "02302",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:27fac077-3105-3983-8b0f-cc4f30f9e7c1",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "27fac077-3105-3983-8b0f-cc4f30f9e7c1",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 8
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "460"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Fay398",
+            "given": [
+              "Deneen201"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "235 NORTH PEARL STREET"
+            ],
+            "city": "BROCKTON",
+            "state": "MA",
+            "postalCode": "02301",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:ba314750-701e-3370-ade0-270e178d80e0",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "ba314750-701e-3370-ade0-270e178d80e0",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 17
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "22240"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Pacocha935",
+            "given": [
+              "Ula130"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "158 A BELMONT ST"
+            ],
+            "city": "WATERTOWN",
+            "state": "MA",
+            "postalCode": "02472-2912",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:f9f09686-21e4-3b27-ba68-9b7313d9a553",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "f9f09686-21e4-3b27-ba68-9b7313d9a553",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 15
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "22570"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Homenick806",
+            "given": [
+              "Evan94"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "198 COLUMBIA RD"
+            ],
+            "city": "HANOVER",
+            "state": "MA",
+            "postalCode": "02339-2380",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:29e6e246-9052-309c-a47f-c2e5bc60c886",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "29e6e246-9052-309c-a47f-c2e5bc60c886",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 9
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "24070"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Waelchi213",
+            "given": [
+              "Cristopher265"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "625 MOUNT AUBURN ST"
+            ],
+            "city": "CAMBRIDGE",
+            "state": "MA",
+            "postalCode": "02138-4518",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:d726e757-2975-3d6a-bdf9-517546432499",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "d726e757-2975-3d6a-bdf9-517546432499",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 8
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "80690"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Abernathy524",
+            "given": [
+              "Ulrike696"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "0 GOVERNORS AVE"
+            ],
+            "city": "MEDFORD",
+            "state": "MA",
+            "postalCode": "02155-3084",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:3dde31b6-dbc2-394b-b2af-a3167d1f6841",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "3dde31b6-dbc2-394b-b2af-a3167d1f6841",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 20
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "81770"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Ondricka197",
+            "given": [
+              "Leisa54"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "360 BROCKTON AVE"
+            ],
+            "city": "ABINGTON",
+            "state": "MA",
+            "postalCode": "02351-2186",
+            "country": "US"
+          }
+        ],
+        "gender": "female"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:7212c355-6c66-3c09-b527-bb8d33b0a915",
+      "resource": {
+        "resourceType": "Practitioner",
+        "id": "7212c355-6c66-3c09-b527-bb8d33b0a915",
+        "extension": [
+          {
+            "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension",
+            "valueInteger": 34
+          }
+        ],
+        "identifier": [
+          {
+            "system": "http://hl7.org/fhir/sid/us-npi",
+            "value": "85760"
+          }
+        ],
+        "active": true,
+        "name": [
+          {
+            "family": "Kihn564",
+            "given": [
+              "Hayden835"
+            ],
+            "prefix": [
+              "Dr."
+            ]
+          }
+        ],
+        "address": [
+          {
+            "line": [
+              "255 E OLD STURBRIDGE RD"
+            ],
+            "city": "BRIMFIELD",
+            "state": "MA",
+            "postalCode": "01010-9647",
+            "country": "US"
+          }
+        ],
+        "gender": "male"
+      },
+      "request": {
+        "method": "POST",
+        "url": "Practitioner"
+      }
+    }
+  ]
+}

From b33ed49f75e2b3074211a8d907cab91270828fea Mon Sep 17 00:00:00 2001
From: Niel Markwick 
Date: Thu, 21 May 2020 03:24:03 +0200
Subject: [PATCH 041/151] [BEAM-9822] Simplify pipeline when batching is
 disabled. (#11529)

* Disable grouping by default when streaming.

Grouping adds significant latency and memory use, and when streaming
this causes both OOMs and high pipeline latencies.

* Simplify pipeline when batching is disabled.

When batching is disabled, there is no need for SpannerIO to read the
schema, group, sort, batch and write batches, so simplify the pipeline
to just write the mutation.

* Fix noBatching test
---
 .../beam/sdk/io/gcp/spanner/SpannerIO.java    | 166 ++++++++++--------
 .../io/gcp/spanner/SpannerIOWriteTest.java    |  20 ++-
 2 files changed, 109 insertions(+), 77 deletions(-)

diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/spanner/SpannerIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/spanner/SpannerIO.java
index 07f227ad250a..94ad154ff7b0 100644
--- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/spanner/SpannerIO.java
+++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/spanner/SpannerIO.java
@@ -59,6 +59,7 @@
 import org.apache.beam.sdk.transforms.Create;
 import org.apache.beam.sdk.transforms.DoFn;
 import org.apache.beam.sdk.transforms.Flatten;
+import org.apache.beam.sdk.transforms.MapElements;
 import org.apache.beam.sdk.transforms.PTransform;
 import org.apache.beam.sdk.transforms.ParDo;
 import org.apache.beam.sdk.transforms.Reshuffle;
@@ -81,6 +82,7 @@
 import org.apache.beam.sdk.values.PCollectionView;
 import org.apache.beam.sdk.values.TupleTag;
 import org.apache.beam.sdk.values.TupleTagList;
+import org.apache.beam.sdk.values.TypeDescriptor;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.annotations.VisibleForTesting;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Stopwatch;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
@@ -1022,84 +1024,98 @@ public void populateDisplayData(DisplayData.Builder builder) {
 
     @Override
     public SpannerWriteResult expand(PCollection input) {
+      PCollection> batches;
+
+      if (spec.getBatchSizeBytes() <= 1
+          || spec.getMaxNumMutations() <= 1
+          || spec.getMaxNumRows() <= 1) {
+        LOG.info("Batching of mutationGroups is disabled");
+        TypeDescriptor> descriptor =
+            new TypeDescriptor>() {};
+        batches =
+            input.apply(MapElements.into(descriptor).via(element -> ImmutableList.of(element)));
+      } else {
 
-      // First, read the Cloud Spanner schema.
-      PCollection schemaSeed =
-          input.getPipeline().apply("Create Seed", Create.of((Void) null));
-      if (spec.getSchemaReadySignal() != null) {
-        // Wait for external signal before reading schema.
-        schemaSeed = schemaSeed.apply("Wait for schema", Wait.on(spec.getSchemaReadySignal()));
+        // First, read the Cloud Spanner schema.
+        PCollection schemaSeed =
+            input.getPipeline().apply("Create Seed", Create.of((Void) null));
+        if (spec.getSchemaReadySignal() != null) {
+          // Wait for external signal before reading schema.
+          schemaSeed = schemaSeed.apply("Wait for schema", Wait.on(spec.getSchemaReadySignal()));
+        }
+        final PCollectionView schemaView =
+            schemaSeed
+                .apply(
+                    "Read information schema",
+                    ParDo.of(new ReadSpannerSchema(spec.getSpannerConfig())))
+                .apply("Schema View", View.asSingleton());
+
+        // Split the mutations into batchable and unbatchable mutations.
+        // Filter out mutation groups too big to be batched.
+        PCollectionTuple filteredMutations =
+            input
+                .apply(
+                    "RewindowIntoGlobal",
+                    Window.into(new GlobalWindows())
+                        .triggering(DefaultTrigger.of())
+                        .discardingFiredPanes())
+                .apply(
+                    "Filter Unbatchable Mutations",
+                    ParDo.of(
+                            new BatchableMutationFilterFn(
+                                schemaView,
+                                UNBATCHABLE_MUTATIONS_TAG,
+                                spec.getBatchSizeBytes(),
+                                spec.getMaxNumMutations(),
+                                spec.getMaxNumRows()))
+                        .withSideInputs(schemaView)
+                        .withOutputTags(
+                            BATCHABLE_MUTATIONS_TAG, TupleTagList.of(UNBATCHABLE_MUTATIONS_TAG)));
+
+        // Build a set of Mutation groups from the current bundle,
+        // sort them by table/key then split into batches.
+        PCollection> batchedMutations =
+            filteredMutations
+                .get(BATCHABLE_MUTATIONS_TAG)
+                .apply(
+                    "Gather And Sort",
+                    ParDo.of(
+                            new GatherBundleAndSortFn(
+                                spec.getBatchSizeBytes(),
+                                spec.getMaxNumMutations(),
+                                spec.getMaxNumRows(),
+                                // Do not group on streaming unless explicitly set.
+                                spec.getGroupingFactor()
+                                    .orElse(
+                                        input.isBounded() == IsBounded.BOUNDED
+                                            ? DEFAULT_GROUPING_FACTOR
+                                            : 1),
+                                schemaView))
+                        .withSideInputs(schemaView))
+                .apply(
+                    "Create Batches",
+                    ParDo.of(
+                            new BatchFn(
+                                spec.getBatchSizeBytes(),
+                                spec.getMaxNumMutations(),
+                                spec.getMaxNumRows(),
+                                schemaView))
+                        .withSideInputs(schemaView));
+
+        // Merge the batched and unbatchable mutation PCollections and write to Spanner.
+        batches =
+            PCollectionList.of(filteredMutations.get(UNBATCHABLE_MUTATIONS_TAG))
+                .and(batchedMutations)
+                .apply("Merge", Flatten.pCollections());
       }
-      final PCollectionView schemaView =
-          schemaSeed
-              .apply(
-                  "Read information schema",
-                  ParDo.of(new ReadSpannerSchema(spec.getSpannerConfig())))
-              .apply("Schema View", View.asSingleton());
-
-      // Split the mutations into batchable and unbatchable mutations.
-      // Filter out mutation groups too big to be batched.
-      PCollectionTuple filteredMutations =
-          input
-              .apply(
-                  "RewindowIntoGlobal",
-                  Window.into(new GlobalWindows())
-                      .triggering(DefaultTrigger.of())
-                      .discardingFiredPanes())
-              .apply(
-                  "Filter Unbatchable Mutations",
-                  ParDo.of(
-                          new BatchableMutationFilterFn(
-                              schemaView,
-                              UNBATCHABLE_MUTATIONS_TAG,
-                              spec.getBatchSizeBytes(),
-                              spec.getMaxNumMutations(),
-                              spec.getMaxNumRows()))
-                      .withSideInputs(schemaView)
-                      .withOutputTags(
-                          BATCHABLE_MUTATIONS_TAG, TupleTagList.of(UNBATCHABLE_MUTATIONS_TAG)));
-
-      // Build a set of Mutation groups from the current bundle,
-      // sort them by table/key then split into batches.
-      PCollection> batchedMutations =
-          filteredMutations
-              .get(BATCHABLE_MUTATIONS_TAG)
-              .apply(
-                  "Gather And Sort",
-                  ParDo.of(
-                          new GatherBundleAndSortFn(
-                              spec.getBatchSizeBytes(),
-                              spec.getMaxNumMutations(),
-                              spec.getMaxNumRows(),
-                              // Do not group on streaming unless explicitly set.
-                              spec.getGroupingFactor()
-                                  .orElse(
-                                      input.isBounded() == IsBounded.BOUNDED
-                                          ? DEFAULT_GROUPING_FACTOR
-                                          : 1),
-                              schemaView))
-                      .withSideInputs(schemaView))
-              .apply(
-                  "Create Batches",
-                  ParDo.of(
-                          new BatchFn(
-                              spec.getBatchSizeBytes(),
-                              spec.getMaxNumMutations(),
-                              spec.getMaxNumRows(),
-                              schemaView))
-                      .withSideInputs(schemaView));
-
-      // Merge the batchable and unbatchable mutation PCollections and write to Spanner.
+
       PCollectionTuple result =
-          PCollectionList.of(filteredMutations.get(UNBATCHABLE_MUTATIONS_TAG))
-              .and(batchedMutations)
-              .apply("Merge", Flatten.pCollections())
-              .apply(
-                  "Write mutations to Spanner",
-                  ParDo.of(
-                          new WriteToSpannerFn(
-                              spec.getSpannerConfig(), spec.getFailureMode(), FAILED_MUTATIONS_TAG))
-                      .withOutputTags(MAIN_OUT_TAG, TupleTagList.of(FAILED_MUTATIONS_TAG)));
+          batches.apply(
+              "Write batches to Spanner",
+              ParDo.of(
+                      new WriteToSpannerFn(
+                          spec.getSpannerConfig(), spec.getFailureMode(), FAILED_MUTATIONS_TAG))
+                  .withOutputTags(MAIN_OUT_TAG, TupleTagList.of(FAILED_MUTATIONS_TAG)));
 
       return new SpannerWriteResult(
           input.getPipeline(),
diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/spanner/SpannerIOWriteTest.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/spanner/SpannerIOWriteTest.java
index ffcbaefff9a5..816556cf1bc3 100644
--- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/spanner/SpannerIOWriteTest.java
+++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/spanner/SpannerIOWriteTest.java
@@ -263,18 +263,34 @@ private void verifyBatches(Iterable... batches) {
 
   @Test
   public void noBatching() throws Exception {
+
+    // This test uses a different mock/fake because it explicitly does not want to populate the
+    // Spanner schema.
+    FakeServiceFactory fakeServiceFactory = new FakeServiceFactory();
+    ReadOnlyTransaction tx = mock(ReadOnlyTransaction.class);
+    when(fakeServiceFactory.mockDatabaseClient().readOnlyTransaction()).thenReturn(tx);
+
+    // Capture batches sent to writeAtLeastOnce.
+    when(fakeServiceFactory.mockDatabaseClient().writeAtLeastOnce(mutationBatchesCaptor.capture()))
+        .thenReturn(null);
+
     PCollection mutations = pipeline.apply(Create.of(g(m(1L)), g(m(2L))));
     mutations.apply(
         SpannerIO.write()
             .withProjectId("test-project")
             .withInstanceId("test-instance")
             .withDatabaseId("test-database")
-            .withServiceFactory(serviceFactory)
+            .withServiceFactory(fakeServiceFactory)
             .withBatchSizeBytes(1)
             .grouped());
     pipeline.run();
 
-    verifyBatches(batch(m(1L)), batch(m(2L)));
+    verify(fakeServiceFactory.mockDatabaseClient(), times(1))
+        .writeAtLeastOnce(mutationsInNoOrder(batch(m(1L))));
+    verify(fakeServiceFactory.mockDatabaseClient(), times(1))
+        .writeAtLeastOnce(mutationsInNoOrder(batch(m(2L))));
+    // If no batching then the DB schema is never read.
+    verify(tx, never()).executeQuery(any());
   }
 
   @Test

From 9cf6f5f3b0beb27b53fac6bd895114fef4b0fe6d Mon Sep 17 00:00:00 2001
From: Brian Hulette 
Date: Wed, 20 May 2020 18:52:31 -0700
Subject: [PATCH 042/151] Moving to 2.23.0-SNAPSHOT on master branch.

---
 .../groovy/org/apache/beam/gradle/BeamModulePlugin.groovy     | 2 +-
 gradle.properties                                             | 4 ++--
 sdks/python/apache_beam/version.py                            | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy b/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy
index eaf79fbdd696..5757ef79af81 100644
--- a/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy
+++ b/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy
@@ -311,7 +311,7 @@ class BeamModulePlugin implements Plugin {
 
     // Automatically use the official release version if we are performing a release
     // otherwise append '-SNAPSHOT'
-    project.version = '2.22.0'
+    project.version = '2.23.0'
     if (!isRelease(project)) {
       project.version += '-SNAPSHOT'
     }
diff --git a/gradle.properties b/gradle.properties
index e29a95f52554..22f2c251bd7e 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -23,8 +23,8 @@ offlineRepositoryRoot=offline-repository
 signing.gnupg.executable=gpg
 signing.gnupg.useLegacyGpg=true
 
-version=2.22.0-SNAPSHOT
-sdk_version=2.22.0.dev
+version=2.23.0-SNAPSHOT
+sdk_version=2.23.0.dev
 
 javaVersion=1.8
 
diff --git a/sdks/python/apache_beam/version.py b/sdks/python/apache_beam/version.py
index 154e15b9a6f5..964e46428565 100644
--- a/sdks/python/apache_beam/version.py
+++ b/sdks/python/apache_beam/version.py
@@ -17,4 +17,4 @@
 
 """Apache Beam SDK version information and utilities."""
 
-__version__ = '2.22.0.dev'
+__version__ = '2.23.0.dev'

From ffd74b0c07bd9a89ffe021cfcb15cc5fbf40d9f9 Mon Sep 17 00:00:00 2001
From: Lukasz Cwik 
Date: Wed, 20 May 2020 20:13:13 -0700
Subject: [PATCH 043/151] [BEAM-10028] Add support for the state backed
 iterable coder to the Java SDK harness. (#11746)

* [BEAM-10028] Add support for the state backed iterable coder to the Java SDK harness.

This required supporting a translation context through CoderTranslator to give access to the BeamFnStateClient and current process bundle instruction id.

* fixup! Address PR comments
---
 .../AvroGenericCoderTranslator.java           |   4 +-
 .../core/construction/CoderTranslation.java   |  35 ++-
 .../core/construction/CoderTranslator.java    |   8 +-
 .../core/construction/CoderTranslators.java   |   9 +-
 .../construction/ModelCoderRegistrar.java     |  11 +-
 .../core/construction/ModelCoders.java        |  12 +-
 .../construction/RehydratedComponents.java    |   4 +-
 .../construction/CoderTranslationTest.java    |   5 +-
 .../core/construction/CommonCoderTest.java    |   3 +-
 .../construction/ParDoTranslationTest.java    |   4 +-
 .../construction/PipelineTranslationTest.java |   5 +-
 .../beam/runners/dataflow/DataflowRunner.java |   4 +-
 .../dataflow/worker/FnApiWindowMappingFn.java |   9 +-
 .../beam/sdk/coders/IterableLikeCoder.java    |  22 +-
 .../BufferedElementCountingOutputStream.java  |  14 +-
 ...fferedElementCountingOutputStreamTest.java |  16 +-
 .../expansion/service/ExpansionService.java   |   3 +-
 .../beam/fn/harness/BeamFnDataReadRunner.java |  18 +-
 .../fn/harness/BeamFnDataWriteRunner.java     |  26 +-
 .../beam/fn/harness/state/BagUserState.java   |   2 +-
 .../fn/harness/state/MultimapSideInput.java   |   6 +-
 .../fn/harness/state/StateBackedIterable.java | 224 ++++++++++++++++++
 .../harness/state/StateFetchingIterators.java |   2 +-
 .../fn/harness/BeamFnDataReadRunnerTest.java  |   1 +
 .../fn/harness/BeamFnDataWriteRunnerTest.java |   3 +-
 .../beam/fn/harness/FnApiDoFnRunnerTest.java  |   7 +-
 .../state/StateBackedIterableTest.java        | 184 ++++++++++++++
 27 files changed, 600 insertions(+), 41 deletions(-)
 create mode 100644 sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/StateBackedIterable.java
 create mode 100644 sdks/java/harness/src/test/java/org/apache/beam/fn/harness/state/StateBackedIterableTest.java

diff --git a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/AvroGenericCoderTranslator.java b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/AvroGenericCoderTranslator.java
index 564a8d3db3cc..53a566c1b52c 100644
--- a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/AvroGenericCoderTranslator.java
+++ b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/AvroGenericCoderTranslator.java
@@ -20,6 +20,7 @@
 import java.util.Collections;
 import java.util.List;
 import org.apache.avro.Schema;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.sdk.coders.AvroGenericCoder;
 import org.apache.beam.sdk.coders.Coder;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Charsets;
@@ -37,7 +38,8 @@ public byte[] getPayload(AvroGenericCoder from) {
   }
 
   @Override
-  public AvroGenericCoder fromComponents(List> components, byte[] payload) {
+  public AvroGenericCoder fromComponents(
+      List> components, byte[] payload, TranslationContext context) {
     Schema schema = new Schema.Parser().parse(new String(payload, Charsets.UTF_8));
     return AvroGenericCoder.of(schema);
   }
diff --git a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslation.java b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslation.java
index 86f017814d53..6f6c59b20df9 100644
--- a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslation.java
+++ b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslation.java
@@ -36,6 +36,22 @@
 
 /** Converts to and from Beam Runner API representations of {@link Coder Coders}. */
 public class CoderTranslation {
+
+  /**
+   * Pass through additional parameters beyond the components and payload to be able to translate
+   * specific coders.
+   *
+   * 
    Portability state API backed coders is an example of such a coder translator requiring
+   * additional parameters.
+   */
+  public interface TranslationContext {
+    /** The default translation context containing no additional parameters. */
+    TranslationContext DEFAULT = new DefaultTranslationContext();
+  }
+
+  /** A convenient class representing a default context containing no additional parameters. */
+  private static class DefaultTranslationContext implements TranslationContext {}
+
   // This URN says that the coder is just a UDF blob this SDK understands
   // TODO: standardize such things
   public static final String JAVA_SERIALIZED_CODER_URN = "beam:coders:javasdk:0.1";
@@ -115,21 +131,29 @@ private static RunnerApi.Coder toCustomCoder(Coder coder) throws IOException
         .build();
   }
 
-  public static Coder fromProto(RunnerApi.Coder protoCoder, RehydratedComponents components)
+  public static Coder fromProto(
+      RunnerApi.Coder protoCoder, RehydratedComponents components, TranslationContext context)
       throws IOException {
     String coderSpecUrn = protoCoder.getSpec().getUrn();
     if (coderSpecUrn.equals(JAVA_SERIALIZED_CODER_URN)) {
       return fromCustomCoder(protoCoder);
     }
-    return fromKnownCoder(protoCoder, components);
+    return fromKnownCoder(protoCoder, components, context);
   }
 
-  private static Coder fromKnownCoder(RunnerApi.Coder coder, RehydratedComponents components)
+  private static Coder fromKnownCoder(
+      RunnerApi.Coder coder, RehydratedComponents components, TranslationContext context)
       throws IOException {
     String coderUrn = coder.getSpec().getUrn();
     List> coderComponents = new ArrayList<>();
     for (String componentId : coder.getComponentCoderIdsList()) {
-      Coder innerCoder = components.getCoder(componentId);
+      // Only store coders in RehydratedComponents as long as we are not using a custom
+      // translation context.
+      Coder innerCoder =
+          context == TranslationContext.DEFAULT
+              ? components.getCoder(componentId)
+              : fromProto(
+                  components.getComponents().getCodersOrThrow(componentId), components, context);
       coderComponents.add(innerCoder);
     }
     Class coderType = KNOWN_CODER_URNS.inverse().get(coderUrn);
@@ -139,7 +163,8 @@ private static Coder fromKnownCoder(RunnerApi.Coder coder, RehydratedComponen
         "Unknown Coder URN %s. Known URNs: %s",
         coderUrn,
         KNOWN_CODER_URNS.values());
-    return translator.fromComponents(coderComponents, coder.getSpec().getPayload().toByteArray());
+    return translator.fromComponents(
+        coderComponents, coder.getSpec().getPayload().toByteArray(), context);
   }
 
   private static Coder fromCustomCoder(RunnerApi.Coder protoCoder) throws IOException {
diff --git a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslator.java b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslator.java
index 442a445df355..434ac1b0957b 100644
--- a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslator.java
+++ b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslator.java
@@ -18,6 +18,7 @@
 package org.apache.beam.runners.core.construction;
 
 import java.util.List;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.sdk.coders.Coder;
 
 /**
@@ -41,6 +42,9 @@ default byte[] getPayload(T from) {
     return new byte[0];
   }
 
-  /** Create a {@link Coder} from its component {@link Coder coders}. */
-  T fromComponents(List> components, byte[] payload);
+  /**
+   * Create a {@link Coder} from its component {@link Coder coders} using the specified translation
+   * context.
+   */
+  T fromComponents(List> components, byte[] payload, TranslationContext context);
 }
diff --git a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslators.java b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslators.java
index ae7e9dc4b425..c4f45023d912 100644
--- a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslators.java
+++ b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/CoderTranslators.java
@@ -22,6 +22,7 @@
 import java.util.Collections;
 import java.util.List;
 import org.apache.beam.model.pipeline.v1.SchemaApi;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.sdk.coders.Coder;
 import org.apache.beam.sdk.coders.IterableCoder;
 import org.apache.beam.sdk.coders.KvCoder;
@@ -139,7 +140,7 @@ public byte[] getPayload(WindowedValue.ParamWindowedValueCoder from) {
 
       @Override
       public WindowedValue.ParamWindowedValueCoder fromComponents(
-          List> components, byte[] payload) {
+          List> components, byte[] payload, TranslationContext context) {
         return WindowedValue.ParamWindowedValueCoder.fromComponents(components, payload);
       }
     };
@@ -158,7 +159,8 @@ public byte[] getPayload(RowCoder from) {
       }
 
       @Override
-      public RowCoder fromComponents(List> components, byte[] payload) {
+      public RowCoder fromComponents(
+          List> components, byte[] payload, TranslationContext context) {
         checkArgument(
             components.isEmpty(), "Expected empty component list, but received: " + components);
         Schema schema;
@@ -175,7 +177,8 @@ public RowCoder fromComponents(List> components, byte[] payload) {
   public abstract static class SimpleStructuredCoderTranslator>
       implements CoderTranslator {
     @Override
-    public final T fromComponents(List> components, byte[] payload) {
+    public final T fromComponents(
+        List> components, byte[] payload, TranslationContext context) {
       return fromComponents(components);
     }
 
diff --git a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/ModelCoderRegistrar.java b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/ModelCoderRegistrar.java
index 8ff90630f396..501a82379506 100644
--- a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/ModelCoderRegistrar.java
+++ b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/ModelCoderRegistrar.java
@@ -20,6 +20,7 @@
 import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkState;
 
 import com.google.auto.service.AutoService;
+import java.util.Collections;
 import java.util.Map;
 import java.util.Set;
 import org.apache.beam.sdk.coders.BooleanCoder;
@@ -97,7 +98,15 @@ public class ModelCoderRegistrar implements CoderTranslatorRegistrar {
         CoderTranslator.class.getSimpleName(),
         Sets.difference(BEAM_MODEL_CODER_URNS.keySet(), BEAM_MODEL_CODERS.keySet()));
     checkState(
-        ModelCoders.urns().equals(BEAM_MODEL_CODER_URNS.values()),
+        Sets.symmetricDifference(
+                ModelCoders.urns(),
+                /**
+                 * The state backed iterable coder implementation is environment specific and hence
+                 * is not part of the coder translation checks as these are meant to be used only
+                 * during pipeline construction.
+                 */
+                Collections.singleton(ModelCoders.STATE_BACKED_ITERABLE_CODER_URN))
+            .equals(BEAM_MODEL_CODER_URNS.values()),
         "All Model %ss should have an associated java %s",
         Coder.class.getSimpleName(),
         Coder.class.getSimpleName());
diff --git a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/ModelCoders.java b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/ModelCoders.java
index 7685b730510b..e1c204748bb4 100644
--- a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/ModelCoders.java
+++ b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/ModelCoders.java
@@ -19,6 +19,7 @@
 
 import static org.apache.beam.runners.core.construction.BeamUrns.getUrn;
 import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkArgument;
+import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkState;
 
 import com.google.auto.value.AutoValue;
 import java.util.Set;
@@ -59,6 +60,14 @@ private ModelCoders() {}
 
   public static final String ROW_CODER_URN = getUrn(StandardCoders.Enum.ROW);
 
+  public static final String STATE_BACKED_ITERABLE_CODER_URN =
+      "beam:coder:state_backed_iterable:v1";
+
+  static {
+    checkState(
+        STATE_BACKED_ITERABLE_CODER_URN.equals(getUrn(StandardCoders.Enum.STATE_BACKED_ITERABLE)));
+  }
+
   private static final Set MODEL_CODER_URNS =
       ImmutableSet.of(
           BYTES_CODER_URN,
@@ -74,7 +83,8 @@ private ModelCoders() {}
           WINDOWED_VALUE_CODER_URN,
           DOUBLE_CODER_URN,
           ROW_CODER_URN,
-          PARAM_WINDOWED_VALUE_CODER_URN);
+          PARAM_WINDOWED_VALUE_CODER_URN,
+          STATE_BACKED_ITERABLE_CODER_URN);
 
   public static Set urns() {
     return MODEL_CODER_URNS;
diff --git a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/RehydratedComponents.java b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/RehydratedComponents.java
index 11d24042c626..c51508b14bfd 100644
--- a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/RehydratedComponents.java
+++ b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/RehydratedComponents.java
@@ -27,6 +27,7 @@
 import org.apache.beam.model.pipeline.v1.RunnerApi;
 import org.apache.beam.model.pipeline.v1.RunnerApi.Components;
 import org.apache.beam.model.pipeline.v1.RunnerApi.Environment;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.sdk.Pipeline;
 import org.apache.beam.sdk.coders.Coder;
 import org.apache.beam.sdk.values.PCollection;
@@ -81,7 +82,8 @@ public class RehydratedComponents {
                 public Coder load(String id) throws Exception {
                   @Nullable RunnerApi.Coder coder = components.getCodersOrDefault(id, null);
                   checkState(coder != null, "No coder with id '%s' in serialized components", id);
-                  return CoderTranslation.fromProto(coder, RehydratedComponents.this);
+                  return CoderTranslation.fromProto(
+                      coder, RehydratedComponents.this, TranslationContext.DEFAULT);
                 }
               });
 
diff --git a/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/CoderTranslationTest.java b/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/CoderTranslationTest.java
index e6b45c475d52..8bc677214c86 100644
--- a/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/CoderTranslationTest.java
+++ b/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/CoderTranslationTest.java
@@ -31,6 +31,7 @@
 import org.apache.avro.SchemaBuilder;
 import org.apache.beam.model.pipeline.v1.RunnerApi;
 import org.apache.beam.model.pipeline.v1.RunnerApi.Components;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.sdk.coders.AtomicCoder;
 import org.apache.beam.sdk.coders.AvroCoder;
 import org.apache.beam.sdk.coders.BooleanCoder;
@@ -165,7 +166,9 @@ public void toAndFromProto() throws Exception {
       Components encodedComponents = sdkComponents.toComponents();
       Coder decodedCoder =
           CoderTranslation.fromProto(
-              coderProto, RehydratedComponents.forComponents(encodedComponents));
+              coderProto,
+              RehydratedComponents.forComponents(encodedComponents),
+              TranslationContext.DEFAULT);
       assertThat(decodedCoder, equalTo(coder));
 
       if (KNOWN_CODERS.contains(coder)) {
diff --git a/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/CommonCoderTest.java b/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/CommonCoderTest.java
index fe08582b9bbb..7b0d5453f829 100644
--- a/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/CommonCoderTest.java
+++ b/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/CommonCoderTest.java
@@ -49,6 +49,7 @@
 import javax.annotation.Nullable;
 import org.apache.beam.model.pipeline.v1.RunnerApi.StandardCoders;
 import org.apache.beam.model.pipeline.v1.SchemaApi;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.sdk.coders.BooleanCoder;
 import org.apache.beam.sdk.coders.ByteCoder;
 import org.apache.beam.sdk.coders.Coder;
@@ -407,7 +408,7 @@ private static Coder instantiateCoder(CommonCoder coder) {
     checkNotNull(
         translator, "No translator found for common coder class: " + coderType.getSimpleName());
 
-    return translator.fromComponents(components, coder.getPayload());
+    return translator.fromComponents(components, coder.getPayload(), new TranslationContext() {});
   }
 
   @Test
diff --git a/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/ParDoTranslationTest.java b/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/ParDoTranslationTest.java
index 113186eafc7f..5c3b388447fa 100644
--- a/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/ParDoTranslationTest.java
+++ b/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/ParDoTranslationTest.java
@@ -29,6 +29,7 @@
 import org.apache.beam.model.pipeline.v1.RunnerApi;
 import org.apache.beam.model.pipeline.v1.RunnerApi.ParDoPayload;
 import org.apache.beam.model.pipeline.v1.RunnerApi.SideInput;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.sdk.Pipeline;
 import org.apache.beam.sdk.coders.Coder;
 import org.apache.beam.sdk.coders.KvCoder;
@@ -200,7 +201,8 @@ public void toTransformProto() throws Exception {
         Coder timerCoder =
             CoderTranslation.fromProto(
                 components.getCodersOrThrow(timerFamilySpec.getTimerFamilyCoderId()),
-                rehydratedComponents);
+                rehydratedComponents,
+                TranslationContext.DEFAULT);
         assertEquals(
             org.apache.beam.runners.core.construction.Timer.Coder.of(
                 VarLongCoder.of(), GlobalWindow.Coder.INSTANCE),
diff --git a/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/PipelineTranslationTest.java b/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/PipelineTranslationTest.java
index 9cffd69ab3ac..63264a6897f3 100644
--- a/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/PipelineTranslationTest.java
+++ b/runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/PipelineTranslationTest.java
@@ -29,6 +29,7 @@
 import org.apache.beam.model.pipeline.v1.RunnerApi;
 import org.apache.beam.model.pipeline.v1.RunnerApi.CombinePayload;
 import org.apache.beam.model.pipeline.v1.RunnerApi.Components;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.sdk.Pipeline;
 import org.apache.beam.sdk.Pipeline.PipelineVisitor;
 import org.apache.beam.sdk.coders.BigEndianLongCoder;
@@ -213,7 +214,9 @@ private static Coder getAccumulatorCoder(AppliedPTransform transform
             .orElseThrow(() -> new IOException("Transform does not contain an AccumulatorCoder"));
     Components components = sdkComponents.toComponents();
     return CoderTranslation.fromProto(
-        components.getCodersOrThrow(id), RehydratedComponents.forComponents(components));
+        components.getCodersOrThrow(id),
+        RehydratedComponents.forComponents(components),
+        TranslationContext.DEFAULT);
   }
 
   private static Optional getCombinePayload(
diff --git a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/DataflowRunner.java b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/DataflowRunner.java
index a4ea1c952094..457634fe6d23 100644
--- a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/DataflowRunner.java
+++ b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/DataflowRunner.java
@@ -62,6 +62,7 @@
 import org.apache.beam.model.pipeline.v1.RunnerApi;
 import org.apache.beam.runners.core.construction.BeamUrns;
 import org.apache.beam.runners.core.construction.CoderTranslation;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.runners.core.construction.DeduplicatedFlattenFactory;
 import org.apache.beam.runners.core.construction.EmptyFlattenAsCreateFactory;
 import org.apache.beam.runners.core.construction.Environments;
@@ -1531,7 +1532,8 @@ private Coder getCoder() throws IOException {
               (Coder)
                   CoderTranslation.fromProto(
                       coderSpec.getCoder(),
-                      RehydratedComponents.forComponents(coderSpec.getComponents()));
+                      RehydratedComponents.forComponents(coderSpec.getComponents()),
+                      TranslationContext.DEFAULT);
         }
         return coder;
       }
diff --git a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/FnApiWindowMappingFn.java b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/FnApiWindowMappingFn.java
index 07f032416167..d8889b936741 100644
--- a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/FnApiWindowMappingFn.java
+++ b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/FnApiWindowMappingFn.java
@@ -35,6 +35,7 @@
 import org.apache.beam.model.pipeline.v1.RunnerApi.FunctionSpec;
 import org.apache.beam.model.pipeline.v1.RunnerApi.PCollection;
 import org.apache.beam.runners.core.construction.CoderTranslation;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.runners.core.construction.RehydratedComponents;
 import org.apache.beam.runners.core.construction.SdkComponents;
 import org.apache.beam.runners.fnexecution.control.InstructionRequestHandler;
@@ -136,11 +137,15 @@ public static CacheKey create(FunctionSpec windowMappingFn, BoundedWindow mainWi
       outboundCoder =
           (Coder)
               CoderTranslation.fromProto(
-                  components.getCodersOrThrow(mainInputWindowCoderId), rehydratedComponents);
+                  components.getCodersOrThrow(mainInputWindowCoderId),
+                  rehydratedComponents,
+                  TranslationContext.DEFAULT);
       inboundCoder =
           (Coder)
               CoderTranslation.fromProto(
-                  components.getCodersOrThrow(sideInputWindowCoderId), rehydratedComponents);
+                  components.getCodersOrThrow(sideInputWindowCoderId),
+                  rehydratedComponents,
+                  TranslationContext.DEFAULT);
     } catch (IOException e) {
       throw new IllegalStateException(
           "Unable to create side input window mapping process bundle specification.", e);
diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/coders/IterableLikeCoder.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/coders/IterableLikeCoder.java
index fcd744caf67b..a4e9c86992a5 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/coders/IterableLikeCoder.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/coders/IterableLikeCoder.java
@@ -66,9 +66,25 @@ public Coder getElemCoder() {
   /**
    * Builds an instance of {@code IterableT}, this coder's associated {@link Iterable}-like subtype,
    * from a list of decoded elements.
+   *
+   * 
    Override {@link #decodeToIterable(List, long, InputStream)} if you need access to the
+   * terminator value and the {@link InputStream}.
    */
   protected abstract IterableT decodeToIterable(List decodedElements);
 
+  /**
+   * Builds an instance of {@code IterableT}, this coder's associated {@link Iterable}-like subtype,
+   * from a list of decoded elements with the {@link InputStream} at the position where this coder
+   * detected the end of the stream.
+   */
+  protected IterableT decodeToIterable(
+      List decodedElements, long terminatorValue, InputStream in) throws IOException {
+    throw new IllegalStateException(
+        String.format(
+            "%s does not support non zero terminator values. Received stream with terminator %s.",
+            iterableName, terminatorValue));
+  }
+
   /////////////////////////////////////////////////////////////////////////////
   // Internal operations below here.
 
@@ -136,7 +152,11 @@ public IterableT decode(InputStream inStream) throws IOException, CoderException
         count = VarInt.decodeLong(dataInStream);
       }
     }
-    return decodeToIterable(elements);
+    if (count == 0) {
+      return decodeToIterable(elements);
+    } else {
+      return decodeToIterable(elements, count, inStream);
+    }
   }
 
   @Override
diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/util/BufferedElementCountingOutputStream.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/util/BufferedElementCountingOutputStream.java
index 15aab64787ad..3470dbfd55bd 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/util/BufferedElementCountingOutputStream.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/util/BufferedElementCountingOutputStream.java
@@ -79,6 +79,7 @@ public class BufferedElementCountingOutputStream extends OutputStream {
   public static final int DEFAULT_BUFFER_SIZE = 64 * 1024;
   private final ByteBuffer buffer;
   private final OutputStream os;
+  private final long terminatorValue;
   private boolean finished;
   private long count;
 
@@ -87,15 +88,20 @@ public class BufferedElementCountingOutputStream extends OutputStream {
    * manner.
    */
   public BufferedElementCountingOutputStream(OutputStream os) {
-    this(os, DEFAULT_BUFFER_SIZE);
+    this(os, DEFAULT_BUFFER_SIZE, 0);
+  }
+
+  public BufferedElementCountingOutputStream(OutputStream os, long terminatorValue) {
+    this(os, DEFAULT_BUFFER_SIZE, terminatorValue);
   }
 
   /**
    * Creates an output stream which encodes the number of elements output to it in a streaming
    * manner with the given {@code bufferSize}.
    */
-  BufferedElementCountingOutputStream(OutputStream os, int bufferSize) {
+  BufferedElementCountingOutputStream(OutputStream os, int bufferSize, long terminatorValue) {
     this.os = os;
+    this.terminatorValue = terminatorValue;
     this.finished = false;
     this.count = 0;
     ByteBuffer buffer = BUFFER_POOL.poll();
@@ -111,8 +117,8 @@ public void finish() throws IOException {
       return;
     }
     flush();
-    // Finish the stream by stating that there are 0 elements that follow.
-    VarInt.encode(0, os);
+    // Finish the stream with the terminatorValue.
+    VarInt.encode(terminatorValue, os);
     if (!BUFFER_POOL.offer(buffer)) {
       // The pool is full, we can't store the buffer. We just drop the buffer.
     }
diff --git a/sdks/java/core/src/test/java/org/apache/beam/sdk/util/BufferedElementCountingOutputStreamTest.java b/sdks/java/core/src/test/java/org/apache/beam/sdk/util/BufferedElementCountingOutputStreamTest.java
index 205f1afe1e52..0d1f7d89b719 100644
--- a/sdks/java/core/src/test/java/org/apache/beam/sdk/util/BufferedElementCountingOutputStreamTest.java
+++ b/sdks/java/core/src/test/java/org/apache/beam/sdk/util/BufferedElementCountingOutputStreamTest.java
@@ -41,14 +41,22 @@
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
 import org.junit.runner.RunWith;
-import org.junit.runners.JUnit4;
+import org.junit.runners.Parameterized;
 
 /** Tests for {@link BufferedElementCountingOutputStream}. */
-@RunWith(JUnit4.class)
+@RunWith(Parameterized.class)
 public class BufferedElementCountingOutputStreamTest {
   @Rule public final ExpectedException expectedException = ExpectedException.none();
   private static final int BUFFER_SIZE = 8;
 
+  @Parameterized.Parameters
+  public static Iterable data() {
+    return ImmutableList.builder().add(new Object[] {0L}).add(new Object[] {-1L}).build();
+  }
+
+  @Parameterized.Parameter(0)
+  public long terminatorValue;
+
   @Test
   public void testEmptyValues() throws Exception {
     testValues(Collections.emptyList());
@@ -219,6 +227,8 @@ private void verifyValues(List expectedValues, InputStream is) throws Ex
       }
     } while (count > 0);
 
+    assertEquals(terminatorValue, count);
+
     if (expectedValues.isEmpty()) {
       assertTrue(values.isEmpty());
     } else {
@@ -229,7 +239,7 @@ private void verifyValues(List expectedValues, InputStream is) throws Ex
   private BufferedElementCountingOutputStream createAndWriteValues(
       List values, OutputStream output) throws Exception {
     BufferedElementCountingOutputStream os =
-        new BufferedElementCountingOutputStream(output, BUFFER_SIZE);
+        new BufferedElementCountingOutputStream(output, BUFFER_SIZE, terminatorValue);
 
     for (byte[] value : values) {
       os.markElementStart();
diff --git a/sdks/java/expansion-service/src/main/java/org/apache/beam/sdk/expansion/service/ExpansionService.java b/sdks/java/expansion-service/src/main/java/org/apache/beam/sdk/expansion/service/ExpansionService.java
index 578e87583438..f5707eaafca0 100644
--- a/sdks/java/expansion-service/src/main/java/org/apache/beam/sdk/expansion/service/ExpansionService.java
+++ b/sdks/java/expansion-service/src/main/java/org/apache/beam/sdk/expansion/service/ExpansionService.java
@@ -39,6 +39,7 @@
 import org.apache.beam.model.pipeline.v1.RunnerApi;
 import org.apache.beam.runners.core.construction.BeamUrns;
 import org.apache.beam.runners.core.construction.CoderTranslation;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.runners.core.construction.Environments;
 import org.apache.beam.runners.core.construction.PipelineTranslation;
 import org.apache.beam.runners.core.construction.RehydratedComponents;
@@ -203,7 +204,7 @@ private static Coder resolveCoder(List coderUrns) throws Exception {
 
       RehydratedComponents rehydratedComponents =
           RehydratedComponents.forComponents(componentsBuilder.build());
-      return CoderTranslation.fromProto(coder, rehydratedComponents);
+      return CoderTranslation.fromProto(coder, rehydratedComponents, TranslationContext.DEFAULT);
     }
 
     private static RunnerApi.Coder buildProto(
diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/BeamFnDataReadRunner.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/BeamFnDataReadRunner.java
index eedb42c2a05f..3b10b33dcdd9 100644
--- a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/BeamFnDataReadRunner.java
+++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/BeamFnDataReadRunner.java
@@ -34,6 +34,7 @@
 import org.apache.beam.fn.harness.data.PCollectionConsumerRegistry;
 import org.apache.beam.fn.harness.data.PTransformFunctionRegistry;
 import org.apache.beam.fn.harness.state.BeamFnStateClient;
+import org.apache.beam.fn.harness.state.StateBackedIterable.StateBackedIterableTranslationContext;
 import org.apache.beam.model.fnexecution.v1.BeamFnApi;
 import org.apache.beam.model.fnexecution.v1.BeamFnApi.ProcessBundleSplitRequest;
 import org.apache.beam.model.fnexecution.v1.BeamFnApi.ProcessBundleSplitRequest.DesiredSplit;
@@ -120,6 +121,7 @@ public BeamFnDataReadRunner createRunnerForPTransform(
               processBundleInstructionId,
               coders,
               beamFnDataClient,
+              beamFnStateClient,
               addProgressRequestCallback,
               consumer);
       startFunctionRegistry.register(pTransformId, runner::registerInputLocation);
@@ -149,6 +151,7 @@ public BeamFnDataReadRunner createRunnerForPTransform(
       Supplier processBundleInstructionIdSupplier,
       Map coders,
       BeamFnDataClient beamFnDataClient,
+      BeamFnStateClient beamFnStateClient,
       Consumer addProgressRequestCallback,
       FnDataReceiver> consumer)
       throws IOException {
@@ -163,7 +166,20 @@ public BeamFnDataReadRunner createRunnerForPTransform(
         RehydratedComponents.forComponents(Components.newBuilder().putAllCoders(coders).build());
     this.coder =
         (Coder>)
-            CoderTranslation.fromProto(coders.get(port.getCoderId()), components);
+            CoderTranslation.fromProto(
+                coders.get(port.getCoderId()),
+                components,
+                new StateBackedIterableTranslationContext() {
+                  @Override
+                  public BeamFnStateClient getStateClient() {
+                    return beamFnStateClient;
+                  }
+
+                  @Override
+                  public Supplier getCurrentInstructionId() {
+                    return processBundleInstructionIdSupplier;
+                  }
+                });
 
     addProgressRequestCallback.accept(
         () -> {
diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/BeamFnDataWriteRunner.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/BeamFnDataWriteRunner.java
index c2570c1c8490..684f39911320 100644
--- a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/BeamFnDataWriteRunner.java
+++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/BeamFnDataWriteRunner.java
@@ -30,6 +30,7 @@
 import org.apache.beam.fn.harness.data.PCollectionConsumerRegistry;
 import org.apache.beam.fn.harness.data.PTransformFunctionRegistry;
 import org.apache.beam.fn.harness.state.BeamFnStateClient;
+import org.apache.beam.fn.harness.state.StateBackedIterable.StateBackedIterableTranslationContext;
 import org.apache.beam.model.fnexecution.v1.BeamFnApi;
 import org.apache.beam.model.fnexecution.v1.BeamFnApi.RemoteGrpcPort;
 import org.apache.beam.model.pipeline.v1.Endpoints;
@@ -99,7 +100,12 @@ public BeamFnDataWriteRunner createRunnerForPTransform(
 
       BeamFnDataWriteRunner runner =
           new BeamFnDataWriteRunner<>(
-              pTransformId, pTransform, processBundleInstructionId, coders, beamFnDataClient);
+              pTransformId,
+              pTransform,
+              processBundleInstructionId,
+              coders,
+              beamFnDataClient,
+              beamFnStateClient);
       startFunctionRegistry.register(pTransformId, runner::registerForOutput);
       pCollectionConsumerRegistry.register(
           getOnlyElement(pTransform.getInputsMap().values()),
@@ -124,7 +130,8 @@ public BeamFnDataWriteRunner createRunnerForPTransform(
       RunnerApi.PTransform remoteWriteNode,
       Supplier processBundleInstructionIdSupplier,
       Map coders,
-      BeamFnDataClient beamFnDataClientFactory)
+      BeamFnDataClient beamFnDataClientFactory,
+      BeamFnStateClient beamFnStateClient)
       throws IOException {
     this.pTransformId = pTransformId;
     RemoteGrpcPort port = RemoteGrpcPortWrite.fromPTransform(remoteWriteNode).getPort();
@@ -136,7 +143,20 @@ public BeamFnDataWriteRunner createRunnerForPTransform(
         RehydratedComponents.forComponents(Components.newBuilder().putAllCoders(coders).build());
     this.coder =
         (Coder>)
-            CoderTranslation.fromProto(coders.get(port.getCoderId()), components);
+            CoderTranslation.fromProto(
+                coders.get(port.getCoderId()),
+                components,
+                new StateBackedIterableTranslationContext() {
+                  @Override
+                  public BeamFnStateClient getStateClient() {
+                    return beamFnStateClient;
+                  }
+
+                  @Override
+                  public Supplier getCurrentInstructionId() {
+                    return processBundleInstructionIdSupplier;
+                  }
+                });
   }
 
   public void registerForOutput() {
diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/BagUserState.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/BagUserState.java
index 38e202700ed0..cb3c1953aa53 100644
--- a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/BagUserState.java
+++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/BagUserState.java
@@ -77,7 +77,7 @@ public BagUserState(
             new DataStreams.DataStreamDecoder(
                 valueCoder,
                 DataStreams.inbound(
-                    StateFetchingIterators.forFirstChunk(beamFnStateClient, request))));
+                    StateFetchingIterators.readAllStartingFrom(beamFnStateClient, request))));
     this.newValues = new ArrayList<>();
   }
 
diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/MultimapSideInput.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/MultimapSideInput.java
index d795d44f163f..795561047d1a 100644
--- a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/MultimapSideInput.java
+++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/MultimapSideInput.java
@@ -71,7 +71,8 @@ public Iterable get() {
         new DataStreams.DataStreamDecoder(
             keyCoder,
             DataStreams.inbound(
-                StateFetchingIterators.forFirstChunk(beamFnStateClient, requestBuilder.build()))));
+                StateFetchingIterators.readAllStartingFrom(
+                    beamFnStateClient, requestBuilder.build()))));
   }
 
   @Override
@@ -97,6 +98,7 @@ public Iterable get(K k) {
         new DataStreams.DataStreamDecoder(
             valueCoder,
             DataStreams.inbound(
-                StateFetchingIterators.forFirstChunk(beamFnStateClient, requestBuilder.build()))));
+                StateFetchingIterators.readAllStartingFrom(
+                    beamFnStateClient, requestBuilder.build()))));
   }
 }
diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/StateBackedIterable.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/StateBackedIterable.java
new file mode 100644
index 000000000000..94c8f9a8f614
--- /dev/null
+++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/StateBackedIterable.java
@@ -0,0 +1,224 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.fn.harness.state;
+
+import static org.apache.beam.runners.core.construction.ModelCoders.STATE_BACKED_ITERABLE_CODER_URN;
+
+import com.google.auto.service.AutoService;
+import java.io.DataOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.function.Supplier;
+import org.apache.beam.model.fnexecution.v1.BeamFnApi.StateRequest;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
+import org.apache.beam.runners.core.construction.CoderTranslator;
+import org.apache.beam.runners.core.construction.CoderTranslatorRegistrar;
+import org.apache.beam.sdk.coders.IterableLikeCoder;
+import org.apache.beam.sdk.fn.stream.DataStreams;
+import org.apache.beam.sdk.util.BufferedElementCountingOutputStream;
+import org.apache.beam.sdk.util.VarInt;
+import org.apache.beam.vendor.grpc.v1p26p0.com.google.protobuf.ByteString;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.annotations.VisibleForTesting;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Iterables;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Iterators;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.io.ByteStreams;
+
+/**
+ * A {@link BeamFnStateClient state} backed iterable which allows for fetching elements over the
+ * portability state API. See remote references for
+ * additional details.
+ *
+ * 
    One must supply a {@link StateBackedIterableTranslationContext} when using {@link
+ * CoderTranslator#fromComponents} to be able to create a {@link StateBackedIterable.Coder}.
+ */
+public class StateBackedIterable implements Iterable {
+
+  private final BeamFnStateClient beamFnStateClient;
+  private final org.apache.beam.sdk.coders.Coder elemCoder;
+  @VisibleForTesting final StateRequest request;
+  @VisibleForTesting final List prefix;
+
+  public StateBackedIterable(
+      BeamFnStateClient beamFnStateClient,
+      String instructionId,
+      ByteString runnerKey,
+      org.apache.beam.sdk.coders.Coder elemCoder,
+      List prefix) {
+    this.beamFnStateClient = beamFnStateClient;
+    this.elemCoder = elemCoder;
+
+    StateRequest.Builder requestBuilder = StateRequest.newBuilder();
+    requestBuilder
+        .setInstructionId(instructionId)
+        .getStateKeyBuilder()
+        .getRunnerBuilder()
+        .setKey(runnerKey);
+    this.request = requestBuilder.build();
+    this.prefix = prefix;
+  }
+
+  @Override
+  public Iterator iterator() {
+    return Iterators.concat(
+        prefix.iterator(),
+        new DataStreams.DataStreamDecoder(
+            elemCoder,
+            DataStreams.inbound(
+                StateFetchingIterators.readAllStartingFrom(beamFnStateClient, request))));
+  }
+
+  /**
+   * Decodes an {@link Iterable} that might be backed by state. If the terminator at the end of the
+   * value stream is {@code -1} then we return a {@link StateBackedIterable} otherwise we return an
+   * {@link Iterable}.
+   */
+  public static class Coder extends IterableLikeCoder> {
+
+    private final BeamFnStateClient beamFnStateClient;
+    private final Supplier instructionId;
+
+    public Coder(
+        BeamFnStateClient beamFnStateClient,
+        Supplier instructionId,
+        org.apache.beam.sdk.coders.Coder elemCoder) {
+      super(elemCoder, "StateBackedIterable");
+      this.beamFnStateClient = beamFnStateClient;
+      this.instructionId = instructionId;
+    }
+
+    @Override
+    protected Iterable decodeToIterable(List decodedElements) {
+      return decodedElements;
+    }
+
+    @Override
+    protected Iterable decodeToIterable(
+        List decodedElements, long terminatorValue, InputStream in) throws IOException {
+      if (terminatorValue == -1L) {
+        long tokenLength = VarInt.decodeLong(in);
+        ByteString token = ByteString.readFrom(ByteStreams.limit(in, tokenLength));
+        return new StateBackedIterable<>(
+            beamFnStateClient, instructionId.get(), token, getElemCoder(), decodedElements);
+      } else {
+        throw new IllegalStateException(
+            String.format(
+                "StateBackedIterable expected terminator of 0 or -1 but received %s.",
+                terminatorValue));
+      }
+    }
+
+    @Override
+    public void encode(Iterable iterable, OutputStream outStream) throws IOException {
+      if (!(iterable instanceof StateBackedIterable)) {
+        super.encode(iterable, outStream);
+        return;
+      }
+
+      StateBackedIterable stateBackedIterable = (StateBackedIterable) iterable;
+
+      DataOutputStream dataOutStream = new DataOutputStream(outStream);
+      // We don't know the size without traversing it so use a fixed size buffer
+      // and encode as many elements as possible into it before outputting the size followed
+      // by the elements.
+      dataOutStream.writeInt(-1);
+      BufferedElementCountingOutputStream countingOutputStream =
+          new BufferedElementCountingOutputStream(dataOutStream, -1L);
+      // Encode only the prefix
+      for (T elem : stateBackedIterable.prefix) {
+        countingOutputStream.markElementStart();
+        getElemCoder().encode(elem, countingOutputStream);
+      }
+      countingOutputStream.finish();
+      // Make sure all our output gets pushed to the underlying outStream.
+      dataOutStream.flush();
+
+      // Append 'len(token) token' after the -1 stream terminator.
+      VarInt.encode(
+          stateBackedIterable.request.getStateKey().getRunner().getKey().size(), outStream);
+      stateBackedIterable.request.getStateKey().getRunner().getKey().writeTo(outStream);
+    }
+  }
+
+  /** Additional parameters required by the {@link StateBackedIterable.Coder}. */
+  public interface StateBackedIterableTranslationContext extends TranslationContext {
+    BeamFnStateClient getStateClient();
+
+    Supplier getCurrentInstructionId();
+  }
+
+  /** A {@link CoderTranslatorRegistrar} for {@code beam:coder:state_backed_iterable:v1}. */
+  @AutoService(CoderTranslatorRegistrar.class)
+  public static class Registrar implements CoderTranslatorRegistrar {
+
+    @Override
+    public Map, String> getCoderURNs() {
+      return Collections.singletonMap(
+          StateBackedIterable.Coder.class, STATE_BACKED_ITERABLE_CODER_URN);
+    }
+
+    @Override
+    public Map<
+            Class,
+            CoderTranslator>
+        getCoderTranslators() {
+      return ImmutableMap.of(StateBackedIterable.Coder.class, new Translator());
+    }
+  }
+
+  /**
+   * A {@link CoderTranslator} for {@code beam:coder:state_backed_iterable:v1}.
+   *
+   * 
    One must supply a {@link StateBackedIterableTranslationContext} during {@link
+   * CoderTranslator#fromComponents} to be able to successfully create an instance.
+   */
+  private static class Translator implements CoderTranslator> {
+
+    @Override
+    public List> getComponents(
+        StateBackedIterable.Coder from) {
+      return Collections.>singletonList(from.getElemCoder());
+    }
+
+    @Override
+    public StateBackedIterable.Coder fromComponents(
+        List> components,
+        byte[] payload,
+        TranslationContext context) {
+      if (context instanceof StateBackedIterableTranslationContext) {
+        return new StateBackedIterable.Coder<>(
+            ((StateBackedIterableTranslationContext) context).getStateClient(),
+            ((StateBackedIterableTranslationContext) context).getCurrentInstructionId(),
+            Iterables.getOnlyElement(components));
+      } else {
+        throw new IllegalStateException(
+            String.format(
+                "Unable to construct coder %s. Expected translation context %s but received %s.",
+                STATE_BACKED_ITERABLE_CODER_URN,
+                StateBackedIterableTranslationContext.class.getName(),
+                context.getClass().getName()));
+      }
+    }
+  }
+}
diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/StateFetchingIterators.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/StateFetchingIterators.java
index a7cb38d7b25a..7af431de0659 100644
--- a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/StateFetchingIterators.java
+++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/state/StateFetchingIterators.java
@@ -46,7 +46,7 @@ private StateFetchingIterators() {}
    *     only) chunk of a state stream. This state request will be populated with a continuation
    *     token to request further chunks of the stream if required.
    */
-  public static Iterator forFirstChunk(
+  public static Iterator readAllStartingFrom(
       BeamFnStateClient beamFnStateClient, StateRequest stateRequestForFirstChunk) {
     return new LazyBlockingStateFetchingIterator(beamFnStateClient, stateRequestForFirstChunk);
   }
diff --git a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/BeamFnDataReadRunnerTest.java b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/BeamFnDataReadRunnerTest.java
index 75f3105b0b22..9293d011c35a 100644
--- a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/BeamFnDataReadRunnerTest.java
+++ b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/BeamFnDataReadRunnerTest.java
@@ -235,6 +235,7 @@ public void testReuseForMultipleBundles() throws Exception {
               bundleId::get,
               COMPONENTS.getCodersMap(),
               mockBeamFnDataClient,
+              null /* beamFnStateClient */,
               (PTransformRunnerFactory.ProgressRequestCallback callback) -> {
                 progressCallbacks.add(callback);
               },
diff --git a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/BeamFnDataWriteRunnerTest.java b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/BeamFnDataWriteRunnerTest.java
index 7159801d1eee..a2f4c8f27511 100644
--- a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/BeamFnDataWriteRunnerTest.java
+++ b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/BeamFnDataWriteRunnerTest.java
@@ -213,7 +213,8 @@ public void testReuseForMultipleBundles() throws Exception {
             RemoteGrpcPortWrite.writeToPort("myWrite", PORT_SPEC).toPTransform(),
             bundleId::get,
             COMPONENTS.getCodersMap(),
-            mockBeamFnDataClient);
+            mockBeamFnDataClient,
+            null /* beamFnStateClient */);
 
     // Process for bundle id 0
     writeRunner.registerForOutput();
diff --git a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java
index 1da967269b32..b5e23685e731 100644
--- a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java
+++ b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java
@@ -59,6 +59,7 @@
 import org.apache.beam.model.pipeline.v1.RunnerApi;
 import org.apache.beam.model.pipeline.v1.RunnerApi.Environment;
 import org.apache.beam.runners.core.construction.CoderTranslation;
+import org.apache.beam.runners.core.construction.CoderTranslation.TranslationContext;
 import org.apache.beam.runners.core.construction.PTransformTranslation;
 import org.apache.beam.runners.core.construction.ParDoTranslation;
 import org.apache.beam.runners.core.construction.PipelineTranslation;
@@ -1188,7 +1189,8 @@ public void testProcessElementForSizedElementAndRestriction() throws Exception {
         WindowedValue.getFullCoder(
             CoderTranslation.fromProto(
                 pProto.getComponents().getCodersOrThrow(inputPCollection.getCoderId()),
-                rehydratedComponents),
+                rehydratedComponents,
+                TranslationContext.DEFAULT),
             (Coder)
                 CoderTranslation.fromProto(
                     pProto
@@ -1199,7 +1201,8 @@ public void testProcessElementForSizedElementAndRestriction() throws Exception {
                                 .getWindowingStrategiesOrThrow(
                                     inputPCollection.getWindowingStrategyId())
                                 .getWindowCoderId()),
-                    rehydratedComponents));
+                    rehydratedComponents,
+                    TranslationContext.DEFAULT));
     String outputPCollectionId = pTransform.getOutputsOrThrow("output");
 
     ImmutableMap stateData =
diff --git a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/state/StateBackedIterableTest.java b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/state/StateBackedIterableTest.java
new file mode 100644
index 000000000000..fc6549b294a2
--- /dev/null
+++ b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/state/StateBackedIterableTest.java
@@ -0,0 +1,184 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.fn.harness.state;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Random;
+import org.apache.beam.model.fnexecution.v1.BeamFnApi.StateKey;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import org.apache.beam.vendor.grpc.v1p26p0.com.google.protobuf.ByteString;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.FluentIterable;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Lists;
+import org.junit.Test;
+import org.junit.experimental.runners.Enclosed;
+import org.junit.runner.RunWith;
+import org.junit.runners.JUnit4;
+import org.junit.runners.Parameterized;
+
+/** Tests for {@link StateBackedIterable}. */
+@RunWith(Enclosed.class)
+public class StateBackedIterableTest {
+
+  @RunWith(Parameterized.class)
+  public static class IterationTest {
+    @Parameterized.Parameters
+    public static Iterable data() {
+      return ImmutableList.builder()
+          .add(new Object[] {Collections.emptyList(), "emptySuffix", ImmutableList.of()})
+          .add(new Object[] {ImmutableList.of("A", "B"), "emptySuffix", ImmutableList.of("A", "B")})
+          .add(
+              new Object[] {
+                Collections.emptyList(),
+                "nonEmptySuffix",
+                ImmutableList.of("C", "D", "E", "F", "G", "H", "I", "J", "K")
+              })
+          .add(
+              new Object[] {
+                ImmutableList.of("A", "B"),
+                "nonEmptySuffix",
+                ImmutableList.of("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K")
+              })
+          .build();
+    }
+
+    @Parameterized.Parameter(0)
+    public List prefix;
+
+    @Parameterized.Parameter(1)
+    public String suffixKey;
+
+    @Parameterized.Parameter(2)
+    public List expected;
+
+    @Test
+    public void testReiteration() throws Exception {
+      FakeBeamFnStateClient fakeBeamFnStateClient =
+          new FakeBeamFnStateClient(
+              ImmutableMap.of(
+                  key("nonEmptySuffix"), encode("C", "D", "E", "F", "G", "H", "I", "J", "K"),
+                  key("emptySuffix"), encode()));
+
+      StateBackedIterable iterable =
+          new StateBackedIterable<>(
+              fakeBeamFnStateClient,
+              "instruction",
+              encode(suffixKey),
+              StringUtf8Coder.of(),
+              prefix);
+
+      assertEquals(expected, Lists.newArrayList(iterable));
+      assertEquals(expected, Lists.newArrayList(iterable));
+      assertEquals(expected, Lists.newArrayList(iterable));
+    }
+
+    @Test
+    public void testUsingInterleavedReiteration() throws Exception {
+      FakeBeamFnStateClient fakeBeamFnStateClient =
+          new FakeBeamFnStateClient(
+              ImmutableMap.of(
+                  key("nonEmptySuffix"), encode("C", "D", "E", "F", "G", "H", "I", "J", "K"),
+                  key("emptySuffix"), encode()));
+
+      StateBackedIterable iterable =
+          new StateBackedIterable<>(
+              fakeBeamFnStateClient,
+              "instruction",
+              encode(suffixKey),
+              StringUtf8Coder.of(),
+              prefix);
+
+      List> iterators = new ArrayList<>();
+      List> results = new ArrayList<>();
+      for (int i = 0; i < 3; ++i) {
+        iterators.add(iterable.iterator());
+        results.add(new ArrayList<>());
+      }
+
+      Random random = new Random(42L);
+      while (!iterators.isEmpty()) {
+        int current = random.nextInt(iterators.size());
+        if (!iterators.get(current).hasNext()) {
+          iterators.remove(current);
+          assertEquals(expected, results.remove(current));
+        } else {
+          results.get(current).add(iterators.get(current).next());
+        }
+      }
+    }
+  }
+
+  @RunWith(JUnit4.class)
+  public static class CoderTest {
+    @Test
+    public void testDecodeEncodeRegularIterable() throws Exception {
+      Iterable iterable = FluentIterable.of("A", "B", "C");
+      StateBackedIterable.Coder coder =
+          new StateBackedIterable.Coder<>(null, () -> "instructionId", StringUtf8Coder.of());
+
+      // We can't rely on CoderProperties since it requires serialization of the coder
+      ByteArrayOutputStream baos = new ByteArrayOutputStream();
+      coder.encode(iterable, baos);
+      Iterable result = coder.decode(new ByteArrayInputStream(baos.toByteArray()));
+
+      assertEquals(Lists.newArrayList(iterable), Lists.newArrayList(result));
+    }
+
+    @Test
+    public void testEncodeDecodeStateBackedIterable() throws Exception {
+      StateBackedIterable iterable =
+          new StateBackedIterable(
+              null, "instructionId", encode("key"), StringUtf8Coder.of(), Arrays.asList("A", "B"));
+      StateBackedIterable.Coder coder =
+          new StateBackedIterable.Coder<>(null, () -> "instructionId", StringUtf8Coder.of());
+
+      // We can't rely on CoderProperties since it requires serialization of the coder
+      ByteArrayOutputStream baos = new ByteArrayOutputStream();
+      coder.encode(iterable, baos);
+      StateBackedIterable result =
+          (StateBackedIterable) coder.decode(new ByteArrayInputStream(baos.toByteArray()));
+
+      // Ensure that when we round trip the iterable we correctly convert it back to a state backed
+      // iterable
+      assertEquals(iterable.prefix, result.prefix);
+      assertEquals(iterable.request, result.request);
+    }
+  }
+
+  private static StateKey key(String id) throws IOException {
+    return StateKey.newBuilder().setRunner(StateKey.Runner.newBuilder().setKey(encode(id))).build();
+  }
+
+  private static ByteString encode(String... values) throws IOException {
+    ByteString.Output out = ByteString.newOutput();
+    for (String value : values) {
+      StringUtf8Coder.of().encode(value, out);
+    }
+    return out.toByteString();
+  }
+}

From 22d604b45b2597c9f863a82bf688430f4f2d8679 Mon Sep 17 00:00:00 2001
From: Rehman 
Date: Thu, 21 May 2020 17:42:36 +0500
Subject: [PATCH 044/151] Update changes.md

---
 CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGES.md b/CHANGES.md
index 9aff55608c1d..107e7dc8dff1 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -63,6 +63,7 @@
 * `--workerCacheMB` flag is supported in Dataflow streaming pipeline ([BEAM-9964](https://issues.apache.org/jira/browse/BEAM-9964))
 * `--direct_num_workers=0` is supported for FnApi runner. It will set the number of threads/subprocesses to number of cores of the machine executing the pipeline ([BEAM-9443](https://issues.apache.org/jira/browse/BEAM-9443)).
 * Python SDK now has experimental support for SqlTransform ([BEAM-8603](https://issues.apache.org/jira/browse/BEAM-8603)).
+* Add OnWindowExpiration method to Stateful DoFn ([BEAM-1589](https://issues.apache.org/jira/browse/BEAM-1589)).
 
 ## Breaking Changes
 

From d3dfa30f7b6d1ac1ad693e98b29d09cc0586d6de Mon Sep 17 00:00:00 2001
From: Yichi Zhang 
Date: Thu, 21 May 2020 09:05:24 -0700
Subject: [PATCH 045/151] comments

---
 .../beam/fn/harness/FnApiDoFnRunnerTest.java  | 77 +++++++++++--------
 1 file changed, 45 insertions(+), 32 deletions(-)

diff --git a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java
index e763fface9f4..07086aa8015d 100644
--- a/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java
+++ b/sdks/java/harness/src/test/java/org/apache/beam/fn/harness/FnApiDoFnRunnerTest.java
@@ -864,10 +864,11 @@ public void testTimers() throws Exception {
         processingTimer, timerInGlobalWindow("B", new Instant(1900L), new Instant(2900L)));
     fakeTimerClient.sendTimer(
         eventFamilyTimer,
-        timerInGlobalWindow("B", "event-timer2", new Instant(2000L), new Instant(3000L)));
+        dynamicTimerInGlobalWindow("B", "event-timer2", new Instant(2000L), new Instant(3000L)));
     fakeTimerClient.sendTimer(
         processingFamilyTimer,
-        timerInGlobalWindow("Y", "processing-timer2", new Instant(2100L), new Instant(3100L)));
+        dynamicTimerInGlobalWindow(
+            "Y", "processing-timer2", new Instant(2100L), new Instant(3100L)));
     assertThat(
         mainOutputValues,
         contains(
@@ -916,33 +917,45 @@ public void testTimers() throws Exception {
     assertThat(
         fakeTimerClient.getTimers(eventFamilyTimer),
         contains(
-            timerInGlobalWindow("X", "event-timer1", new Instant(1000L), new Instant(1003L)),
-            timerInGlobalWindow("Y", "event-timer1", new Instant(1100L), new Instant(1103L)),
-            timerInGlobalWindow("X", "event-timer1", new Instant(1200L), new Instant(1203L)),
-            timerInGlobalWindow("Y", "event-timer1", new Instant(1300L), new Instant(1303L)),
-            timerInGlobalWindow("A", "event-timer1", new Instant(1400L), new Instant(2413L)),
-            timerInGlobalWindow("B", "event-timer1", new Instant(1500L), new Instant(2513L)),
-            timerInGlobalWindow("A", "event-timer1", new Instant(1600L), new Instant(2613L)),
-            timerInGlobalWindow("X", "event-timer1", new Instant(1700L), new Instant(1723L)),
-            timerInGlobalWindow("C", "event-timer1", new Instant(1800L), new Instant(1823L)),
-            timerInGlobalWindow("B", "event-timer1", new Instant(1900L), new Instant(1923L)),
-            timerInGlobalWindow("B", "event-timer1", new Instant(2000L), new Instant(2033L)),
-            timerInGlobalWindow("Y", "event-timer1", new Instant(2100L), new Instant(2143L))));
+            dynamicTimerInGlobalWindow("X", "event-timer1", new Instant(1000L), new Instant(1003L)),
+            dynamicTimerInGlobalWindow("Y", "event-timer1", new Instant(1100L), new Instant(1103L)),
+            dynamicTimerInGlobalWindow("X", "event-timer1", new Instant(1200L), new Instant(1203L)),
+            dynamicTimerInGlobalWindow("Y", "event-timer1", new Instant(1300L), new Instant(1303L)),
+            dynamicTimerInGlobalWindow("A", "event-timer1", new Instant(1400L), new Instant(2413L)),
+            dynamicTimerInGlobalWindow("B", "event-timer1", new Instant(1500L), new Instant(2513L)),
+            dynamicTimerInGlobalWindow("A", "event-timer1", new Instant(1600L), new Instant(2613L)),
+            dynamicTimerInGlobalWindow("X", "event-timer1", new Instant(1700L), new Instant(1723L)),
+            dynamicTimerInGlobalWindow("C", "event-timer1", new Instant(1800L), new Instant(1823L)),
+            dynamicTimerInGlobalWindow("B", "event-timer1", new Instant(1900L), new Instant(1923L)),
+            dynamicTimerInGlobalWindow("B", "event-timer1", new Instant(2000L), new Instant(2033L)),
+            dynamicTimerInGlobalWindow(
+                "Y", "event-timer1", new Instant(2100L), new Instant(2143L))));
     assertThat(
         fakeTimerClient.getTimers(processingFamilyTimer),
         contains(
-            timerInGlobalWindow("X", "processing-timer1", new Instant(1000L), new Instant(10004L)),
-            timerInGlobalWindow("Y", "processing-timer1", new Instant(1100L), new Instant(10004L)),
-            timerInGlobalWindow("X", "processing-timer1", new Instant(1200L), new Instant(10004L)),
-            timerInGlobalWindow("Y", "processing-timer1", new Instant(1300L), new Instant(10004L)),
-            timerInGlobalWindow("A", "processing-timer1", new Instant(1400L), new Instant(10014L)),
-            timerInGlobalWindow("B", "processing-timer1", new Instant(1500L), new Instant(10014L)),
-            timerInGlobalWindow("A", "processing-timer1", new Instant(1600L), new Instant(10014L)),
-            timerInGlobalWindow("X", "processing-timer1", new Instant(1700L), new Instant(10024L)),
-            timerInGlobalWindow("C", "processing-timer1", new Instant(1800L), new Instant(10024L)),
-            timerInGlobalWindow("B", "processing-timer1", new Instant(1900L), new Instant(10024L)),
-            timerInGlobalWindow("B", "processing-timer1", new Instant(2000L), new Instant(10034L)),
-            timerInGlobalWindow(
+            dynamicTimerInGlobalWindow(
+                "X", "processing-timer1", new Instant(1000L), new Instant(10004L)),
+            dynamicTimerInGlobalWindow(
+                "Y", "processing-timer1", new Instant(1100L), new Instant(10004L)),
+            dynamicTimerInGlobalWindow(
+                "X", "processing-timer1", new Instant(1200L), new Instant(10004L)),
+            dynamicTimerInGlobalWindow(
+                "Y", "processing-timer1", new Instant(1300L), new Instant(10004L)),
+            dynamicTimerInGlobalWindow(
+                "A", "processing-timer1", new Instant(1400L), new Instant(10014L)),
+            dynamicTimerInGlobalWindow(
+                "B", "processing-timer1", new Instant(1500L), new Instant(10014L)),
+            dynamicTimerInGlobalWindow(
+                "A", "processing-timer1", new Instant(1600L), new Instant(10014L)),
+            dynamicTimerInGlobalWindow(
+                "X", "processing-timer1", new Instant(1700L), new Instant(10024L)),
+            dynamicTimerInGlobalWindow(
+                "C", "processing-timer1", new Instant(1800L), new Instant(10024L)),
+            dynamicTimerInGlobalWindow(
+                "B", "processing-timer1", new Instant(1900L), new Instant(10024L)),
+            dynamicTimerInGlobalWindow(
+                "B", "processing-timer1", new Instant(2000L), new Instant(10034L)),
+            dynamicTimerInGlobalWindow(
                 "Y", "processing-timer1", new Instant(2100L), new Instant(10044L))));
     mainOutputValues.clear();
 
@@ -979,14 +992,10 @@ public void testTimers() throws Exception {
 
   private  org.apache.beam.runners.core.construction.Timer timerInGlobalWindow(
       K userKey, Instant holdTimestamp, Instant fireTimestamp) {
-    return timerInGlobalWindow(userKey, "", holdTimestamp, fireTimestamp);
+    return dynamicTimerInGlobalWindow(userKey, "", holdTimestamp, fireTimestamp);
   }
 
-  private  WindowedValue valueInWindow(T value, BoundedWindow window) {
-    return WindowedValue.of(value, window.maxTimestamp(), window, PaneInfo.NO_FIRING);
-  }
-
-  private  org.apache.beam.runners.core.construction.Timer timerInGlobalWindow(
+  private  org.apache.beam.runners.core.construction.Timer dynamicTimerInGlobalWindow(
       K userKey, String dynamicTimerTag, Instant holdTimestamp, Instant fireTimestamp) {
     return org.apache.beam.runners.core.construction.Timer.of(
         userKey,
@@ -997,6 +1006,10 @@ private  org.apache.beam.runners.core.construction.Timer timerInGlobalWind
         PaneInfo.NO_FIRING);
   }
 
+  private  WindowedValue valueInWindow(T value, BoundedWindow window) {
+    return WindowedValue.of(value, window.maxTimestamp(), window, PaneInfo.NO_FIRING);
+  }
+
   private static class TestTimerfulDoFn extends DoFn, String> {
     @StateId("bag")
     private final StateSpec> bagStateSpec = StateSpecs.bag(StringUtf8Coder.of());

From 79e84e98f7de076de72302a4bce9086236e1e947 Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Thu, 21 May 2020 12:40:06 -0400
Subject: [PATCH 046/151] Include additional instructions for staging
 repository.

---
 website/www/site/content/en/contribute/release-guide.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/website/www/site/content/en/contribute/release-guide.md b/website/www/site/content/en/contribute/release-guide.md
index 3da9fbcc3973..230cae418ed8 100644
--- a/website/www/site/content/en/contribute/release-guide.md
+++ b/website/www/site/content/en/contribute/release-guide.md
@@ -607,7 +607,10 @@ For this step, we recommend you using automation script to create a RC, but you
           ls -al /opt/apache/beam/third_party_licenses/ | wc -l
           ```
   1. Publish staging artifacts
-      1. Go to the staging repo to close the staging repository on [Apache Nexus](https://repository.apache.org/#stagingRepositories).
+      1. Log in to the [Apache Nexus](https://repository.apache.org/#stagingRepositories) website.
+      1. Navigate to Build Promotion -> Staging Repositories (in the left sidebar).
+      1. Select repository `orgapachebeam-NNNN`.
+      1. Click the Close button.
       1. When prompted for a description, enter “Apache Beam, version X, release candidate Y”.
       1. Review all staged artifacts on https://repository.apache.org/content/repositories/orgapachebeam-NNNN/. They should contain all relevant parts for each module, including `pom.xml`, jar, test jar, javadoc, etc. Artifact names should follow [the existing format](https://search.maven.org/#search%7Cga%7C1%7Cg%3A%22org.apache.beam%22) in which artifact name mirrors directory structure, e.g., `beam-sdks-java-io-kafka`. Carefully review any new artifacts.
   1. Build and stage python wheels.

From b8e582ffaf39918819640c83f4b3fdf9f0190abf Mon Sep 17 00:00:00 2001
From: Heejong Lee 
Date: Thu, 21 May 2020 01:01:24 -0700
Subject: [PATCH 047/151] [BEAM-10052] check hash and avoid duplicated
 artifacts

---
 .../runners/dataflow/internal/apiclient.py           | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py b/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
index 06bb26029aeb..55649a761af7 100644
--- a/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
+++ b/sdks/python/apache_beam/runners/dataflow/internal/apiclient.py
@@ -583,6 +583,7 @@ def _stage_resources(self, pipeline, options):
       raise RuntimeError('The --temp_location option must be specified.')
 
     resources = []
+    hashs = {}
     for _, env in sorted(pipeline.components.environments.items(),
                          key=lambda kv: kv[0]):
       for dep in env.dependencies:
@@ -595,7 +596,16 @@ def _stage_resources(self, pipeline, options):
         role_payload = (
             beam_runner_api_pb2.ArtifactStagingToRolePayload.FromString(
                 dep.role_payload))
-        resources.append((type_payload.path, role_payload.staged_name))
+        if type_payload.sha256 and type_payload.sha256 in hashs:
+          _LOGGER.info(
+              'Found duplicated artifact: %s (%s)',
+              type_payload.path,
+              type_payload.sha256)
+          dep.role_payload = beam_runner_api_pb2.ArtifactStagingToRolePayload(
+              staged_name=hashs[type_payload.sha256]).SerializeToString()
+        else:
+          resources.append((type_payload.path, role_payload.staged_name))
+          hashs[type_payload.sha256] = role_payload.staged_name
 
     resource_stager = _LegacyDataflowStager(self)
     staged_resources = resource_stager.stage_job_resources(

From 0c3780c438bc1e3c9e314e87e8646e3f4e8972b4 Mon Sep 17 00:00:00 2001
From: Kyle Weaver 
Date: Thu, 21 May 2020 13:54:42 -0400
Subject: [PATCH 048/151] Clarify the usage of sign_hash_python_wheels.sh.

---
 website/www/site/content/en/contribute/release-guide.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/website/www/site/content/en/contribute/release-guide.md b/website/www/site/content/en/contribute/release-guide.md
index 230cae418ed8..3037698002f8 100644
--- a/website/www/site/content/en/contribute/release-guide.md
+++ b/website/www/site/content/en/contribute/release-guide.md
@@ -617,8 +617,8 @@ For this step, we recommend you using automation script to create a RC, but you
       - There is a wrapper repo [beam-wheels](https://github.com/apache/beam-wheels) to help build python wheels.
       - If you are interested in how it works, please refer to the [structure section](https://github.com/apache/beam-wheels#structure).
       - Please follow the [user guide](https://github.com/apache/beam-wheels#user-guide) to build python wheels.
-      - Once all python wheels have been staged [dist.apache.org](https://dist.apache.org/repos/dist/dev/beam/),
-      please run [./sign_hash_python_wheels.sh](https://github.com/apache/beam/blob/master/release/src/main/scripts/sign_hash_python_wheels.sh) to sign and hash python wheels.
+      - Once all python wheels have been staged to GCS,
+      please run [./sign_hash_python_wheels.sh](https://github.com/apache/beam/blob/master/release/src/main/scripts/sign_hash_python_wheels.sh), which copies the wheels along with signatures and hashes to [dist.apache.org](https://dist.apache.org/repos/dist/dev/beam/).
   1. Update Beam website ([example](https://github.com/apache/beam/pull/11727))
       1. Update release version in `website/www/site/config.toml`.
       1. Add new release in `website/www/site/content/en/get-started/downloads.md`.

From 105f2657a730672b70fbb3ec4a2f111247a5cae1 Mon Sep 17 00:00:00 2001
From: Brian Hulette 
Date: Thu, 21 May 2020 15:03:23 -0700
Subject: [PATCH 049/151] Website build: Remove -u root (#11625)

---
 website/build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/website/build.gradle b/website/build.gradle
index 235cb8426e6d..b5988d8e2b42 100644
--- a/website/build.gradle
+++ b/website/build.gradle
@@ -119,7 +119,7 @@ task setupDockerContainer(type: Exec) {
   }
 
   // Create the config to point to a GitHub or Colab blob in the repo, e.g. apache/beam/blob/master
-  commandLine 'docker', 'exec', '-u', 'root',
+  commandLine 'docker', 'exec',
     "${->startDockerContainer.containerId()}", '/bin/bash', '-c',
     """echo '[params]\n  branch_repo = "${getBranchRepo()}"' > /tmp/_config_branch_repo.toml"""
 }

From 393f1bacffa64360d359b646655ead3e090373f4 Mon Sep 17 00:00:00 2001
From: Ankur Goenka 
Date: Thu, 21 May 2020 15:03:38 -0700
Subject: [PATCH 050/151] [BEAM-10060] Upgrading Python containers to
 beam-master-20200521

---
 sdks/python/apache_beam/runners/dataflow/internal/names.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sdks/python/apache_beam/runners/dataflow/internal/names.py b/sdks/python/apache_beam/runners/dataflow/internal/names.py
index 9be60ff497fa..446f00cda49b 100644
--- a/sdks/python/apache_beam/runners/dataflow/internal/names.py
+++ b/sdks/python/apache_beam/runners/dataflow/internal/names.py
@@ -40,10 +40,10 @@
 
 # Update this version to the next version whenever there is a change that will
 # require changes to legacy Dataflow worker execution environment.
-BEAM_CONTAINER_VERSION = 'beam-master-20200518'
+BEAM_CONTAINER_VERSION = 'beam-master-20200521'
 # Update this version to the next version whenever there is a change that
 # requires changes to SDK harness container or SDK harness launcher.
-BEAM_FNAPI_CONTAINER_VERSION = 'beam-master-20200518'
+BEAM_FNAPI_CONTAINER_VERSION = 'beam-master-20200521'
 
 # TODO(BEAM-5939): Remove these shared names once Dataflow worker is updated.
 PICKLED_MAIN_SESSION_FILE = 'pickled_main_session'

From 73fa1356e4bc2d04e51c06cbf7c3aa860264f9ee Mon Sep 17 00:00:00 2001
From: Dariusz Aniszewski 
Date: Fri, 22 May 2020 00:39:16 +0200
Subject: [PATCH 051/151] [BEAM-9722] added SnowflakeIO with Read operation
 (#11360)

* [BEAM-9722] added SnowflakeIO with Read operation

* [BEAM-9722] Added SnowflakeCloudProvider to enable use various clouds with Snowflake

* [BEAM-9722] added docstrings for public methods

* [BEAM-9722] Added changed cleanup staged GCS files to Beam FileSystems

* [BEAM-9722] Added javadocs for public methods in DataSourceConfiguration

* add testing p8 file to RAT exclude
refactor SnowflakeCredentials
add information about possibly left files on cloud storage
small docs changes

* documentation changes

* [BEAM-9722] Added TestRule and changed Unit tests to use pipeline.run

* [BEAM-9722] Renamed Snowflake Read unit test and applied spotless

* [BEAM-9722] remove SnowflakeCloudProvider interface

* [BEAM-9722] doc changes

* [BEAM-9722] add `withoutValidation` to disable verifying connection to Snowflake during pipeline construction

* [BEAM-9722] added MoveOption and removed leftover file

* [BEAM-9722] fixed tests. Add tests for `withQuery`

* [BEAM-9722] make `CopyIntoStageFn` retryable

* [BEAM-9722] added `Reshuffle` step after `CopyIntoStageFn`

Co-authored-by: Kasia Kucharczyk 
Co-authored-by: pawel.urbanowicz 
---
 CHANGES.md                                    |   1 +
 build.gradle                                  |   3 +
 sdks/java/io/snowflake/build.gradle           |  42 +
 .../beam/sdk/io/snowflake/CloudProvider.java  |  32 +
 .../beam/sdk/io/snowflake/SnowflakeIO.java    | 759 ++++++++++++++++++
 .../snowflake/SnowflakePipelineOptions.java   | 133 +++
 .../sdk/io/snowflake/SnowflakeService.java    |  36 +
 .../io/snowflake/SnowflakeServiceImpl.java    |  90 +++
 .../KeyPairSnowflakeCredentials.java          |  81 ++
 .../OAuthTokenSnowflakeCredentials.java       |  31 +
 .../credentials/SnowflakeCredentials.java     |  24 +
 .../SnowflakeCredentialsFactory.java          |  55 ++
 .../UsernamePasswordSnowflakeCredentials.java |  37 +
 .../snowflake/credentials/package-info.java   |  20 +
 .../beam/sdk/io/snowflake/package-info.java   |  20 +
 .../test/FakeSnowflakeBasicDataSource.java    | 298 +++++++
 .../snowflake/test/FakeSnowflakeDatabase.java |  81 ++
 .../test/FakeSnowflakeServiceImpl.java        |  64 ++
 .../beam/sdk/io/snowflake/test/TestUtils.java |  40 +
 .../sdk/io/snowflake/test/package-info.java   |  20 +
 .../test/unit/BatchTestPipelineOptions.java   |  28 +
 .../unit/DataSourceConfigurationTest.java     | 159 ++++
 .../KeyPairSnowflakeCredentialsTest.java      |  38 +
 .../OAuthTokenSnowflakeCredentialsTest.java   |  46 ++
 .../SnowflakeCredentialsFactoryTest.java      |  77 ++
 ...rnamePasswordSnowflakeCredentialsTest.java |  50 ++
 .../test/unit/read/SnowflakeIOReadTest.java   | 278 +++++++
 .../src/test/resources/test_rsa_key.p8        |  29 +
 settings.gradle                               |   1 +
 29 files changed, 2573 insertions(+)
 create mode 100644 sdks/java/io/snowflake/build.gradle
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/CloudProvider.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeIO.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakePipelineOptions.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeService.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeServiceImpl.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/KeyPairSnowflakeCredentials.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/OAuthTokenSnowflakeCredentials.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/SnowflakeCredentials.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/SnowflakeCredentialsFactory.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/UsernamePasswordSnowflakeCredentials.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/package-info.java
 create mode 100644 sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/package-info.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeBasicDataSource.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeDatabase.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeServiceImpl.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/TestUtils.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/package-info.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/BatchTestPipelineOptions.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/DataSourceConfigurationTest.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/KeyPairSnowflakeCredentialsTest.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/OAuthTokenSnowflakeCredentialsTest.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/SnowflakeCredentialsFactoryTest.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/UsernamePasswordSnowflakeCredentialsTest.java
 create mode 100644 sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/read/SnowflakeIOReadTest.java
 create mode 100644 sdks/java/io/snowflake/src/test/resources/test_rsa_key.p8

diff --git a/CHANGES.md b/CHANGES.md
index 107e7dc8dff1..59082149617a 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -57,6 +57,7 @@
 ## I/Os
 
 * Support for X source added (Java/Python) ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)).
+* Support for reading from Snowflake added (Java) ([BEAM-9722](https://issues.apache.org/jira/browse/BEAM-9722)).
 
 ## New Features / Improvements
 
diff --git a/build.gradle b/build.gradle
index c26a02067da3..65363b7569dc 100644
--- a/build.gradle
+++ b/build.gradle
@@ -112,6 +112,9 @@ rat {
     "learning/katas/**/task-remote-info.yaml",
     "learning/katas/*/IO/**/*.txt",
 
+    // test p8 file for SnowflakeIO
+    "sdks/java/io/snowflake/src/test/resources/test_rsa_key.p8",
+
     // Mockito extensions
     "sdks/java/io/amazon-web-services2/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker",
     "sdks/java/extensions/ml/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker"
diff --git a/sdks/java/io/snowflake/build.gradle b/sdks/java/io/snowflake/build.gradle
new file mode 100644
index 000000000000..c51c0348efc0
--- /dev/null
+++ b/sdks/java/io/snowflake/build.gradle
@@ -0,0 +1,42 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * License); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an AS IS BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+plugins { id 'org.apache.beam.module' }
+applyJavaNature(automaticModuleName: 'org.apache.beam.sdk.io.snowflake')
+provideIntegrationTestingDependencies()
+enableJavaPerformanceTesting()
+description = "Apache Beam :: SDKs :: Java :: IO :: Snowflake"
+ext.summary = "IO to read and write on Snowflake."
+dependencies {
+  compile library.java.vendored_guava_26_0_jre
+  compile project(path: ":sdks:java:core", configuration: "shadow")
+  compile project(path: ":sdks:java:extensions:google-cloud-platform-core")
+  compile library.java.slf4j_api
+  compile group: 'net.snowflake', name: 'snowflake-jdbc', version: '3.11.0'
+  compile group: 'com.opencsv', name: 'opencsv', version: '5.0'
+  testCompile project(path: ":sdks:java:core", configuration: "shadowTest")
+  testCompile project(path: ":sdks:java:io:common", configuration: "testRuntime")
+  testCompile project(path: ":sdks:java:testing:test-utils", configuration: "testRuntime")
+  testCompile library.java.avro
+  testCompile library.java.junit
+  testCompile library.java.hamcrest_core
+  testCompile library.java.hamcrest_library
+  testCompile library.java.slf4j_api
+  testRuntimeOnly library.java.hadoop_client
+  testRuntimeOnly library.java.slf4j_jdk14
+  testRuntimeOnly project(path: ":runners:direct-java", configuration: "shadow")
+}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/CloudProvider.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/CloudProvider.java
new file mode 100644
index 000000000000..404859c96d81
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/CloudProvider.java
@@ -0,0 +1,32 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake;
+
+public enum CloudProvider {
+  GCS("gs://");
+
+  private final String prefix;
+
+  private CloudProvider(String prefix) {
+    this.prefix = prefix;
+  }
+
+  public String getPrefix() {
+    return prefix;
+  }
+}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeIO.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeIO.java
new file mode 100644
index 000000000000..a67ba320d361
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeIO.java
@@ -0,0 +1,759 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake;
+
+import static org.apache.beam.sdk.io.TextIO.readFiles;
+import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkArgument;
+
+import com.google.auto.value.AutoValue;
+import com.opencsv.CSVParser;
+import com.opencsv.CSVParserBuilder;
+import java.io.IOException;
+import java.io.Serializable;
+import java.security.PrivateKey;
+import java.sql.Connection;
+import java.sql.SQLException;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.stream.Collectors;
+import javax.annotation.Nullable;
+import javax.sql.DataSource;
+import net.snowflake.client.jdbc.SnowflakeBasicDataSource;
+import org.apache.beam.sdk.coders.Coder;
+import org.apache.beam.sdk.io.FileIO;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.MoveOptions;
+import org.apache.beam.sdk.io.fs.ResourceId;
+import org.apache.beam.sdk.io.snowflake.credentials.KeyPairSnowflakeCredentials;
+import org.apache.beam.sdk.io.snowflake.credentials.OAuthTokenSnowflakeCredentials;
+import org.apache.beam.sdk.io.snowflake.credentials.SnowflakeCredentials;
+import org.apache.beam.sdk.io.snowflake.credentials.UsernamePasswordSnowflakeCredentials;
+import org.apache.beam.sdk.transforms.Create;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.transforms.Reshuffle;
+import org.apache.beam.sdk.transforms.SerializableFunction;
+import org.apache.beam.sdk.transforms.Wait;
+import org.apache.beam.sdk.transforms.display.DisplayData;
+import org.apache.beam.sdk.transforms.display.HasDisplayData;
+import org.apache.beam.sdk.values.PBegin;
+import org.apache.beam.sdk.values.PCollection;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * IO to read and write data on Snowflake.
+ *
+ * 
    SnowflakeIO uses Snowflake
+ * JDBC driver under the hood, but data isn't read/written using JDBC directly. Instead,
+ * SnowflakeIO uses dedicated COPY operations to read/write data from/to a cloud bucket. By
+ * now only Google Cloud Storage is supported.
+ *
+ * 
    To configure SnowflakeIO to read/write from your Snowflake instance, you have to provide a
+ * {@link DataSourceConfiguration} using {@link
+ * DataSourceConfiguration#create(SnowflakeCredentials)}, where {@link SnowflakeCredentials might be
+ * created using {@link org.apache.beam.sdk.io.snowflake.credentials.SnowflakeCredentialsFactory}}.
+ * Additionally one of {@link DataSourceConfiguration#withServerName(String)} or {@link
+ * DataSourceConfiguration#withUrl(String)} must be used to tell SnowflakeIO which instance to use.
+ * 
    
+ * There are also other options available to configure connection to Snowflake:
+ *
+ * 
      
+ *   
    • {@link DataSourceConfiguration#withWarehouse(String)} to specify which Warehouse to use
+ *   
    • {@link DataSourceConfiguration#withDatabase(String)} to specify which Database to connect
+ *       to
+ *   
    • {@link DataSourceConfiguration#withSchema(String)} to specify which schema to use
+ *   
    • {@link DataSourceConfiguration#withRole(String)} to specify which role to use
+ *   
    • {@link DataSourceConfiguration#withLoginTimeout(Integer)} to specify the timeout for the
+ *       login
+ *   
    • {@link DataSourceConfiguration#withPortNumber(Integer)} to specify custom port of Snowflake
+ *       instance
+ * 
    
+ *
+ * 
    For example:
+ *
+ * 
    {@code
+ * SnowflakeIO.DataSourceConfiguration dataSourceConfiguration =
+ *     SnowflakeIO.DataSourceConfiguration.create(SnowflakeCredentialsFactory.of(options))
+ *         .withServerName(options.getServerName())
+ *         .withWarehouse(options.getWarehouse())
+ *         .withDatabase(options.getDatabase())
+ *         .withSchema(options.getSchema());
+ * }
    
+ *
+ * 
    Reading from Snowflake
    
+ *
+ * 
    SnowflakeIO.Read returns a bounded collection of {@code T} as a {@code PCollection}. T is
+ * the type returned by the provided {@link CsvMapper}.
+ *
+ * 
    For example
+ *
+ * 
    {@code
+ * PCollection items = pipeline.apply(
+ *  SnowflakeIO.read()
+ *    .withDataSourceConfiguration(dataSourceConfiguration)
+ *    .fromQuery(QUERY)
+ *    .withStagingBucketName(stagingBucketName)
+ *    .withIntegrationName(integrationName)
+ *    .withCsvMapper(...)
+ *    .withCoder(...));
+ * }
    
+ *
+ * 
    Important When reading data from Snowflake, temporary CSV files are created on the
+ * specified stagingBucketName in directory named `sf_copy_csv_[RANDOM CHARS]_[TIMESTAMP]`. This
+ * directory and all the files are cleaned up automatically by default, but in case of failed
+ * pipeline they may remain and will have to be cleaned up manually.
+ */
+public class SnowflakeIO {
+  private static final Logger LOG = LoggerFactory.getLogger(SnowflakeIO.class);
+
+  private static final String CSV_QUOTE_CHAR = "'";
+  /**
+   * Read data from Snowflake.
+   *
+   * @param snowflakeService user-defined {@link SnowflakeService}
+   * @param  Type of the data to be read.
+   */
+  public static  Read read(SnowflakeService snowflakeService) {
+    return new AutoValue_SnowflakeIO_Read.Builder()
+        .setSnowflakeService(snowflakeService)
+        .build();
+  }
+
+  /**
+   * Read data from Snowflake.
+   *
+   * @param  Type of the data to be read.
+   */
+  public static  Read read() {
+    return read(new SnowflakeServiceImpl());
+  }
+
+  /**
+   * Interface for user-defined function mapping parts of CSV line into T. Used for
+   * SnowflakeIO.Read.
+   *
+   * @param  Type of data to be read.
+   */
+  @FunctionalInterface
+  public interface CsvMapper extends Serializable {
+    T mapRow(String[] parts) throws Exception;
+  }
+
+  /** Implementation of {@link #read()}. */
+  @AutoValue
+  public abstract static class Read extends PTransform> {
+    @Nullable
+    abstract SerializableFunction getDataSourceProviderFn();
+
+    @Nullable
+    abstract String getQuery();
+
+    @Nullable
+    abstract String getTable();
+
+    @Nullable
+    abstract String getIntegrationName();
+
+    @Nullable
+    abstract String getStagingBucketName();
+
+    @Nullable
+    abstract CsvMapper getCsvMapper();
+
+    @Nullable
+    abstract Coder getCoder();
+
+    @Nullable
+    abstract SnowflakeService getSnowflakeService();
+
+    abstract Builder toBuilder();
+
+    @AutoValue.Builder
+    abstract static class Builder {
+      abstract Builder setDataSourceProviderFn(
+          SerializableFunction dataSourceProviderFn);
+
+      abstract Builder setQuery(String query);
+
+      abstract Builder setTable(String table);
+
+      abstract Builder setIntegrationName(String integrationName);
+
+      abstract Builder setStagingBucketName(String stagingBucketName);
+
+      abstract Builder setCsvMapper(CsvMapper csvMapper);
+
+      abstract Builder setCoder(Coder coder);
+
+      abstract Builder setSnowflakeService(SnowflakeService snowflakeService);
+
+      abstract Read build();
+    }
+
+    /**
+     * Setting information about Snowflake server.
+     *
+     * @param config - An instance of {@link DataSourceConfiguration}.
+     */
+    public Read withDataSourceConfiguration(final DataSourceConfiguration config) {
+      if (config.getValidate()) {
+        try {
+          Connection connection = config.buildDatasource().getConnection();
+          connection.close();
+        } catch (SQLException e) {
+          throw new IllegalArgumentException(
+              "Invalid DataSourceConfiguration. Underlying cause: " + e);
+        }
+      }
+      return withDataSourceProviderFn(new DataSourceProviderFromDataSourceConfiguration(config));
+    }
+
+    /**
+     * Setting function that will provide {@link DataSourceConfiguration} in runtime.
+     *
+     * @param dataSourceProviderFn a {@link SerializableFunction}.
+     */
+    public Read withDataSourceProviderFn(
+        SerializableFunction dataSourceProviderFn) {
+      return toBuilder().setDataSourceProviderFn(dataSourceProviderFn).build();
+    }
+
+    /**
+     * A query to be executed in Snowflake.
+     *
+     * @param query - String with query.
+     */
+    public Read fromQuery(String query) {
+      return toBuilder().setQuery(query).build();
+    }
+
+    /**
+     * A table name to be read in Snowflake.
+     *
+     * @param table - String with the name of the table.
+     */
+    public Read fromTable(String table) {
+      return toBuilder().setTable(table).build();
+    }
+
+    /**
+     * Name of the cloud bucket (GCS by now) to use as tmp location of CSVs during COPY statement.
+     *
+     * @param stagingBucketName - String with the name of the bucket.
+     */
+    public Read withStagingBucketName(String stagingBucketName) {
+      return toBuilder().setStagingBucketName(stagingBucketName).build();
+    }
+
+    /**
+     * Name of the Storage Integration in Snowflake to be used. See
+     * https://docs.snowflake.com/en/sql-reference/sql/create-storage-integration.html for
+     * reference.
+     *
+     * @param integrationName - String with the name of the Storage Integration.
+     */
+    public Read withIntegrationName(String integrationName) {
+      return toBuilder().setIntegrationName(integrationName).build();
+    }
+
+    /**
+     * User-defined function mapping CSV lines into user data.
+     *
+     * @param csvMapper - an instance of {@link CsvMapper}.
+     */
+    public Read withCsvMapper(CsvMapper csvMapper) {
+      return toBuilder().setCsvMapper(csvMapper).build();
+    }
+
+    /**
+     * A Coder to be used by the output PCollection generated by the source.
+     *
+     * @param coder - an instance of {@link Coder}.
+     */
+    public Read withCoder(Coder coder) {
+      return toBuilder().setCoder(coder).build();
+    }
+
+    @Override
+    public PCollection expand(PBegin input) {
+      // Either table or query is required. If query is present, it's being used, table is used
+      // otherwise
+      checkArgument(
+          getQuery() != null || getTable() != null, "fromTable() or fromQuery() is required");
+      checkArgument(
+          !(getQuery() != null && getTable() != null),
+          "fromTable() and fromQuery() are not allowed together");
+      checkArgument(getCsvMapper() != null, "withCsvMapper() is required");
+      checkArgument(getCoder() != null, "withCoder() is required");
+      checkArgument(getIntegrationName() != null, "withIntegrationName() is required");
+      checkArgument(getStagingBucketName() != null, "withStagingBucketName() is required");
+      checkArgument(
+          (getDataSourceProviderFn() != null),
+          "withDataSourceConfiguration() or withDataSourceProviderFn() is required");
+
+      String tmpDirName = makeTmpDirName();
+      String stagingBucketDir = String.format("%s/%s", getStagingBucketName(), tmpDirName);
+
+      PCollection emptyCollection = input.apply(Create.of((Void) null));
+
+      PCollection output =
+          emptyCollection
+              .apply(
+                  ParDo.of(
+                      new CopyIntoStageFn(
+                          getDataSourceProviderFn(),
+                          getQuery(),
+                          getTable(),
+                          getIntegrationName(),
+                          stagingBucketDir,
+                          getSnowflakeService())))
+              .apply(Reshuffle.viaRandomKey())
+              .apply(FileIO.matchAll())
+              .apply(FileIO.readMatches())
+              .apply(readFiles())
+              .apply(ParDo.of(new MapCsvToStringArrayFn()))
+              .apply(ParDo.of(new MapStringArrayToUserDataFn<>(getCsvMapper())));
+
+      output.setCoder(getCoder());
+
+      emptyCollection
+          .apply(Wait.on(output))
+          .apply(ParDo.of(new CleanTmpFilesFromGcsFn(stagingBucketDir)));
+
+      return output;
+    }
+
+    private String makeTmpDirName() {
+      return String.format(
+          "sf_copy_csv_%s_%s",
+          new SimpleDateFormat("yyyyMMdd_HHmmss").format(new Date()),
+          UUID.randomUUID().toString().subSequence(0, 8) // first 8 chars of UUID should be enough
+          );
+    }
+
+    private static class CopyIntoStageFn extends DoFn {
+      private final SerializableFunction dataSourceProviderFn;
+      private final String query;
+      private final String table;
+      private final String integrationName;
+      private final String stagingBucketDir;
+      private final SnowflakeService snowflakeService;
+
+      private CopyIntoStageFn(
+          SerializableFunction dataSourceProviderFn,
+          String query,
+          String table,
+          String integrationName,
+          String stagingBucketDir,
+          SnowflakeService snowflakeService) {
+        this.dataSourceProviderFn = dataSourceProviderFn;
+        this.query = query;
+        this.table = table;
+        this.integrationName = integrationName;
+        this.stagingBucketDir =
+            String.format(
+                "%s/run_%s/", stagingBucketDir, UUID.randomUUID().toString().subSequence(0, 8));
+        this.snowflakeService = snowflakeService;
+      }
+
+      @ProcessElement
+      public void processElement(ProcessContext context) throws Exception {
+        String output =
+            snowflakeService.copyIntoStage(
+                dataSourceProviderFn, query, table, integrationName, stagingBucketDir);
+
+        context.output(output);
+      }
+    }
+
+    public static class MapCsvToStringArrayFn extends DoFn {
+      @ProcessElement
+      public void processElement(ProcessContext c) throws IOException {
+        String csvLine = c.element();
+        CSVParser parser = new CSVParserBuilder().withQuoteChar(CSV_QUOTE_CHAR.charAt(0)).build();
+        String[] parts = parser.parseLine(csvLine);
+        c.output(parts);
+      }
+    }
+
+    private static class MapStringArrayToUserDataFn extends DoFn {
+      private final CsvMapper csvMapper;
+
+      public MapStringArrayToUserDataFn(CsvMapper csvMapper) {
+        this.csvMapper = csvMapper;
+      }
+
+      @ProcessElement
+      public void processElement(ProcessContext context) throws Exception {
+        context.output(csvMapper.mapRow(context.element()));
+      }
+    }
+
+    public static class CleanTmpFilesFromGcsFn extends DoFn {
+      private final String stagingBucketDir;
+
+      public CleanTmpFilesFromGcsFn(String stagingBucketDir) {
+        this.stagingBucketDir = stagingBucketDir;
+      }
+
+      @ProcessElement
+      public void processElement(ProcessContext c) throws IOException {
+        String combinedPath = stagingBucketDir + "/**";
+        List paths =
+            FileSystems.match(combinedPath).metadata().stream()
+                .map(metadata -> metadata.resourceId())
+                .collect(Collectors.toList());
+
+        FileSystems.delete(paths, MoveOptions.StandardMoveOptions.IGNORE_MISSING_FILES);
+      }
+    }
+
+    @Override
+    public void populateDisplayData(DisplayData.Builder builder) {
+      super.populateDisplayData(builder);
+      if (getQuery() != null) {
+        builder.add(DisplayData.item("query", getQuery()));
+      }
+      if (getTable() != null) {
+        builder.add(DisplayData.item("table", getTable()));
+      }
+      builder.add(DisplayData.item("integrationName", getIntegrationName()));
+      builder.add(DisplayData.item("stagingBucketName", getStagingBucketName()));
+      builder.add(DisplayData.item("csvMapper", getCsvMapper().getClass().getName()));
+      builder.add(DisplayData.item("coder", getCoder().getClass().getName()));
+      if (getDataSourceProviderFn() instanceof HasDisplayData) {
+        ((HasDisplayData) getDataSourceProviderFn()).populateDisplayData(builder);
+      }
+    }
+  }
+
+  /**
+   * A POJO describing a {@link DataSource}, providing all properties allowing to create a {@link
+   * DataSource}.
+   */
+  @AutoValue
+  public abstract static class DataSourceConfiguration implements Serializable {
+    @Nullable
+    public abstract String getUrl();
+
+    @Nullable
+    public abstract String getUsername();
+
+    @Nullable
+    public abstract String getPassword();
+
+    @Nullable
+    public abstract PrivateKey getPrivateKey();
+
+    @Nullable
+    public abstract String getOauthToken();
+
+    @Nullable
+    public abstract String getDatabase();
+
+    @Nullable
+    public abstract String getWarehouse();
+
+    @Nullable
+    public abstract String getSchema();
+
+    @Nullable
+    public abstract String getServerName();
+
+    @Nullable
+    public abstract Integer getPortNumber();
+
+    @Nullable
+    public abstract String getRole();
+
+    @Nullable
+    public abstract Integer getLoginTimeout();
+
+    @Nullable
+    public abstract Boolean getSsl();
+
+    @Nullable
+    public abstract Boolean getValidate();
+
+    @Nullable
+    public abstract DataSource getDataSource();
+
+    abstract Builder builder();
+
+    @AutoValue.Builder
+    abstract static class Builder {
+      abstract Builder setUrl(String url);
+
+      abstract Builder setUsername(String username);
+
+      abstract Builder setPassword(String password);
+
+      abstract Builder setPrivateKey(PrivateKey privateKey);
+
+      abstract Builder setOauthToken(String oauthToken);
+
+      abstract Builder setDatabase(String database);
+
+      abstract Builder setWarehouse(String warehouse);
+
+      abstract Builder setSchema(String schema);
+
+      abstract Builder setServerName(String serverName);
+
+      abstract Builder setPortNumber(Integer portNumber);
+
+      abstract Builder setRole(String role);
+
+      abstract Builder setLoginTimeout(Integer loginTimeout);
+
+      abstract Builder setSsl(Boolean ssl);
+
+      abstract Builder setValidate(Boolean validate);
+
+      abstract Builder setDataSource(DataSource dataSource);
+
+      abstract DataSourceConfiguration build();
+    }
+
+    /**
+     * Creates {@link DataSourceConfiguration} from existing instance of {@link DataSource}.
+     *
+     * @param dataSource - an instance of {@link DataSource}.
+     */
+    public static DataSourceConfiguration create(DataSource dataSource) {
+      checkArgument(dataSource instanceof Serializable, "dataSource must be Serializable");
+      return new AutoValue_SnowflakeIO_DataSourceConfiguration.Builder()
+          .setValidate(true)
+          .setDataSource(dataSource)
+          .build();
+    }
+
+    /**
+     * Creates {@link DataSourceConfiguration} from instance of {@link SnowflakeCredentials}.
+     *
+     * @param credentials - an instance of {@link SnowflakeCredentials}.
+     */
+    public static DataSourceConfiguration create(SnowflakeCredentials credentials) {
+      if (credentials instanceof UsernamePasswordSnowflakeCredentials) {
+        return new AutoValue_SnowflakeIO_DataSourceConfiguration.Builder()
+            .setValidate(true)
+            .setUsername(((UsernamePasswordSnowflakeCredentials) credentials).getUsername())
+            .setPassword(((UsernamePasswordSnowflakeCredentials) credentials).getPassword())
+            .build();
+      } else if (credentials instanceof OAuthTokenSnowflakeCredentials) {
+        return new AutoValue_SnowflakeIO_DataSourceConfiguration.Builder()
+            .setValidate(true)
+            .setOauthToken(((OAuthTokenSnowflakeCredentials) credentials).getToken())
+            .build();
+      } else if (credentials instanceof KeyPairSnowflakeCredentials) {
+        return new AutoValue_SnowflakeIO_DataSourceConfiguration.Builder()
+            .setValidate(true)
+            .setUsername(((KeyPairSnowflakeCredentials) credentials).getUsername())
+            .setPrivateKey(((KeyPairSnowflakeCredentials) credentials).getPrivateKey())
+            .build();
+      }
+      throw new IllegalArgumentException(
+          "Can't create DataSourceConfiguration from given credentials");
+    }
+
+    /**
+     * Sets URL of Snowflake server in following format:
+     * jdbc:snowflake://.snowflakecomputing.com
+     *
+     * 
    Either withUrl or withServerName is required.
+     *
+     * @param url - String with URL of the Snowflake server.
+     */
+    public DataSourceConfiguration withUrl(String url) {
+      checkArgument(
+          url.startsWith("jdbc:snowflake://"),
+          "url must have format: jdbc:snowflake://.snowflakecomputing.com");
+      checkArgument(
+          url.endsWith("snowflakecomputing.com"),
+          "url must have format: jdbc:snowflake://.snowflakecomputing.com");
+      return builder().setUrl(url).build();
+    }
+
+    /**
+     * Sets database to use.
+     *
+     * @param database - String with database name.
+     */
+    public DataSourceConfiguration withDatabase(String database) {
+      return builder().setDatabase(database).build();
+    }
+
+    /**
+     * Sets Snowflake Warehouse to use.
+     *
+     * @param warehouse - String with warehouse name.
+     */
+    public DataSourceConfiguration withWarehouse(String warehouse) {
+      return builder().setWarehouse(warehouse).build();
+    }
+
+    /**
+     * Sets schema to use when connecting to Snowflake.
+     *
+     * @param schema - String with schema name.
+     */
+    public DataSourceConfiguration withSchema(String schema) {
+      return builder().setSchema(schema).build();
+    }
+
+    /**
+     * Sets the name of the Snowflake server. Following format is required:
+     * .snowflakecomputing.com
+     *
+     * 
    Either withServerName or withUrl is required.
+     *
+     * @param serverName - String with server name.
+     */
+    public DataSourceConfiguration withServerName(String serverName) {
+      checkArgument(
+          serverName.endsWith("snowflakecomputing.com"),
+          "serverName must be in format .snowflakecomputing.com");
+      return builder().setServerName(serverName).build();
+    }
+
+    /**
+     * Sets port number to use to connect to Snowflake.
+     *
+     * @param portNumber - Integer with port number.
+     */
+    public DataSourceConfiguration withPortNumber(Integer portNumber) {
+      return builder().setPortNumber(portNumber).build();
+    }
+
+    /**
+     * Sets user's role to be used when running queries on Snowflake.
+     *
+     * @param role - String with role name.
+     */
+    public DataSourceConfiguration withRole(String role) {
+      return builder().setRole(role).build();
+    }
+
+    /**
+     * Sets loginTimeout that will be used in {@link SnowflakeBasicDataSource:setLoginTimeout}.
+     *
+     * @param loginTimeout - Integer with timeout value.
+     */
+    public DataSourceConfiguration withLoginTimeout(Integer loginTimeout) {
+      return builder().setLoginTimeout(loginTimeout).build();
+    }
+
+    /**
+     * Disables validation of connection parameters prior to pipeline submission.
+     *
+     * @return
+     */
+    public DataSourceConfiguration withoutValidation() {
+      return builder().setValidate(false).build();
+    }
+
+    void populateDisplayData(DisplayData.Builder builder) {
+      if (getDataSource() != null) {
+        builder.addIfNotNull(DisplayData.item("dataSource", getDataSource().getClass().getName()));
+      } else {
+        builder.addIfNotNull(DisplayData.item("jdbcUrl", getUrl()));
+        builder.addIfNotNull(DisplayData.item("username", getUsername()));
+      }
+    }
+
+    /** Builds {@link SnowflakeBasicDataSource} based on the current configuration. */
+    public DataSource buildDatasource() {
+      if (getDataSource() == null) {
+        SnowflakeBasicDataSource basicDataSource = new SnowflakeBasicDataSource();
+
+        if (getUrl() != null) {
+          basicDataSource.setUrl(getUrl());
+        }
+        if (getUsername() != null) {
+          basicDataSource.setUser(getUsername());
+        }
+        if (getPassword() != null) {
+          basicDataSource.setPassword(getPassword());
+        }
+        if (getPrivateKey() != null) {
+          basicDataSource.setPrivateKey(getPrivateKey());
+        }
+        if (getDatabase() != null) {
+          basicDataSource.setDatabaseName(getDatabase());
+        }
+        if (getWarehouse() != null) {
+          basicDataSource.setWarehouse(getWarehouse());
+        }
+        if (getSchema() != null) {
+          basicDataSource.setSchema(getSchema());
+        }
+        if (getServerName() != null) {
+          basicDataSource.setServerName(getServerName());
+        }
+        if (getPortNumber() != null) {
+          basicDataSource.setPortNumber(getPortNumber());
+        }
+        if (getRole() != null) {
+          basicDataSource.setRole(getRole());
+        }
+        if (getLoginTimeout() != null) {
+          try {
+            basicDataSource.setLoginTimeout(getLoginTimeout());
+          } catch (SQLException e) {
+            throw new RuntimeException("Failed to setLoginTimeout");
+          }
+        }
+        if (getOauthToken() != null) {
+          basicDataSource.setOauthToken(getOauthToken());
+        }
+        return basicDataSource;
+      }
+      return getDataSource();
+    }
+  }
+
+  public static class DataSourceProviderFromDataSourceConfiguration
+      implements SerializableFunction, HasDisplayData {
+    private static final ConcurrentHashMap instances =
+        new ConcurrentHashMap<>();
+    private final DataSourceConfiguration config;
+
+    private DataSourceProviderFromDataSourceConfiguration(DataSourceConfiguration config) {
+      this.config = config;
+    }
+
+    public static SerializableFunction of(DataSourceConfiguration config) {
+      return new DataSourceProviderFromDataSourceConfiguration(config);
+    }
+
+    @Override
+    public DataSource apply(Void input) {
+      return instances.computeIfAbsent(config, (config) -> config.buildDatasource());
+    }
+
+    @Override
+    public void populateDisplayData(DisplayData.Builder builder) {
+      config.populateDisplayData(builder);
+    }
+  }
+}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakePipelineOptions.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakePipelineOptions.java
new file mode 100644
index 000000000000..783230edbb8d
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakePipelineOptions.java
@@ -0,0 +1,133 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake;
+
+import org.apache.beam.sdk.options.Default;
+import org.apache.beam.sdk.options.Description;
+import org.apache.beam.sdk.options.PipelineOptions;
+import org.apache.beam.sdk.options.Validation;
+
+public interface SnowflakePipelineOptions extends PipelineOptions {
+  String BASIC_CONNECTION_INFO_VALIDATION_GROUP = "BASIC_CONNECTION_INFO_GROUP";
+  String AUTH_VALIDATION_GROUP = "AUTH_VALIDATION_GROUP";
+
+  @Description(
+      "Snowflake's JDBC-like url including account name and region without any parameters.")
+  @Validation.Required(groups = BASIC_CONNECTION_INFO_VALIDATION_GROUP)
+  String getUrl();
+
+  void setUrl(String url);
+
+  @Description("Server Name - full server name with account, zone and domain.")
+  @Validation.Required(groups = BASIC_CONNECTION_INFO_VALIDATION_GROUP)
+  String getServerName();
+
+  void setServerName(String serverName);
+
+  @Description("Username. Required for username/password and Private Key authentication.")
+  @Validation.Required(groups = AUTH_VALIDATION_GROUP)
+  String getUsername();
+
+  void setUsername(String username);
+
+  @Description("OAuth token. Required for OAuth authentication only.")
+  @Validation.Required(groups = AUTH_VALIDATION_GROUP)
+  String getOauthToken();
+
+  void setOauthToken(String oauthToken);
+
+  @Description("Password. Required for username/password authentication only.")
+  @Default.String("")
+  String getPassword();
+
+  void setPassword(String password);
+
+  @Description("Path to Private Key file. Required for Private Key authentication only.")
+  @Default.String("")
+  String getPrivateKeyPath();
+
+  void setPrivateKeyPath(String privateKeyPath);
+
+  @Description("Private Key's passphrase. Required for Private Key authentication only.")
+  @Default.String("")
+  String getPrivateKeyPassphrase();
+
+  void setPrivateKeyPassphrase(String keyPassphrase);
+
+  @Description("Warehouse to use. Optional.")
+  @Default.String("")
+  String getWarehouse();
+
+  void setWarehouse(String warehouse);
+
+  @Description("Database name to connect to. Optional.")
+  @Default.String("")
+  String getDatabase();
+
+  void setDatabase(String database);
+
+  @Description("Schema to use. Optional.")
+  @Default.String("")
+  String getSchema();
+
+  void setSchema(String schema);
+
+  @Description("Role to use. Optional.")
+  @Default.String("")
+  String getRole();
+
+  void setRole(String role);
+
+  @Description("Authenticator to use. Optional.")
+  @Default.String("")
+  String getAuthenticator();
+
+  void setAuthenticator(String authenticator);
+
+  @Description("Port number. Optional.")
+  @Default.String("")
+  String getPortNumber();
+
+  void setPortNumber(String portNumber);
+
+  @Description("Login timeout. Optional.")
+  @Default.String("")
+  String getLoginTimeout();
+
+  void setLoginTimeout(String loginTimeout);
+
+  @Description("External location name to connect to.")
+  String getExternalLocation();
+
+  void setExternalLocation(String externalLocation);
+
+  @Description("Temporary GCS bucket name")
+  String getStagingBucketName();
+
+  void setStagingBucketName(String stagingBucketName);
+
+  @Description("Storage integration - required in case the external stage is not specified.")
+  String getStorageIntegration();
+
+  void setStorageIntegration(String integration);
+
+  @Description("Stage name. Optional.")
+  String getStage();
+
+  void setStage(String stage);
+}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeService.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeService.java
new file mode 100644
index 000000000000..6375e79e74ce
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeService.java
@@ -0,0 +1,36 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake;
+
+import java.io.Serializable;
+import java.sql.SQLException;
+import javax.sql.DataSource;
+import org.apache.beam.sdk.transforms.SerializableFunction;
+
+/** Interface which defines common methods for interacting with SnowFlake. */
+public interface SnowflakeService extends Serializable {
+  String CSV_QUOTE_CHAR_FOR_COPY = "''";
+
+  String copyIntoStage(
+      SerializableFunction dataSourceProviderFn,
+      String query,
+      String table,
+      String integrationName,
+      String stagingBucketDir)
+      throws SQLException;
+}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeServiceImpl.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeServiceImpl.java
new file mode 100644
index 000000000000..5aaad06b7ed2
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/SnowflakeServiceImpl.java
@@ -0,0 +1,90 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake;
+
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.function.Consumer;
+import javax.sql.DataSource;
+import org.apache.beam.sdk.transforms.SerializableFunction;
+
+/**
+ * Implemenation of {@link org.apache.beam.sdk.io.snowflake.SnowflakeService} used in production.
+ */
+public class SnowflakeServiceImpl implements SnowflakeService {
+  private static final String SNOWFLAKE_GCS_PREFIX = "gcs://";
+
+  @Override
+  public String copyIntoStage(
+      SerializableFunction dataSourceProviderFn,
+      String query,
+      String table,
+      String integrationName,
+      String stagingBucketDir)
+      throws SQLException {
+
+    String from;
+    if (query != null) {
+      // Query must be surrounded with brackets
+      from = String.format("(%s)", query);
+    } else {
+      from = table;
+    }
+
+    String copyQuery =
+        String.format(
+            "COPY INTO '%s' FROM %s STORAGE_INTEGRATION=%s FILE_FORMAT=(TYPE=CSV COMPRESSION=GZIP FIELD_OPTIONALLY_ENCLOSED_BY='%s');",
+            getProperBucketDir(stagingBucketDir), from, integrationName, CSV_QUOTE_CHAR_FOR_COPY);
+
+    runStatement(copyQuery, getConnection(dataSourceProviderFn), null);
+
+    return stagingBucketDir.concat("*");
+  }
+
+  private static void runStatement(String query, Connection connection, Consumer resultSetMethod)
+      throws SQLException {
+    PreparedStatement statement = connection.prepareStatement(query);
+    try {
+      if (resultSetMethod != null) {
+        ResultSet resultSet = statement.executeQuery();
+        resultSetMethod.accept(resultSet);
+      } else {
+        statement.execute();
+      }
+    } finally {
+      statement.close();
+      connection.close();
+    }
+  }
+
+  private Connection getConnection(SerializableFunction dataSourceProviderFn)
+      throws SQLException {
+    DataSource dataSource = dataSourceProviderFn.apply(null);
+    return dataSource.getConnection();
+  }
+
+  // Snowflake is expecting "gcs://" prefix for GCS and Beam "gs://"
+  private String getProperBucketDir(String bucketDir) {
+    if (bucketDir.contains(CloudProvider.GCS.getPrefix())) {
+      return bucketDir.replace(CloudProvider.GCS.getPrefix(), SNOWFLAKE_GCS_PREFIX);
+    }
+    return bucketDir;
+  }
+}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/KeyPairSnowflakeCredentials.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/KeyPairSnowflakeCredentials.java
new file mode 100644
index 000000000000..286ec628fc8b
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/KeyPairSnowflakeCredentials.java
@@ -0,0 +1,81 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.credentials;
+
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.security.InvalidKeyException;
+import java.security.KeyFactory;
+import java.security.NoSuchAlgorithmException;
+import java.security.PrivateKey;
+import java.security.spec.InvalidKeySpecException;
+import java.security.spec.PKCS8EncodedKeySpec;
+import java.util.Base64;
+import javax.crypto.EncryptedPrivateKeyInfo;
+import javax.crypto.SecretKeyFactory;
+import javax.crypto.spec.PBEKeySpec;
+
+/** POJO for handling Key-Pair authentication against Snowflake. */
+public class KeyPairSnowflakeCredentials implements SnowflakeCredentials {
+  private String username;
+  private PrivateKey privateKey;
+
+  public KeyPairSnowflakeCredentials(
+      String username, String privateKeyPath, String privateKeyPassword) {
+    this.username = username;
+    this.privateKey = getPrivateKey(privateKeyPath, privateKeyPassword);
+  }
+
+  public KeyPairSnowflakeCredentials(String username, PrivateKey privateKey) {
+    this.username = username;
+    this.privateKey = privateKey;
+  }
+
+  private PrivateKey getPrivateKey(String privateKeyPath, String privateKeyPassphrase) {
+    try {
+      byte[] keyBytes = Files.readAllBytes(Paths.get(privateKeyPath));
+
+      String encrypted = new String(keyBytes, Charset.defaultCharset());
+      encrypted = encrypted.replace("-----BEGIN ENCRYPTED PRIVATE KEY-----", "");
+      encrypted = encrypted.replace("-----END ENCRYPTED PRIVATE KEY-----", "");
+      EncryptedPrivateKeyInfo pkInfo =
+          new EncryptedPrivateKeyInfo(Base64.getMimeDecoder().decode(encrypted));
+      PBEKeySpec keySpec = new PBEKeySpec(privateKeyPassphrase.toCharArray());
+      SecretKeyFactory pbeKeyFactory = SecretKeyFactory.getInstance(pkInfo.getAlgName());
+      PKCS8EncodedKeySpec encodedKeySpec = pkInfo.getKeySpec(pbeKeyFactory.generateSecret(keySpec));
+
+      KeyFactory keyFactory = KeyFactory.getInstance("RSA");
+      return keyFactory.generatePrivate(encodedKeySpec);
+    } catch (IOException
+        | NoSuchAlgorithmException
+        | InvalidKeySpecException
+        | InvalidKeyException ex) {
+      throw new RuntimeException("Can't create PrivateKey from options");
+    }
+  }
+
+  public String getUsername() {
+    return username;
+  }
+
+  public PrivateKey getPrivateKey() {
+    return privateKey;
+  }
+}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/OAuthTokenSnowflakeCredentials.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/OAuthTokenSnowflakeCredentials.java
new file mode 100644
index 000000000000..be102a8b0f41
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/OAuthTokenSnowflakeCredentials.java
@@ -0,0 +1,31 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.credentials;
+
+/** POJO for handling OAuth authentication against Snowflake, using pre-obtained OAuth token. */
+public class OAuthTokenSnowflakeCredentials implements SnowflakeCredentials {
+  private String token;
+
+  public OAuthTokenSnowflakeCredentials(String token) {
+    this.token = token;
+  }
+
+  public String getToken() {
+    return token;
+  }
+}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/SnowflakeCredentials.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/SnowflakeCredentials.java
new file mode 100644
index 000000000000..e3abf91f7d12
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/SnowflakeCredentials.java
@@ -0,0 +1,24 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.credentials;
+
+/**
+ * Interface for holding credentials. Allows creating {@link
+ * org.apache.beam.sdk.io.snowflake.SnowflakeIO.DataSourceConfiguration}.
+ */
+public interface SnowflakeCredentials {}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/SnowflakeCredentialsFactory.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/SnowflakeCredentialsFactory.java
new file mode 100644
index 000000000000..3876c2f10d71
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/SnowflakeCredentialsFactory.java
@@ -0,0 +1,55 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.credentials;
+
+import org.apache.beam.sdk.io.snowflake.SnowflakePipelineOptions;
+
+/**
+ * Factory class for creating implementations of {@link SnowflakeCredentials} from {@link
+ * SnowflakePipelineOptions}.
+ */
+public class SnowflakeCredentialsFactory {
+  public static SnowflakeCredentials of(SnowflakePipelineOptions options) {
+    if (oauthOptionsAvailable(options)) {
+      return new OAuthTokenSnowflakeCredentials(options.getOauthToken());
+    } else if (usernamePasswordOptionsAvailable(options)) {
+      return new UsernamePasswordSnowflakeCredentials(options.getUsername(), options.getPassword());
+    } else if (keyPairOptionsAvailable(options)) {
+      return new KeyPairSnowflakeCredentials(
+          options.getUsername(), options.getPrivateKeyPath(), options.getPrivateKeyPassphrase());
+    }
+    throw new RuntimeException("Can't get credentials from Options");
+  }
+
+  private static boolean oauthOptionsAvailable(SnowflakePipelineOptions options) {
+    return options.getOauthToken() != null && !options.getOauthToken().isEmpty();
+  }
+
+  private static boolean usernamePasswordOptionsAvailable(SnowflakePipelineOptions options) {
+    return options.getUsername() != null
+        && !options.getUsername().isEmpty()
+        && !options.getPassword().isEmpty();
+  }
+
+  private static boolean keyPairOptionsAvailable(SnowflakePipelineOptions options) {
+    return options.getUsername() != null
+        && !options.getUsername().isEmpty()
+        && !options.getPrivateKeyPath().isEmpty()
+        && !options.getPrivateKeyPassphrase().isEmpty();
+  }
+}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/UsernamePasswordSnowflakeCredentials.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/UsernamePasswordSnowflakeCredentials.java
new file mode 100644
index 000000000000..1d8bdce0cc2e
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/UsernamePasswordSnowflakeCredentials.java
@@ -0,0 +1,37 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.credentials;
+
+/** POJO for handling Username & Password authentication against Snowflake. */
+public class UsernamePasswordSnowflakeCredentials implements SnowflakeCredentials {
+  private String username;
+  private String password;
+
+  public UsernamePasswordSnowflakeCredentials(String username, String password) {
+    this.username = username;
+    this.password = password;
+  }
+
+  public String getUsername() {
+    return username;
+  }
+
+  public String getPassword() {
+    return password;
+  }
+}
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/package-info.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/package-info.java
new file mode 100644
index 000000000000..f76d2419b8ce
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/credentials/package-info.java
@@ -0,0 +1,20 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+/** Credentials for SnowflakeIO. */
+package org.apache.beam.sdk.io.snowflake.credentials;
diff --git a/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/package-info.java b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/package-info.java
new file mode 100644
index 000000000000..9dbcf05a4074
--- /dev/null
+++ b/sdks/java/io/snowflake/src/main/java/org/apache/beam/sdk/io/snowflake/package-info.java
@@ -0,0 +1,20 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+/** Snowflake IO transforms. */
+package org.apache.beam.sdk.io.snowflake;
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeBasicDataSource.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeBasicDataSource.java
new file mode 100644
index 000000000000..5fc694fb9d0c
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeBasicDataSource.java
@@ -0,0 +1,298 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test;
+
+import java.io.Serializable;
+import java.sql.Array;
+import java.sql.Blob;
+import java.sql.CallableStatement;
+import java.sql.Clob;
+import java.sql.Connection;
+import java.sql.DatabaseMetaData;
+import java.sql.NClob;
+import java.sql.PreparedStatement;
+import java.sql.SQLClientInfoException;
+import java.sql.SQLException;
+import java.sql.SQLWarning;
+import java.sql.SQLXML;
+import java.sql.Savepoint;
+import java.sql.Statement;
+import java.sql.Struct;
+import java.util.Map;
+import java.util.Properties;
+import java.util.concurrent.Executor;
+import net.snowflake.client.jdbc.SnowflakeBasicDataSource;
+
+/**
+ * Fake implementation of {@link net.snowflake.client.jdbc.SnowflakeBasicDataSource} used in tests.
+ */
+public class FakeSnowflakeBasicDataSource extends SnowflakeBasicDataSource implements Serializable {
+  @Override
+  public FakeConnection getConnection() throws SQLException {
+    return new FakeConnection();
+  }
+
+  private class FakeConnection implements Connection {
+
+    @Override
+    public Statement createStatement() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public PreparedStatement prepareStatement(String sql) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public CallableStatement prepareCall(String sql) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public String nativeSQL(String sql) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public void setAutoCommit(boolean autoCommit) throws SQLException {}
+
+    @Override
+    public boolean getAutoCommit() throws SQLException {
+      return false;
+    }
+
+    @Override
+    public void commit() throws SQLException {}
+
+    @Override
+    public void rollback() throws SQLException {}
+
+    @Override
+    public void close() throws SQLException {}
+
+    @Override
+    public boolean isClosed() throws SQLException {
+      return false;
+    }
+
+    @Override
+    public DatabaseMetaData getMetaData() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public void setReadOnly(boolean readOnly) throws SQLException {}
+
+    @Override
+    public boolean isReadOnly() throws SQLException {
+      return false;
+    }
+
+    @Override
+    public void setCatalog(String catalog) throws SQLException {}
+
+    @Override
+    public String getCatalog() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public void setTransactionIsolation(int level) throws SQLException {}
+
+    @Override
+    public int getTransactionIsolation() throws SQLException {
+      return 0;
+    }
+
+    @Override
+    public SQLWarning getWarnings() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public void clearWarnings() throws SQLException {}
+
+    @Override
+    public Statement createStatement(int resultSetType, int resultSetConcurrency)
+        throws SQLException {
+      return null;
+    }
+
+    @Override
+    public PreparedStatement prepareStatement(
+        String sql, int resultSetType, int resultSetConcurrency) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public CallableStatement prepareCall(String sql, int resultSetType, int resultSetConcurrency)
+        throws SQLException {
+      return null;
+    }
+
+    @Override
+    public Map> getTypeMap() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public void setTypeMap(Map> map) throws SQLException {}
+
+    @Override
+    public void setHoldability(int holdability) throws SQLException {}
+
+    @Override
+    public int getHoldability() throws SQLException {
+      return 0;
+    }
+
+    @Override
+    public Savepoint setSavepoint() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public Savepoint setSavepoint(String name) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public void rollback(Savepoint savepoint) throws SQLException {}
+
+    @Override
+    public void releaseSavepoint(Savepoint savepoint) throws SQLException {}
+
+    @Override
+    public Statement createStatement(
+        int resultSetType, int resultSetConcurrency, int resultSetHoldability) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public PreparedStatement prepareStatement(
+        String sql, int resultSetType, int resultSetConcurrency, int resultSetHoldability)
+        throws SQLException {
+      return null;
+    }
+
+    @Override
+    public CallableStatement prepareCall(
+        String sql, int resultSetType, int resultSetConcurrency, int resultSetHoldability)
+        throws SQLException {
+      return null;
+    }
+
+    @Override
+    public PreparedStatement prepareStatement(String sql, int autoGeneratedKeys)
+        throws SQLException {
+      return null;
+    }
+
+    @Override
+    public PreparedStatement prepareStatement(String sql, int[] columnIndexes) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public PreparedStatement prepareStatement(String sql, String[] columnNames)
+        throws SQLException {
+      return null;
+    }
+
+    @Override
+    public Clob createClob() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public Blob createBlob() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public NClob createNClob() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public SQLXML createSQLXML() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public boolean isValid(int timeout) throws SQLException {
+      return false;
+    }
+
+    @Override
+    public void setClientInfo(String name, String value) throws SQLClientInfoException {}
+
+    @Override
+    public void setClientInfo(Properties properties) throws SQLClientInfoException {}
+
+    @Override
+    public String getClientInfo(String name) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public Properties getClientInfo() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public Array createArrayOf(String typeName, Object[] elements) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public Struct createStruct(String typeName, Object[] attributes) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public void setSchema(String schema) throws SQLException {}
+
+    @Override
+    public String getSchema() throws SQLException {
+      return null;
+    }
+
+    @Override
+    public void abort(Executor executor) throws SQLException {}
+
+    @Override
+    public void setNetworkTimeout(Executor executor, int milliseconds) throws SQLException {}
+
+    @Override
+    public int getNetworkTimeout() throws SQLException {
+      return 0;
+    }
+
+    @Override
+    public  T unwrap(Class iface) throws SQLException {
+      return null;
+    }
+
+    @Override
+    public boolean isWrapperFor(Class iface) throws SQLException {
+      return false;
+    }
+  }
+}
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeDatabase.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeDatabase.java
new file mode 100644
index 000000000000..5bf8b21afa18
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeDatabase.java
@@ -0,0 +1,81 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test;
+
+import java.io.Serializable;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+import net.snowflake.client.jdbc.SnowflakeSQLException;
+
+/** Fake implementation of SnowFlake warehouse used in test code. */
+public class FakeSnowflakeDatabase implements Serializable {
+  private static Map> tables = new HashMap<>();
+
+  private FakeSnowflakeDatabase() {
+    tables = new HashMap<>();
+  }
+
+  public static void createTable(String table) {
+    FakeSnowflakeDatabase.tables.put(table, Collections.emptyList());
+  }
+
+  public static List getElements(String table) throws SnowflakeSQLException {
+    if (!isTableExist(table)) {
+      throw new SnowflakeSQLException(
+          null, "SQL compilation error: Table does not exist", table, 0);
+    }
+
+    return FakeSnowflakeDatabase.tables.get(table);
+  }
+
+  public static List runQuery(String query) throws SnowflakeSQLException {
+    if (query.startsWith("SELECT * FROM ")) {
+      String tableName = query.replace("SELECT * FROM ", "");
+      return getElements(tableName);
+    }
+    throw new SnowflakeSQLException(null, "SQL compilation error: Invalid query", query, 0);
+  }
+
+  public static List getElementsAsLong(String table) throws SnowflakeSQLException {
+    List elements = getElements(table);
+    return elements.stream().map(Long::parseLong).collect(Collectors.toList());
+  }
+
+  public static boolean isTableExist(String table) {
+    return FakeSnowflakeDatabase.tables.containsKey(table);
+  }
+
+  public static boolean isTableEmpty(String table) {
+    return FakeSnowflakeDatabase.tables.get(table).isEmpty();
+  }
+
+  public static void createTableWithElements(String table, List rows) {
+    FakeSnowflakeDatabase.tables.put(table, rows);
+  }
+
+  public static void clean() {
+    FakeSnowflakeDatabase.tables = new HashMap<>();
+  }
+
+  public static void truncateTable(String table) {
+    FakeSnowflakeDatabase.createTable(table);
+  }
+}
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeServiceImpl.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeServiceImpl.java
new file mode 100644
index 000000000000..4a62dcd3181d
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/FakeSnowflakeServiceImpl.java
@@ -0,0 +1,64 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.sql.SQLException;
+import java.util.List;
+import javax.sql.DataSource;
+import org.apache.beam.sdk.io.snowflake.SnowflakeService;
+import org.apache.beam.sdk.transforms.SerializableFunction;
+
+/**
+ * Fake implementation of {@link org.apache.beam.sdk.io.snowflake.SnowflakeService} used in tests.
+ */
+public class FakeSnowflakeServiceImpl implements SnowflakeService {
+
+  @Override
+  public String copyIntoStage(
+      SerializableFunction dataSourceProviderFn,
+      String query,
+      String table,
+      String integrationName,
+      String stagingBucketName)
+      throws SQLException {
+
+    if (table != null) {
+      writeToFile(stagingBucketName, FakeSnowflakeDatabase.getElements(table));
+    }
+    if (query != null) {
+      writeToFile(stagingBucketName, FakeSnowflakeDatabase.runQuery(query));
+    }
+
+    return String.format("./%s/*", stagingBucketName);
+  }
+
+  private void writeToFile(String stagingBucketNameTmp, List rows) {
+    Path filePath = Paths.get(String.format("./%s/table.csv.gz", stagingBucketNameTmp));
+    try {
+      Files.createDirectories(filePath.getParent());
+      Files.createFile(filePath);
+      Files.write(filePath, rows);
+    } catch (IOException e) {
+      throw new RuntimeException("Failed to create files", e);
+    }
+  }
+}
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/TestUtils.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/TestUtils.java
new file mode 100644
index 000000000000..aab8d7de9660
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/TestUtils.java
@@ -0,0 +1,40 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test;
+
+import java.io.File;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class TestUtils {
+
+  private static final Logger LOG = LoggerFactory.getLogger(TestUtils.class);
+
+  private static final String PRIVATE_KEY_FILE_NAME = "test_rsa_key.p8";
+  private static final String PRIVATE_KEY_PASSPHRASE = "snowflake";
+
+  public static String getPrivateKeyPath(Class klass) {
+    ClassLoader classLoader = klass.getClassLoader();
+    File file = new File(classLoader.getResource(PRIVATE_KEY_FILE_NAME).getFile());
+    return file.getAbsolutePath();
+  }
+
+  public static String getPrivateKeyPassphrase() {
+    return PRIVATE_KEY_PASSPHRASE;
+  }
+}
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/package-info.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/package-info.java
new file mode 100644
index 000000000000..2e2cf2f7645c
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/package-info.java
@@ -0,0 +1,20 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+/** Snowflake IO tests. */
+package org.apache.beam.sdk.io.snowflake.test;
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/BatchTestPipelineOptions.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/BatchTestPipelineOptions.java
new file mode 100644
index 000000000000..3504c455851b
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/BatchTestPipelineOptions.java
@@ -0,0 +1,28 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test.unit;
+
+import org.apache.beam.sdk.io.snowflake.SnowflakePipelineOptions;
+import org.apache.beam.sdk.options.Description;
+
+public interface BatchTestPipelineOptions extends SnowflakePipelineOptions {
+  @Description("Table name to connect to.")
+  String getTable();
+
+  void setTable(String table);
+}
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/DataSourceConfigurationTest.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/DataSourceConfigurationTest.java
new file mode 100644
index 000000000000..98f22132c77f
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/DataSourceConfigurationTest.java
@@ -0,0 +1,159 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test.unit;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThrows;
+
+import javax.sql.DataSource;
+import net.snowflake.client.jdbc.SnowflakeBasicDataSource;
+import org.apache.beam.sdk.io.snowflake.SnowflakeIO;
+import org.apache.beam.sdk.io.snowflake.credentials.OAuthTokenSnowflakeCredentials;
+import org.junit.Before;
+import org.junit.Test;
+
+/** Unit tests for {@link org.apache.beam.sdk.io.snowflake.SnowflakeIO.DataSourceConfiguration}. */
+public class DataSourceConfigurationTest {
+
+  private SnowflakeIO.DataSourceConfiguration configuration;
+
+  @Before
+  public void setUp() {
+    configuration =
+        SnowflakeIO.DataSourceConfiguration.create(
+            new OAuthTokenSnowflakeCredentials("some-token"));
+  }
+
+  @Test
+  public void testSettingUrlWithBadPrefix() {
+    assertThrows(
+        IllegalArgumentException.class,
+        () -> configuration.withUrl("account.snowflakecomputing.com"));
+  }
+
+  @Test
+  public void testSettingUrlWithBadSuffix() {
+    assertThrows(
+        IllegalArgumentException.class, () -> configuration.withUrl("jdbc:snowflake://account"));
+  }
+
+  @Test
+  public void testSettingStringUrl() {
+    String url = "jdbc:snowflake://account.snowflakecomputing.com";
+    configuration = configuration.withUrl(url);
+    assertEquals(url, configuration.getUrl());
+  }
+
+  @Test
+  public void testSettingServerNameWithBadSuffix() {
+    assertThrows(
+        IllegalArgumentException.class, () -> configuration.withServerName("not.properly.ended"));
+  }
+
+  @Test
+  public void testSettingStringServerName() {
+    String serverName = "account.snowflakecomputing.com";
+    configuration = configuration.withServerName(serverName);
+    assertEquals(serverName, configuration.getServerName());
+  }
+
+  @Test
+  public void testSettingStringDatabase() {
+    String database = "dbname";
+    configuration = configuration.withDatabase(database);
+    assertEquals(database, configuration.getDatabase());
+  }
+
+  @Test
+  public void testSettingStringWarehouse() {
+    String warehouse = "warehouse";
+    configuration = configuration.withWarehouse(warehouse);
+    assertEquals(warehouse, configuration.getWarehouse());
+  }
+
+  @Test
+  public void testSettingStringSchema() {
+    String schema = "schema";
+    configuration = configuration.withSchema(schema);
+    assertEquals(schema, configuration.getSchema());
+  }
+
+  @Test
+  public void testSettingStringRole() {
+    String role = "role";
+    configuration = configuration.withRole(role);
+    assertEquals(role, configuration.getRole());
+  }
+
+  @Test
+  public void testSettingStringPortNumber() {
+    Integer portNumber = 1234;
+    configuration = configuration.withPortNumber(portNumber);
+    assertEquals(portNumber, configuration.getPortNumber());
+  }
+
+  @Test
+  public void testSettingStringLoginTimeout() {
+    Integer loginTimeout = 999;
+    configuration = configuration.withLoginTimeout(loginTimeout);
+    assertEquals(loginTimeout, configuration.getLoginTimeout());
+  }
+
+  @Test
+  public void testSettingValidate() {
+    configuration = configuration.withoutValidation();
+    assertEquals(false, configuration.getValidate());
+  }
+
+  @Test
+  public void testDataSourceCreatedFromUrl() {
+    String url = "jdbc:snowflake://account.snowflakecomputing.com";
+    configuration = configuration.withUrl(url);
+
+    DataSource dataSource = configuration.buildDatasource();
+
+    assertEquals(SnowflakeBasicDataSource.class, dataSource.getClass());
+    assertEquals(url, ((SnowflakeBasicDataSource) dataSource).getUrl());
+  }
+
+  @Test
+  public void testDataSourceCreatedFromServerName() {
+    String serverName = "account.snowflakecomputing.com";
+    configuration = configuration.withServerName(serverName);
+
+    DataSource dataSource = configuration.buildDatasource();
+
+    String expectedUrl = "jdbc:snowflake://account.snowflakecomputing.com";
+    assertEquals(SnowflakeBasicDataSource.class, dataSource.getClass());
+    assertEquals(expectedUrl, ((SnowflakeBasicDataSource) dataSource).getUrl());
+  }
+
+  @Test
+  public void testDataSourceCreatedFromServerNameAndPort() {
+    String serverName = "account.snowflakecomputing.com";
+    int portNumber = 1234;
+
+    configuration = configuration.withServerName(serverName);
+    configuration = configuration.withPortNumber(portNumber);
+
+    DataSource dataSource = configuration.buildDatasource();
+    assertEquals(SnowflakeBasicDataSource.class, dataSource.getClass());
+    String expectedUrl = "jdbc:snowflake://account.snowflakecomputing.com:1234";
+    assertEquals(expectedUrl, ((SnowflakeBasicDataSource) dataSource).getUrl());
+  }
+}
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/KeyPairSnowflakeCredentialsTest.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/KeyPairSnowflakeCredentialsTest.java
new file mode 100644
index 000000000000..b231a2dde665
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/KeyPairSnowflakeCredentialsTest.java
@@ -0,0 +1,38 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test.unit.credentials;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import org.apache.beam.sdk.io.snowflake.credentials.KeyPairSnowflakeCredentials;
+import org.apache.beam.sdk.io.snowflake.test.TestUtils;
+import org.junit.Test;
+
+public class KeyPairSnowflakeCredentialsTest {
+  @Test
+  public void testFilePathConstructor() {
+    KeyPairSnowflakeCredentials credentials =
+        new KeyPairSnowflakeCredentials(
+            "username",
+            TestUtils.getPrivateKeyPath(getClass()),
+            TestUtils.getPrivateKeyPassphrase());
+    assertEquals("username", credentials.getUsername());
+    assertNotNull(credentials.getPrivateKey());
+  }
+}
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/OAuthTokenSnowflakeCredentialsTest.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/OAuthTokenSnowflakeCredentialsTest.java
new file mode 100644
index 000000000000..a1dee76f1601
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/OAuthTokenSnowflakeCredentialsTest.java
@@ -0,0 +1,46 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test.unit.credentials;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.beam.sdk.io.snowflake.SnowflakeIO;
+import org.apache.beam.sdk.io.snowflake.credentials.OAuthTokenSnowflakeCredentials;
+import org.junit.Test;
+
+public class OAuthTokenSnowflakeCredentialsTest {
+
+  @Test
+  public void testConstructor() {
+    OAuthTokenSnowflakeCredentials credentials = new OAuthTokenSnowflakeCredentials("token");
+
+    assertEquals("token", credentials.getToken());
+  }
+
+  @Test
+  public void testBuildingDataSource() {
+    OAuthTokenSnowflakeCredentials credentials = new OAuthTokenSnowflakeCredentials("token");
+
+    SnowflakeIO.DataSourceConfiguration configuration =
+        SnowflakeIO.DataSourceConfiguration.create(credentials);
+
+    assertEquals(credentials.getToken(), configuration.getOauthToken());
+    assertTrue(configuration.getValidate());
+  }
+}
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/SnowflakeCredentialsFactoryTest.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/SnowflakeCredentialsFactoryTest.java
new file mode 100644
index 000000000000..f9f612d8f002
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/SnowflakeCredentialsFactoryTest.java
@@ -0,0 +1,77 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test.unit.credentials;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThrows;
+
+import org.apache.beam.sdk.io.snowflake.SnowflakePipelineOptions;
+import org.apache.beam.sdk.io.snowflake.credentials.KeyPairSnowflakeCredentials;
+import org.apache.beam.sdk.io.snowflake.credentials.OAuthTokenSnowflakeCredentials;
+import org.apache.beam.sdk.io.snowflake.credentials.SnowflakeCredentials;
+import org.apache.beam.sdk.io.snowflake.credentials.SnowflakeCredentialsFactory;
+import org.apache.beam.sdk.io.snowflake.credentials.UsernamePasswordSnowflakeCredentials;
+import org.apache.beam.sdk.io.snowflake.test.TestUtils;
+import org.apache.beam.sdk.options.PipelineOptionsFactory;
+import org.junit.Test;
+
+public class SnowflakeCredentialsFactoryTest {
+
+  @Test
+  public void usernamePasswordTest() {
+    SnowflakePipelineOptions options = PipelineOptionsFactory.as(SnowflakePipelineOptions.class);
+    options.setUsername("username");
+    options.setPassword("password");
+
+    SnowflakeCredentials credentials = SnowflakeCredentialsFactory.of(options);
+
+    assertEquals(UsernamePasswordSnowflakeCredentials.class, credentials.getClass());
+  }
+
+  @Test
+  public void oauthTokenTest() {
+    SnowflakePipelineOptions options = PipelineOptionsFactory.as(SnowflakePipelineOptions.class);
+    options.setOauthToken("token");
+
+    SnowflakeCredentials credentials = SnowflakeCredentialsFactory.of(options);
+
+    assertEquals(OAuthTokenSnowflakeCredentials.class, credentials.getClass());
+  }
+
+  @Test
+  public void keyPairTest() {
+    SnowflakePipelineOptions options = PipelineOptionsFactory.as(SnowflakePipelineOptions.class);
+    System.out.println(TestUtils.getPrivateKeyPath(getClass()));
+    options.setUsername("username");
+    options.setPrivateKeyPath(TestUtils.getPrivateKeyPath(getClass()));
+    options.setPrivateKeyPassphrase(TestUtils.getPrivateKeyPassphrase());
+
+    SnowflakeCredentials credentials = SnowflakeCredentialsFactory.of(options);
+
+    assertEquals(KeyPairSnowflakeCredentials.class, credentials.getClass());
+  }
+
+  @Test
+  public void emptyOptionsTest() {
+    SnowflakePipelineOptions options = PipelineOptionsFactory.as(SnowflakePipelineOptions.class);
+
+    Exception ex =
+        assertThrows(RuntimeException.class, () -> SnowflakeCredentialsFactory.of(options));
+    assertEquals("Can't get credentials from Options", ex.getMessage());
+  }
+}
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/UsernamePasswordSnowflakeCredentialsTest.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/UsernamePasswordSnowflakeCredentialsTest.java
new file mode 100644
index 000000000000..0c7503a079b8
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/credentials/UsernamePasswordSnowflakeCredentialsTest.java
@@ -0,0 +1,50 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test.unit.credentials;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.beam.sdk.io.snowflake.SnowflakeIO;
+import org.apache.beam.sdk.io.snowflake.credentials.UsernamePasswordSnowflakeCredentials;
+import org.junit.Test;
+
+public class UsernamePasswordSnowflakeCredentialsTest {
+
+  @Test
+  public void testConstructor() {
+    UsernamePasswordSnowflakeCredentials credentials =
+        new UsernamePasswordSnowflakeCredentials("username", "password");
+
+    assertEquals("username", credentials.getUsername());
+    assertEquals("password", credentials.getPassword());
+  }
+
+  @Test
+  public void testBuildingDataSource() {
+    UsernamePasswordSnowflakeCredentials credentials =
+        new UsernamePasswordSnowflakeCredentials("username", "password");
+
+    SnowflakeIO.DataSourceConfiguration configuration =
+        SnowflakeIO.DataSourceConfiguration.create(credentials);
+
+    assertEquals("username", configuration.getUsername());
+    assertEquals("password", configuration.getPassword());
+    assertTrue(configuration.getValidate());
+  }
+}
diff --git a/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/read/SnowflakeIOReadTest.java b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/read/SnowflakeIOReadTest.java
new file mode 100644
index 000000000000..e4eda0d7520b
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/java/org/apache/beam/sdk/io/snowflake/test/unit/read/SnowflakeIOReadTest.java
@@ -0,0 +1,278 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.snowflake.test.unit.read;
+
+import java.io.Serializable;
+import java.util.Arrays;
+import java.util.List;
+import org.apache.avro.generic.GenericRecord;
+import org.apache.avro.generic.GenericRecordBuilder;
+import org.apache.beam.sdk.Pipeline.PipelineExecutionException;
+import org.apache.beam.sdk.coders.AvroCoder;
+import org.apache.beam.sdk.io.AvroGeneratedUser;
+import org.apache.beam.sdk.io.snowflake.SnowflakeIO;
+import org.apache.beam.sdk.io.snowflake.SnowflakeService;
+import org.apache.beam.sdk.io.snowflake.test.FakeSnowflakeBasicDataSource;
+import org.apache.beam.sdk.io.snowflake.test.FakeSnowflakeDatabase;
+import org.apache.beam.sdk.io.snowflake.test.FakeSnowflakeServiceImpl;
+import org.apache.beam.sdk.io.snowflake.test.unit.BatchTestPipelineOptions;
+import org.apache.beam.sdk.testing.PAssert;
+import org.apache.beam.sdk.testing.TestPipeline;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
+import org.junit.BeforeClass;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.ExpectedException;
+import org.junit.runner.RunWith;
+import org.junit.runners.JUnit4;
+
+@RunWith(JUnit4.class)
+public class SnowflakeIOReadTest implements Serializable {
+  public static final String FAKE_TABLE = "FAKE_TABLE";
+  public static final String FAKE_QUERY = "SELECT * FROM FAKE_TABLE";
+
+  private static final BatchTestPipelineOptions options =
+      TestPipeline.testingPipelineOptions().as(BatchTestPipelineOptions.class);;
+  @Rule public final transient TestPipeline pipeline = TestPipeline.create();
+
+  @Rule public transient ExpectedException thrown = ExpectedException.none();
+
+  private static SnowflakeIO.DataSourceConfiguration dataSourceConfiguration;
+  private static SnowflakeService snowflakeService;
+  private static String stagingBucketName;
+  private static String integrationName;
+  private static List avroTestData;
+
+  @BeforeClass
+  public static void setup() {
+
+    List testData = Arrays.asList("Paul,51,red", "Jackson,41,green");
+
+    avroTestData =
+        ImmutableList.of(
+            new AvroGeneratedUser("Paul", 51, "red"),
+            new AvroGeneratedUser("Jackson", 41, "green"));
+
+    FakeSnowflakeDatabase.createTableWithElements(FAKE_TABLE, testData);
+
+    options.setServerName("NULL.snowflakecomputing.com");
+    options.setStorageIntegration("STORAGE_INTEGRATION");
+    options.setStagingBucketName("BUCKET");
+
+    stagingBucketName = options.getStagingBucketName();
+    integrationName = options.getStorageIntegration();
+
+    dataSourceConfiguration =
+        SnowflakeIO.DataSourceConfiguration.create(new FakeSnowflakeBasicDataSource())
+            .withServerName(options.getServerName());
+
+    snowflakeService = new FakeSnowflakeServiceImpl();
+  }
+
+  @Test
+  public void testConfigIsMissingStagingBucketName() {
+    thrown.expect(IllegalArgumentException.class);
+    thrown.expectMessage("withStagingBucketName() is required");
+
+    pipeline.apply(
+        SnowflakeIO.read(snowflakeService)
+            .withDataSourceConfiguration(dataSourceConfiguration)
+            .fromTable(FAKE_TABLE)
+            .withIntegrationName(integrationName)
+            .withIntegrationName(integrationName)
+            .withCsvMapper(getCsvMapper())
+            .withCoder(AvroCoder.of(AvroGeneratedUser.getClassSchema())));
+
+    pipeline.run();
+  }
+
+  @Test
+  public void testConfigIsMissingIntegrationName() {
+    thrown.expect(IllegalArgumentException.class);
+    thrown.expectMessage("withIntegrationName() is required");
+
+    pipeline.apply(
+        SnowflakeIO.read(snowflakeService)
+            .withDataSourceConfiguration(dataSourceConfiguration)
+            .fromTable(FAKE_TABLE)
+            .withStagingBucketName(stagingBucketName)
+            .withCsvMapper(getCsvMapper())
+            .withCoder(AvroCoder.of(AvroGeneratedUser.getClassSchema())));
+
+    pipeline.run();
+  }
+
+  @Test
+  public void testConfigIsMissingCsvMapper() {
+    thrown.expect(IllegalArgumentException.class);
+    thrown.expectMessage("withCsvMapper() is required");
+
+    pipeline.apply(
+        SnowflakeIO.read(snowflakeService)
+            .withDataSourceConfiguration(dataSourceConfiguration)
+            .fromTable(FAKE_TABLE)
+            .withStagingBucketName(stagingBucketName)
+            .withIntegrationName(integrationName)
+            .withCoder(AvroCoder.of(AvroGeneratedUser.getClassSchema())));
+
+    pipeline.run();
+  }
+
+  @Test
+  public void testConfigIsMissingCoder() {
+    thrown.expect(IllegalArgumentException.class);
+    thrown.expectMessage("withCoder() is required");
+
+    pipeline.apply(
+        SnowflakeIO.read(snowflakeService)
+            .withDataSourceConfiguration(dataSourceConfiguration)
+            .fromTable(FAKE_TABLE)
+            .withStagingBucketName(stagingBucketName)
+            .withIntegrationName(integrationName)
+            .withCsvMapper(getCsvMapper()));
+
+    pipeline.run();
+  }
+
+  @Test
+  public void testConfigIsMissingFromTableOrFromQuery() {
+    thrown.expect(IllegalArgumentException.class);
+    thrown.expectMessage("fromTable() or fromQuery() is required");
+
+    pipeline.apply(
+        SnowflakeIO.read(snowflakeService)
+            .withDataSourceConfiguration(dataSourceConfiguration)
+            .withStagingBucketName(stagingBucketName)
+            .withIntegrationName(integrationName)
+            .withCsvMapper(getCsvMapper())
+            .withCoder(AvroCoder.of(AvroGeneratedUser.getClassSchema())));
+
+    pipeline.run();
+  }
+
+  @Test
+  public void testConfigIsMissingDataSourceConfiguration() {
+    thrown.expect(IllegalArgumentException.class);
+    thrown.expectMessage("withDataSourceConfiguration() or withDataSourceProviderFn() is required");
+
+    pipeline.apply(
+        SnowflakeIO.read(snowflakeService)
+            .fromTable(FAKE_TABLE)
+            .withStagingBucketName(stagingBucketName)
+            .withIntegrationName(integrationName)
+            .withCsvMapper(getCsvMapper())
+            .withCoder(AvroCoder.of(AvroGeneratedUser.getClassSchema())));
+
+    pipeline.run();
+  }
+
+  @Test
+  public void testConfigContainsFromQueryAndFromTable() {
+    thrown.expect(IllegalArgumentException.class);
+    thrown.expectMessage("fromTable() and fromQuery() are not allowed together");
+
+    pipeline.apply(
+        SnowflakeIO.read(snowflakeService)
+            .withDataSourceConfiguration(dataSourceConfiguration)
+            .fromQuery("")
+            .fromTable(FAKE_TABLE)
+            .withStagingBucketName(stagingBucketName)
+            .withIntegrationName(integrationName)
+            .withCsvMapper(getCsvMapper())
+            .withCoder(AvroCoder.of(AvroGeneratedUser.getClassSchema())));
+
+    pipeline.run();
+  }
+
+  @Test
+  public void testTableDoesntExist() {
+    thrown.expect(PipelineExecutionException.class);
+    thrown.expectMessage("SQL compilation error: Table does not exist");
+
+    pipeline.apply(
+        SnowflakeIO.read(snowflakeService)
+            .withDataSourceConfiguration(dataSourceConfiguration)
+            .fromTable("NON_EXIST")
+            .withStagingBucketName(stagingBucketName)
+            .withIntegrationName(integrationName)
+            .withCsvMapper(getCsvMapper())
+            .withCoder(AvroCoder.of(AvroGeneratedUser.getClassSchema())));
+
+    pipeline.run();
+  }
+
+  @Test
+  public void testInvalidQuery() {
+    thrown.expect(PipelineExecutionException.class);
+    thrown.expectMessage("SQL compilation error: Invalid query");
+
+    pipeline.apply(
+        SnowflakeIO.read(snowflakeService)
+            .withDataSourceConfiguration(dataSourceConfiguration)
+            .fromQuery("BAD_QUERY")
+            .withStagingBucketName(stagingBucketName)
+            .withIntegrationName(integrationName)
+            .withCsvMapper(getCsvMapper())
+            .withCoder(AvroCoder.of(AvroGeneratedUser.getClassSchema())));
+
+    pipeline.run();
+  }
+
+  @Test
+  public void testReadFromTable() {
+    PCollection items =
+        pipeline.apply(
+            SnowflakeIO.read(snowflakeService)
+                .withDataSourceConfiguration(dataSourceConfiguration)
+                .fromTable(FAKE_TABLE)
+                .withStagingBucketName(stagingBucketName)
+                .withIntegrationName(integrationName)
+                .withCsvMapper(getCsvMapper())
+                .withCoder(AvroCoder.of(AvroGeneratedUser.getClassSchema())));
+
+    PAssert.that(items).containsInAnyOrder(avroTestData);
+    pipeline.run();
+  }
+
+  @Test
+  public void testReadFromQuery() {
+    PCollection items =
+        pipeline.apply(
+            SnowflakeIO.read(snowflakeService)
+                .withDataSourceConfiguration(dataSourceConfiguration)
+                .fromQuery(FAKE_QUERY)
+                .withStagingBucketName(stagingBucketName)
+                .withIntegrationName(integrationName)
+                .withCsvMapper(getCsvMapper())
+                .withCoder(AvroCoder.of(AvroGeneratedUser.getClassSchema())));
+
+    PAssert.that(items).containsInAnyOrder(avroTestData);
+    pipeline.run();
+  }
+
+  static SnowflakeIO.CsvMapper getCsvMapper() {
+    return (SnowflakeIO.CsvMapper)
+        parts ->
+            new GenericRecordBuilder(AvroGeneratedUser.getClassSchema())
+                .set("name", String.valueOf(parts[0]))
+                .set("favorite_number", Integer.valueOf(parts[1]))
+                .set("favorite_color", String.valueOf(parts[2]))
+                .build();
+  }
+}
diff --git a/sdks/java/io/snowflake/src/test/resources/test_rsa_key.p8 b/sdks/java/io/snowflake/src/test/resources/test_rsa_key.p8
new file mode 100644
index 000000000000..ee86a8dd39dd
--- /dev/null
+++ b/sdks/java/io/snowflake/src/test/resources/test_rsa_key.p8
@@ -0,0 +1,29 @@
+-----BEGIN ENCRYPTED PRIVATE KEY-----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+-----END ENCRYPTED PRIVATE KEY-----
diff --git a/settings.gradle b/settings.gradle
index 0c642309dfed..8a80ffd06298 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -119,6 +119,7 @@ include ":sdks:java:io:parquet"
 include ":sdks:java:io:rabbitmq"
 include ":sdks:java:io:redis"
 include ":sdks:java:io:solr"
+include ":sdks:java:io:snowflake"
 include ":sdks:java:io:thrift"
 include ":sdks:java:io:tika"
 include ":sdks:java:io:xml"

From 9f8783d4d1d759d6c37fe4bfa1113723a4f5d37b Mon Sep 17 00:00:00 2001
From: Brian Hulette 
Date: Thu, 21 May 2020 17:19:22 -0700
Subject: [PATCH 052/151] add def args

---
 release/src/main/groovy/MobileGamingCommands.groovy | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/release/src/main/groovy/MobileGamingCommands.groovy b/release/src/main/groovy/MobileGamingCommands.groovy
index 505fbcf691c0..1042062e4cb5 100644
--- a/release/src/main/groovy/MobileGamingCommands.groovy
+++ b/release/src/main/groovy/MobileGamingCommands.groovy
@@ -146,7 +146,7 @@ class MobileGamingCommands {
   }
 
   private Map getLeaderBoardWithStreamingEngineArgs(String runner, String jobName){
-    args = [project: testScripts.gcpProject(),
+    def args = [project: testScripts.gcpProject(),
             dataset: testScripts.bqDataset(),
             topic: "projects/${testScripts.gcpProject()}/topics/${testScripts.pubsubTopic()}",
             leaderBoardTableName: "leaderboard_${runner}",
@@ -160,7 +160,7 @@ class MobileGamingCommands {
   }
 
   private Map getGameStatsArgs(String runner, String jobName){
-    args = [project: testScripts.gcpProject(),
+    def args = [project: testScripts.gcpProject(),
       dataset: testScripts.bqDataset(),
       topic: "projects/${testScripts.gcpProject()}/topics/${testScripts.pubsubTopic()}",
       fixedWindowDuration: 5,

From 8f53b99c8567ab25f51cb85239a2e3fe70fa0898 Mon Sep 17 00:00:00 2001
From: Ashwin Ramaswami 
Date: Thu, 21 May 2020 22:16:45 -0400
Subject: [PATCH 053/151] Fix typo Portabillity -> Portability

---
 website/www/site/content/en/roadmap/go-sdk.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/website/www/site/content/en/roadmap/go-sdk.md b/website/www/site/content/en/roadmap/go-sdk.md
index 8e003e689cca..4172cb09cb59 100644
--- a/website/www/site/content/en/roadmap/go-sdk.md
+++ b/website/www/site/content/en/roadmap/go-sdk.md
@@ -18,7 +18,7 @@ limitations under the License.
 # Go SDK Roadmap
 
 The Go SDK is currently experimental. As the first purely portable Beam SDK, the Go SDK is constrained
-by the status of the [Beam Portabillity Framework](https://beam.apache.org/roadmap/portability/) and the existence of
+by the status of the [Beam Portability Framework](https://beam.apache.org/roadmap/portability/) and the existence of
 portable runners.
 
 **April 2020 Update**

From 1095db056dbd9095c35effbff07cbcd90dc87c54 Mon Sep 17 00:00:00 2001
From: Daniel Oliveira 
Date: Wed, 20 May 2020 12:06:49 -0700
Subject: [PATCH 054/151] [BEAM-9978] Adding functionality and tests to Go
 offset range tracker.

Pretty simple. Moves some commonly desired behaviors out of the SDF
code and into the offset range tracker/restriction code + adds tests.
---
 sdks/go/examples/stringsplit/stringsplit.go   |  16 +-
 .../io/rtrackers/offsetrange/offsetrange.go   |  63 +++++-
 .../rtrackers/offsetrange/offsetrange_test.go | 212 ++++++++++++++++++
 sdks/go/pkg/beam/io/synthetic/source.go       |  31 +--
 sdks/go/pkg/beam/io/synthetic/step.go         |  31 +--
 5 files changed, 276 insertions(+), 77 deletions(-)
 create mode 100644 sdks/go/pkg/beam/io/rtrackers/offsetrange/offsetrange_test.go

diff --git a/sdks/go/examples/stringsplit/stringsplit.go b/sdks/go/examples/stringsplit/stringsplit.go
index eff55bf90cc6..d96a3417ac08 100644
--- a/sdks/go/examples/stringsplit/stringsplit.go
+++ b/sdks/go/examples/stringsplit/stringsplit.go
@@ -71,19 +71,7 @@ func (fn *StringSplitFn) CreateInitialRestriction(s string) offsetrange.Restrict
 // SplitRestriction performs initial splits so that each restriction is split
 // into 5.
 func (fn *StringSplitFn) SplitRestriction(s string, rest offsetrange.Restriction) []offsetrange.Restriction {
-	size := rest.End - rest.Start
-	splitPts := []int64{
-		rest.Start,
-		rest.Start + (size / 5),
-		rest.Start + (size * 2 / 5),
-		rest.Start + (size * 3 / 5),
-		rest.Start + (size * 4 / 5),
-		rest.End,
-	}
-	var splits []offsetrange.Restriction
-	for i := 0; i < len(splitPts)-1; i++ {
-		splits = append(splits, offsetrange.Restriction{Start: splitPts[i], End: splitPts[i+1]})
-	}
+	splits := rest.EvenSplits(5)
 	log.Debugf(context.Background(), "StringSplit SplitRestrictions: %v -> %v", rest, splits)
 	return splits
 }
@@ -91,7 +79,7 @@ func (fn *StringSplitFn) SplitRestriction(s string, rest offsetrange.Restriction
 // RestrictionSize returns the size as the difference between the restriction's
 // start and end.
 func (fn *StringSplitFn) RestrictionSize(s string, rest offsetrange.Restriction) float64 {
-	size := float64(rest.End - rest.Start)
+	size := rest.Size()
 	log.Debugf(context.Background(), "StringSplit RestrictionSize: %v -> %v", rest, size)
 	return size
 }
diff --git a/sdks/go/pkg/beam/io/rtrackers/offsetrange/offsetrange.go b/sdks/go/pkg/beam/io/rtrackers/offsetrange/offsetrange.go
index 5e55f35ea592..fb1e5965431a 100644
--- a/sdks/go/pkg/beam/io/rtrackers/offsetrange/offsetrange.go
+++ b/sdks/go/pkg/beam/io/rtrackers/offsetrange/offsetrange.go
@@ -21,6 +21,7 @@ package offsetrange
 
 import (
 	"errors"
+	"math"
 	"reflect"
 
 	"github.com/apache/beam/sdks/go/pkg/beam"
@@ -31,8 +32,43 @@ func init() {
 	beam.RegisterType(reflect.TypeOf((*Restriction)(nil)))
 }
 
+// Restriction is an offset range restriction, which represents a range of
+// integers as a half-closed interval with boundaries [start, end).
 type Restriction struct {
-	Start, End int64 // Half-closed interval with boundaries [start, end).
+	Start, End int64
+}
+
+// EvenSplits splits a restriction into a number of evenly sized restrictions.
+// Each split restriction is guaranteed to not be empty, and each unit from the
+// original restriction is guaranteed to be contained in one split restriction.
+//
+// Num should be greater than 0. Otherwise there is no way to split the
+// restriction and this function will return the original restriction.
+func (r *Restriction) EvenSplits(num int64) (splits []Restriction) {
+	if num <= 1 {
+		// Don't split, just return original restriction.
+		return append(splits, *r)
+	}
+
+	offset := r.Start
+	size := r.End - r.Start
+	for i := int64(0); i < num; i++ {
+		split := Restriction{
+			Start: offset + (i * size / num),
+			End:   offset + ((i + 1) * size / num),
+		}
+		// Skip restrictions that end up empty.
+		if split.End-split.Start <= 0 {
+			continue
+		}
+		splits = append(splits, split)
+	}
+	return splits
+}
+
+// Size returns the restriction's size as the difference between Start and End.
+func (r *Restriction) Size() float64 {
+	return float64(r.End - r.Start)
 }
 
 // Tracker tracks a restriction  that can be represented as a range of integer values,
@@ -42,9 +78,8 @@ type Restriction struct {
 type Tracker struct {
 	Rest    Restriction
 	Claimed int64 // Tracks the last claimed position.
-	Stopped bool  // Tracks whether TryClaim has already indicated to stop processing elements for
-	// any reason.
-	Err error
+	Stopped bool  // Tracks whether TryClaim has indicated to stop processing elements.
+	Err     error
 }
 
 // NewTracker is a constructor for an Tracker given a start and end range.
@@ -57,10 +92,15 @@ func NewTracker(rest Restriction) *Tracker {
 	}
 }
 
-// TryClaim accepts an int64 position and successfully claims it if that position is greater than
-// the previously claimed position and less than the end of the restriction. Note that the
-// Tracker is not considered done until a position >= tracker.end tries to be claimed,
-// at which point this method signals to end processing.
+// TryClaim accepts an int64 position representing the starting position of a block of work. It
+// successfully claims it if the position is greater than the previously claimed position and within
+// the restriction. Claiming a position at or beyond the end of the restriction signals that the
+// entire restriction has been processed and is now done, at which point this method signals to end
+// processing.
+//
+// The tracker stops with an error if a claim is attempted after the tracker has signalled to stop,
+// if a position is claimed before the start of the restriction, or if a position is claimed before
+// the latest successfully claimed.
 func (tracker *Tracker) TryClaim(rawPos interface{}) bool {
 	if tracker.Stopped == true {
 		tracker.Err = errors.New("cannot claim work after restriction tracker returns false")
@@ -88,7 +128,7 @@ func (tracker *Tracker) TryClaim(rawPos interface{}) bool {
 	return true
 }
 
-// IsDone returns true if the most recent claimed element is past the end of the restriction.
+// GetError returns the error that caused the tracker to stop, if there is one.
 func (tracker *Tracker) GetError() error {
 	return tracker.Err
 }
@@ -105,7 +145,8 @@ func (tracker *Tracker) TrySplit(fraction float64) (primary, residual interface{
 		fraction = 1
 	}
 
-	splitPt := tracker.Claimed + int64(fraction*float64(tracker.Rest.End-tracker.Claimed))
+	// Use Ceil to always round up from float split point.
+	splitPt := tracker.Claimed + int64(math.Ceil(fraction*float64(tracker.Rest.End-tracker.Claimed)))
 	if splitPt >= tracker.Rest.End {
 		return tracker.Rest, nil, nil
 	}
@@ -123,5 +164,5 @@ func (tracker *Tracker) GetProgress() (done, remaining float64) {
 
 // IsDone returns true if the most recent claimed element is past the end of the restriction.
 func (tracker *Tracker) IsDone() bool {
-	return tracker.Claimed >= tracker.Rest.End
+	return tracker.Err == nil && tracker.Claimed >= tracker.Rest.End
 }
diff --git a/sdks/go/pkg/beam/io/rtrackers/offsetrange/offsetrange_test.go b/sdks/go/pkg/beam/io/rtrackers/offsetrange/offsetrange_test.go
new file mode 100644
index 000000000000..489e25146249
--- /dev/null
+++ b/sdks/go/pkg/beam/io/rtrackers/offsetrange/offsetrange_test.go
@@ -0,0 +1,212 @@
+// Licensed to the Apache Software Foundation (ASF) under one or more
+// contributor license agreements.  See the NOTICE file distributed with
+// this work for additional information regarding copyright ownership.
+// The ASF licenses this file to You under the Apache License, Version 2.0
+// (the "License"); you may not use this file except in compliance with
+// the License.  You may obtain a copy of the License at
+//
+//    http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package offsetrange
+
+import (
+	"fmt"
+	"github.com/google/go-cmp/cmp"
+	"testing"
+)
+
+// TestRestriction_EvenSplits tests various splits and checks that they all
+// follow the contract for EvenSplits. This means that all restrictions are
+// evenly split, that each restriction has at least one element, and that each
+// element is present in the split restrictions.
+func TestRestriction_EvenSplits(t *testing.T) {
+	tests := []struct {
+		rest Restriction
+		num  int64
+	}{
+		{rest: Restriction{Start: 0, End: 21}, num: 4},
+		{rest: Restriction{Start: 21, End: 42}, num: 4},
+		{rest: Restriction{Start: 0, End: 5}, num: 10},
+		{rest: Restriction{Start: 0, End: 21}, num: -1},
+	}
+	for _, test := range tests {
+		test := test
+		t.Run(fmt.Sprintf("(rest[%v, %v], splits = %v)",
+			test.rest.Start, test.rest.End, test.num), func(t *testing.T) {
+			r := test.rest
+
+			// Get the minimum size that a split restriction can be. Max size
+			// should be min + 1. This way we can check the size of each split.
+			num := test.num
+			if num <= 1 {
+				num = 1
+			}
+			min := (r.End - r.Start) / num
+
+			splits := r.EvenSplits(test.num)
+			prevEnd := r.Start
+			for _, split := range splits {
+				size := split.End - split.Start
+				// Check: Each restriction has at least 1 element.
+				if size == 0 {
+					t.Errorf("split restriction [%v, %v] is empty, size must be greater than 0.",
+						split.Start, split.End)
+				}
+				// Check: Restrictions are evenly split.
+				if size != min && size != min+1 {
+					t.Errorf("split restriction [%v, %v] has unexpected size. got: %v, want: %v or %v",
+						split.Start, split.End, size, min, min+1)
+				}
+				// Check: All elements are still in a split restrictions. This
+				// logic assumes that the splits are returned in order which
+				// isn't guaranteed by EvenSplits, but this check is way easier
+				// with the assumption.
+				if split.Start != prevEnd {
+					t.Errorf("restriction range [%v, %v] missing after splits.",
+						prevEnd, split.Start)
+				} else {
+					prevEnd = split.End
+				}
+			}
+			if prevEnd != r.End {
+				t.Errorf("restriction range [%v, %v] missing after splits.",
+					prevEnd, r.End)
+			}
+		})
+	}
+}
+
+// TestTracker_TryClaim validates both success and failure cases for TryClaim.
+func TestTracker_TryClaim(t *testing.T) {
+	// Test that TryClaim works as expected when called correctly.
+	t.Run("Correctness", func(t *testing.T) {
+		tests := []struct {
+			rest   Restriction
+			claims []int64
+		}{
+			{rest: Restriction{Start: 0, End: 3}, claims: []int64{0, 1, 2, 3}},
+			{rest: Restriction{Start: 10, End: 40}, claims: []int64{15, 20, 50}},
+			{rest: Restriction{Start: 0, End: 3}, claims: []int64{4}},
+		}
+		for _, test := range tests {
+			test := test
+			t.Run(fmt.Sprintf("(rest[%v, %v], claims = %v)",
+				test.rest.Start, test.rest.End, test.claims), func(t *testing.T) {
+				rt := NewTracker(test.rest)
+				for _, pos := range test.claims {
+					// If TryClaim returns false, check if there was an error.
+					if !rt.TryClaim(pos) && !rt.IsDone() {
+						t.Fatalf("tracker claiming %v failed, error: %v", pos, rt.GetError())
+					}
+				}
+			})
+		}
+	})
+
+	// Test that each invalid error case actually results in an error.
+	t.Run("Errors", func(t *testing.T) {
+		tests := []struct {
+			rest   Restriction
+			claims []int64
+		}{
+			// Claiming backwards.
+			{rest: Restriction{Start: 0, End: 3}, claims: []int64{0, 2, 1}},
+			// Claiming before start of restriction.
+			{rest: Restriction{Start: 10, End: 40}, claims: []int64{8}},
+			// Claiming after tracker signalled to stop.
+			{rest: Restriction{Start: 0, End: 3}, claims: []int64{4, 5}},
+		}
+		for _, test := range tests {
+			test := test
+			t.Run(fmt.Sprintf("(rest[%v, %v], claims = %v)",
+				test.rest.Start, test.rest.End, test.claims), func(t *testing.T) {
+				rt := NewTracker(test.rest)
+				for _, pos := range test.claims {
+					// Finish successfully if we got an error.
+					if !rt.TryClaim(pos) && !rt.IsDone() && rt.GetError() != nil {
+						return
+					}
+				}
+				t.Fatal("tracker did not fail on invalid claim")
+			})
+		}
+	})
+}
+
+// TestTracker_TrySplit tests that TrySplit follows its contract, meaning that
+// splits don't lose any elements, split fractions are clamped to 0 or 1, and
+// that TrySplit always splits at the nearest integer greater than the given
+// fraction.
+func TestTracker_TrySplit(t *testing.T) {
+	tests := []struct {
+		rest     Restriction
+		claimed  int64
+		fraction float64
+		// Index where we want the split to happen. This will be the end
+		// (exclusive) of the primary and first element of the residual.
+		splitPt int64
+	}{
+		{
+			rest:     Restriction{Start: 0, End: 1},
+			claimed:  0,
+			fraction: 0.5,
+			splitPt:  1,
+		},
+		{
+			rest:     Restriction{Start: 0, End: 5},
+			claimed:  0,
+			fraction: 0.5,
+			splitPt:  3,
+		},
+		{
+			rest:     Restriction{Start: 0, End: 10},
+			claimed:  5,
+			fraction: 0.5,
+			splitPt:  8,
+		},
+		{
+			rest:     Restriction{Start: 0, End: 10},
+			claimed:  5,
+			fraction: -0.5,
+			splitPt:  5,
+		},
+		{
+			rest:     Restriction{Start: 0, End: 10},
+			claimed:  5,
+			fraction: 1.5,
+			splitPt:  10,
+		},
+	}
+	for _, test := range tests {
+		test := test
+		t.Run(fmt.Sprintf("(split at %v of [%v, %v])",
+			test.fraction, test.claimed, test.rest.End), func(t *testing.T) {
+			rt := NewTracker(test.rest)
+			ok := rt.TryClaim(test.claimed)
+			if !ok {
+				t.Fatalf("tracker failed on initial claim: %v", test.claimed)
+			}
+			gotP, gotR, err := rt.TrySplit(test.fraction)
+			if err != nil {
+				t.Fatalf("tracker failed on split: %v", err)
+			}
+			var wantP interface{} = Restriction{Start: test.rest.Start, End: test.splitPt}
+			var wantR interface{} = Restriction{Start: test.splitPt, End: test.rest.End}
+			if test.splitPt == test.rest.End {
+				wantR = nil // When residuals are empty we should get nil.
+			}
+			if !cmp.Equal(gotP, wantP) {
+				t.Errorf("split got incorrect primary: got: %v, want: %v", gotP, wantP)
+			}
+			if !cmp.Equal(gotR, wantR) {
+				t.Errorf("split got incorrect residual: got: %v, want: %v", gotR, wantR)
+			}
+		})
+	}
+}
diff --git a/sdks/go/pkg/beam/io/synthetic/source.go b/sdks/go/pkg/beam/io/synthetic/source.go
index 00033206cf62..fbe385c6bd32 100644
--- a/sdks/go/pkg/beam/io/synthetic/source.go
+++ b/sdks/go/pkg/beam/io/synthetic/source.go
@@ -24,10 +24,11 @@ package synthetic
 
 import (
 	"fmt"
-	"github.com/apache/beam/sdks/go/pkg/beam"
-	"github.com/apache/beam/sdks/go/pkg/beam/io/rtrackers/offsetrange"
 	"math/rand"
 	"time"
+
+	"github.com/apache/beam/sdks/go/pkg/beam"
+	"github.com/apache/beam/sdks/go/pkg/beam/io/rtrackers/offsetrange"
 )
 
 // Source creates a synthetic source transform that emits randomly
@@ -95,35 +96,13 @@ func (fn *sourceFn) CreateInitialRestriction(config SourceConfig) offsetrange.Re
 // method will contain at least one element, so the number of splits will not
 // exceed the number of elements.
 func (fn *sourceFn) SplitRestriction(config SourceConfig, rest offsetrange.Restriction) (splits []offsetrange.Restriction) {
-	if config.InitialSplits <= 1 {
-		// Don't split, just return original restriction.
-		return append(splits, rest)
-	}
-
-	// TODO(BEAM-9978) Move this implementation of the offset range restriction
-	// splitting to the restriction itself, and add testing.
-	num := int64(config.InitialSplits)
-	offset := rest.Start
-	size := rest.End - rest.Start
-	for i := int64(0); i < num; i++ {
-		split := offsetrange.Restriction{
-			Start: offset + (i * size / num),
-			End:   offset + ((i + 1) * size / num),
-		}
-		// Skip restrictions that end up empty.
-		if split.End-split.Start <= 0 {
-			continue
-		}
-		splits = append(splits, split)
-	}
-	return splits
+	return rest.EvenSplits(int64(config.InitialSplits))
 }
 
 // RestrictionSize outputs the size of the restriction as the number of elements
 // that restriction will output.
 func (fn *sourceFn) RestrictionSize(config SourceConfig, rest offsetrange.Restriction) float64 {
-	// TODO(BEAM-9978) Move this size implementation to the offset range restriction itself.
-	return float64(rest.End - rest.Start)
+	return rest.Size()
 }
 
 // CreateTracker just creates an offset range restriction tracker for the
diff --git a/sdks/go/pkg/beam/io/synthetic/step.go b/sdks/go/pkg/beam/io/synthetic/step.go
index 977d5540e410..4fc23bc15d56 100644
--- a/sdks/go/pkg/beam/io/synthetic/step.go
+++ b/sdks/go/pkg/beam/io/synthetic/step.go
@@ -17,10 +17,11 @@ package synthetic
 
 import (
 	"fmt"
-	"github.com/apache/beam/sdks/go/pkg/beam"
-	"github.com/apache/beam/sdks/go/pkg/beam/io/rtrackers/offsetrange"
 	"math/rand"
 	"time"
+
+	"github.com/apache/beam/sdks/go/pkg/beam"
+	"github.com/apache/beam/sdks/go/pkg/beam/io/rtrackers/offsetrange"
 )
 
 // Step creates a synthetic step transform that receives KV<[]byte, []byte>
@@ -98,35 +99,13 @@ func (fn *sdfStepFn) CreateInitialRestriction(key, val []byte) offsetrange.Restr
 // method will contain at least one element, so the number of splits will not
 // exceed the number of elements.
 func (fn *sdfStepFn) SplitRestriction(key, val []byte, rest offsetrange.Restriction) (splits []offsetrange.Restriction) {
-	if fn.cfg.InitialSplits <= 1 {
-		// Don't split, just return original restriction.
-		return append(splits, rest)
-	}
-
-	// TODO(BEAM-9978) Move this implementation of the offset range restriction
-	// splitting to the restriction itself, and add testing.
-	num := int64(fn.cfg.InitialSplits)
-	offset := rest.Start
-	size := rest.End - rest.Start
-	for i := int64(0); i < num; i++ {
-		split := offsetrange.Restriction{
-			Start: offset + (i * size / num),
-			End:   offset + ((i + 1) * size / num),
-		}
-		// Skip restrictions that end up empty.
-		if split.End-split.Start <= 0 {
-			continue
-		}
-		splits = append(splits, split)
-	}
-	return splits
+	return rest.EvenSplits(int64(fn.cfg.InitialSplits))
 }
 
 // RestrictionSize outputs the size of the restriction as the number of elements
 // that restriction will output.
 func (fn *sdfStepFn) RestrictionSize(key, val []byte, rest offsetrange.Restriction) float64 {
-	// TODO(BEAM-9978) Move this size implementation to the offset range restriction itself.
-	return float64(rest.End - rest.Start)
+	return rest.Size()
 }
 
 // CreateTracker creates an offset range restriction tracker for the

From 64f8a40c26afeae7fead09f06ed18b930ce1731b Mon Sep 17 00:00:00 2001
From: Heejong Lee 
Date: Thu, 21 May 2020 23:37:02 -0700
Subject: [PATCH 055/151] [BEAM-10064] Fix google3 import error for BEAM-9383

---
 .../apache_beam/runners/dataflow/internal/apiclient_test.py    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sdks/python/apache_beam/runners/dataflow/internal/apiclient_test.py b/sdks/python/apache_beam/runners/dataflow/internal/apiclient_test.py
index 7776156bd460..7a780a6a5192 100644
--- a/sdks/python/apache_beam/runners/dataflow/internal/apiclient_test.py
+++ b/sdks/python/apache_beam/runners/dataflow/internal/apiclient_test.py
@@ -944,7 +944,8 @@ def test_stage_resources(self):
         '--temp_location',
         'gs://test-location/temp',
         '--staging_location',
-        'gs://test-location/staging'
+        'gs://test-location/staging',
+        '--no_auth'
     ])
     pipeline = beam_runner_api_pb2.Pipeline(
         components=beam_runner_api_pb2.Components(

From 6766d0c2b929f74152c4d4a60bd0898c918ad667 Mon Sep 17 00:00:00 2001
From: Kamil Wasilewski 
Date: Fri, 22 May 2020 12:06:27 +0200
Subject: [PATCH 056/151] [BEAM-10058] Provide less strict assertion to make
 the test more resistant against future changes in a model

---
 .../apache_beam/ml/gcp/videointelligenceml_test_it.py       | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/sdks/python/apache_beam/ml/gcp/videointelligenceml_test_it.py b/sdks/python/apache_beam/ml/gcp/videointelligenceml_test_it.py
index f411549d7b9c..397256e5f153 100644
--- a/sdks/python/apache_beam/ml/gcp/videointelligenceml_test_it.py
+++ b/sdks/python/apache_beam/ml/gcp/videointelligenceml_test_it.py
@@ -44,7 +44,7 @@
 
 def extract_entities_descriptions(response):
   for result in response.annotation_results:
-    for segment in result.segment_label_annotations:
+    for segment in result.segment_presence_label_annotations:
       yield segment.entity.description
 
 
@@ -69,7 +69,9 @@ def test_label_detection_with_video_context(self):
           | beam.ParDo(extract_entities_descriptions)
           | beam.combiners.ToList())
 
-      assert_that(output, matches_all([hc.has_items('bicycle', 'dinosaur')]))
+      # Search for at least one entity that contains 'bicycle'.
+      assert_that(
+          output, matches_all([hc.has_item(hc.contains_string('bicycle'))]))
 
 
 if __name__ == '__main__':

From 790ed4427429292ae14931ca5c3ad9af73438e94 Mon Sep 17 00:00:00 2001
From: Ashwin Ramaswami 
Date: Fri, 22 May 2020 10:36:42 -0400
Subject: [PATCH 057/151] Fix typo copyLicenseScrips -> copyLicenseScripts

---
 sdks/python/container/py2/build.gradle  | 4 ++--
 sdks/python/container/py35/build.gradle | 4 ++--
 sdks/python/container/py36/build.gradle | 4 ++--
 sdks/python/container/py37/build.gradle | 4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/sdks/python/container/py2/build.gradle b/sdks/python/container/py2/build.gradle
index 4e5848208fa0..2821600419d7 100644
--- a/sdks/python/container/py2/build.gradle
+++ b/sdks/python/container/py2/build.gradle
@@ -43,7 +43,7 @@ task copyDockerfileDependencies(type: Copy) {
   }
 }
 
-task copyLicenseScrips(type: Copy){
+task copyLicenseScripts(type: Copy){
   from ("../license_scripts")
   into "build/target/license_scripts"
 }
@@ -72,4 +72,4 @@ docker {
 
 dockerPrepare.dependsOn copyLauncherDependencies
 dockerPrepare.dependsOn copyDockerfileDependencies
-dockerPrepare.dependsOn copyLicenseScrips
+dockerPrepare.dependsOn copyLicenseScripts
diff --git a/sdks/python/container/py35/build.gradle b/sdks/python/container/py35/build.gradle
index ce1fbe91b16a..6a0133dd9916 100644
--- a/sdks/python/container/py35/build.gradle
+++ b/sdks/python/container/py35/build.gradle
@@ -43,7 +43,7 @@ task copyDockerfileDependencies(type: Copy) {
   }
 }
 
-task copyLicenseScrips(type: Copy){
+task copyLicenseScripts(type: Copy){
   from ("../license_scripts")
   into "build/target/license_scripts"
 }
@@ -72,4 +72,4 @@ docker {
 
 dockerPrepare.dependsOn copyLauncherDependencies
 dockerPrepare.dependsOn copyDockerfileDependencies
-dockerPrepare.dependsOn copyLicenseScrips
+dockerPrepare.dependsOn copyLicenseScripts
diff --git a/sdks/python/container/py36/build.gradle b/sdks/python/container/py36/build.gradle
index c5417169c76b..b50267c29201 100644
--- a/sdks/python/container/py36/build.gradle
+++ b/sdks/python/container/py36/build.gradle
@@ -43,7 +43,7 @@ task copyDockerfileDependencies(type: Copy) {
   }
 }
 
-task copyLicenseScrips(type: Copy){
+task copyLicenseScripts(type: Copy){
   from ("../license_scripts")
   into "build/target/license_scripts"
 }
@@ -72,4 +72,4 @@ docker {
 
 dockerPrepare.dependsOn copyLauncherDependencies
 dockerPrepare.dependsOn copyDockerfileDependencies
-dockerPrepare.dependsOn copyLicenseScrips
+dockerPrepare.dependsOn copyLicenseScripts
diff --git a/sdks/python/container/py37/build.gradle b/sdks/python/container/py37/build.gradle
index 1225332d9535..969a58db7945 100644
--- a/sdks/python/container/py37/build.gradle
+++ b/sdks/python/container/py37/build.gradle
@@ -43,7 +43,7 @@ task copyDockerfileDependencies(type: Copy) {
   }
 }
 
-task copyLicenseScrips(type: Copy){
+task copyLicenseScripts(type: Copy){
   from ("../license_scripts")
   into "build/target/license_scripts"
 }
@@ -72,4 +72,4 @@ docker {
 
 dockerPrepare.dependsOn copyLauncherDependencies
 dockerPrepare.dependsOn copyDockerfileDependencies
-dockerPrepare.dependsOn copyLicenseScrips
+dockerPrepare.dependsOn copyLicenseScripts

From 0e484983febc9ed6be0ddf5b68452380e208db56 Mon Sep 17 00:00:00 2001
From: Ashwin Ramaswami 
Date: Fri, 22 May 2020 11:06:58 -0400
Subject: [PATCH 058/151] [BEAM-10067] Minify website assets with --minify flag

---
 website/www/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/website/www/package.json b/website/www/package.json
index a5b1cbea637d..d68017f163e1 100644
--- a/website/www/package.json
+++ b/website/www/package.json
@@ -7,7 +7,7 @@
   "scripts": {
     "build_github_samples": "./build_github_samples.sh",
     "develop": "cd site && hugo server",
-    "build": "cross-env HUGO_ENV=production hugo -d ../dist -s site -v",
+    "build": "cross-env HUGO_ENV=production hugo --minify -d ../dist -s site -v",
     "start": "hugo -d ../dist -s site -vw"
   },
   "dependencies": {},

From e45623e5d7f72b28c0ec1bde1c1795982cbe9ffe Mon Sep 17 00:00:00 2001
From: Robert Burke 
Date: Fri, 22 May 2020 10:01:42 -0700
Subject: [PATCH 059/151] [BEAM-10051] Move closed reader check after sentinel.
 (#11768)

---
 .../pkg/beam/core/runtime/harness/datamgr.go  | 24 +++++++++++--------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/sdks/go/pkg/beam/core/runtime/harness/datamgr.go b/sdks/go/pkg/beam/core/runtime/harness/datamgr.go
index 81e813e4f93b..3fb9401dd017 100644
--- a/sdks/go/pkg/beam/core/runtime/harness/datamgr.go
+++ b/sdks/go/pkg/beam/core/runtime/harness/datamgr.go
@@ -266,18 +266,14 @@ func (c *DataChannel) read(ctx context.Context) {
 				cache[id] = r
 			}
 
-			if r.completed {
-				// The local reader has closed but the remote is still sending data.
-				// Just ignore it. We keep the reader config in the cache so we don't
-				// treat it as a new reader. Eventually the stream will finish and go
-				// through normal teardown.
-				continue
-			}
 			// TODO(BEAM-9558): Cleanup once dataflow is updated.
 			if len(elm.GetData()) == 0 || elm.GetIsLast() {
-				// Sentinel EOF segment for stream. Close buffer to signal EOF.
-				r.completed = true
-				close(r.buf)
+				// If this reader hasn't closed yet, do so now.
+				if !r.completed {
+					// Sentinel EOF segment for stream. Close buffer to signal EOF.
+					r.completed = true
+					close(r.buf)
+				}
 
 				// Clean up local bookkeeping. We'll never see another message
 				// for it again. We have to be careful not to remove the real
@@ -287,6 +283,14 @@ func (c *DataChannel) read(ctx context.Context) {
 				continue
 			}
 
+			if r.completed {
+				// The local reader has closed but the remote is still sending data.
+				// Just ignore it. We keep the reader config in the cache so we don't
+				// treat it as a new reader. Eventually the stream will finish and go
+				// through normal teardown.
+				continue
+			}
+
 			// This send is deliberately blocking, if we exceed the buffering for
 			// a reader. We can't buffer the entire main input, if some user code
 			// is slow (or gets stuck). If the local side closes, the reader

From 455fca5ab79f74d4e79a81e66942878f35aaa08c Mon Sep 17 00:00:00 2001
From: Robert Burke 
Date: Fri, 22 May 2020 10:02:42 -0700
Subject: [PATCH 060/151] [BEAM-10056] Fix validation for struct CoGBKs
 (#11782)

---
 sdks/go/pkg/beam/core/graph/fn.go      | 24 ++++---
 sdks/go/pkg/beam/core/graph/fn_test.go | 91 +++++++++++++++++++++-----
 sdks/go/pkg/beam/pardo.go              | 11 ++--
 3 files changed, 97 insertions(+), 29 deletions(-)

diff --git a/sdks/go/pkg/beam/core/graph/fn.go b/sdks/go/pkg/beam/core/graph/fn.go
index 6b4f64bd03e8..1711d7cf7db8 100644
--- a/sdks/go/pkg/beam/core/graph/fn.go
+++ b/sdks/go/pkg/beam/core/graph/fn.go
@@ -297,6 +297,19 @@ func NumMainInputs(num mainInputs) func(*config) {
 	}
 }
 
+// CoGBKMainInput is an optional config to NewDoFn which specifies the number
+// of components of a CoGBK input to the DoFn being created, allowing for more complete
+// validation.
+//
+// Example usage:
+//   var col beam.PCollection
+//   graph.NewDoFn(fn, graph.CoGBKMainInput(len(col.Type().Components())))
+func CoGBKMainInput(components int) func(*config) {
+	return func(cfg *config) {
+		cfg.numMainIn = mainInputs(components)
+	}
+}
+
 // NewDoFn constructs a DoFn from the given value, if possible.
 func NewDoFn(fn interface{}, options ...func(*config)) (*DoFn, error) {
 	ret, err := NewFn(fn)
@@ -586,14 +599,9 @@ func validateSideInputsNumUnknown(processFnInputs []funcx.FnParam, method *funcx
 
 	// Handle cases where method has no inputs.
 	if !ok {
-		if numProcessIn <= int(MainKv) {
-			return nil // We're good, possible for there to be no side inputs.
-		}
-		err := errors.Errorf("side inputs expected in method %v", methodName)
-		return errors.SetTopLevelMsgf(err,
-			"Missing side inputs in the %v method of a DoFn. "+
-				"If side inputs are present in %v those side inputs must also be present in %v.",
-			methodName, processElementName, methodName)
+		// If there's no inputs, this is fine, as the ProcessElement method could be a
+		// CoGBK, and not have side inputs.
+		return nil
 	}
 
 	// Error if number of side inputs doesn't match any of the possible numbers of side inputs,
diff --git a/sdks/go/pkg/beam/core/graph/fn_test.go b/sdks/go/pkg/beam/core/graph/fn_test.go
index e5305123a4ed..f75410970fc7 100644
--- a/sdks/go/pkg/beam/core/graph/fn_test.go
+++ b/sdks/go/pkg/beam/core/graph/fn_test.go
@@ -26,22 +26,26 @@ import (
 func TestNewDoFn(t *testing.T) {
 	t.Run("valid", func(t *testing.T) {
 		tests := []struct {
-			dfn  interface{}
-			main mainInputs
+			dfn interface{}
+			opt func(*config)
 		}{
-			{dfn: func(string) int { return 0 }, main: MainSingle},
-			{dfn: func(string, int) int { return 0 }, main: MainKv},
+			{dfn: func(string) int { return 0 }, opt: NumMainInputs(MainSingle)},
+			{dfn: func(string, int) int { return 0 }, opt: NumMainInputs(MainKv)},
 			{dfn: func(context.Context, typex.Window, typex.EventTime, reflect.Type, string, int, func(*int) bool, func() func(*int) bool, func(int)) (typex.EventTime, int, error) {
 				return 0, 0, nil
-			}, main: MainKv},
-			{dfn: &GoodDoFn{}, main: MainSingle},
-			{dfn: &GoodDoFnOmittedMethods{}, main: MainSingle},
-			{dfn: &GoodDoFnEmits{}, main: MainSingle},
-			{dfn: &GoodDoFnSideInputs{}, main: MainSingle},
-			{dfn: &GoodDoFnKv{}, main: MainKv},
-			{dfn: &GoodDoFnKvSideInputs{}, main: MainKv},
-			{dfn: &GoodDoFnAllExtras{}, main: MainKv},
-			{dfn: &GoodDoFnUnexportedExtraMethod{}, main: MainSingle},
+			}, opt: NumMainInputs(MainKv)},
+			{dfn: &GoodDoFn{}, opt: NumMainInputs(MainSingle)},
+			{dfn: &GoodDoFnOmittedMethods{}, opt: NumMainInputs(MainSingle)},
+			{dfn: &GoodDoFnEmits{}, opt: NumMainInputs(MainSingle)},
+			{dfn: &GoodDoFnSideInputs{}, opt: NumMainInputs(MainSingle)},
+			{dfn: &GoodDoFnKv{}, opt: NumMainInputs(MainKv)},
+			{dfn: &GoodDoFnKvSideInputs{}, opt: NumMainInputs(MainKv)},
+			{dfn: &GoodDoFnAllExtras{}, opt: NumMainInputs(MainKv)},
+			{dfn: &GoodDoFnUnexportedExtraMethod{}, opt: NumMainInputs(MainSingle)},
+			{dfn: &GoodDoFnCoGbk1{}, opt: NumMainInputs(MainKv)},
+			{dfn: &GoodDoFnCoGbk2{}, opt: CoGBKMainInput(3)},
+			{dfn: &GoodDoFnCoGbk7{}, opt: CoGBKMainInput(8)},
+			{dfn: &GoodDoFnCoGbk1wSide{}, opt: NumMainInputs(MainKv)},
 		}
 
 		for _, test := range tests {
@@ -50,8 +54,10 @@ func TestNewDoFn(t *testing.T) {
 				if _, err := NewDoFn(test.dfn); err != nil {
 					t.Fatalf("NewDoFn failed: %v", err)
 				}
-				if _, err := NewDoFn(test.dfn, NumMainInputs(test.main)); err != nil {
-					t.Fatalf("NewDoFn(NumMainInputs(%v)) failed: %v", test.main, err)
+				if _, err := NewDoFn(test.dfn, test.opt); err != nil {
+					cfg := defaultConfig()
+					test.opt(cfg)
+					t.Fatalf("NewDoFn(%#v) failed: %v", cfg, err)
 				}
 			})
 		}
@@ -72,10 +78,8 @@ func TestNewDoFn(t *testing.T) {
 			{dfn: &BadDoFnMismatchedEmitsStartBundle{}},
 			{dfn: &BadDoFnNoEmitsFinishBundle{}},
 			// Validate side inputs.
-			{dfn: &BadDoFnNoSideInputsStartBundle{}},
 			{dfn: &BadDoFnMissingSideInputsStartBundle{}},
 			{dfn: &BadDoFnMismatchedSideInputsStartBundle{}},
-			{dfn: &BadDoFnNoSideInputsFinishBundle{}},
 			// Validate setup/teardown.
 			{dfn: &BadDoFnParamsInSetup{}},
 			{dfn: &BadDoFnParamsInTeardown{}},
@@ -121,6 +125,11 @@ func TestNewDoFn(t *testing.T) {
 			}, main: MainKv},
 			{dfn: &BadDoFnAmbiguousMainInput{}, main: MainKv},
 			{dfn: &BadDoFnAmbiguousSideInput{}, main: MainSingle},
+			// These are ambiguous with CoGBKs, but should fail with known MainInputs.
+			{dfn: &BadDoFnNoSideInputsStartBundle{}, main: MainSingle},
+			{dfn: &BadDoFnNoSideInputsStartBundle{}, main: MainKv},
+			{dfn: &BadDoFnNoSideInputsFinishBundle{}, main: MainSingle},
+			{dfn: &BadDoFnNoSideInputsFinishBundle{}, main: MainKv},
 		}
 		for _, test := range tests {
 			t.Run(reflect.TypeOf(test.dfn).String(), func(t *testing.T) {
@@ -368,6 +377,54 @@ func (fn *GoodDoFnKvSideInputs) StartBundle(string, func(*int) bool, func() func
 func (fn *GoodDoFnKvSideInputs) FinishBundle(string, func(*int) bool, func() func(*int) bool) {
 }
 
+type GoodDoFnCoGbk1 struct{}
+
+func (fn *GoodDoFnCoGbk1) ProcessElement(int, func(*string) bool) int {
+	return 0
+}
+
+func (fn *GoodDoFnCoGbk1) StartBundle() {
+}
+
+func (fn *GoodDoFnCoGbk1) FinishBundle() {
+}
+
+type GoodDoFnCoGbk2 struct{}
+
+func (fn *GoodDoFnCoGbk2) ProcessElement(int, func(*int) bool, func(*string) bool) int {
+	return 0
+}
+
+func (fn *GoodDoFnCoGbk2) StartBundle() {
+}
+
+func (fn *GoodDoFnCoGbk2) FinishBundle() {
+}
+
+type GoodDoFnCoGbk7 struct{}
+
+func (fn *GoodDoFnCoGbk7) ProcessElement(k int, v1, v2, v3, v4, v5, v6, v7 func(*int) bool) int {
+	return 0
+}
+
+func (fn *GoodDoFnCoGbk7) StartBundle() {
+}
+
+func (fn *GoodDoFnCoGbk7) FinishBundle() {
+}
+
+type GoodDoFnCoGbk1wSide struct{}
+
+func (fn *GoodDoFnCoGbk1wSide) ProcessElement(int, func(*string) bool, func(*int) bool) int {
+	return 0
+}
+
+func (fn *GoodDoFnCoGbk1wSide) StartBundle(func(*int) bool) {
+}
+
+func (fn *GoodDoFnCoGbk1wSide) FinishBundle(func(*int) bool) {
+}
+
 type GoodDoFnAllExtras struct{}
 
 func (fn *GoodDoFnAllExtras) ProcessElement(context.Context, typex.Window, typex.EventTime, reflect.Type, string, int, func(*int) bool, func() func(*int) bool, func(int)) (typex.EventTime, int, error) {
diff --git a/sdks/go/pkg/beam/pardo.go b/sdks/go/pkg/beam/pardo.go
index d53e270e6a35..de3063446c79 100644
--- a/sdks/go/pkg/beam/pardo.go
+++ b/sdks/go/pkg/beam/pardo.go
@@ -17,6 +17,7 @@ package beam
 
 import (
 	"fmt"
+
 	"github.com/apache/beam/sdks/go/pkg/beam/core/graph/coder"
 	"github.com/apache/beam/sdks/go/pkg/beam/core/typex"
 
@@ -37,12 +38,14 @@ func TryParDo(s Scope, dofn interface{}, col PCollection, opts ...Option) ([]PCo
 		return nil, addParDoCtx(err, s)
 	}
 
-	num := graph.MainSingle
+	doFnOpt := graph.NumMainInputs(graph.MainSingle)
 	// Check the PCollection for any keyed type (not just KV specifically).
-	if typex.IsKV(col.Type()) || typex.IsCoGBK(col.Type()) {
-		num = graph.MainKv
+	if typex.IsKV(col.Type()) {
+		doFnOpt = graph.NumMainInputs(graph.MainKv)
+	} else if typex.IsCoGBK(col.Type()) {
+		doFnOpt = graph.CoGBKMainInput(len(col.Type().Components()))
 	}
-	fn, err := graph.NewDoFn(dofn, graph.NumMainInputs(num))
+	fn, err := graph.NewDoFn(dofn, doFnOpt)
 	if err != nil {
 		return nil, addParDoCtx(err, s)
 	}

From f387df7d01ab1355f7f522ee20233b7674222b10 Mon Sep 17 00:00:00 2001
From: Ashwin Ramaswami 
Date: Fri, 22 May 2020 22:16:32 -0400
Subject: [PATCH 061/151] add io-matrix

---
 .../content/en/documentation/io/built-in.md   |  82 +---
 website/www/site/data/io_matrix.yaml          | 373 ++++++++++++++++++
 .../site/layouts/shortcodes/io-matrix.html    |  48 +++
 3 files changed, 424 insertions(+), 79 deletions(-)
 create mode 100644 website/www/site/data/io_matrix.yaml
 create mode 100644 website/www/site/layouts/shortcodes/io-matrix.html

diff --git a/website/www/site/content/en/documentation/io/built-in.md b/website/www/site/content/en/documentation/io/built-in.md
index 481c532327f9..ba72908a885f 100644
--- a/website/www/site/content/en/documentation/io/built-in.md
+++ b/website/www/site/content/en/documentation/io/built-in.md
@@ -19,87 +19,11 @@ limitations under the License.
 
 This table contains the currently available I/O transforms.
 
-Consult the [Programming Guide I/O section](/documentation/programming-guide#pipeline-io) for general usage instructions, and see the javadoc/pydoc for the particular I/O transforms.
+Consult the [Programming Guide I/O section](/documentation/programming-guide#pipeline-io) for general usage instructions.
 
+{{< language-switcher java py go >}}
 
-
-
-  
-  
-  
-  
-
-
-  
-  
-  
-  
-
-
-  
-  
-  
-  
-
-
-  
-  
-  
-  
-
-
    LanguageFile-basedMessagingDatabase
    Java
-    
    Beam Java supports Apache HDFS, Amazon S3, Google Cloud Storage, and local filesystems.
    
-    
    FileIO (general-purpose reading, writing, and matching of files)
    
-    
    AvroIO
    
-    
    TextIO
    
-    
    TFRecordIO
    
-    
    XmlIO
    
-    
    TikaIO
    
-    
    ParquetIO
    
-    
    ThriftIO
    
-      		
-    
    Amazon Kinesis
    
-    
    AMQP
    
-    
    Apache Kafka
    
-    
    Google Cloud Pub/Sub
    
-    
    JMS
    
-    
    MQTT
    
-    
    RabbitMqIO
    
-    
    SqsIO
    
-      		
-    
    Apache Cassandra
    
-    
    Apache Hadoop Input/Output Format
    
-    
    Apache HBase
    
-    
    Apache Hive (HCatalog)
    
-    
    Apache Kudu
    
-    
    Apache Solr
    
-    
    Elasticsearch (v2.x, v5.x, v6.x)
    
-    
    Google BigQuery
    
-    
    Google Cloud Bigtable
    
-    
    Google Cloud Datastore
    
-    
    Google Cloud Spanner
    
-    
    JDBC
    
-    
    MongoDB
    
-    
    Redis
    
-  
    Python/Batch
-    
    Beam Python supports Apache HDFS, Amazon S3, Google Cloud Storage, and local filesystems.
    
-    
    avroio
    
-    
    parquetio.py
    
-    
    textio
    
-    
    tfrecordio
    
-    
    vcfio
    
-      		
-  
-    
    Google BigQuery
    
-    
    Google Cloud Datastore
    
-    
    Google Cloud Bigtable (Write)
    
-    
    MongoDB
    
-  
    Python/Streaming
-  
-    
    Google Cloud Pub/Sub
    
-      		
-    
    Google BigQuery (sink only)
    
-  
    
+{{< io-matrix >}}
 
 # In-Progress I/O Transforms
 
diff --git a/website/www/site/data/io_matrix.yaml b/website/www/site/data/io_matrix.yaml
new file mode 100644
index 000000000000..4b64189ab730
--- /dev/null
+++ b/website/www/site/data/io_matrix.yaml
@@ -0,0 +1,373 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+categories:
+  - name: File-based
+    description: These I/O connectors involve working with files.
+    rows:
+      - transform: FileIO
+        description: "General-purpose transforms for working with files: listing files (matching), reading and writing."
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.FileIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/FileIO.html
+          - language: py
+            name: apache_beam.io.FileIO
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.fileio.html
+      - transform: AvroIO
+        description: PTransforms for reading from and writing to Avro files.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.AvroIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/AvroIO.html
+          - language: py
+            name: apache_beam.io.avroio
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.avroio.html
+          - language: go
+            name: github.com/apache/beam/sdks/go/pkg/beam/io/avroio
+            url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/avroio
+      - transform: TextIO
+        description: PTransforms for reading and writing text files.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.TextIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/TextIO.html
+          - language: py
+            name: apache_beam.io.textio
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.textio.html
+          - language: go
+            name: github.com/apache/beam/sdks/go/pkg/beam/io/textio
+            url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/textio
+      - transform: TFRecordIO
+        description: PTransforms for reading and writing TensorFlow TFRecord files.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.TFRecordIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/TFRecordIO.html
+          - language: py
+            name: apache_beam.io.tfrecordio
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.tfrecordio.html
+      - transform: XmlIO
+        description: Transforms for reading and writing XML files using JAXB mappers.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.xml.XmlIO
+            url: https://beam.apache.org/releases/javadoc/2.3.0/org/apache/beam/sdk/io/xml/XmlIO.html
+      - transform: TikaIO
+        description: Transforms for parsing arbitrary files using [Apache Tika](https://tika.apache.org/).
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.tika.TikaIO
+            url: https://beam.apache.org/releases/javadoc/2.3.0/org/apache/beam/sdk/io/tika/TikaIO.html
+      - transform: ParquetIO
+        description: IO for reading from and writing to Parquet files.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.parquet.ParquetIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/parquet/ParquetIO.html
+          - language: py
+            name: apache_beam.io.parquetio
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.parquetio.html
+      - transform: ThriftIO
+        description: PTransforms for reading and writing files containing Thrift encoded data.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.thrift.ThriftIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/thrift/ThriftIO.html
+      - transform: VcfIO
+        description: A source for reading from [VCF files](https://samtools.github.io/hts-specs/VCFv4.2.pdf) (version 4.x).
+        implementations:
+          - language: py
+            name: apache_beam.io.vcfio
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.vcfio.html
+      - transform: S3IO
+        description: A source for reading from and writing to Amazon S3.
+        implementations:
+          - language: py
+            name: apache_beam.io.aws.s3io
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.aws.s3io.html
+      - transform: GcsIO
+        description: A source for reading from and writing to Google Cloud Storage.
+        implementations:
+          - language: py
+            name: apache_beam.io.gcp.gcsio
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.gcp.gcsio.html
+  - name: FileSystem
+    description: Beam provides a File system interface that defines APIs for writing file systems agnostic code. Several I/O connectors are implemented as a FileSystem implementation.
+    rows:
+      - transform: HadoopFileSystem
+        description: "`FileSystem` implementation for accessing Hadoop Distributed File System files."
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.hdfs.HadoopFileSystemRegistrar
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/hdfs/HadoopFileSystemRegistrar.html
+          - language: py
+            name: apache_beam.io.hadoopfilesystem
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.hadoopfilesystem.html
+      - transform: GcsFileSystem
+        description: "`FileSystem` implementation for Google Cloud Storage."
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.extensions.gcp.storage.GcsFileSystemRegistrar
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/extensions/gcp/storage/GcsFileSystemRegistrar.html
+          - language: py
+            name: apache_beam.io.gcp.gcsfilesystem
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.gcp.gcsfilesystem.html
+          - language: go
+            name: github.com/apache/beam/sdks/go/pkg/beam/io/filesystem/gcs
+            url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/filesystem/gcs
+      - transform: LocalFileSystem
+        description: "`FileSystem` implementation for accessing files on disk."
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.LocalFileSystemRegistrar
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/LocalFileSystemRegistrar.html
+          - language: py
+            name: apache_beam.io.localfilesystem
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.localfilesystem.html
+          - language: go
+            name: github.com/apache/beam/sdks/go/pkg/beam/io/filesystem/local
+            url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/filesystem/local
+      - transform: S3FileSystem
+        description: "`FileSystem` implementation for Amazon S3."
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.aws.s3.S3FileSystemRegistrar
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/hdfs/package-summary.html
+      - transform: In-memory
+        description: "`FileSystem` implementation in memory; useful for testing."
+        implementations:
+          - language: go
+            name: github.com/apache/beam/sdks/go/pkg/beam/io/filesystem/memfs
+            url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/filesystem/memfs
+  - name: Messaging
+    description: These I/O connectors typically involve working with unbounded sources that come from messaging sources.
+    rows:
+      - transform: KinesisIO
+        description: PTransforms for reading from and writing to [Kinesis](https://aws.amazon.com/kinesis/) streams.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.kinesis.KinesisIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/kinesis/KinesisIO.html
+      - transform: AmqpIO
+        description: AMQP 1.0 protocol using the Apache QPid Proton-J library
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.amqp.AmqpIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/amqp/AmqpIO.html
+      - transform: KafkaIO
+        description: Read and Write PTransforms for Cloud Pub/Sub streams. These transforms create and consume unbounded PCollections.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.kafka.KafkaIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/kafka/KafkaIO.html
+          - language: py
+            name: apache_beam.io.external.kafka
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.external.kafka.html
+      - transform: PubSubIO
+        description: Read and Write PTransforms for Google Cloud Pub/Sub streams. These transforms create and consume unbounded PCollections.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.gcp.pubsub.PubsubIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/gcp/pubsub/PubsubIO.html
+          - language: py
+            name: apache_beam.io.gcp.pubsub
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.gcp.pubsub.html
+          - language: py
+            name: apache_beam.io.external.gcp.pubsub
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.external.gcp.pubsub.html
+          - language: go
+            name: github.com/apache/beam/sdks/go/pkg/beam/io/pubsubio
+            url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/pubsubio
+      - transform: JmsIO
+        description: An unbounded source for JMS destinations (queues or topics).
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.jms.JmsIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/jms/JmsIO.html
+      - transform: MqttIO
+        description: An unbounded source for MQTT broker.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.mqtt.MqttIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/mqtt/MqttIO.html
+      - transform: RabbitMqIO
+        description: A IO to publish or consume messages with a RabbitMQ broker.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.rabbitmq.RabbitMqIO
+            url: https://github.com/apache/beam/blob/master/sdks/java/io/rabbitmq/src/main/java/org/apache/beam/sdk/io/rabbitmq/RabbitMqIO.java
+      - transform: SqsIO
+        description: An unbounded source for Amazon Simple Queue Service (SQS).
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.aws.sqs.SqsIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/aws/sqs/SqsIO.html
+          - language: java
+            name: org.apache.beam.sdk.io.aws2.sqs.SqsIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/aws2/sqs/SqsIO.html
+      - transform: SnsIO
+        description: PTransforms for writing to SNS.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.aws.sns.SnsIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/aws/sns/SnsIO.html
+          - language: java
+            name: org.apache.beam.sdk.io.aws2.sns.SnsIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/aws2/sns/SnsIO.html
+  - name: Database
+    description: These I/O connectors are used to connect to database systems.
+    rows:
+      - transform: CassandraIO
+        description: An IO to read from Apache Cassandra.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.cassandra.CassandraIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/cassandra/CassandraIO.html
+      - transform: HadoopFormatIO
+        description: Allows for reading data from any source or writing data to any sink which implements Hadoop InputFormat or OutputFormat.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.hadoop.format.HadoopFormatIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/hadoop/format/HadoopFormatIO.html
+      - transform: HBaseIO
+        description: A bounded source and sink for HBase.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.hbase.HBaseIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/hbase/HBaseIO.html
+      - transform: HCatalogIO
+        description: HCatalog source supports reading of HCatRecord from a HCatalog managed source, for e.g. Hive.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.hcatalog.HCatalogIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/hcatalog/HCatalogIO.html
+      - transform: KuduIO
+        description: A bounded source and sink for (Kudu)[https://kudu.apache.org/].
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.kudu
+            url: https://github.com/apache/beam/blob/master/sdks/java/io/kudu/src/main/java/org/apache/beam/sdk/io/kudu/KuduIO.java
+      - transform: SolrIO
+        description: Transforms for reading and writing data from/to Solr.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.solr.SolrIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/solr/SolrIO.html
+      - transform: ElasticsearchIO
+        description: Transforms for reading and writing data from/to Elasticsearch.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.elasticsearch.ElasticsearchIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/elasticsearch/ElasticsearchIO.html
+      - transform: BigQueryIO
+        description: Read from and write to Google Cloud BigQuery.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.gcp.bigquery.BigQueryIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/gcp/bigquery/BigQueryIO.html
+          - language: py
+            name: apache_beam.io.gcp.bigquery
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.gcp.bigquery.html
+          - language: go
+            name: github.com/apache/beam/sdks/go/pkg/beam/io/bigqueryio
+            url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/bigqueryio
+      - transform: BigTableIO
+        description: Read from and write to [Google Cloud Bigtable](https://cloud.google.com/bigtable/).
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.gcp.bigtable.BigtableIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/gcp/bigtable/BigtableIO.html
+          - language: py
+            name: apache_beam.io.gcp.bigtableio module
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.gcp.bigtableio.html
+      - transform: DatastoreIO
+        description: Read from and write to Google Cloud Datastore.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.gcp.datastore.DatastoreIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/gcp/datastore/DatastoreIO.html
+          - language: py
+            name: apache_beam.io.gcp.datastore.v1new.datastoreio
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.gcp.datastore.v1new.datastoreio.html
+      - transform: SpannerIO
+        description: Experimental Transforms for reading from and writing to Google Cloud Spanner.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.gcp.spanner.SpannerIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/gcp/spanner/SpannerIO.html
+      - transform: JdbcIO
+        description: IO to read and write data on JDBC.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.jdbc.JdbcIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/jdbc/JdbcIO.html
+      - transform: MongoDbIO
+        description: IO to read and write data on MongoDB.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.mongodb.MongoDbIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/mongodb/MongoDbIO.html
+          - language: py
+            name: apache_beam.io.mongodbio
+            url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.mongodbio.html
+      - transform: MongoDbGridFSIO
+        description: IO to read and write data on MongoDB GridFS.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.mongodb.MongoDbGridFSIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/mongodb/MongoDbGridFSIO.html
+      - transform: RedisIO
+        description: An IO to manipulate Redis key/value database.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.redis.RedisIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/redis/RedisIO.html
+      - transform: DynamoDBIO
+        description:
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.aws.dynamodb.DynamoDBIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/aws/dynamodb/DynamoDBIO.html
+          - language: java
+            name: org.apache.beam.sdk.io.aws2.dynamodb.DynamoDBIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/aws2/dynamodb/DynamoDBIO.html
+      - transform: ClickHouseIO
+        description: Transform for writing to [ClickHouse](https://clickhouse.tech/).
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.clickhouse.ClickHouseIO
+            url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/clickhouse/ClickHouseIO.html
+      - transform: DatabaseIO
+        description: Package databaseio provides transformations and utilities to interact with a generic database / SQL API.
+        implementations:
+          - language: go
+            name: github.com/apache/beam/sdks/go/pkg/beam/io/databaseio
+            url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/databaseio
+  - name: Miscellaneous
+    description: Miscellaneous I/O sources.
+    rows:
+      - transform: FlinkStreamingImpulseSource
+        description: A PTransform that provides an unbounded, streaming source of empty byte arrays. This can only be used with the Flink runner.
+        implementations:
+          - language: py
+            name: apache_beam.io.flink.flink_streaming_impulse_source
+            url: https://beam.apache.org/releases/pydoc/2.20.0/apache_beam.io.flink.flink_streaming_impulse_source.html
+      - transform: GenerateSequence
+        description: Generates a bounded or unbounded stream of integers.
+        implementations:
+          - language: java
+            name: org.apache.beam.sdk.io.GenerateSequence
+            url: https://beam.apache.org/releases/javadoc/2.20.0/org/apache/beam/sdk/io/GenerateSequence.html
+          - language: py
+            name: apache_beam.io.external.generate_sequence.GenerateSequence
+            url: https://beam.apache.org/releases/pydoc/2.20.0/apache_beam.io.external.generate_sequence.html
\ No newline at end of file
diff --git a/website/www/site/layouts/shortcodes/io-matrix.html b/website/www/site/layouts/shortcodes/io-matrix.html
new file mode 100644
index 000000000000..3717361c913b
--- /dev/null
+++ b/website/www/site/layouts/shortcodes/io-matrix.html
@@ -0,0 +1,48 @@
+{{/*
+  Licensed under the Apache License, Version 2.0 (the "License");
+  you may not use this file except in compliance with the License.
+  You may obtain a copy of the License at
+    http://www.apache.org/licenses/LICENSE-2.0
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License. See accompanying LICENSE file.
+ */}}
+ 
+{{ $data := index $.Site.Data.io_matrix }}
+
+{{ define "language-row" }}
+  {{ if len (where .row.implementations "language" .language) }}
+  
+    {{ .row.transform | markdownify }}
+    {{ .row.description | markdownify }}
+    
+      {{ range where .row.implementations "language" .language }}
+        
    
+      {{ else }}
+        N/A
+      {{ end }}
+    
+  
+  {{ else }}
+  {{ end }}
+{{ end }}
+
+
+{{ range $data.categories }}
+
    {{ .name }}
    
+
    {{ .description }}
    
+
+  
+    
+    
+    
+  
+  {{ range .rows }}
+    {{ block "language-row" (dict "row" . "language" "java") }}{{ end }}
+    {{ block "language-row" (dict "row" . "language" "py") }}{{ end }}
+    {{ block "language-row" (dict "row" . "language" "go") }}{{ end }}
+  {{ end }}
+
    NameDescriptionImplementation(s)
    
+{{ end }}
\ No newline at end of file

From 8fe35ade6cb48be0724ad5f055b4101a25e12f6b Mon Sep 17 00:00:00 2001
From: Ashwin Ramaswami 
Date: Fri, 22 May 2020 22:38:14 -0400
Subject: [PATCH 062/151] add descriptions, links to guides

---
 website/www/site/data/io_matrix.yaml          | 64 ++++++++++---------
 .../section-menu/en/documentation.html        | 12 ++++
 .../site/layouts/shortcodes/io-matrix.html    | 13 +++-
 3 files changed, 56 insertions(+), 33 deletions(-)

diff --git a/website/www/site/data/io_matrix.yaml b/website/www/site/data/io_matrix.yaml
index 4b64189ab730..804d93f45a7a 100644
--- a/website/www/site/data/io_matrix.yaml
+++ b/website/www/site/data/io_matrix.yaml
@@ -24,7 +24,7 @@ categories:
             name: apache_beam.io.FileIO
             url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.fileio.html
       - transform: AvroIO
-        description: PTransforms for reading from and writing to Avro files.
+        description: PTransforms for reading from and writing to [Avro](https://avro.apache.org/) files.
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.AvroIO
@@ -48,7 +48,7 @@ categories:
             name: github.com/apache/beam/sdks/go/pkg/beam/io/textio
             url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/textio
       - transform: TFRecordIO
-        description: PTransforms for reading and writing TensorFlow TFRecord files.
+        description: PTransforms for reading and writing [TensorFlow TFRecord](https://www.tensorflow.org/tutorials/load_data/tfrecord) files.
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.TFRecordIO
@@ -57,7 +57,7 @@ categories:
             name: apache_beam.io.tfrecordio
             url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.tfrecordio.html
       - transform: XmlIO
-        description: Transforms for reading and writing XML files using JAXB mappers.
+        description: Transforms for reading and writing XML files using [JAXB](https://www.oracle.com/technical-resources/articles/javase/jaxb.html) mappers.
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.xml.XmlIO
@@ -69,7 +69,8 @@ categories:
             name: org.apache.beam.sdk.io.tika.TikaIO
             url: https://beam.apache.org/releases/javadoc/2.3.0/org/apache/beam/sdk/io/tika/TikaIO.html
       - transform: ParquetIO
-        description: IO for reading from and writing to Parquet files.
+        description: IO for reading from and writing to [Parquet](https://parquet.apache.org/) files.
+        docs: /documentation/io/built-in/parquet/
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.parquet.ParquetIO
@@ -78,7 +79,7 @@ categories:
             name: apache_beam.io.parquetio
             url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.parquetio.html
       - transform: ThriftIO
-        description: PTransforms for reading and writing files containing Thrift encoded data.
+        description: PTransforms for reading and writing files containing [Thrift](https://thrift.apache.org/)-encoded data.
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.thrift.ThriftIO
@@ -90,13 +91,13 @@ categories:
             name: apache_beam.io.vcfio
             url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.vcfio.html
       - transform: S3IO
-        description: A source for reading from and writing to Amazon S3.
+        description: A source for reading from and writing to [Amazon S3](https://aws.amazon.com/s3/).
         implementations:
           - language: py
             name: apache_beam.io.aws.s3io
             url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.aws.s3io.html
       - transform: GcsIO
-        description: A source for reading from and writing to Google Cloud Storage.
+        description: A source for reading from and writing to [Google Cloud Storage](https://cloud.google.com/storage).
         implementations:
           - language: py
             name: apache_beam.io.gcp.gcsio
@@ -105,7 +106,7 @@ categories:
     description: Beam provides a File system interface that defines APIs for writing file systems agnostic code. Several I/O connectors are implemented as a FileSystem implementation.
     rows:
       - transform: HadoopFileSystem
-        description: "`FileSystem` implementation for accessing Hadoop Distributed File System files."
+        description: "`FileSystem` implementation for accessing [Hadoop](https://hadoop.apache.org/) Distributed File System files."
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.hdfs.HadoopFileSystemRegistrar
@@ -114,7 +115,7 @@ categories:
             name: apache_beam.io.hadoopfilesystem
             url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.hadoopfilesystem.html
       - transform: GcsFileSystem
-        description: "`FileSystem` implementation for Google Cloud Storage."
+        description: "`FileSystem` implementation for [Google Cloud Storage](https://cloud.google.com/storage)."
         implementations:
           - language: java
             name: org.apache.beam.sdk.extensions.gcp.storage.GcsFileSystemRegistrar
@@ -138,7 +139,7 @@ categories:
             name: github.com/apache/beam/sdks/go/pkg/beam/io/filesystem/local
             url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/filesystem/local
       - transform: S3FileSystem
-        description: "`FileSystem` implementation for Amazon S3."
+        description: "`FileSystem` implementation for [Amazon S3](https://aws.amazon.com/s3/)."
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.aws.s3.S3FileSystemRegistrar
@@ -165,7 +166,7 @@ categories:
             name: org.apache.beam.sdk.io.amqp.AmqpIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/amqp/AmqpIO.html
       - transform: KafkaIO
-        description: Read and Write PTransforms for Cloud Pub/Sub streams. These transforms create and consume unbounded PCollections.
+        description: Read and Write PTransforms for [Apache Kafka](https://kafka.apache.org/).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.kafka.KafkaIO
@@ -174,7 +175,7 @@ categories:
             name: apache_beam.io.external.kafka
             url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.external.kafka.html
       - transform: PubSubIO
-        description: Read and Write PTransforms for Google Cloud Pub/Sub streams. These transforms create and consume unbounded PCollections.
+        description: Read and Write PTransforms for [Google Cloud Pub/Sub](https://cloud.google.com/pubsub) streams.
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.gcp.pubsub.PubsubIO
@@ -189,13 +190,13 @@ categories:
             name: github.com/apache/beam/sdks/go/pkg/beam/io/pubsubio
             url: https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam/io/pubsubio
       - transform: JmsIO
-        description: An unbounded source for JMS destinations (queues or topics).
+        description: An unbounded source for [JMS](https://www.oracle.com/java/technologies/java-message-service.html) destinations (queues or topics).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.jms.JmsIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/jms/JmsIO.html
       - transform: MqttIO
-        description: An unbounded source for MQTT broker.
+        description: An unbounded source for [MQTT](https://mqtt.org/) broker.
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.mqtt.MqttIO
@@ -207,7 +208,7 @@ categories:
             name: org.apache.beam.sdk.io.rabbitmq.RabbitMqIO
             url: https://github.com/apache/beam/blob/master/sdks/java/io/rabbitmq/src/main/java/org/apache/beam/sdk/io/rabbitmq/RabbitMqIO.java
       - transform: SqsIO
-        description: An unbounded source for Amazon Simple Queue Service (SQS).
+        description: An unbounded source for [Amazon Simple Queue Service (SQS)](https://aws.amazon.com/sqs/).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.aws.sqs.SqsIO
@@ -216,7 +217,7 @@ categories:
             name: org.apache.beam.sdk.io.aws2.sqs.SqsIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/aws2/sqs/SqsIO.html
       - transform: SnsIO
-        description: PTransforms for writing to SNS.
+        description: PTransforms for writing to [Amazon Simple Notification Service (SNS)](https://aws.amazon.com/sns/).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.aws.sns.SnsIO
@@ -228,25 +229,27 @@ categories:
     description: These I/O connectors are used to connect to database systems.
     rows:
       - transform: CassandraIO
-        description: An IO to read from Apache Cassandra.
+        description: An IO to read from [Apache Cassandra](https://cassandra.apache.org/).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.cassandra.CassandraIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/cassandra/CassandraIO.html
       - transform: HadoopFormatIO
-        description: Allows for reading data from any source or writing data to any sink which implements Hadoop InputFormat or OutputFormat.
+        description: Allows for reading data from any source or writing data to any sink which implements [Hadoop](https://hadoop.apache.org/) InputFormat or OutputFormat.
+        docs: /documentation/io/built-in/hadoop/
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.hadoop.format.HadoopFormatIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/hadoop/format/HadoopFormatIO.html
       - transform: HBaseIO
-        description: A bounded source and sink for HBase.
+        description: A bounded source and sink for [HBase])https://hbase.apache.org/.
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.hbase.HBaseIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/hbase/HBaseIO.html
       - transform: HCatalogIO
-        description: HCatalog source supports reading of HCatRecord from a HCatalog managed source, for e.g. Hive.
+        description: HCatalog source supports reading of HCatRecord from a [HCatalog](https://cwiki.apache.org/confluence/display/Hive/HCatalog)-managed source, for example [Hive](https://hive.apache.org/).
+        docs: /documentation/io/built-in/hcatalog/
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.hcatalog.HCatalogIO
@@ -258,19 +261,20 @@ categories:
             name: org.apache.beam.sdk.io.kudu
             url: https://github.com/apache/beam/blob/master/sdks/java/io/kudu/src/main/java/org/apache/beam/sdk/io/kudu/KuduIO.java
       - transform: SolrIO
-        description: Transforms for reading and writing data from/to Solr.
+        description: Transforms for reading and writing data from/to [Solr](https://lucene.apache.org/solr/).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.solr.SolrIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/solr/SolrIO.html
       - transform: ElasticsearchIO
-        description: Transforms for reading and writing data from/to Elasticsearch.
+        description: Transforms for reading and writing data from/to [Elasticsearch](https://www.elastic.co/elasticsearch/).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.elasticsearch.ElasticsearchIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/elasticsearch/ElasticsearchIO.html
       - transform: BigQueryIO
-        description: Read from and write to Google Cloud BigQuery.
+        description: Read from and write to [Google Cloud BigQuery](https://cloud.google.com/bigquery).
+        docs: /documentation/io/built-in/google-bigquery/
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.gcp.bigquery.BigQueryIO
@@ -291,7 +295,7 @@ categories:
             name: apache_beam.io.gcp.bigtableio module
             url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.gcp.bigtableio.html
       - transform: DatastoreIO
-        description: Read from and write to Google Cloud Datastore.
+        description: Read from and write to [Google Cloud Datastore](https://cloud.google.com/datastore).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.gcp.datastore.DatastoreIO
@@ -300,19 +304,19 @@ categories:
             name: apache_beam.io.gcp.datastore.v1new.datastoreio
             url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.gcp.datastore.v1new.datastoreio.html
       - transform: SpannerIO
-        description: Experimental Transforms for reading from and writing to Google Cloud Spanner.
+        description: Experimental Transforms for reading from and writing to [Google Cloud Spanner](https://cloud.google.com/spanner).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.gcp.spanner.SpannerIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/gcp/spanner/SpannerIO.html
       - transform: JdbcIO
-        description: IO to read and write data on JDBC.
+        description: IO to read and write data on [JDBC](https://docs.oracle.com/javase/tutorial/jdbc/basics/index.html).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.jdbc.JdbcIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/jdbc/JdbcIO.html
       - transform: MongoDbIO
-        description: IO to read and write data on MongoDB.
+        description: IO to read and write data on [MongoDB](https://www.mongodb.com/).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.mongodb.MongoDbIO
@@ -321,19 +325,19 @@ categories:
             name: apache_beam.io.mongodbio
             url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.mongodbio.html
       - transform: MongoDbGridFSIO
-        description: IO to read and write data on MongoDB GridFS.
+        description: IO to read and write data on [MongoDB GridFS](https://docs.mongodb.com/manual/core/gridfs/).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.mongodb.MongoDbGridFSIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/mongodb/MongoDbGridFSIO.html
       - transform: RedisIO
-        description: An IO to manipulate Redis key/value database.
+        description: An IO to manipulate a [Redis](https://redis.io/) key/value database.
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.redis.RedisIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/redis/RedisIO.html
       - transform: DynamoDBIO
-        description:
+        description: Read from and write to [Amazon DynamoDB](https://aws.amazon.com/dynamodb/).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.aws.dynamodb.DynamoDBIO
diff --git a/website/www/site/layouts/partials/section-menu/en/documentation.html b/website/www/site/layouts/partials/section-menu/en/documentation.html
index a44e0455a7d1..93c16ce25b48 100644
--- a/website/www/site/layouts/partials/section-menu/en/documentation.html
+++ b/website/www/site/layouts/partials/section-menu/en/documentation.html
@@ -66,6 +66,18 @@
         
  • Using I/O transforms
    • 
         
  • Built-in I/O connectors
    • 
 
+        
  • 
+          Built-in I/O connector guides
+          
+       
    • 
+
+
         
  • 
            Developing new I/O connectors
 
diff --git a/website/www/site/layouts/shortcodes/io-matrix.html b/website/www/site/layouts/shortcodes/io-matrix.html
index 3717361c913b..3fd1eef025ac 100644
--- a/website/www/site/layouts/shortcodes/io-matrix.html
+++ b/website/www/site/layouts/shortcodes/io-matrix.html
@@ -15,9 +15,12 @@
 {{ define "language-row" }}
   {{ if len (where .row.implementations "language" .language) }}
   
-    {{ .row.transform | markdownify }}
-    {{ .row.description | markdownify }}
     
+      {{ .row.transform | markdownify }}
+      {{ if .row.docs }} (guide){{ else }}{{ end }}
+    
+    {{ .row.description | markdownify }}
+    
       {{ range where .row.implementations "language" .language }}
         
       {{ else }}
@@ -37,7 +40,11 @@ 
    {{ .name }}
    
   
     Name
     Description
-    Implementation(s)
+    
+      Javadoc
+      pydoc
+      Godoc
+    
   
   {{ range .rows }}
     {{ block "language-row" (dict "row" . "language" "java") }}{{ end }}

From ff1f9f1e482cc5a8335a069610fc5a322263abfd Mon Sep 17 00:00:00 2001
From: Ashwin Ramaswami 
Date: Fri, 22 May 2020 22:41:49 -0400
Subject: [PATCH 063/151] fix typo

---
 website/www/site/data/io_matrix.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/website/www/site/data/io_matrix.yaml b/website/www/site/data/io_matrix.yaml
index 804d93f45a7a..4368386ef59c 100644
--- a/website/www/site/data/io_matrix.yaml
+++ b/website/www/site/data/io_matrix.yaml
@@ -242,7 +242,7 @@ categories:
             name: org.apache.beam.sdk.io.hadoop.format.HadoopFormatIO
             url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/hadoop/format/HadoopFormatIO.html
       - transform: HBaseIO
-        description: A bounded source and sink for [HBase])https://hbase.apache.org/.
+        description: A bounded source and sink for [HBase](https://hbase.apache.org/).
         implementations:
           - language: java
             name: org.apache.beam.sdk.io.hbase.HBaseIO

From fa805b693464df0cf1e04ec3d7723bf677a40971 Mon Sep 17 00:00:00 2001
From: Ashwin Ramaswami 
Date: Fri, 22 May 2020 22:42:01 -0400
Subject: [PATCH 064/151] format

---
 website/www/site/data/io_matrix.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/website/www/site/data/io_matrix.yaml b/website/www/site/data/io_matrix.yaml
index 4368386ef59c..f1e4c962f0e0 100644
--- a/website/www/site/data/io_matrix.yaml
+++ b/website/www/site/data/io_matrix.yaml
@@ -374,4 +374,4 @@ categories:
             url: https://beam.apache.org/releases/javadoc/2.20.0/org/apache/beam/sdk/io/GenerateSequence.html
           - language: py
             name: apache_beam.io.external.generate_sequence.GenerateSequence
-            url: https://beam.apache.org/releases/pydoc/2.20.0/apache_beam.io.external.generate_sequence.html
\ No newline at end of file
+            url: https://beam.apache.org/releases/pydoc/2.20.0/apache_beam.io.external.generate_sequence.html

From 37ac9ee8bbd4a9a90bf149a2d599ed735909e1a8 Mon Sep 17 00:00:00 2001
From: Ashwin Ramaswami 
Date: Fri, 22 May 2020 22:43:31 -0400
Subject: [PATCH 065/151] update CHANGES.md

---
 CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGES.md b/CHANGES.md
index 59082149617a..6445baba5df5 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -65,6 +65,7 @@
 * `--direct_num_workers=0` is supported for FnApi runner. It will set the number of threads/subprocesses to number of cores of the machine executing the pipeline ([BEAM-9443](https://issues.apache.org/jira/browse/BEAM-9443)).
 * Python SDK now has experimental support for SqlTransform ([BEAM-8603](https://issues.apache.org/jira/browse/BEAM-8603)).
 * Add OnWindowExpiration method to Stateful DoFn ([BEAM-1589](https://issues.apache.org/jira/browse/BEAM-1589)).
+* Add a more complete I/O support matrix in the documentation site ([BEAM-9916](https://issues.apache.org/jira/browse/BEAM-9916)).
 
 ## Breaking Changes
 

From e3b6a43de2251c55ec142cbe8070eacb72d7effc Mon Sep 17 00:00:00 2001
From: Michal Walenia <32354134+mwalenia@users.noreply.github.com>
Date: Mon, 25 May 2020 10:27:50 +0200
Subject: [PATCH 066/151] [BEAM-10050] Change labels checked in
 VideoIntelligenceIT (#11775)

[BEAM-10050] Change labels checked in VideoIntelligenceIT to make the test more resistant to future ML model changes.
---
 .../apache/beam/sdk/extensions/ml/VideoIntelligenceIT.java  | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/VideoIntelligenceIT.java b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/VideoIntelligenceIT.java
index 642722562384..20e9145d5e78 100644
--- a/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/VideoIntelligenceIT.java
+++ b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/VideoIntelligenceIT.java
@@ -58,7 +58,7 @@ private static class VerifyVideoAnnotationResult
     @Override
     public Void apply(Iterable> input) {
       List labelEvaluations = new ArrayList<>();
-      input.forEach(findStringMatchesInVideoAnnotationResultList(labelEvaluations, "dinosaur"));
+      input.forEach(findStringMatchesInVideoAnnotationResultList(labelEvaluations, "bicycle"));
       assertEquals(Boolean.TRUE, labelEvaluations.contains(Boolean.TRUE));
       return null;
     }
@@ -73,9 +73,9 @@ private Consumer> findStringMatchesInVideoAnnotatio
 
     private boolean entityWithDescriptionFoundInSegmentLabels(
         String toMatch, VideoAnnotationResults result) {
-      return result.getSegmentLabelAnnotationsList().stream()
+      return result.getSegmentPresenceLabelAnnotationsList().stream()
           .anyMatch(
-              labelAnnotation -> labelAnnotation.getEntity().getDescription().equals(toMatch));
+              labelAnnotation -> labelAnnotation.getEntity().getDescription().contains(toMatch));
     }
   }
 }

From 0f97499b4473e21742a2aa2875b512964fbad43c Mon Sep 17 00:00:00 2001
From: Maximilian Michels 
Date: Mon, 25 May 2020 03:48:05 -0700
Subject: [PATCH 067/151] [BEAM-9930] Update blog post for new Beam Summit
 Digital dates (#11772)

---
 .../content/en/blog/beam-summit-digital-2020.md |  10 +++++-----
 .../blog/beamsummit/beamsummit-digital-2020.png | Bin 0 -> 72388 bytes
 .../blog/beamsummit/beamsummit-digital.png      | Bin 63238 -> 0 bytes
 3 files changed, 5 insertions(+), 5 deletions(-)
 create mode 100644 website/www/site/static/images/blog/beamsummit/beamsummit-digital-2020.png
 delete mode 100644 website/www/site/static/images/blog/beamsummit/beamsummit-digital.png

diff --git a/website/www/site/content/en/blog/beam-summit-digital-2020.md b/website/www/site/content/en/blog/beam-summit-digital-2020.md
index ed0853c58d58..dfbe9fdd7c1c 100644
--- a/website/www/site/content/en/blog/beam-summit-digital-2020.md
+++ b/website/www/site/content/en/blog/beam-summit-digital-2020.md
@@ -1,6 +1,6 @@
 ---
 layout: post
-title:  "Beam Digital Summit is Coming, and it's Coming Fast!"
+title:  "Beam Summit Digital Is Coming - Register Now!"
 date:   2020-05-08 00:00:01 -0800
 aliases:
   - /blog/2020/05/08/beam-summit-digital-2020.html
@@ -23,13 +23,13 @@ See the License for the specific language governing permissions and
 limitations under the License.
 -->
 
-As some of you are already aware, the 2020 edition of the Beam Summit will be completely **digital and free**. And as you would expect from the Apache Beam community, it is coming in fast; the Beam Digital Summit will be from **June 15th to 19th**, one moth away! The conference will be spread across the course of one week with a couple of hours of program each day.
+As some of you are already aware, the 2020 edition of the Beam Summit will be completely **digital and free**. Beam Summit Digital will take place from **August 24th to 28th**. The conference will be spread across the course of one week with a couple of hours of program each day.
 
 
 
 Beam Summit Digital 2020
+    src="/images/blog/beamsummit/beamsummit-digital-2020.png"
+    alt="Beam Summit Digital 2020, August 24-28">
 
 While we would have loved to see all of you in person, we have to accept that 2020 will not be the year for that. So, we are looking at this as an opportunity to have a bigger and more inclusive event, where people who would normally not be able to travel to the summit will now be able to join, learn and share with the rest of the community.
 
@@ -43,7 +43,7 @@ So, what we want to say with this is: We will have a great event! And if you hav
 
 As all things Beam, this is a community effort. The door is open for participation:
 
-1. Submit a proposal to talk. Please check out the **[Call for Papers](https://sessionize.com/beam-digital-summit-2020/)** and submit a talk. The deadline for submissions is _May 20th_!
+1. Submit a proposal to talk. Please check out the **[Call for Papers](https://sessionize.com/beam-digital-summit-2020/)** and submit a talk. The deadline for submissions is _June 15th_!
 2. Register to join as an attendee. Registration is now open at the **[registration page](https://crowdcast.io/e/beamsummit)**. Registration is free!
 3. Consider sponsoring the event. If your company is interested in engaging with members of the community please check out our [sponsoring prospectus](https://drive.google.com/open?id=1EbijvZKpkWwWyMryLY9sJfyZzZk1k44v).
 4. Help us get the word out. Please make sure to let your colleagues and friends in the data engineering field (and beyond!) know about the Beam Summit.
diff --git a/website/www/site/static/images/blog/beamsummit/beamsummit-digital-2020.png b/website/www/site/static/images/blog/beamsummit/beamsummit-digital-2020.png
new file mode 100644
index 0000000000000000000000000000000000000000..36025d3e44f2a8fa596f9ffa904043b01ffa40e1
GIT binary patch
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e`~S2TaSBu=xzjKRAuj>`qo$($tm>&%#Qy+k``Qrz


From 1d84d00bcf20c8f7cbf43c33a8ce293f8167a9be Mon Sep 17 00:00:00 2001
From: Heejong Lee 
Date: Mon, 25 May 2020 17:17:02 -0700
Subject: [PATCH 068/151] [BEAM-10077] using filename + hash instead of UUID
 for staging name

---
 .../core/construction/Environments.java       | 23 ++++++++++-------
 .../beam/runners/dataflow/DataflowRunner.java | 12 +++------
 .../runners/dataflow/util/PackageUtil.java    | 25 ++++++-------------
 .../runners/dataflow/util/GCSUploadMain.java  |  7 +++++-
 .../dataflow/util/PackageUtilTest.java        | 24 ++++++++++--------
 5 files changed, 46 insertions(+), 45 deletions(-)

diff --git a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/Environments.java b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/Environments.java
index c324b92e7f33..72ebd13b681c 100644
--- a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/Environments.java
+++ b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/Environments.java
@@ -17,6 +17,7 @@
  */
 package org.apache.beam.runners.core.construction;
 
+import com.fasterxml.jackson.core.Base64Variants;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -215,25 +216,19 @@ public static List getArtifacts(List stagingFiles)
     Set deduplicatedStagingFiles = new LinkedHashSet<>(stagingFiles);
     for (String path : deduplicatedStagingFiles) {
       File file;
-      String stagedName;
+      String stagedName = null;
       if (path.contains("=")) {
         String[] components = path.split("=", 2);
         file = new File(components[1]);
         stagedName = components[0];
       } else {
         file = new File(path);
-        stagedName = createStagingFileName(file);
       }
       // Spurious items get added to the classpath. Filter by just those that exist.
       if (file.exists()) {
         ArtifactInformation.Builder artifactBuilder = ArtifactInformation.newBuilder();
         artifactBuilder.setTypeUrn(BeamUrns.getUrn(StandardArtifacts.Types.FILE));
         artifactBuilder.setRoleUrn(BeamUrns.getUrn(StandardArtifacts.Roles.STAGING_TO));
-        artifactBuilder.setRolePayload(
-            RunnerApi.ArtifactStagingToRolePayload.newBuilder()
-                .setStagedName(stagedName)
-                .build()
-                .toByteString());
         HashCode hashCode;
         if (file.isDirectory()) {
           File zippedFile;
@@ -264,6 +259,14 @@ public static List getArtifacts(List stagingFiles)
                   .build()
                   .toByteString());
         }
+        if (stagedName == null) {
+          stagedName = createStagingFileName(file, hashCode);
+        }
+        artifactBuilder.setRolePayload(
+            RunnerApi.ArtifactStagingToRolePayload.newBuilder()
+                .setStagedName(stagedName)
+                .build()
+                .toByteString());
         artifactsBuilder.add(artifactBuilder.build());
       }
     }
@@ -314,10 +317,12 @@ public static Set getJavaCapabilities() {
     return capabilities.build();
   }
 
-  public static String createStagingFileName(File path) {
+  public static String createStagingFileName(File path, HashCode hash) {
+    String encodedHash = Base64Variants.MODIFIED_FOR_URL.encode(hash.asBytes());
+    String fileName = Files.getNameWithoutExtension(path.getAbsolutePath());
     String ext = path.isDirectory() ? "jar" : Files.getFileExtension(path.getAbsolutePath());
     String suffix = Strings.isNullOrEmpty(ext) ? "" : "." + ext;
-    return UUID.randomUUID().toString() + suffix;
+    return String.format("%s-%s%s", fileName, encodedHash, suffix);
   }
 
   private static File zipDirectory(File directory) throws IOException {
diff --git a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/DataflowRunner.java b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/DataflowRunner.java
index 457634fe6d23..a6358c120435 100644
--- a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/DataflowRunner.java
+++ b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/DataflowRunner.java
@@ -55,7 +55,6 @@
 import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
-import java.util.UUID;
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
@@ -211,8 +210,8 @@ public class DataflowRunner extends PipelineRunner {
 
   @VisibleForTesting static final int GCS_UPLOAD_BUFFER_SIZE_BYTES_DEFAULT = 1024 * 1024;
 
-  @VisibleForTesting static final String PIPELINE_FILE_FORMAT = "pipeline-%s.pb";
-  @VisibleForTesting static final String DATAFLOW_GRAPH_FILE_FORMAT = "dataflow_graph-%s.json";
+  @VisibleForTesting static final String PIPELINE_FILE_NAME = "pipeline.pb";
+  @VisibleForTesting static final String DATAFLOW_GRAPH_FILE_NAME = "dataflow_graph.json";
 
   private static final ObjectMapper MAPPER = new ObjectMapper();
 
@@ -893,10 +892,7 @@ public DataflowPipelineJob run(Pipeline pipeline) {
     LOG.info("Staging pipeline description to {}", options.getStagingLocation());
     byte[] serializedProtoPipeline = jobSpecification.getPipelineProto().toByteArray();
     DataflowPackage stagedPipeline =
-        options
-            .getStager()
-            .stageToFile(
-                serializedProtoPipeline, String.format(PIPELINE_FILE_FORMAT, UUID.randomUUID()));
+        options.getStager().stageToFile(serializedProtoPipeline, PIPELINE_FILE_NAME);
     dataflowOptions.setPipelineUrl(stagedPipeline.getLocation());
 
     if (!isNullOrEmpty(dataflowOptions.getDataflowWorkerJar())) {
@@ -996,7 +992,7 @@ public DataflowPipelineJob run(Pipeline pipeline) {
               .getStager()
               .stageToFile(
                   DataflowPipelineTranslator.jobToString(newJob).getBytes(UTF_8),
-                  String.format(DATAFLOW_GRAPH_FILE_FORMAT, UUID.randomUUID()));
+                  DATAFLOW_GRAPH_FILE_NAME);
       newJob.getSteps().clear();
       newJob.setStepsLocation(stagedGraph.getLocation());
     }
diff --git a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/util/PackageUtil.java b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/util/PackageUtil.java
index 0b5e47828dc7..72139931edfd 100644
--- a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/util/PackageUtil.java
+++ b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/util/PackageUtil.java
@@ -34,7 +34,6 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
-import java.util.UUID;
 import java.util.concurrent.CompletionStage;
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
@@ -52,7 +51,7 @@
 import org.apache.beam.sdk.util.FluentBackoff;
 import org.apache.beam.sdk.util.MimeTypes;
 import org.apache.beam.sdk.util.MoreFutures;
-import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.hash.Hasher;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.hash.HashCode;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.hash.Hashing;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.io.ByteSource;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.io.Files;
@@ -360,21 +359,15 @@ List stageClasspathElements(
 
   @AutoValue
   public abstract static class StagedFile {
-    public static PackageUtil.StagedFile of(
-        String source, String sha256, @Nullable String destination) {
+    public static PackageUtil.StagedFile of(String source, String sha256, String destination) {
       return new AutoValue_PackageUtil_StagedFile(source, sha256, destination);
     }
 
-    public static PackageUtil.StagedFile of(String source, String sha256) {
-      return new AutoValue_PackageUtil_StagedFile(source, sha256, null);
-    }
-
     /** The file to stage. */
     public abstract String getSource();
     /** The SHA-256 hash of the source file. */
     public abstract String getSha256();
     /** Staged target for this file. */
-    @Nullable
     public abstract String getDestination();
   }
 
@@ -405,25 +398,22 @@ public static PackageAttributes forFileToStage(
       }
       checkState(!file.isDirectory(), "Source file must not be a directory.");
       DataflowPackage destination = new DataflowPackage();
-      String target = dest == null ? Environments.createStagingFileName(file) : dest;
       String resourcePath =
           FileSystems.matchNewResource(stagingPath, true)
-              .resolve(target, StandardResolveOptions.RESOLVE_FILE)
+              .resolve(dest, StandardResolveOptions.RESOLVE_FILE)
               .toString();
       destination.setLocation(resourcePath);
-      destination.setName(target);
+      destination.setName(dest);
       return new AutoValue_PackageUtil_PackageAttributes(
           file, null, destination, file.length(), hash);
     }
 
     public static PackageAttributes forBytesToStage(
         byte[] bytes, String targetName, String stagingPath) {
-
-      Hasher hasher = Hashing.sha256().newHasher();
-      String hash = hasher.putBytes(bytes).hash().toString();
+      HashCode hashCode = Hashing.sha256().newHasher().putBytes(bytes).hash();
       long size = bytes.length;
 
-      String target = targetName == null ? UUID.randomUUID().toString() : targetName;
+      String target = Environments.createStagingFileName(new File(targetName), hashCode);
 
       String resourcePath =
           FileSystems.matchNewResource(stagingPath, true)
@@ -433,7 +423,8 @@ public static PackageAttributes forBytesToStage(
       targetPackage.setName(target);
       targetPackage.setLocation(resourcePath);
 
-      return new AutoValue_PackageUtil_PackageAttributes(null, bytes, targetPackage, size, hash);
+      return new AutoValue_PackageUtil_PackageAttributes(
+          null, bytes, targetPackage, size, hashCode.toString());
     }
 
     public PackageAttributes withPackageName(String overridePackageName) {
diff --git a/runners/google-cloud-dataflow-java/src/test/java/org/apache/beam/runners/dataflow/util/GCSUploadMain.java b/runners/google-cloud-dataflow-java/src/test/java/org/apache/beam/runners/dataflow/util/GCSUploadMain.java
index fb07652f38a1..468ec958334e 100644
--- a/runners/google-cloud-dataflow-java/src/test/java/org/apache/beam/runners/dataflow/util/GCSUploadMain.java
+++ b/runners/google-cloud-dataflow-java/src/test/java/org/apache/beam/runners/dataflow/util/GCSUploadMain.java
@@ -21,9 +21,11 @@
 import java.io.IOException;
 import java.io.UncheckedIOException;
 import java.util.stream.Collectors;
+import org.apache.beam.runners.core.construction.Environments;
 import org.apache.beam.runners.dataflow.options.DataflowPipelineOptions;
 import org.apache.beam.sdk.io.FileSystems;
 import org.apache.beam.sdk.options.PipelineOptionsFactory;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.hash.HashCode;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.hash.Hashing;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.io.Files;
 
@@ -39,9 +41,12 @@ public static void main(String[] args) {
             .map(
                 (String source) -> {
                   try {
+                    File file = new File(source);
+                    HashCode hashCode = Files.asByteSource(file).hash(Hashing.sha256());
                     return PackageUtil.StagedFile.of(
                         source,
-                        Files.asByteSource(new File(source)).hash(Hashing.sha256()).toString());
+                        hashCode.toString(),
+                        Environments.createStagingFileName(file, hashCode));
                   } catch (IOException e) {
                     throw new UncheckedIOException(e);
                   }
diff --git a/runners/google-cloud-dataflow-java/src/test/java/org/apache/beam/runners/dataflow/util/PackageUtilTest.java b/runners/google-cloud-dataflow-java/src/test/java/org/apache/beam/runners/dataflow/util/PackageUtilTest.java
index 2847279babff..535fbce76355 100644
--- a/runners/google-cloud-dataflow-java/src/test/java/org/apache/beam/runners/dataflow/util/PackageUtilTest.java
+++ b/runners/google-cloud-dataflow-java/src/test/java/org/apache/beam/runners/dataflow/util/PackageUtilTest.java
@@ -66,6 +66,7 @@
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 import javax.annotation.Nullable;
+import org.apache.beam.runners.core.construction.Environments;
 import org.apache.beam.runners.dataflow.util.PackageUtil.PackageAttributes;
 import org.apache.beam.runners.dataflow.util.PackageUtil.StagedFile;
 import org.apache.beam.sdk.extensions.gcp.options.GcsOptions;
@@ -85,6 +86,7 @@
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Iterables;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Lists;
+import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.hash.HashCode;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.hash.Hashing;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.io.Files;
 import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.io.LineReader;
@@ -140,12 +142,12 @@ private File makeFileWithContents(String name, String contents) throws Exception
 
   private static PackageAttributes makePackageAttributes(
       File file, @Nullable String overridePackageName) throws IOException {
-    File sourceFile = file.isDirectory() ? zipDirectory(file) : file;
+    StagedFile stagedFile = makeStagedFile(file.getPath());
     PackageAttributes attributes =
         PackageUtil.PackageAttributes.forFileToStage(
-            sourceFile.getPath(),
-            Files.asByteSource(sourceFile).hash(Hashing.sha256()).toString(),
-            null,
+            stagedFile.getSource(),
+            stagedFile.getSha256(),
+            stagedFile.getDestination(),
             STAGING_PATH);
     if (overridePackageName != null) {
       attributes = attributes.withPackageName(overridePackageName);
@@ -160,15 +162,17 @@ private static StagedFile makeStagedFile(String source) throws IOException {
   private static StagedFile makeStagedFile(String source, String destName) throws IOException {
     File file = new File(source);
     File sourceFile;
-    String sha256;
+    HashCode hashCode;
     if (file.exists()) {
       sourceFile = file.isDirectory() ? zipDirectory(file) : file;
-      sha256 = Files.asByteSource(sourceFile).hash(Hashing.sha256()).toString();
+      hashCode = Files.asByteSource(sourceFile).hash(Hashing.sha256());
     } else {
       sourceFile = file;
-      sha256 = "";
+      hashCode = Hashing.sha256().hashBytes(new byte[] {});
     }
-    return StagedFile.of(sourceFile.getPath(), sha256, destName);
+    String destination =
+        destName == null ? Environments.createStagingFileName(file, hashCode) : destName;
+    return StagedFile.of(sourceFile.getPath(), hashCode.toString(), destination);
   }
 
   private static File zipDirectory(File directory) throws IOException {
@@ -218,8 +222,8 @@ public void testPackageNamingWithFilesHavingSameContentsAndSameNames() throws Ex
     makeFileWithContents("folder2/folderA/sameName", "This is a test!");
     DataflowPackage target2 = makePackageAttributes(tmpDirectory2, null).getDestination();
 
-    assertNotEquals(target1.getName(), target2.getName());
-    assertNotEquals(target1.getLocation(), target2.getLocation());
+    assertEquals(target1.getName(), target2.getName());
+    assertEquals(target1.getLocation(), target2.getLocation());
   }
 
   @Test

From 27f0dbae8080b93801ce56ef208470e41673062a Mon Sep 17 00:00:00 2001
From: rarokni 
Date: Tue, 26 May 2020 17:23:44 +0800
Subject: [PATCH 069/151] [BEAM-9770] BigQueryIO Patterns. Add Document update
 to snippit update.

---
 .../en/documentation/patterns/bigqueryio.md   | 46 +++++++++++++++++++
 .../en/documentation/patterns/overview.md     |  3 ++
 .../section-menu/en/documentation.html        |  1 +
 3 files changed, 50 insertions(+)
 create mode 100644 website/www/site/content/en/documentation/patterns/bigqueryio.md

diff --git a/website/www/site/content/en/documentation/patterns/bigqueryio.md b/website/www/site/content/en/documentation/patterns/bigqueryio.md
new file mode 100644
index 000000000000..49393b873b41
--- /dev/null
+++ b/website/www/site/content/en/documentation/patterns/bigqueryio.md
@@ -0,0 +1,46 @@
+---
+layout: section
+title: "BigQuery patterns"
+section_menu: section-menu/documentation.html
+permalink: /documentation/patterns/bigqueryio/
+---
+
+
+# Google BigQuery patterns
+
+The samples on this page show you common patterns for use with BigQueryIO.
+
+{{< language-switcher java py >}}
+
+## BigQueryIO deadletter pattern
+In production systems, it is useful to implement the deadletter pattern with BigQueryIO outputting any elements which had errors during processing by BigQueryIO into another PCollection for further processing. 
+The samples below print the errors, but in a production system they can be sent to a deadletter table for later correction.  
+
+{{< paragraph class="language-java" >}}
+When using `STREAMING_INSERTS`  you can use the `WriteResult` object to access a `PCollection` with the `TableRows` that failed to be inserted into BigQuery. 
+If you also set the `withExtendedErrorInfo` property , you will be able to access a `PCollection` from the `WriteResult`. The `PCollection` will then include a reference to the table, the data row and the `InsertErrors`. Which errors are added to the deadletter queue is determined via the `InsertRetryPolicy`.
+{{< /paragraph >}}
+
+{{< paragraph class="language-py" >}}
+In the result tuple you can access `FailedRows` to access the failed inserts.
+{{< /paragraph >}}
+
+{{< highlight java >}}
+{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryIODeadLetter >}}
+{{< /highlight >}}
+
+{{< highlight py >}}
+{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" BigQueryIODeadLetter >}}
+{{< /highlight >}}
diff --git a/website/www/site/content/en/documentation/patterns/overview.md b/website/www/site/content/en/documentation/patterns/overview.md
index a610c3c83243..561c8f00187c 100644
--- a/website/www/site/content/en/documentation/patterns/overview.md
+++ b/website/www/site/content/en/documentation/patterns/overview.md
@@ -35,6 +35,9 @@ Pipeline patterns demonstrate common Beam use cases. Pipeline patterns are based
 **Custom window patterns** - Patterns for windowing functions
 * [Using data to dynamically set session window gaps](/documentation/patterns/custom-windows/#using-data-to-dynamically-set-session-window-gaps)
 
+**BigQuery patterns** - Patterns for BigQueryIO
+* [Google BigQuery patterns](/documentation/patterns/bigqueryio/#google-bigquery-patterns)
+
 ## Contributing a pattern
 
 To contribute a new pipeline pattern, create an issue with the [`pipeline-patterns` label](https://issues.apache.org/jira/browse/BEAM-7449?jql=labels%20%3D%20pipeline-patterns) and add details to the issue description. See [Get started contributing](/contribute/) for more information.
diff --git a/website/www/site/layouts/partials/section-menu/en/documentation.html b/website/www/site/layouts/partials/section-menu/en/documentation.html
index a44e0455a7d1..9baa95c26f6c 100644
--- a/website/www/site/layouts/partials/section-menu/en/documentation.html
+++ b/website/www/site/layouts/partials/section-menu/en/documentation.html
@@ -276,6 +276,7 @@
     
  • Pipeline options
    • 
     
  • Custom I/O
    • 
     
  • Custom windows
    • 
+    
  • BigQueryIO
    •
    • From 79dcab9cab04b70d9e16f8c924fc52237f13622f Mon Sep 17 00:00:00 2001 From: Piotr Szuberski Date: Tue, 26 May 2020 13:26:53 +0200 Subject: [PATCH 070/151] [BEAM-10073] Add pubsub performance tests results to the grafana dashboards (#11809) --- ...ob_PerformanceTests_PubsubIO_Python.groovy | 5 +- .test-infra/metrics/beamgrafana-deploy.yaml | 2 +- .../Python_IO_IT_Tests_Dataflow.json | 256 +++++++++++++++++- 3 files changed, 255 insertions(+), 8 deletions(-) diff --git a/.test-infra/jenkins/job_PerformanceTests_PubsubIO_Python.groovy b/.test-infra/jenkins/job_PerformanceTests_PubsubIO_Python.groovy index 5ca1458c4fcd..96361c007920 100644 --- a/.test-infra/jenkins/job_PerformanceTests_PubsubIO_Python.groovy +++ b/.test-infra/jenkins/job_PerformanceTests_PubsubIO_Python.groovy @@ -39,7 +39,10 @@ def psio_test = [ temp_location : 'gs://temp-storage-for-perf-tests/loadtests', publish_to_big_query : true, metrics_dataset : 'beam_performance', - metrics_table : 'psio_io_2GB_msg_results', + metrics_table : 'psio_io_2GB_results', + influx_measurement : 'python_psio_2GB_results', + influx_db_name : InfluxDBCredentialsHelper.InfluxDBDatabaseName, + influx_hostname : InfluxDBCredentialsHelper.InfluxDBHostname, input_options : '\'{' + '"num_records": 2097152,' + '"key_size": 1,' + diff --git a/.test-infra/metrics/beamgrafana-deploy.yaml b/.test-infra/metrics/beamgrafana-deploy.yaml index 8a4ecb7a474a..7c5a83dd6784 100644 --- a/.test-infra/metrics/beamgrafana-deploy.yaml +++ b/.test-infra/metrics/beamgrafana-deploy.yaml @@ -37,7 +37,7 @@ spec: fsGroup: 1000 containers: - name: beamgrafana - image: gcr.io/apache-beam-testing/beamgrafana:beammetrics20200515 + image: gcr.io/apache-beam-testing/beamgrafana:beammetrics20200526 securityContext: runAsUser: 0 env: diff --git a/.test-infra/metrics/grafana/dashboards/perftests_metrics/Python_IO_IT_Tests_Dataflow.json b/.test-infra/metrics/grafana/dashboards/perftests_metrics/Python_IO_IT_Tests_Dataflow.json index 60d9a86dba56..d11465bc14fb 100644 --- a/.test-infra/metrics/grafana/dashboards/perftests_metrics/Python_IO_IT_Tests_Dataflow.json +++ b/.test-infra/metrics/grafana/dashboards/perftests_metrics/Python_IO_IT_Tests_Dataflow.json @@ -35,7 +35,7 @@ }, "hiddenSeries": false, "id": 2, - "interval": "", + "interval": "24h", "legend": { "avg": false, "current": false, @@ -75,7 +75,7 @@ "measurement": "python_bqio_read", "orderByTime": "ASC", "policy": "default", - "query": "SELECT value FROM \"python_bqio_read_10GB_results\" WHERE \"metric\" =~ /runtime/", + "query": "SELECT mean(\"value\") FROM \"python_bqio_read_10GB_results\" WHERE \"metric\" =~ /runtime/ AND $timeFilter GROUP BY time($__interval), \"metric\"", "rawQuery": true, "refId": "A", "resultFormat": "time_series", @@ -157,7 +157,7 @@ }, "hiddenSeries": false, "id": 3, - "interval": "", + "interval": "24h", "legend": { "avg": false, "current": false, @@ -197,7 +197,7 @@ "measurement": "python_bqio_read", "orderByTime": "ASC", "policy": "default", - "query": "SELECT value FROM \"python_bqio_write_10GB_results\" WHERE \"metric\" =~ /runtime/", + "query": "SELECT mean(\"value\") FROM \"python_bqio_write_10GB_results\" WHERE \"metric\" =~ /runtime/ AND $timeFilter GROUP BY time($__interval), \"metric\"", "rawQuery": true, "refId": "A", "resultFormat": "time_series", @@ -261,6 +261,250 @@ "align": false, "alignLevel": null } + }, + { + "aliasColors": {}, + "bars": false, + "cacheTimeout": null, + "dashLength": 10, + "dashes": false, + "datasource": "BeamInfluxDB", + "fill": 1, + "fillGradient": 0, + "gridPos": { + "h": 9, + "w": 12, + "x": 0, + "y": 9 + }, + "hiddenSeries": false, + "id": 4, + "interval": "24h", + "legend": { + "avg": false, + "current": false, + "max": false, + "min": false, + "show": false, + "total": false, + "values": false + }, + "lines": true, + "linewidth": 2, + "links": [], + "nullPointMode": "connected", + "options": { + "dataLinks": [] + }, + "percentage": false, + "pluginVersion": "6.7.2", + "pointradius": 2, + "points": true, + "renderer": "flot", + "seriesOverrides": [], + "spaceLength": 10, + "stack": false, + "steppedLine": false, + "targets": [ + { + "alias": "read_time", + "groupBy": [ + { + "params": [ + "$__interval" + ], + "type": "time" + } + ], + "measurement": "python_bqio_read", + "orderByTime": "ASC", + "policy": "default", + "query": "SELECT mean(\"value\") FROM \"python_psio_2GB_results\" WHERE \"metric\" = \"pubsub_io_perf_read_runtime\" AND $timeFilter GROUP BY time($__interval), \"metric\"", + "rawQuery": true, + "refId": "A", + "resultFormat": "time_series", + "select": [ + [ + { + "params": [ + "value" + ], + "type": "field" + }, + { + "params": [], + "type": "mean" + } + ] + ], + "tags": [] + } + ], + "thresholds": [], + "timeFrom": null, + "timeRegions": [], + "timeShift": null, + "title": "Reading 2GB of data | Pubsub native Dataflow IO | streaming", + "tooltip": { + "shared": true, + "sort": 0, + "value_type": "individual" + }, + "transparent": true, + "type": "graph", + "xaxis": { + "buckets": null, + "mode": "time", + "name": null, + "show": true, + "values": [] + }, + "yaxes": [ + { + "$$hashKey": "object:403", + "format": "s", + "label": null, + "logBase": 1, + "max": null, + "min": null, + "show": true + }, + { + "$$hashKey": "object:404", + "format": "short", + "label": null, + "logBase": 1, + "max": null, + "min": null, + "show": true + } + ], + "yaxis": { + "align": false, + "alignLevel": null + } + }, + { + "aliasColors": {}, + "bars": false, + "cacheTimeout": null, + "dashLength": 10, + "dashes": false, + "datasource": "BeamInfluxDB", + "fill": 1, + "fillGradient": 0, + "gridPos": { + "h": 9, + "w": 12, + "x": 12, + "y": 9 + }, + "hiddenSeries": false, + "id": 5, + "interval": "24h", + "legend": { + "avg": false, + "current": false, + "max": false, + "min": false, + "show": false, + "total": false, + "values": false + }, + "lines": true, + "linewidth": 2, + "links": [], + "nullPointMode": "connected", + "options": { + "dataLinks": [] + }, + "percentage": false, + "pluginVersion": "6.7.2", + "pointradius": 2, + "points": true, + "renderer": "flot", + "seriesOverrides": [], + "spaceLength": 10, + "stack": false, + "steppedLine": false, + "targets": [ + { + "alias": "write_time", + "groupBy": [ + { + "params": [ + "$__interval" + ], + "type": "time" + } + ], + "measurement": "python_bqio_read", + "orderByTime": "ASC", + "policy": "default", + "query": "SELECT mean(\"value\") FROM \"python_psio_2GB_results\" WHERE \"metric\" = 'pubsub_io_perf_write_runtime' AND $timeFilter GROUP BY time($__interval), \"metric\"", + "rawQuery": true, + "refId": "A", + "resultFormat": "time_series", + "select": [ + [ + { + "params": [ + "value" + ], + "type": "field" + }, + { + "params": [], + "type": "mean" + } + ] + ], + "tags": [] + } + ], + "thresholds": [], + "timeFrom": null, + "timeRegions": [], + "timeShift": null, + "title": "Writing 2GB of data | Pubsub native Dataflow IO | streaming", + "tooltip": { + "shared": true, + "sort": 0, + "value_type": "individual" + }, + "transparent": true, + "type": "graph", + "xaxis": { + "buckets": null, + "mode": "time", + "name": null, + "show": true, + "values": [] + }, + "yaxes": [ + { + "$$hashKey": "object:403", + "format": "s", + "label": null, + "logBase": 1, + "max": null, + "min": null, + "show": true + }, + { + "$$hashKey": "object:404", + "format": "short", + "label": null, + "logBase": 1, + "max": null, + "min": null, + "show": true + } + ], + "yaxis": { + "align": false, + "alignLevel": null + } } ], "schemaVersion": 22, @@ -293,5 +537,5 @@ "variables": { "list": [] }, - "version": 1 -} + "version": 2 +} \ No newline at end of file From fa028e68e47c2a47858783a5a5f7adc15569c654 Mon Sep 17 00:00:00 2001 From: darshan jani Date: Tue, 26 May 2020 22:36:35 +0800 Subject: [PATCH 071/151] [BEAM-10074] | implement hashing functions --- .../sql/impl/udf/BuiltinHashFunctions.java | 139 ++++++++++++++++++ .../sdk/extensions/sql/BeamSqlDslBase.java | 6 + .../BeamSalUhfSpecialTypeAndValueTest.java | 69 +++++++++ .../impl/udf/BeamSqlUdfExpressionTest.java | 41 ++++++ 4 files changed, 255 insertions(+) create mode 100644 sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/udf/BuiltinHashFunctions.java diff --git a/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/udf/BuiltinHashFunctions.java b/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/udf/BuiltinHashFunctions.java new file mode 100644 index 000000000000..c3fc82b1fdb5 --- /dev/null +++ b/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/udf/BuiltinHashFunctions.java @@ -0,0 +1,139 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.sql.impl.udf; + +import com.google.auto.service.AutoService; +import org.apache.beam.sdk.schemas.Schema; +import org.apache.beam.vendor.calcite.v1_20_0.org.apache.calcite.linq4j.function.Strict; + +/** Hash Functions. */ +@AutoService(BeamBuiltinFunctionProvider.class) +public class BuiltinHashFunctions extends BeamBuiltinFunctionProvider { + + /** + * MD5(X) + * + *

    Calculates the MD5 digest and returns the value as a 16 element {@code byte[]}. + */ + @UDF( + funcName = "MD5", + parameterArray = {Schema.TypeName.STRING}, + returnType = Schema.TypeName.BYTES) + @Strict + public byte[] md5String(String str) { + return org.apache.commons.codec.digest.DigestUtils.md5(str); + } + + /** + * MD5(X) + * + *

    Calculates the MD5 digest and returns the value as a 16 element {@code byte[]}. + */ + @UDF( + funcName = "MD5", + parameterArray = {Schema.TypeName.BYTES}, + returnType = Schema.TypeName.BYTES) + @Strict + public byte[] md5Bytes(byte[] bytes) { + return org.apache.commons.codec.digest.DigestUtils.md5(bytes); + } + + /** + * SHA1(X) + * + *

    Calculates the SHA-1 digest and returns the value as a {@code byte[]}. + */ + @UDF( + funcName = "SHA1", + parameterArray = {Schema.TypeName.STRING}, + returnType = Schema.TypeName.BYTES) + @Strict + public byte[] sha1String(String str) { + return org.apache.commons.codec.digest.DigestUtils.sha1(str); + } + + /** + * SHA1(X) + * + *

    Calculates the SHA-1 digest and returns the value as a {@code byte[]}. + */ + @UDF( + funcName = "SHA1", + parameterArray = {Schema.TypeName.BYTES}, + returnType = Schema.TypeName.BYTES) + @Strict + public byte[] sha1Bytes(byte[] bytes) { + return org.apache.commons.codec.digest.DigestUtils.sha1(bytes); + } + + /** + * SHA256(X) + * + *

    Calculates the SHA-1 digest and returns the value as a {@code byte[]}. + */ + @UDF( + funcName = "SHA256", + parameterArray = {Schema.TypeName.STRING}, + returnType = Schema.TypeName.BYTES) + @Strict + public byte[] sha256String(String str) { + return org.apache.commons.codec.digest.DigestUtils.sha256(str); + } + + /** + * SHA256(X) + * + *

    Calculates the SHA-1 digest and returns the value as a {@code byte[]}. + */ + @UDF( + funcName = "SHA256", + parameterArray = {Schema.TypeName.BYTES}, + returnType = Schema.TypeName.BYTES) + @Strict + public byte[] sha256Bytes(byte[] bytes) { + return org.apache.commons.codec.digest.DigestUtils.sha256(bytes); + } + + /** + * SHA512(X) + * + *

    Calculates the SHA-1 digest and returns the value as a {@code byte[]}. + */ + @UDF( + funcName = "SHA512", + parameterArray = {Schema.TypeName.STRING}, + returnType = Schema.TypeName.BYTES) + @Strict + public byte[] sha512String(String str) { + return org.apache.commons.codec.digest.DigestUtils.sha512(str); + } + + /** + * SHA512(X) + * + *

    Calculates the SHA-1 digest and returns the value as a {@code byte[]}. + */ + @UDF( + funcName = "SHA512", + parameterArray = {Schema.TypeName.BYTES}, + returnType = Schema.TypeName.BYTES) + @Strict + public byte[] sha512Bytes(byte[] bytes) { + return org.apache.commons.codec.digest.DigestUtils.sha512(bytes); + } +} diff --git a/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/BeamSqlDslBase.java b/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/BeamSqlDslBase.java index ad26d4a27f5b..4298c0711cc4 100644 --- a/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/BeamSqlDslBase.java +++ b/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/BeamSqlDslBase.java @@ -213,6 +213,12 @@ public static void prepareClass() throws ParseException { "TO_HEX", "abcABC".getBytes(UTF_8), "TO_HEX", + "abcABCжщфЖЩФ".getBytes(UTF_8), + "HashingFn", + "foobar".getBytes(UTF_8), + "HashingFn", + " ".getBytes(UTF_8), + "HashingFn", "abcABCжщфЖЩФ".getBytes(UTF_8)) .getRows(); diff --git a/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/impl/udf/BeamSalUhfSpecialTypeAndValueTest.java b/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/impl/udf/BeamSalUhfSpecialTypeAndValueTest.java index 1370c62db0f9..db87eb77a203 100644 --- a/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/impl/udf/BeamSalUhfSpecialTypeAndValueTest.java +++ b/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/impl/udf/BeamSalUhfSpecialTypeAndValueTest.java @@ -27,6 +27,7 @@ import org.apache.beam.sdk.testing.PAssert; import org.apache.beam.sdk.values.PCollection; import org.apache.beam.sdk.values.Row; +import org.apache.commons.codec.digest.DigestUtils; import org.junit.Test; import org.junit.runner.RunWith; import org.junit.runners.JUnit4; @@ -167,4 +168,72 @@ public void testRightPad() throws Exception { resultRow8); pipeline.run().waitUntilFinish(); } + + @Test + public void testMd5() throws Exception { + Schema resultType = Schema.builder().addByteArrayField("field").build(); + Row resultRow1 = + Row.withSchema(resultType).addValues(DigestUtils.md5("foobar".getBytes(UTF_8))).build(); + Row resultRow2 = + Row.withSchema(resultType).addValues(DigestUtils.md5(" ".getBytes(UTF_8))).build(); + Row resultRow3 = + Row.withSchema(resultType) + .addValues(DigestUtils.md5("abcABCжщфЖЩФ".getBytes(UTF_8))) + .build(); + String sql = "SELECT MD5(f_bytes) FROM PCOLLECTION WHERE f_func = 'HashingFn'"; + PCollection result = boundedInputBytes.apply("testUdf", SqlTransform.query(sql)); + PAssert.that(result).containsInAnyOrder(resultRow1, resultRow2, resultRow3); + pipeline.run().waitUntilFinish(); + } + + @Test + public void testSHA1() throws Exception { + Schema resultType = Schema.builder().addByteArrayField("field").build(); + Row resultRow1 = + Row.withSchema(resultType).addValues(DigestUtils.sha1("foobar".getBytes(UTF_8))).build(); + Row resultRow2 = + Row.withSchema(resultType).addValues(DigestUtils.sha1(" ".getBytes(UTF_8))).build(); + Row resultRow3 = + Row.withSchema(resultType) + .addValues(DigestUtils.sha1("abcABCжщфЖЩФ".getBytes(UTF_8))) + .build(); + String sql = "SELECT SHA1(f_bytes) FROM PCOLLECTION WHERE f_func = 'HashingFn'"; + PCollection result = boundedInputBytes.apply("testUdf", SqlTransform.query(sql)); + PAssert.that(result).containsInAnyOrder(resultRow1, resultRow2, resultRow3); + pipeline.run().waitUntilFinish(); + } + + @Test + public void testSHA256() throws Exception { + Schema resultType = Schema.builder().addByteArrayField("field").build(); + Row resultRow1 = + Row.withSchema(resultType).addValues(DigestUtils.sha256("foobar".getBytes(UTF_8))).build(); + Row resultRow2 = + Row.withSchema(resultType).addValues(DigestUtils.sha256(" ".getBytes(UTF_8))).build(); + Row resultRow3 = + Row.withSchema(resultType) + .addValues(DigestUtils.sha256("abcABCжщфЖЩФ".getBytes(UTF_8))) + .build(); + String sql = "SELECT SHA256(f_bytes) FROM PCOLLECTION WHERE f_func = 'HashingFn'"; + PCollection result = boundedInputBytes.apply("testUdf", SqlTransform.query(sql)); + PAssert.that(result).containsInAnyOrder(resultRow1, resultRow2, resultRow3); + pipeline.run().waitUntilFinish(); + } + + @Test + public void testSHA512() throws Exception { + Schema resultType = Schema.builder().addByteArrayField("field").build(); + Row resultRow1 = + Row.withSchema(resultType).addValues(DigestUtils.sha512("foobar".getBytes(UTF_8))).build(); + Row resultRow2 = + Row.withSchema(resultType).addValues(DigestUtils.sha512(" ".getBytes(UTF_8))).build(); + Row resultRow3 = + Row.withSchema(resultType) + .addValues(DigestUtils.sha512("abcABCжщфЖЩФ".getBytes(UTF_8))) + .build(); + String sql = "SELECT SHA512(f_bytes) FROM PCOLLECTION WHERE f_func = 'HashingFn'"; + PCollection result = boundedInputBytes.apply("testUdf", SqlTransform.query(sql)); + PAssert.that(result).containsInAnyOrder(resultRow1, resultRow2, resultRow3); + pipeline.run().waitUntilFinish(); + } } diff --git a/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/impl/udf/BeamSqlUdfExpressionTest.java b/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/impl/udf/BeamSqlUdfExpressionTest.java index 82ffccf9fb6f..495f32941f6f 100644 --- a/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/impl/udf/BeamSqlUdfExpressionTest.java +++ b/sdks/java/extensions/sql/src/test/java/org/apache/beam/sdk/extensions/sql/impl/udf/BeamSqlUdfExpressionTest.java @@ -21,6 +21,7 @@ import org.apache.beam.sdk.extensions.sql.integrationtest.BeamSqlBuiltinFunctionsIntegrationTestBase; import org.apache.beam.sdk.schemas.Schema.TypeName; +import org.apache.commons.codec.digest.DigestUtils; import org.junit.Test; import org.junit.runner.RunWith; import org.junit.runners.JUnit4; @@ -199,4 +200,44 @@ public void testRightPad() throws Exception { checker.buildRunAndCheck(); } + + @Test + public void testMd5() throws Exception { + ExpressionChecker checker = + new ExpressionChecker() + .addExpr("MD5('foobar')", DigestUtils.md5("foobar")) + .addExpr("MD5('中文')", DigestUtils.md5("中文")) + .addExprWithNullExpectedValue("MD5(CAST(NULL AS VARCHAR(0)))", TypeName.BYTES); + checker.buildRunAndCheck(); + } + + @Test + public void testSHA1() throws Exception { + ExpressionChecker checker = + new ExpressionChecker() + .addExpr("SHA1('foobar')", DigestUtils.sha1("foobar")) + .addExpr("SHA1('中文')", DigestUtils.sha1("中文")) + .addExprWithNullExpectedValue("SHA1(CAST(NULL AS VARCHAR(0)))", TypeName.BYTES); + checker.buildRunAndCheck(); + } + + @Test + public void testSHA256() throws Exception { + ExpressionChecker checker = + new ExpressionChecker() + .addExpr("SHA256('foobar')", DigestUtils.sha256("foobar")) + .addExpr("SHA256('中文')", DigestUtils.sha256("中文")) + .addExprWithNullExpectedValue("SHA256(CAST(NULL AS VARCHAR(0)))", TypeName.BYTES); + checker.buildRunAndCheck(); + } + + @Test + public void testSHA512() throws Exception { + ExpressionChecker checker = + new ExpressionChecker() + .addExpr("SHA512('foobar')", DigestUtils.sha512("foobar")) + .addExpr("SHA512('中文')", DigestUtils.sha512("中文")) + .addExprWithNullExpectedValue("SHA512(CAST(NULL AS VARCHAR(0)))", TypeName.BYTES); + checker.buildRunAndCheck(); + } } From f83bc7569864509a4ba2e7a5051fb0a4dd62281d Mon Sep 17 00:00:00 2001 From: Ashwin Ramaswami Date: Tue, 26 May 2020 12:42:13 -0400 Subject: [PATCH 072/151] [BEAM-10065] Fix beam release guide template (#11797) [BEAM-10065] Fix beam release guide template --- .../content/en/contribute/release-guide.md | 60 +++++++++---------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/website/www/site/content/en/contribute/release-guide.md b/website/www/site/content/en/contribute/release-guide.md index 81d39b4fa09b..4f949e2d4bd8 100644 --- a/website/www/site/content/en/contribute/release-guide.md +++ b/website/www/site/content/en/contribute/release-guide.md @@ -712,53 +712,53 @@ all major features and bug fixes, and all known issues. Template: ``` - We are happy to present the new {$RELEASE_VERSION} release of Beam. This release includes both improvements and new functionality. - See the [download page](/get-started/downloads/{$DOWNLOAD_ANCHOR}) for this release. - For more information on changes in {$RELEASE_VERSION}, check out the - [detailed release notes]({$JIRA_RELEASE_NOTES}). +We are happy to present the new {$RELEASE_VERSION} release of Beam. This release includes both improvements and new functionality. +See the [download page](/get-started/downloads/{$DOWNLOAD_ANCHOR}) for this release. +For more information on changes in {$RELEASE_VERSION}, check out the +[detailed release notes]({$JIRA_RELEASE_NOTES}). - ## Highlights +## Highlights - * New highly anticipated feature X added to Python SDK ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). - * New highly anticipated feature Y added to JavaSDK ([BEAM-Y](https://issues.apache.org/jira/browse/BEAM-Y)). + * New highly anticipated feature X added to Python SDK ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). + * New highly anticipated feature Y added to JavaSDK ([BEAM-Y](https://issues.apache.org/jira/browse/BEAM-Y)). - {$TOPICS e.g.:} - ### I/Os - * Support for X source added (Java) ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). - {$TOPICS} +{$TOPICS e.g.:} +### I/Os +* Support for X source added (Java) ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). +{$TOPICS} - ### New Features / Improvements +### New Features / Improvements - * X feature added (Python) ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). - * Y feature added (Java) [BEAM-Y](https://issues.apache.org/jira/browse/BEAM-Y). +* X feature added (Python) ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). +* Y feature added (Java) [BEAM-Y](https://issues.apache.org/jira/browse/BEAM-Y). - ### Breaking Changes +### Breaking Changes - * X behavior was changed ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). - * Y behavior was changed ([BEAM-Y](https://issues.apache.org/jira/browse/BEAM-Y)). +* X behavior was changed ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). +* Y behavior was changed ([BEAM-Y](https://issues.apache.org/jira/browse/BEAM-Y)). - ### Deprecations +### Deprecations - * X behavior is deprecated and will be removed in X versions ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). +* X behavior is deprecated and will be removed in X versions ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). - ### Bugfixes +### Bugfixes - * Fixed X (Python) ([BEAM-Y](https://issues.apache.org/jira/browse/BEAM-X)). - * Fixed Y (Java) ([BEAM-Y](https://issues.apache.org/jira/browse/BEAM-Y)). +* Fixed X (Python) ([BEAM-Y](https://issues.apache.org/jira/browse/BEAM-X)). +* Fixed Y (Java) ([BEAM-Y](https://issues.apache.org/jira/browse/BEAM-Y)). - ### Known Issues +### Known Issues - * {$KNOWN_ISSUE_1} - * {$KNOWN_ISSUE_2} - * See a full list of open [issues that affect](https://issues.apache.org/jira/issues/?jql=project%20%3D%20BEAM%20AND%20affectedVersion%20%3D%20{$RELEASE}%20ORDER%20BY%20priority%20DESC%2C%20updated%20DESC) this version. +* {$KNOWN_ISSUE_1} +* {$KNOWN_ISSUE_2} +* See a full list of open [issues that affect](https://issues.apache.org/jira/issues/?jql=project%20%3D%20BEAM%20AND%20affectedVersion%20%3D%20{$RELEASE}%20ORDER%20BY%20priority%20DESC%2C%20updated%20DESC) this version. - ## List of Contributors +## List of Contributors - According to git shortlog, the following people contributed to the 2.XX.0 release. Thank you to all contributors! +According to git shortlog, the following people contributed to the 2.XX.0 release. Thank you to all contributors! - ${CONTRIBUTORS} - ``` +${CONTRIBUTORS} +``` #### Checklist to proceed to the next step From f452e098242e7f4f48e5be7d34fe94039600f6c2 Mon Sep 17 00:00:00 2001 From: Ashwin Ramaswami Date: Tue, 26 May 2020 14:04:42 -0400 Subject: [PATCH 073/151] Fix typo in doc "and and" -> "and" (#11810) --- sdks/python/apache_beam/io/textio.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sdks/python/apache_beam/io/textio.py b/sdks/python/apache_beam/io/textio.py index 4099e87215e7..0660b8747f3a 100644 --- a/sdks/python/apache_beam/io/textio.py +++ b/sdks/python/apache_beam/io/textio.py @@ -438,7 +438,7 @@ def _create_text_source( class ReadAllFromText(PTransform): """A ``PTransform`` for reading a ``PCollection`` of text files. - Reads a ``PCollection`` of text files or file patterns and and produces a + Reads a ``PCollection`` of text files or file patterns and produces a ``PCollection`` of strings. Parses a text file as newline-delimited elements, by default assuming From d86219ffb478c7ecd130668858673cb5f6786c2e Mon Sep 17 00:00:00 2001 From: Lukasz Cwik Date: Tue, 26 May 2020 11:07:46 -0700 Subject: [PATCH 074/151] [BEAM-2939, BEAM-10057] Ensure that we can process an EmptyUnboundedSource and also prevent splitting on it. (#11781) --- .../src/main/java/org/apache/beam/sdk/io/Read.java | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/io/Read.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/io/Read.java index e02c938e68d6..19baa8d4cb0a 100644 --- a/sdks/java/core/src/main/java/org/apache/beam/sdk/io/Read.java +++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/io/Read.java @@ -725,7 +725,7 @@ public void close() throws IOException {} @Override public Instant getWatermark() { - throw new UnsupportedOperationException("getWatermark is never meant to be invoked."); + return BoundedWindow.TIMESTAMP_MAX_VALUE; } @Override @@ -836,16 +836,20 @@ public UnboundedSourceRestriction currentRestriction() { @Override public SplitResult> trySplit( double fractionOfRemainder) { - // Don't split if we have claimed all since the SDF wrapper will be finishing soon. + // Don't split if we have the empty sources since the SDF wrapper will be finishing soon. + UnboundedSourceRestriction currentRestriction = currentRestriction(); + if (currentRestriction.getSource() instanceof EmptyUnboundedSource) { + return null; + } + // Our split result sets the primary to have no checkpoint mark associated // with it since when we resume we don't have any state but we specifically pass // the checkpoint mark to the current reader so that when we finish the current bundle // we may register for finalization. - UnboundedSourceRestriction currentRestriction = currentRestriction(); SplitResult> result = SplitResult.of( UnboundedSourceRestriction.create( - EmptyUnboundedSource.INSTANCE, null, currentRestriction.getWatermark()), + EmptyUnboundedSource.INSTANCE, null, BoundedWindow.TIMESTAMP_MAX_VALUE), currentRestriction); currentReader = EmptyUnboundedSource.INSTANCE.createReader(null, currentRestriction.getCheckpoint()); From 90a79d6c8e37a183678c9e3d0c046908334f2a48 Mon Sep 17 00:00:00 2001 From: Ashwin Ramaswami Date: Tue, 26 May 2020 18:41:55 -0400 Subject: [PATCH 075/151] [BEAM-7370] Upgrade sphinx to 3.0.3 (#11798) * Upgrade sphinx to 3.0.3 * update CHANGES.md --- CHANGES.md | 1 + sdks/python/tox.ini | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGES.md b/CHANGES.md index 59082149617a..7e57f487958b 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -65,6 +65,7 @@ * `--direct_num_workers=0` is supported for FnApi runner. It will set the number of threads/subprocesses to number of cores of the machine executing the pipeline ([BEAM-9443](https://issues.apache.org/jira/browse/BEAM-9443)). * Python SDK now has experimental support for SqlTransform ([BEAM-8603](https://issues.apache.org/jira/browse/BEAM-8603)). * Add OnWindowExpiration method to Stateful DoFn ([BEAM-1589](https://issues.apache.org/jira/browse/BEAM-1589)). +* Upgrade Sphinx to 3.0.3 for building PyDoc. ## Breaking Changes diff --git a/sdks/python/tox.ini b/sdks/python/tox.ini index 3b66c28592a0..2726a74d39a1 100644 --- a/sdks/python/tox.ini +++ b/sdks/python/tox.ini @@ -200,7 +200,7 @@ commands = [testenv:py37-docs] extras = test,gcp,docs,interactive deps = - Sphinx==1.8.5 + Sphinx==3.0.3 sphinx_rtd_theme==0.4.3 commands = time {toxinidir}/scripts/generate_pydoc.sh From c77bee6b83f76775945e92bda9e9a8e295a2ce4a Mon Sep 17 00:00:00 2001 From: Yichi Zhang Date: Tue, 26 May 2020 15:43:22 -0700 Subject: [PATCH 076/151] Clear redundant debug statements in pr-11756 --- .../main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java index ab07ca319ac0..0baf76b9dcdf 100644 --- a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java +++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/FnApiDoFnRunner.java @@ -1049,9 +1049,6 @@ private class FnApiTimer implements org.apache.beam.sdk.state.Timer { Instant elementTimestampOrTimerFireTimestamp, PaneInfo paneInfo, TimeDomain timeDomain) { - if (timerId.equals("ts-event") && timeDomain.equals(TimeDomain.PROCESSING_TIME)) { - throw new IllegalStateException("illegal"); - } this.timerId = timerId; this.userKey = userKey; this.dynamicTimerTag = dynamicTimerTag; From 60220792034c5103760b5b6f605ab5795f61903b Mon Sep 17 00:00:00 2001 From: Steven Niemitz Date: Tue, 26 May 2020 23:04:29 -0400 Subject: [PATCH 077/151] [BEAM-10076] Fix dataflow worker status page rendering (#11812) --- .../beam/runners/dataflow/worker/StreamingDataflowWorker.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/StreamingDataflowWorker.java b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/StreamingDataflowWorker.java index 58aa30486d45..2f0871964685 100644 --- a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/StreamingDataflowWorker.java +++ b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/StreamingDataflowWorker.java @@ -2310,14 +2310,14 @@ public void printActiveWork(PrintWriter writer) { builder.append(""); builder.append(String.format("%016x", workItem.getShardingKey())); builder.append(""); - builder.append(workItem.getWorkToken()); + builder.append(String.format("%016x", workItem.getWorkToken())); builder.append(""); builder.append(queue.size() - 1); builder.append(""); builder.append(elapsedString(work.getStartTime(), now)); builder.append(""); builder.append(state); - builder.append("\n"); + builder.append(""); builder.append(elapsedString(work.getStateStartTime(), now)); builder.append("\n"); } From 630a4889bf9ebd5aaa9e21adfdcfabbe5f41beac Mon Sep 17 00:00:00 2001 From: Luke Cwik Date: Tue, 26 May 2020 21:49:50 -0700 Subject: [PATCH 078/151] [BEAM-10016, BEAM-10094] Disable single test to get portable validates runner signal back to green Follow-up on fixing the issue should happen separately. --- .../groovy/org/apache/beam/gradle/BeamModulePlugin.groovy | 7 +++++++ runners/flink/job-server/flink_job_server.gradle | 4 ++++ runners/spark/job-server/build.gradle | 4 ++++ 3 files changed, 15 insertions(+) diff --git a/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy b/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy index 534366ab40f2..8ba8a4d12bb4 100644 --- a/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy +++ b/buildSrc/src/main/groovy/org/apache/beam/gradle/BeamModulePlugin.groovy @@ -257,6 +257,12 @@ class BeamModulePlugin implements Plugin { // includeCategories 'org.apache.beam.sdk.testing.ValidatesRunner' // excludeCategories 'org.apache.beam.sdk.testing.FlattenWithHeterogeneousCoders' } + // Tests to include/exclude from running, by default all tests are included + Closure testFilter = { + // Use the following to include / exclude tests: + // includeTestsMatching 'org.apache.beam.sdk.transforms.FlattenTest.testFlattenWithDifferentInputAndOutputCoders2' + // excludeTestsMatching 'org.apache.beam.sdk.transforms.FlattenTest.testFlattenWithDifferentInputAndOutputCoders2' + } // Configuration for the classpath when running the test. Configuration testClasspathConfiguration // Additional system properties. @@ -1689,6 +1695,7 @@ class BeamModulePlugin implements Plugin { testClassesDirs = project.files(project.project(":sdks:java:core").sourceSets.test.output.classesDirs, project.project(":runners:core-java").sourceSets.test.output.classesDirs) maxParallelForks config.numParallelTests useJUnit(config.testCategories) + filter(config.testFilter) // increase maxHeapSize as this is directly correlated to direct memory, // see https://issues.apache.org/jira/browse/BEAM-6698 maxHeapSize = '4g' diff --git a/runners/flink/job-server/flink_job_server.gradle b/runners/flink/job-server/flink_job_server.gradle index ed76e6b89365..0ce92a569dc0 100644 --- a/runners/flink/job-server/flink_job_server.gradle +++ b/runners/flink/job-server/flink_job_server.gradle @@ -163,6 +163,10 @@ def portableValidatesRunnerTask(String name, Boolean streaming) { excludeCategories 'org.apache.beam.sdk.testing.UsesSplittableParDoWithWindowedSideInputs' excludeCategories 'org.apache.beam.sdk.testing.UsesUnboundedSplittableParDo' }, + testFilter: { + // TODO(BEAM-10016) + excludeTestsMatching 'org.apache.beam.sdk.transforms.FlattenTest.testFlattenWithDifferentInputAndOutputCoders2' + }, ) } diff --git a/runners/spark/job-server/build.gradle b/runners/spark/job-server/build.gradle index cc0628cbe595..26a141d9c0df 100644 --- a/runners/spark/job-server/build.gradle +++ b/runners/spark/job-server/build.gradle @@ -117,6 +117,10 @@ def portableValidatesRunnerTask(String name) { excludeCategories 'org.apache.beam.sdk.testing.UsesStrictTimerOrdering' excludeCategories 'org.apache.beam.sdk.testing.UsesBundleFinalizer' }, + testFilter: { + // TODO(BEAM-10094) + excludeTestsMatching 'org.apache.beam.sdk.transforms.FlattenTest.testFlattenWithDifferentInputAndOutputCoders2' + }, ) } From e66734495586d860b163f6e1dad944f6a2f43e26 Mon Sep 17 00:00:00 2001 From: Ahmet Altay Date: Tue, 26 May 2020 22:49:51 -0700 Subject: [PATCH 079/151] Add a bare bones powered by page. --- .../site/content/en/community/powered-by.md | 25 +++++++++++++++++++ .../partials/section-menu/en/community.html | 1 + 2 files changed, 26 insertions(+) create mode 100644 website/www/site/content/en/community/powered-by.md diff --git a/website/www/site/content/en/community/powered-by.md b/website/www/site/content/en/community/powered-by.md new file mode 100644 index 000000000000..ad22039388b9 --- /dev/null +++ b/website/www/site/content/en/community/powered-by.md @@ -0,0 +1,25 @@ +--- +title: 'Powered by Apache Beam' +--- + +# Projects and Products Powered by Apache Beam + +To add yourself to the list, please open a [pull request](https://github.com/apache/beam/edit/master/website/www/site/content/en/community/powered_by.md) adding your organization name, URL, a list of which Beam components you are using, and a short description of your use case. + +* **[Cloud Dataflow](https://cloud.google.com/dataflow):** Google Cloud Dataflow is a fully managed service for executing + Apache Beam pipelines within the Google Cloud Platform ecosystem. +* **[TensorFlow Extended (TFX)](https://www.tensorflow.org/tfx):** TensorFlow Extended (TFX) is an end-to-end platform + for deploying production ML pipelines. + diff --git a/website/www/site/layouts/partials/section-menu/en/community.html b/website/www/site/layouts/partials/section-menu/en/community.html index b2cafee008f7..d90582ffe861 100644 --- a/website/www/site/layouts/partials/section-menu/en/community.html +++ b/website/www/site/layouts/partials/section-menu/en/community.html @@ -14,6 +14,7 @@

  • Integrations
  • Contact Us
  • Policies
    • +
  • Powered by Apache Beam
  • YouTube channel
  • Twitter Handle
  • In Person
    • From 292dea3670853c34aca2ef80089e4bd31a0134eb Mon Sep 17 00:00:00 2001 From: Kamil Wasilewski Date: Thu, 14 May 2020 17:31:38 +0200 Subject: [PATCH 080/151] [BEAM-9936] Reduce the code duplication across python/container/py* --- sdks/python/container/common.gradle | 71 +++++++++++++++++++++++++ sdks/python/container/py2/build.gradle | 53 +----------------- sdks/python/container/py35/build.gradle | 53 ++---------------- sdks/python/container/py36/build.gradle | 53 ++---------------- sdks/python/container/py37/build.gradle | 53 ++---------------- 5 files changed, 82 insertions(+), 201 deletions(-) create mode 100644 sdks/python/container/common.gradle diff --git a/sdks/python/container/common.gradle b/sdks/python/container/common.gradle new file mode 100644 index 000000000000..2a6ec55882d2 --- /dev/null +++ b/sdks/python/container/common.gradle @@ -0,0 +1,71 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * License); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an AS IS BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +def pythonVersionSuffix = project.ext.pythonVersion.replace('.', '') + +description = "Apache Beam :: SDKs :: Python :: Container :: Python ${pythonVersionSuffix} Container" + +configurations { + sdkSourceTarball + sdkHarnessLauncher +} + +dependencies { + sdkSourceTarball project(path: ":sdks:python", configuration: "distTarBall") + sdkHarnessLauncher project(path: ":sdks:python:container", configuration: "sdkHarnessLauncher") +} + +task copyDockerfileDependencies(type: Copy) { + from configurations.sdkSourceTarball + from file("../base_image_requirements.txt") + into "build/target" + if(configurations.sdkSourceTarball.isEmpty()) { + throw new StopExecutionException(); + } +} + +task copyLicenseScripts(type: Copy){ + from ("../license_scripts") + into "build/target/license_scripts" +} + +task copyLauncherDependencies(type: Copy) { + from configurations.sdkHarnessLauncher + into "build/target/launcher" + if(configurations.sdkHarnessLauncher.isEmpty()) { + throw new StopExecutionException(); + } +} + +docker { + name containerImageName( + name: project.docker_image_default_repo_prefix + "python${project.ext.pythonVersion}_sdk", + root: project.rootProject.hasProperty(["docker-repository-root"]) ? + project.rootProject["docker-repository-root"] : + project.docker_image_default_repo_root, + tag: project.rootProject.hasProperty(["docker-tag"]) ? + project.rootProject["docker-tag"] : project.sdk_version) + files "../Dockerfile", "./build" + buildArgs(['py_version': "${project.ext.pythonVersion}", + 'pull_licenses': project.rootProject.hasProperty(["docker-pull-licenses"]) || + project.rootProject.hasProperty(["isRelease"])]) +} + +dockerPrepare.dependsOn copyLauncherDependencies +dockerPrepare.dependsOn copyDockerfileDependencies +dockerPrepare.dependsOn copyLicenseScripts diff --git a/sdks/python/container/py2/build.gradle b/sdks/python/container/py2/build.gradle index 2821600419d7..6d3c94af3cea 100644 --- a/sdks/python/container/py2/build.gradle +++ b/sdks/python/container/py2/build.gradle @@ -21,55 +21,6 @@ plugins { id 'org.apache.beam.module' } applyDockerNature() +applyPythonNature() -description = "Apache Beam :: SDKs :: Python :: Container :: Python 2 Container" - -configurations { - sdkSourceTarball - sdkHarnessLauncher -} - -dependencies { - sdkSourceTarball project(path: ":sdks:python", configuration: "distTarBall") - sdkHarnessLauncher project(path: ":sdks:python:container", configuration: "sdkHarnessLauncher") -} - -task copyDockerfileDependencies(type: Copy) { - from configurations.sdkSourceTarball - from file("../base_image_requirements.txt") - into "build/target" - if(configurations.sdkSourceTarball.isEmpty()) { - throw new StopExecutionException(); - } -} - -task copyLicenseScripts(type: Copy){ - from ("../license_scripts") - into "build/target/license_scripts" -} - -task copyLauncherDependencies(type: Copy) { - from configurations.sdkHarnessLauncher - into "build/target/launcher" - if(configurations.sdkHarnessLauncher.isEmpty()) { - throw new StopExecutionException(); - } -} - -docker { - name containerImageName( - name: project.docker_image_default_repo_prefix + "python2.7_sdk", - root: project.rootProject.hasProperty(["docker-repository-root"]) ? - project.rootProject["docker-repository-root"] : - project.docker_image_default_repo_root, - tag: project.rootProject.hasProperty(["docker-tag"]) ? - project.rootProject["docker-tag"] : project.sdk_version) - files "../Dockerfile", "./build" - buildArgs(['py_version': "2.7", - 'pull_licenses': project.rootProject.hasProperty(["docker-pull-licenses"]) || - project.rootProject.hasProperty(["isRelease"])]) -} - -dockerPrepare.dependsOn copyLauncherDependencies -dockerPrepare.dependsOn copyDockerfileDependencies -dockerPrepare.dependsOn copyLicenseScripts +apply from: "../common.gradle" diff --git a/sdks/python/container/py35/build.gradle b/sdks/python/container/py35/build.gradle index 6a0133dd9916..25aa4f92e14c 100644 --- a/sdks/python/container/py35/build.gradle +++ b/sdks/python/container/py35/build.gradle @@ -21,55 +21,8 @@ plugins { id 'org.apache.beam.module' } applyDockerNature() +applyPythonNature() -description = "Apache Beam :: SDKs :: Python :: Container :: Python 35 Container" +pythonVersion = '3.5' -configurations { - sdkSourceTarball - sdkHarnessLauncher -} - -dependencies { - sdkSourceTarball project(path: ":sdks:python", configuration: "distTarBall") - sdkHarnessLauncher project(path: ":sdks:python:container", configuration: "sdkHarnessLauncher") -} - -task copyDockerfileDependencies(type: Copy) { - from configurations.sdkSourceTarball - from file("../base_image_requirements.txt") - into "build/target" - if(configurations.sdkSourceTarball.isEmpty()) { - throw new StopExecutionException(); - } -} - -task copyLicenseScripts(type: Copy){ - from ("../license_scripts") - into "build/target/license_scripts" -} - -task copyLauncherDependencies(type: Copy) { - from configurations.sdkHarnessLauncher - into "build/target/launcher" - if(configurations.sdkHarnessLauncher.isEmpty()) { - throw new StopExecutionException(); - } -} - -docker { - name containerImageName( - name: project.docker_image_default_repo_prefix + "python3.5_sdk", - root: project.rootProject.hasProperty(["docker-repository-root"]) ? - project.rootProject["docker-repository-root"] : - project.docker_image_default_repo_root, - tag: project.rootProject.hasProperty(["docker-tag"]) ? - project.rootProject["docker-tag"] : project.sdk_version) - files "../Dockerfile", "./build" - buildArgs(['py_version': "3.5", - 'pull_licenses': project.rootProject.hasProperty(["docker-pull-licenses"]) || - project.rootProject.hasProperty(["isRelease"])]) -} - -dockerPrepare.dependsOn copyLauncherDependencies -dockerPrepare.dependsOn copyDockerfileDependencies -dockerPrepare.dependsOn copyLicenseScripts +apply from: "../common.gradle" diff --git a/sdks/python/container/py36/build.gradle b/sdks/python/container/py36/build.gradle index b50267c29201..20fe8755bf50 100644 --- a/sdks/python/container/py36/build.gradle +++ b/sdks/python/container/py36/build.gradle @@ -21,55 +21,8 @@ plugins { id 'org.apache.beam.module' } applyDockerNature() +applyPythonNature() -description = "Apache Beam :: SDKs :: Python :: Container :: Python 36 Container" +pythonVersion = '3.6' -configurations { - sdkSourceTarball - sdkHarnessLauncher -} - -dependencies { - sdkSourceTarball project(path: ":sdks:python", configuration: "distTarBall") - sdkHarnessLauncher project(path: ":sdks:python:container", configuration: "sdkHarnessLauncher") -} - -task copyDockerfileDependencies(type: Copy) { - from configurations.sdkSourceTarball - from file("../base_image_requirements.txt") - into "build/target" - if(configurations.sdkSourceTarball.isEmpty()) { - throw new StopExecutionException(); - } -} - -task copyLicenseScripts(type: Copy){ - from ("../license_scripts") - into "build/target/license_scripts" -} - -task copyLauncherDependencies(type: Copy) { - from configurations.sdkHarnessLauncher - into "build/target/launcher" - if(configurations.sdkHarnessLauncher.isEmpty()) { - throw new StopExecutionException(); - } -} - -docker { - name containerImageName( - name: project.docker_image_default_repo_prefix + "python3.6_sdk", - root: project.rootProject.hasProperty(["docker-repository-root"]) ? - project.rootProject["docker-repository-root"] : - project.docker_image_default_repo_root, - tag: project.rootProject.hasProperty(["docker-tag"]) ? - project.rootProject["docker-tag"] : project.sdk_version) - files "../Dockerfile", "./build" - buildArgs(['py_version': "3.6", - 'pull_licenses': project.rootProject.hasProperty(["docker-pull-licenses"]) || - project.rootProject.hasProperty(["isRelease"])]) -} - -dockerPrepare.dependsOn copyLauncherDependencies -dockerPrepare.dependsOn copyDockerfileDependencies -dockerPrepare.dependsOn copyLicenseScripts +apply from: "../common.gradle" diff --git a/sdks/python/container/py37/build.gradle b/sdks/python/container/py37/build.gradle index 969a58db7945..547163a3514e 100644 --- a/sdks/python/container/py37/build.gradle +++ b/sdks/python/container/py37/build.gradle @@ -21,55 +21,8 @@ plugins { id 'org.apache.beam.module' } applyDockerNature() +applyPythonNature() -description = "Apache Beam :: SDKs :: Python :: Container :: Python 37 Container" +pythonVersion = '3.7' -configurations { - sdkSourceTarball - sdkHarnessLauncher -} - -dependencies { - sdkSourceTarball project(path: ":sdks:python", configuration: "distTarBall") - sdkHarnessLauncher project(path: ":sdks:python:container", configuration: "sdkHarnessLauncher") -} - -task copyDockerfileDependencies(type: Copy) { - from configurations.sdkSourceTarball - from file("../base_image_requirements.txt") - into "build/target" - if(configurations.sdkSourceTarball.isEmpty()) { - throw new StopExecutionException(); - } -} - -task copyLicenseScripts(type: Copy){ - from ("../license_scripts") - into "build/target/license_scripts" -} - -task copyLauncherDependencies(type: Copy) { - from configurations.sdkHarnessLauncher - into "build/target/launcher" - if(configurations.sdkHarnessLauncher.isEmpty()) { - throw new StopExecutionException(); - } -} - -docker { - name containerImageName( - name: project.docker_image_default_repo_prefix + "python3.7_sdk", - root: project.rootProject.hasProperty(["docker-repository-root"]) ? - project.rootProject["docker-repository-root"] : - project.docker_image_default_repo_root, - tag: project.rootProject.hasProperty(["docker-tag"]) ? - project.rootProject["docker-tag"] : project.sdk_version) - files "../Dockerfile", "./build" - buildArgs(['py_version': "3.7", - 'pull_licenses': project.rootProject.hasProperty(["docker-pull-licenses"]) || - project.rootProject.hasProperty(["isRelease"])]) -} - -dockerPrepare.dependsOn copyLauncherDependencies -dockerPrepare.dependsOn copyDockerfileDependencies -dockerPrepare.dependsOn copyLicenseScripts +apply from: "../common.gradle" From 09a1677906cae3a56a76c67e3e622565a1db408a Mon Sep 17 00:00:00 2001 From: Kamil Wasilewski Date: Tue, 19 May 2020 12:22:24 +0200 Subject: [PATCH 081/151] [BEAM-9936] Create SDK harness containers with Python3.8 --- ..._Python_ValidatesContainer_Dataflow.groovy | 2 ++ build.gradle | 1 + sdks/python/container/Dockerfile | 2 +- .../container/base_image_requirements.txt | 12 ++++---- sdks/python/container/build.gradle | 1 + .../license_scripts/dep_urls_py.yaml | 4 ++- sdks/python/container/py38/build.gradle | 28 +++++++++++++++++++ .../container/run_validatescontainer.sh | 20 +++++++------ settings.gradle | 1 + 9 files changed, 54 insertions(+), 17 deletions(-) create mode 100644 sdks/python/container/py38/build.gradle diff --git a/.test-infra/jenkins/job_PostCommit_Python_ValidatesContainer_Dataflow.groovy b/.test-infra/jenkins/job_PostCommit_Python_ValidatesContainer_Dataflow.groovy index f25f133c282e..bd5888f42df3 100644 --- a/.test-infra/jenkins/job_PostCommit_Python_ValidatesContainer_Dataflow.groovy +++ b/.test-infra/jenkins/job_PostCommit_Python_ValidatesContainer_Dataflow.groovy @@ -39,5 +39,7 @@ PostcommitJobBuilder.postCommitJob('beam_PostCommit_Py_ValCont', shell('cd ' + commonJobProperties.checkoutDir + ' && bash sdks/python/container/run_validatescontainer.sh python35') shell('cd ' + commonJobProperties.checkoutDir + ' && bash sdks/python/container/run_validatescontainer.sh python36') shell('cd ' + commonJobProperties.checkoutDir + ' && bash sdks/python/container/run_validatescontainer.sh python37') + // TODO(BEAM-9754): Turn on ValidatesContainer tests on Python 3.8 once BEAM-9754 is resolved. + // shell('cd ' + commonJobProperties.checkoutDir + ' && bash sdks/python/container/run_validatescontainer.sh python38') } } diff --git a/build.gradle b/build.gradle index 65363b7569dc..8de743ab983c 100644 --- a/build.gradle +++ b/build.gradle @@ -229,6 +229,7 @@ task pythonDockerBuildPreCommit() { dependsOn ":sdks:python:container:py35:docker" dependsOn ":sdks:python:container:py36:docker" dependsOn ":sdks:python:container:py37:docker" + dependsOn ":sdks:python:container:py38:docker" } task pythonLintPreCommit() { diff --git a/sdks/python/container/Dockerfile b/sdks/python/container/Dockerfile index 7af872384c18..f28d6e3b34a0 100644 --- a/sdks/python/container/Dockerfile +++ b/sdks/python/container/Dockerfile @@ -17,7 +17,7 @@ ############################################################################### ARG py_version -FROM python:"${py_version}"-stretch +FROM python:"${py_version}"-buster MAINTAINER "Apache Beam " ARG pull_licenses diff --git a/sdks/python/container/base_image_requirements.txt b/sdks/python/container/base_image_requirements.txt index f3d9b8622118..4c3fd767cb06 100644 --- a/sdks/python/container/base_image_requirements.txt +++ b/sdks/python/container/base_image_requirements.txt @@ -25,18 +25,18 @@ avro==1.8.2;python_version<="2.7" avro-python3==1.8.2;python_version>="3.4" -fastavro==0.21.24 +fastavro==0.23.3 crcmod==1.7 dill==0.3.1.1 -future==0.17.1 +future==0.18.2 futures==3.2.0;python_version<"3.0" grpcio==1.24.3 hdfs==2.5.8 httplib2==0.12.0 mock==2.0.0 oauth2client==3.0.0 -protobuf==3.11.1 -pyarrow==0.15.1 +protobuf==3.12.0 +pyarrow==0.16.0 pydot==1.4.1 pytz==2019.3 pyvcf==0.6.8;python_version<"3.0" @@ -66,8 +66,8 @@ pandas==0.24.2;python_version<="2.7" pandas==0.25.2;python_version>="3.4" protorpc==0.12.0 python-gflags==3.0.6 - -tensorflow==2.1.0 +tensorflow==2.1.0;python_version<="2.7" +tensorflow==2.2.0;python_version>="3.5" pymongo==3.9.0 # Packages needed for testing. diff --git a/sdks/python/container/build.gradle b/sdks/python/container/build.gradle index 2f7662caf3a7..f759088fbbbf 100644 --- a/sdks/python/container/build.gradle +++ b/sdks/python/container/build.gradle @@ -55,6 +55,7 @@ task buildAll { dependsOn ':sdks:python:container:py35:docker' dependsOn ':sdks:python:container:py36:docker' dependsOn ':sdks:python:container:py37:docker' + dependsOn ':sdks:python:container:py38:docker' } artifacts { diff --git a/sdks/python/container/license_scripts/dep_urls_py.yaml b/sdks/python/container/license_scripts/dep_urls_py.yaml index 4a2b6f355736..d1e194f0add1 100644 --- a/sdks/python/container/license_scripts/dep_urls_py.yaml +++ b/sdks/python/container/license_scripts/dep_urls_py.yaml @@ -114,7 +114,9 @@ pip_dependencies: license: "https://raw.githubusercontent.com/tensorflow/tensorflow/master/LICENSE" tensorflow-estimator: license: "https://raw.githubusercontent.com/tensorflow/estimator/master/LICENSE" + tensorboard-plugin-wit: + license: "https://raw.githubusercontent.com/PAIR-code/what-if-tool/master/LICENSE" timeloop: license: "https://raw.githubusercontent.com/sankalpjonn/timeloop/master/LICENSE" wget: - license: "https://raw.githubusercontent.com/mirror/wget/master/COPYING" \ No newline at end of file + license: "https://raw.githubusercontent.com/mirror/wget/master/COPYING" diff --git a/sdks/python/container/py38/build.gradle b/sdks/python/container/py38/build.gradle new file mode 100644 index 000000000000..304895a83718 --- /dev/null +++ b/sdks/python/container/py38/build.gradle @@ -0,0 +1,28 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * License); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an AS IS BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +plugins { + id 'base' + id 'org.apache.beam.module' +} +applyDockerNature() +applyPythonNature() + +pythonVersion = '3.8' + +apply from: "../common.gradle" diff --git a/sdks/python/container/run_validatescontainer.sh b/sdks/python/container/run_validatescontainer.sh index 2b48344ff149..330759d71d60 100755 --- a/sdks/python/container/run_validatescontainer.sh +++ b/sdks/python/container/run_validatescontainer.sh @@ -19,22 +19,23 @@ # This script will be run by Jenkins as a post commit test. In order to run # locally make the following changes: # -# LOCAL_PATH -> Path of tox and virtualenv if you have them already installed. # GCS_LOCATION -> Temporary location to use for service tests. # PROJECT -> Project name to use for dataflow and docker images. +# REGION -> Region name to use for Dataflow # # Execute from the root of the repository: # test Python2 container: ./sdks/python/container/run_validatescontainer.sh python2 # test Python3 container: ./sdks/python/container/run_validatescontainer.sh python35 # test Python3 container: ./sdks/python/container/run_validatescontainer.sh python36 # test Python3 container: ./sdks/python/container/run_validatescontainer.sh python37 +# test Python3 container: ./sdks/python/container/run_validatescontainer.sh python38 -echo "This script must be executed in the root of beam project. Please set LOCAL_PATH, GCS_LOCATION, and PROJECT as desired." +echo "This script must be executed in the root of beam project. Please set GCS_LOCATION, PROJECT and REGION as desired." if [[ $# != 1 ]]; then printf "Usage: \n$> ./sdks/python/container/run_validatescontainer.sh " printf "\n\tpython_version: [required] Python version used for container build and run tests." - printf " Use 'python2' for Python2, 'python35' for Python3.5, python36 for Python3.6, python37 for Python3.7." + printf " Use 'python2' for Python2, 'python35' for Python3.5, python36 for Python3.6, python37 for Python3.7, python38 for Python3.8." exit 1 fi @@ -46,31 +47,32 @@ GCS_LOCATION=${GCS_LOCATION:-gs://temp-storage-for-end-to-end-tests} # Project for the container and integration test PROJECT=${PROJECT:-apache-beam-testing} +REGION=${REGION:-us-central1} IMAGE_PREFIX="$(grep 'docker_image_default_repo_prefix' gradle.properties | cut -d'=' -f2)" # Other variables branched by Python version. if [[ $1 == "python2" ]]; then IMAGE_NAME="${IMAGE_PREFIX}python2.7_sdk" # Use this to create CONTAINER_IMAGE variable. CONTAINER_PROJECT="sdks:python:container:py2" # Use this to build container by Gradle. - GRADLE_PY3_FLAG="" # Use this in Gradle command. PY_INTERPRETER="python" # Use this in virtualenv command. elif [[ $1 == "python35" ]]; then IMAGE_NAME="${IMAGE_PREFIX}python3.5_sdk" # Use this to create CONTAINER_IMAGE variable. CONTAINER_PROJECT="sdks:python:container:py35" # Use this to build container by Gradle. - GRADLE_PY3_FLAG="-Ppython3" # Use this in Gradle command. PY_INTERPRETER="python3.5" # Use this in virtualenv command. elif [[ $1 == "python36" ]]; then IMAGE_NAME="${IMAGE_PREFIX}python3.6_sdk" # Use this to create CONTAINER_IMAGE variable. CONTAINER_PROJECT="sdks:python:container:py36" # Use this to build container by Gradle. - GRADLE_PY3_FLAG="-Ppython3" # Use this in Gradle command. PY_INTERPRETER="python3.6" # Use this in virtualenv command. elif [[ $1 == "python37" ]]; then IMAGE_NAME="${IMAGE_PREFIX}python3.7_sdk" # Use this to create CONTAINER_IMAGE variable. CONTAINER_PROJECT="sdks:python:container:py37" # Use this to build container by Gradle. - GRADLE_PY3_FLAG="-Ppython3" # Use this in Gradle command. PY_INTERPRETER="python3.7" # Use this in virtualenv command. +elif [[ $1 == "python38" ]]; then + IMAGE_NAME="${IMAGE_PREFIX}python3.8_sdk" # Use this to create CONTAINER_IMAGE variable. + CONTAINER_PROJECT="sdks:python:container:py38" # Use this to build container by Gradle. + PY_INTERPRETER="python3.8" # Use this in virtualenv command. else - echo "Must set Python version with one of 'python2', 'python35', 'python36' and 'python37' from commandline." + echo "Must set Python version with one of 'python2', 'python35', 'python36', 'python37' and 'python38' from commandline." exit 1 fi XUNIT_FILE="nosetests-$IMAGE_NAME.xml" @@ -88,7 +90,7 @@ gcloud -v TAG=$(date +%Y%m%d-%H%M%S) CONTAINER=us.gcr.io/$PROJECT/$USER/$IMAGE_NAME echo "Using container $CONTAINER" -./gradlew :$CONTAINER_PROJECT:docker -Pdocker-repository-root=us.gcr.io/$PROJECT/$USER -Pdocker-tag=$TAG $GRADLE_PY3_FLAG --info +./gradlew :$CONTAINER_PROJECT:docker -Pdocker-repository-root=us.gcr.io/$PROJECT/$USER -Pdocker-tag=$TAG --info # Verify it exists docker images | grep $TAG diff --git a/settings.gradle b/settings.gradle index 8a80ffd06298..36493decd0e3 100644 --- a/settings.gradle +++ b/settings.gradle @@ -138,6 +138,7 @@ include ":sdks:python:container:py2" include ":sdks:python:container:py35" include ":sdks:python:container:py36" include ":sdks:python:container:py37" +include ":sdks:python:container:py38" include ":sdks:python:test-suites:dataflow:py2" include ":sdks:python:test-suites:dataflow:py35" include ":sdks:python:test-suites:dataflow:py36" From 6654a3daab11bb9428482df9c68cfcee03deadd8 Mon Sep 17 00:00:00 2001 From: Kamil Wasilewski Date: Wed, 13 May 2020 16:33:43 +0200 Subject: [PATCH 082/151] [BEAM-9810] Tox suites for Python 3.8 --- build.gradle | 3 +- sdks/python/test-suites/tox/py37/build.gradle | 3 -- sdks/python/test-suites/tox/py38/build.gradle | 35 +++++++++++++++++++ .../test-suites/tox/pycommon/build.gradle | 2 +- sdks/python/tox.ini | 27 ++++++++++++-- settings.gradle | 1 + 6 files changed, 64 insertions(+), 7 deletions(-) create mode 100644 sdks/python/test-suites/tox/py38/build.gradle diff --git a/build.gradle b/build.gradle index 65363b7569dc..f8fd0a1a0072 100644 --- a/build.gradle +++ b/build.gradle @@ -215,6 +215,7 @@ task pythonPreCommit() { dependsOn ":sdks:python:test-suites:tox:py35:preCommitPy35" dependsOn ":sdks:python:test-suites:tox:py36:preCommitPy36" dependsOn ":sdks:python:test-suites:tox:py37:preCommitPy37" + dependsOn ":sdks:python:test-suites:tox:py38:preCommitPy38" dependsOn ":sdks:python:test-suites:dataflow:py2:preCommitIT" dependsOn ":sdks:python:test-suites:dataflow:py2:preCommitIT_V2" dependsOn ":sdks:python:test-suites:dataflow:py37:preCommitIT" @@ -237,7 +238,7 @@ task pythonLintPreCommit() { } task pythonFormatterPreCommit() { - dependsOn 'sdks:python:test-suites:tox:py37:formatter' + dependsOn 'sdks:python:test-suites:tox:py38:formatter' } task python2PostCommit() { diff --git a/sdks/python/test-suites/tox/py37/build.gradle b/sdks/python/test-suites/tox/py37/build.gradle index f9126da48903..2583d385bc50 100644 --- a/sdks/python/test-suites/tox/py37/build.gradle +++ b/sdks/python/test-suites/tox/py37/build.gradle @@ -35,9 +35,6 @@ lint.dependsOn lintPy37 toxTask "mypyPy37", "py37-mypy" lint.dependsOn mypyPy37 -toxTask "formatter", "py3-yapf-check" -check.dependsOn formatter - apply from: "../common.gradle" // TODO(BEAM-8954): Remove this once tox uses isolated builds. diff --git a/sdks/python/test-suites/tox/py38/build.gradle b/sdks/python/test-suites/tox/py38/build.gradle new file mode 100644 index 000000000000..96b02f805c25 --- /dev/null +++ b/sdks/python/test-suites/tox/py38/build.gradle @@ -0,0 +1,35 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * License); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an AS IS BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +/** + * Unit tests for Python 3.8 + */ + +plugins { id 'org.apache.beam.module' } +applyPythonNature() + +// Required to setup a Python 3 virtualenv and task names. +pythonVersion = '3.8' + +toxTask "formatter", "py3-yapf-check" +check.dependsOn formatter + +apply from: "../common.gradle" + +// TODO(BEAM-8954): Remove this once tox uses isolated builds. +testPy38Cython.mustRunAfter testPython38, testPy38Cloud diff --git a/sdks/python/test-suites/tox/pycommon/build.gradle b/sdks/python/test-suites/tox/pycommon/build.gradle index 80ad2d4175f0..80342ce990d5 100644 --- a/sdks/python/test-suites/tox/pycommon/build.gradle +++ b/sdks/python/test-suites/tox/pycommon/build.gradle @@ -23,7 +23,7 @@ plugins { id 'org.apache.beam.module' } applyPythonNature() -toxTask "docs", "py37-docs" +toxTask "docs", "py38-docs" assemble.dependsOn docs task preCommitPyCommon() { diff --git a/sdks/python/tox.ini b/sdks/python/tox.ini index 2726a74d39a1..745ed926907a 100644 --- a/sdks/python/tox.ini +++ b/sdks/python/tox.ini @@ -17,7 +17,7 @@ [tox] # new environments will be excluded by default unless explicitly added to envlist. -envlist = py27,py35,py36,py37,py27-{cloud,cython,lint,lint3},py35-{cloud,cython},py36-{cloud,cython},py37-{cloud,cython,lint,mypy,docs} +envlist = py27,py35,py36,py37,py27-{cloud,cython,lint,lint3},py35-{cloud,cython},py36-{cloud,cython},py37-{cloud,cython,lint,mypy},py38-{cloud,cython,docs} toxworkdir = {toxinidir}/target/{env:ENV_NAME:.tox} [pycodestyle] @@ -76,6 +76,11 @@ commands = python apache_beam/examples/complete/autocomplete_test.py {toxinidir}/scripts/run_pytest.sh {envname} "{posargs}" +[testenv:py38] +commands = + python apache_beam/examples/complete/autocomplete_test.py + {toxinidir}/scripts/run_pytest.sh {envname} "{posargs}" + [testenv:py27-cython] # cython tests are only expected to work in linux (2.x and 3.x) # If we want to add other platforms in the future, it should be: @@ -128,6 +133,19 @@ commands = python apache_beam/examples/complete/autocomplete_test.py {toxinidir}/scripts/run_pytest.sh {envname} "{posargs}" +[testenv:py38-cython] +# cython tests are only expected to work in linux (2.x and 3.x) +# If we want to add other platforms in the future, it should be: +# `platform = linux2|darwin|...` +# See https://docs.python.org/2/library/sys.html#sys.platform for platform codes +platform = linux +commands = + # TODO(BEAM-8954): Remove this build_ext invocation once local source no longer + # shadows the installed apache_beam. + python setup.py build_ext --inplace + python apache_beam/examples/complete/autocomplete_test.py + {toxinidir}/scripts/run_pytest.sh {envname} "{posargs}" + [testenv:py27-cloud] extras = test,gcp,aws commands = @@ -149,6 +167,11 @@ extras = test,gcp,interactive,aws commands = {toxinidir}/scripts/run_pytest.sh {envname} "{posargs}" +[testenv:py38-cloud] +extras = test,gcp,interactive,aws +commands = + {toxinidir}/scripts/run_pytest.sh {envname} "{posargs}" + [testenv:py27-lint] # Checks for py2 syntax errors deps = @@ -197,7 +220,7 @@ commands = mypy --version python setup.py mypy -[testenv:py37-docs] +[testenv:py38-docs] extras = test,gcp,docs,interactive deps = Sphinx==3.0.3 diff --git a/settings.gradle b/settings.gradle index 8a80ffd06298..e7bceb4c5c03 100644 --- a/settings.gradle +++ b/settings.gradle @@ -155,6 +155,7 @@ include ":sdks:python:test-suites:tox:py2" include ":sdks:python:test-suites:tox:py35" include ":sdks:python:test-suites:tox:py36" include ":sdks:python:test-suites:tox:py37" +include ":sdks:python:test-suites:tox:py38" include ":vendor:grpc-1_26_0" include ":vendor:bytebuddy-1_10_8" include ":vendor:calcite-1_20_0" From c0c786d41e36d1d1359c1fb96046d24f2a0326f3 Mon Sep 17 00:00:00 2001 From: Kamil Wasilewski Date: Thu, 14 May 2020 18:14:49 +0200 Subject: [PATCH 083/151] [BEAM-9810] Fix 'dictionary keys changed during iteration' error --- .../apache_beam/io/hadoopfilesystem_test.py | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/sdks/python/apache_beam/io/hadoopfilesystem_test.py b/sdks/python/apache_beam/io/hadoopfilesystem_test.py index a4b513b5876b..e83091f145c9 100644 --- a/sdks/python/apache_beam/io/hadoopfilesystem_test.py +++ b/sdks/python/apache_beam/io/hadoopfilesystem_test.py @@ -190,12 +190,15 @@ def rename(self, path1, path2): if self.status(path1, strict=False) is None: raise FakeHdfsError('Path1 not found: %s' % path1) - for fullpath in self.files.keys(): # pylint: disable=consider-iterating-dictionary - if fullpath == path1 or fullpath.startswith(path1 + '/'): - f = self.files.pop(fullpath) - newpath = path2 + fullpath[len(path1):] - f.stat['path'] = newpath - self.files[newpath] = f + files_to_rename = [ + path for path in self.files + if path == path1 or path.startswith(path1 + '/') + ] + for fullpath in files_to_rename: + f = self.files.pop(fullpath) + newpath = path2 + fullpath[len(path1):] + f.stat['path'] = newpath + self.files[newpath] = f def checksum(self, path): f = self.files.get(path, None) From c2b9867d9374dde9cc93c65d694e63acf276e4bb Mon Sep 17 00:00:00 2001 From: Kamil Wasilewski Date: Wed, 13 May 2020 16:00:27 +0200 Subject: [PATCH 084/151] [BEAM-9810] Disable all failing tests until Dataflow runner supports Python 3.8 --- .../runners/dataflow/dataflow_runner_test.py | 57 ++++++++++++++++ .../dataflow/internal/apiclient_test.py | 66 +++++++++++++++++++ .../runners/dataflow/template_runner_test.py | 3 + 3 files changed, 126 insertions(+) diff --git a/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py b/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py index 32ace1a8eef8..16ea3362661a 100644 --- a/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py +++ b/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py @@ -225,6 +225,9 @@ def test_environment_override_translation(self): capabilities=environments.python_sdk_capabilities()) ]) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_remote_runner_translation(self): remote_runner = DataflowRunner() with Pipeline(remote_runner, @@ -235,6 +238,9 @@ def test_remote_runner_translation(self): | 'Do' >> ptransform.FlatMap(lambda x: [(x, x)]) | ptransform.GroupByKey()) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_streaming_create_translation(self): remote_runner = DataflowRunner() self.default_properties.append("--streaming") @@ -250,6 +256,9 @@ def test_streaming_create_translation(self): self.assertEqual(job_dict[u'steps'][1][u'kind'], u'ParallelDo') self.assertEqual(job_dict[u'steps'][2][u'kind'], u'ParallelDo') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_bigquery_read_streaming_fail(self): remote_runner = DataflowRunner() self.default_properties.append("--streaming") @@ -259,6 +268,9 @@ def test_bigquery_read_streaming_fail(self): PipelineOptions(self.default_properties)) as p: _ = p | beam.io.Read(beam.io.BigQuerySource('some.table')) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_biqquery_read_fn_api_fail(self): remote_runner = DataflowRunner() for flag in ['beam_fn_api', 'use_unified_worker', 'use_runner_v2']: @@ -271,6 +283,9 @@ def test_biqquery_read_fn_api_fail(self): PipelineOptions(self.default_properties)) as p: _ = p | beam.io.Read(beam.io.BigQuerySource('some.table')) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_remote_runner_display_data(self): remote_runner = DataflowRunner() p = Pipeline( @@ -313,6 +328,9 @@ def test_remote_runner_display_data(self): }] self.assertUnhashableCountEqual(disp_data, expected_data) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_no_group_by_key_directly_after_bigquery(self): remote_runner = DataflowRunner() with self.assertRaises(ValueError, @@ -438,6 +456,9 @@ def test_side_input_visitor(self): common_urns.side_inputs.MULTIMAP.urn, side_input._side_input_data().access_pattern) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_min_cpu_platform_flag_is_propagated_to_experiments(self): remote_runner = DataflowRunner() self.default_properties.append('--min_cpu_platform=Intel Haswell') @@ -448,6 +469,9 @@ def test_min_cpu_platform_flag_is_propagated_to_experiments(self): 'min_cpu_platform=Intel Haswell', remote_runner.job.options.view_as(DebugOptions).experiments) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_streaming_engine_flag_adds_windmill_experiments(self): remote_runner = DataflowRunner() self.default_properties.append('--streaming') @@ -463,6 +487,9 @@ def test_streaming_engine_flag_adds_windmill_experiments(self): self.assertIn('enable_windmill_service', experiments_for_job) self.assertIn('some_other_experiment', experiments_for_job) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_upload_graph_experiment(self): remote_runner = DataflowRunner() self.default_properties.append('--experiment=upload_graph') @@ -474,6 +501,9 @@ def test_upload_graph_experiment(self): remote_runner.job.options.view_as(DebugOptions).experiments) self.assertIn('upload_graph', experiments_for_job) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_dataflow_worker_jar_flag_non_fnapi_noop(self): remote_runner = DataflowRunner() self.default_properties.append('--experiment=some_other_experiment') @@ -487,6 +517,9 @@ def test_dataflow_worker_jar_flag_non_fnapi_noop(self): self.assertIn('some_other_experiment', experiments_for_job) self.assertNotIn('use_staged_dataflow_worker_jar', experiments_for_job) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_dataflow_worker_jar_flag_adds_use_staged_worker_jar_experiment(self): remote_runner = DataflowRunner() self.default_properties.append('--experiment=beam_fn_api') @@ -500,6 +533,9 @@ def test_dataflow_worker_jar_flag_adds_use_staged_worker_jar_experiment(self): self.assertIn('beam_fn_api', experiments_for_job) self.assertIn('use_staged_dataflow_worker_jar', experiments_for_job) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_use_fastavro_experiment_is_added_on_py3_and_onwards(self): remote_runner = DataflowRunner() @@ -511,6 +547,9 @@ def test_use_fastavro_experiment_is_added_on_py3_and_onwards(self): remote_runner.job.options.view_as(DebugOptions).lookup_experiment( 'use_fastavro', False)) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_use_fastavro_experiment_is_not_added_when_use_avro_is_present(self): remote_runner = DataflowRunner() self.default_properties.append('--experiment=use_avro') @@ -522,6 +561,9 @@ def test_use_fastavro_experiment_is_not_added_when_use_avro_is_present(self): self.assertFalse(debug_options.lookup_experiment('use_fastavro', False)) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_unsupported_fnapi_features(self): remote_runner = DataflowRunner() self.default_properties.append('--experiment=beam_fn_api') @@ -575,6 +617,9 @@ def test_get_default_gcp_region_ignores_error( result = runner.get_default_gcp_region() self.assertIsNone(result) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_combine_values_translation(self): runner = DataflowRunner() @@ -625,6 +670,9 @@ def expect_correct_override(self, job, step_name, step_kind): self.assertGreater(len(step[u'properties']['display_data']), 0) self.assertEqual(step[u'properties']['output_info'], expected_output_info) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_read_create_translation(self): runner = DataflowRunner() @@ -635,6 +683,9 @@ def test_read_create_translation(self): self.expect_correct_override(runner.job, u'Create/Read', u'ParallelRead') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_read_bigquery_translation(self): runner = DataflowRunner() @@ -645,6 +696,9 @@ def test_read_bigquery_translation(self): self.expect_correct_override(runner.job, u'Read', u'ParallelRead') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_read_pubsub_translation(self): runner = DataflowRunner() @@ -658,6 +712,9 @@ def test_read_pubsub_translation(self): self.expect_correct_override( runner.job, u'ReadFromPubSub/Read', u'ParallelRead') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_gbk_translation(self): runner = DataflowRunner() with beam.Pipeline(runner=runner, diff --git a/sdks/python/apache_beam/runners/dataflow/internal/apiclient_test.py b/sdks/python/apache_beam/runners/dataflow/internal/apiclient_test.py index 7776156bd460..b42ab12d0e35 100644 --- a/sdks/python/apache_beam/runners/dataflow/internal/apiclient_test.py +++ b/sdks/python/apache_beam/runners/dataflow/internal/apiclient_test.py @@ -61,6 +61,9 @@ def test_create_application_client(self): pipeline_options = PipelineOptions() apiclient.DataflowApplicationClient(pipeline_options) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_pipeline_url(self): pipeline_options = PipelineOptions([ '--subnetwork', @@ -92,6 +95,9 @@ def test_pipeline_url(self): self.assertEqual(pipeline_url.string_value, FAKE_PIPELINE_URL) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_set_network(self): pipeline_options = PipelineOptions([ '--network', @@ -105,6 +111,9 @@ def test_set_network(self): FAKE_PIPELINE_URL) self.assertEqual(env.proto.workerPools[0].network, 'anetworkname') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_set_subnetwork(self): pipeline_options = PipelineOptions([ '--subnetwork', @@ -121,6 +130,9 @@ def test_set_subnetwork(self): env.proto.workerPools[0].subnetwork, '/regions/MY/subnetworks/SUBNETWORK') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_flexrs_blank(self): pipeline_options = PipelineOptions( ['--temp_location', 'gs://any-location/temp']) @@ -131,6 +143,9 @@ def test_flexrs_blank(self): FAKE_PIPELINE_URL) self.assertEqual(env.proto.flexResourceSchedulingGoal, None) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_flexrs_cost(self): pipeline_options = PipelineOptions([ '--flexrs_goal', @@ -149,6 +164,9 @@ def test_flexrs_cost(self): dataflow.Environment.FlexResourceSchedulingGoalValueValuesEnum. FLEXRS_COST_OPTIMIZED)) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_flexrs_speed(self): pipeline_options = PipelineOptions([ '--flexrs_goal', @@ -167,6 +185,9 @@ def test_flexrs_speed(self): dataflow.Environment.FlexResourceSchedulingGoalValueValuesEnum. FLEXRS_SPEED_OPTIMIZED)) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_sdk_harness_container_images_get_set(self): pipeline_options = PipelineOptions([ @@ -350,6 +371,9 @@ def test_translate_means_using_distribution_accumulator(self): self.assertEqual( metric_update.floatingPointMean.count.lowBits, accumulator.count) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_default_ip_configuration(self): pipeline_options = PipelineOptions( ['--temp_location', 'gs://any-location/temp']) @@ -359,6 +383,9 @@ def test_default_ip_configuration(self): FAKE_PIPELINE_URL) self.assertEqual(env.proto.workerPools[0].ipConfiguration, None) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_public_ip_configuration(self): pipeline_options = PipelineOptions( ['--temp_location', 'gs://any-location/temp', '--use_public_ips']) @@ -370,6 +397,9 @@ def test_public_ip_configuration(self): env.proto.workerPools[0].ipConfiguration, dataflow.WorkerPool.IpConfigurationValueValuesEnum.WORKER_IP_PUBLIC) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_private_ip_configuration(self): pipeline_options = PipelineOptions( ['--temp_location', 'gs://any-location/temp', '--no_use_public_ips']) @@ -381,6 +411,9 @@ def test_private_ip_configuration(self): env.proto.workerPools[0].ipConfiguration, dataflow.WorkerPool.IpConfigurationValueValuesEnum.WORKER_IP_PRIVATE) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_number_of_worker_harness_threads(self): pipeline_options = PipelineOptions([ '--temp_location', @@ -398,6 +431,9 @@ def test_number_of_worker_harness_threads(self): 'apache_beam.runners.dataflow.internal.apiclient.' 'beam_version.__version__', '2.2.0') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_harness_override_default_in_released_sdks(self): pipeline_options = PipelineOptions( ['--temp_location', 'gs://any-location/temp', '--streaming']) @@ -416,6 +452,9 @@ def test_harness_override_default_in_released_sdks(self): 'apache_beam.runners.dataflow.internal.apiclient.' 'beam_version.__version__', '2.2.0') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_harness_override_absent_in_released_sdks_with_runner_v2(self): pipeline_options = PipelineOptions([ '--temp_location', @@ -436,6 +475,9 @@ def test_harness_override_absent_in_released_sdks_with_runner_v2(self): 'apache_beam.runners.dataflow.internal.apiclient.' 'beam_version.__version__', '2.2.0') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_harness_override_custom_in_released_sdks(self): pipeline_options = PipelineOptions([ '--temp_location', @@ -460,6 +502,9 @@ def test_harness_override_custom_in_released_sdks(self): 'apache_beam.runners.dataflow.internal.apiclient.' 'beam_version.__version__', '2.2.0') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_harness_override_custom_in_released_sdks_with_runner_v2(self): pipeline_options = PipelineOptions([ '--temp_location', @@ -485,6 +530,9 @@ def test_harness_override_custom_in_released_sdks_with_runner_v2(self): 'apache_beam.runners.dataflow.internal.apiclient.' 'beam_version.__version__', '2.2.0.rc1') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_harness_override_uses_base_version_in_rc_releases(self): pipeline_options = PipelineOptions( ['--temp_location', 'gs://any-location/temp', '--streaming']) @@ -503,6 +551,9 @@ def test_harness_override_uses_base_version_in_rc_releases(self): 'apache_beam.runners.dataflow.internal.apiclient.' 'beam_version.__version__', '2.2.0.dev') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_harness_override_absent_in_unreleased_sdk(self): pipeline_options = PipelineOptions( ['--temp_location', 'gs://any-location/temp', '--streaming']) @@ -518,6 +569,9 @@ def test_harness_override_absent_in_unreleased_sdk(self): 'apache_beam.runners.dataflow.internal.apiclient.' 'beam_version.__version__', '2.2.0.dev') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_pinned_worker_harness_image_tag_used_in_dev_sdk(self): # streaming, fnapi pipeline. pipeline_options = PipelineOptions( @@ -580,6 +634,9 @@ def test_pinned_worker_harness_image_tag_used_in_dev_sdk(self): 'apache_beam.runners.dataflow.internal.apiclient.' 'beam_version.__version__', '2.2.0') + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_worker_harness_image_tag_matches_released_sdk_version(self): # streaming, fnapi pipeline. pipeline_options = PipelineOptions( @@ -630,6 +687,9 @@ def test_worker_harness_image_tag_matches_released_sdk_version(self): 'apache_beam.runners.dataflow.internal.apiclient.' 'beam_version.__version__', '2.2.0.rc1') + @unittest.skipIf( + sys.version_info.minor == 8, 'Re-enable once BEAM-9754 is ' + 'resolved') def test_worker_harness_image_tag_matches_base_sdk_version_of_an_rc(self): # streaming, fnapi pipeline. pipeline_options = PipelineOptions( @@ -676,6 +736,9 @@ def test_worker_harness_image_tag_matches_base_sdk_version_of_an_rc(self): names.DATAFLOW_CONTAINER_IMAGE_REPOSITORY + '/python%d%d:2.2.0' % (sys.version_info[0], sys.version_info[1]))) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_worker_harness_override_takes_precedence_over_sdk_defaults(self): # streaming, fnapi pipeline. pipeline_options = PipelineOptions([ @@ -765,6 +828,9 @@ def test_labels(self): self.assertEqual('key5', job.proto.labels.additionalProperties[4].key) self.assertEqual('', job.proto.labels.additionalProperties[4].value) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_experiment_use_multiple_sdk_containers(self): pipeline_options = PipelineOptions([ '--project', diff --git a/sdks/python/apache_beam/runners/dataflow/template_runner_test.py b/sdks/python/apache_beam/runners/dataflow/template_runner_test.py index 54e39a5ee21a..3c173924f006 100644 --- a/sdks/python/apache_beam/runners/dataflow/template_runner_test.py +++ b/sdks/python/apache_beam/runners/dataflow/template_runner_test.py @@ -22,6 +22,7 @@ from __future__ import absolute_import import json +import sys import tempfile import unittest @@ -40,6 +41,8 @@ @unittest.skipIf(apiclient is None, 'GCP dependencies are not installed') +@unittest.skipIf( + sys.version_info.minor == 8, 'Doesn\'t work on Python 3.8, see: BEAM-9754') class TemplatingDataflowRunnerTest(unittest.TestCase): """TemplatingDataflow tests.""" def test_full_completion(self): From 63b4d3a27a5e6400cf8cf812bc46ed5350f36bde Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Isma=C3=ABl=20Mej=C3=ADa?= Date: Thu, 9 Apr 2020 02:06:21 +0200 Subject: [PATCH 085/151] [BEAM-7770] Make ReplicaInfo part of Read on SolrIO --- .../org/apache/beam/sdk/io/solr/SolrIO.java | 47 ++++++++++++------- 1 file changed, 29 insertions(+), 18 deletions(-) diff --git a/sdks/java/io/solr/src/main/java/org/apache/beam/sdk/io/solr/SolrIO.java b/sdks/java/io/solr/src/main/java/org/apache/beam/sdk/io/solr/SolrIO.java index 747ac86c881b..01fc612d1b52 100644 --- a/sdks/java/io/solr/src/main/java/org/apache/beam/sdk/io/solr/SolrIO.java +++ b/sdks/java/io/solr/src/main/java/org/apache/beam/sdk/io/solr/SolrIO.java @@ -41,7 +41,6 @@ import org.apache.beam.sdk.util.BackOffUtils; import org.apache.beam.sdk.util.FluentBackoff; import org.apache.beam.sdk.util.Sleeper; -import org.apache.beam.sdk.values.KV; import org.apache.beam.sdk.values.PBegin; import org.apache.beam.sdk.values.PCollection; import org.apache.beam.sdk.values.PDone; @@ -306,17 +305,22 @@ public abstract static class Read extends PTransform 0 && batchSize < MAX_BATCH_SIZE, - "Valid values for batchSize are 1 (inclusize) to %s (exclusive), but was: %s ", + "Valid values for batchSize are 1 (inclusive) to %s (exclusive), but was: %s ", MAX_BATCH_SIZE, batchSize); return builder().setBatchSize(batchSize).build(); } + /** Read from a specific Replica (partition). */ + public Read withReplicaInfo(ReplicaInfo replicaInfo) { + checkArgument(replicaInfo != null, "replicaInfo can not be null"); + return builder().setReplicaInfo(replicaInfo).build(); + } + @Override public PCollection expand(PBegin input) { checkArgument( @@ -386,14 +396,18 @@ public PCollection expand(PBegin input) { @Override public void populateDisplayData(DisplayData.Builder builder) { super.populateDisplayData(builder); - builder.addIfNotNull(DisplayData.item("query", getQuery())); getConnectionConfiguration().populateDisplayData(builder); + builder.add(DisplayData.item("collection", getCollection())); + builder.addIfNotNull(DisplayData.item("query", getQuery())); + builder.add(DisplayData.item("batchSize", getBatchSize())); + final String replicaInfo = (getReplicaInfo() != null) ? getReplicaInfo().toString() : null; + builder.addIfNotNull(DisplayData.item("replicaInfo", replicaInfo)); } } /** A POJO describing a replica of Solr. */ @AutoValue - abstract static class ReplicaInfo implements Serializable { + public abstract static class ReplicaInfo implements Serializable { public abstract String coreName(); public abstract String coreUrl(); @@ -408,10 +422,9 @@ static ReplicaInfo create(Replica replica) { } } - static class SplitFn extends DoFn> { + private static class SplitFn extends DoFn { @ProcessElement - public void process(@Element SolrIO.Read spec, OutputReceiver> out) - throws IOException { + public void process(@Element Read spec, OutputReceiver out) throws IOException { ConnectionConfiguration connectionConfig = spec.getConnectionConfiguration(); try (AuthorizedSolrClient client = connectionConfig.createClient()) { String collection = spec.getCollection(); @@ -437,19 +450,17 @@ public void process(@Element SolrIO.Read spec, OutputReceiver, SolrDocument> { + private static class ReadFn extends DoFn { @ProcessElement - public void process( - @Element KV specAndReplica, OutputReceiver out) - throws IOException { - Read spec = specAndReplica.getKey(); - ReplicaInfo replica = specAndReplica.getValue(); + public void process(@Element Read spec, OutputReceiver out) throws IOException { + ReplicaInfo replicaInfo = spec.getReplicaInfo(); + checkArgument(replicaInfo != null, "replicaInfo is required"); String cursorMark = CursorMarkParams.CURSOR_MARK_START; String query = spec.getQuery(); if (query == null) { @@ -459,7 +470,7 @@ public void process( solrQuery.setRows(spec.getBatchSize()); solrQuery.setDistrib(false); try (AuthorizedSolrClient client = - spec.getConnectionConfiguration().createClient(replica.baseUrl())) { + spec.getConnectionConfiguration().createClient(replicaInfo.baseUrl())) { SchemaRequest.UniqueKey request = new SchemaRequest.UniqueKey(); try { SchemaResponse.UniqueKeyResponse response = client.process(spec.getCollection(), request); @@ -472,7 +483,7 @@ public void process( solrQuery.set(CursorMarkParams.CURSOR_MARK_PARAM, cursorMark); try { QueryResponse response; - response = client.query(replica.coreName(), solrQuery); + response = client.query(replicaInfo.coreName(), solrQuery); if (cursorMark.equals(response.getNextCursorMark())) { break; } @@ -599,7 +610,7 @@ static class WriteFn extends DoFn { } @Setup - public void setup() throws Exception { + public void setup() { solrClient = spec.getConnectionConfiguration().createClient(); retryBackoff = From 61eebf0e4623e67ef9f5430052ea5d26c7b69d0a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Isma=C3=ABl=20Mej=C3=ADa?= Date: Thu, 9 Apr 2020 02:33:46 +0200 Subject: [PATCH 086/151] [BEAM-7770] Add ReadAll transform for SolrIO --- .../org/apache/beam/sdk/io/solr/SolrIO.java | 21 +++++++++++++------ .../apache/beam/sdk/io/solr/SolrIOTest.java | 17 +++++++++++++++ 2 files changed, 32 insertions(+), 6 deletions(-) diff --git a/sdks/java/io/solr/src/main/java/org/apache/beam/sdk/io/solr/SolrIO.java b/sdks/java/io/solr/src/main/java/org/apache/beam/sdk/io/solr/SolrIO.java index 01fc612d1b52..7b23839ce083 100644 --- a/sdks/java/io/solr/src/main/java/org/apache/beam/sdk/io/solr/SolrIO.java +++ b/sdks/java/io/solr/src/main/java/org/apache/beam/sdk/io/solr/SolrIO.java @@ -123,6 +123,10 @@ public static Read read() { return new AutoValue_SolrIO_Read.Builder().setBatchSize(1000).setQuery("*:*").build(); } + public static ReadAll readAll() { + return new ReadAll(); + } + public static Write write() { // 1000 for batch size is good enough in many cases, // ex: if document size is large, around 10KB, the request's size will be around 10MB @@ -385,12 +389,7 @@ public PCollection expand(PBegin input) { checkArgument( getConnectionConfiguration() != null, "withConnectionConfiguration() is required"); checkArgument(getCollection() != null, "from() is required"); - - return input - .apply("Create", Create.of(this)) - .apply("Split", ParDo.of(new SplitFn())) - .apply("Reshuffle", Reshuffle.viaRandomKey()) - .apply("Read", ParDo.of(new ReadFn())); + return input.apply("Create", Create.of(this)).apply("ReadAll", readAll()); } @Override @@ -499,6 +498,16 @@ public void process(@Element Read spec, OutputReceiver out) throws } } + public static class ReadAll extends PTransform, PCollection> { + @Override + public PCollection expand(PCollection input) { + return input + .apply("Split", ParDo.of(new SplitFn())) + .apply("Reshuffle", Reshuffle.viaRandomKey()) + .apply("Read", ParDo.of(new ReadFn())); + } + } + /** A {@link PTransform} writing data to Solr. */ @AutoValue public abstract static class Write extends PTransform, PDone> { diff --git a/sdks/java/io/solr/src/test/java/org/apache/beam/sdk/io/solr/SolrIOTest.java b/sdks/java/io/solr/src/test/java/org/apache/beam/sdk/io/solr/SolrIOTest.java index 09c38a2b57e6..6f666b8600db 100644 --- a/sdks/java/io/solr/src/test/java/org/apache/beam/sdk/io/solr/SolrIOTest.java +++ b/sdks/java/io/solr/src/test/java/org/apache/beam/sdk/io/solr/SolrIOTest.java @@ -155,6 +155,23 @@ public void testRead() throws Exception { pipeline.run(); } + @Test + public void testReadAll() throws Exception { + SolrIOTestUtils.insertTestDocuments(SOLR_COLLECTION, NUM_DOCS, solrClient); + + PCollection output = + pipeline + .apply( + Create.of( + SolrIO.read() + .withConnectionConfiguration(connectionConfiguration) + .from(SOLR_COLLECTION) + .withBatchSize(101))) + .apply(SolrIO.readAll()); + PAssert.thatSingleton(output.apply("Count", Count.globally())).isEqualTo(NUM_DOCS); + pipeline.run(); + } + @Test public void testReadWithQuery() throws Exception { SolrIOTestUtils.insertTestDocuments(SOLR_COLLECTION, NUM_DOCS, solrClient); From 9199598ea6bc185822fc888fa6dc376dacb9d641 Mon Sep 17 00:00:00 2001 From: Piotr Szuberski Date: Wed, 27 May 2020 15:41:50 +0200 Subject: [PATCH 087/151] [BEAM-10102] Fix query in pubsub read grafana dashoard --- .../perftests_metrics/Python_IO_IT_Tests_Dataflow.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.test-infra/metrics/grafana/dashboards/perftests_metrics/Python_IO_IT_Tests_Dataflow.json b/.test-infra/metrics/grafana/dashboards/perftests_metrics/Python_IO_IT_Tests_Dataflow.json index d11465bc14fb..c7bf2e390862 100644 --- a/.test-infra/metrics/grafana/dashboards/perftests_metrics/Python_IO_IT_Tests_Dataflow.json +++ b/.test-infra/metrics/grafana/dashboards/perftests_metrics/Python_IO_IT_Tests_Dataflow.json @@ -319,7 +319,7 @@ "measurement": "python_bqio_read", "orderByTime": "ASC", "policy": "default", - "query": "SELECT mean(\"value\") FROM \"python_psio_2GB_results\" WHERE \"metric\" = \"pubsub_io_perf_read_runtime\" AND $timeFilter GROUP BY time($__interval), \"metric\"", + "query": "SELECT mean(\"value\") FROM \"python_psio_2GB_results\" WHERE \"metric\" = 'pubsub_io_perf_read_runtime' AND $timeFilter GROUP BY time($__interval), \"metric\"", "rawQuery": true, "refId": "A", "resultFormat": "time_series", From 4676c438b087b1ddbdb49547fddae6b5edcb1e0c Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 10:13:40 -0400 Subject: [PATCH 088/151] [BEAM-10106] Script the deployment of artifacts to pypi --- release/src/main/scripts/deploy_pypi.sh | 57 +++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100755 release/src/main/scripts/deploy_pypi.sh diff --git a/release/src/main/scripts/deploy_pypi.sh b/release/src/main/scripts/deploy_pypi.sh new file mode 100755 index 000000000000..c6b3dcd5056f --- /dev/null +++ b/release/src/main/scripts/deploy_pypi.sh @@ -0,0 +1,57 @@ +#!/bin/bash +# +# Licensed to the Apache Software Foundation (ASF) under one or more +# contributor license agreements. See the NOTICE file distributed with +# this work for additional information regarding copyright ownership. +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +# This script uploads Python artifacts staged at dist.apache.org to PyPI. + +set -e + +function clean_up(){ + echo "Do you want to clean local clone repo? [y|N]" + read confirmation + if [[ $confirmation = "y" ]]; then + cd ~ + rm -rf ${LOCAL_CLONE_DIR} + echo "Clean up local repo." + fi +} + +echo "Enter the release version, e.g. 2.21.0:" +read RELEASE +LOCAL_CLONE_DIR="beam_release_${RELEASE}" +cd ~ +if [[ -d ${LOCAL_CLONE_DIR} ]]; then + rm -rf ${LOCAL_CLONE_DIR} +fi +mkdir ${LOCAL_CLONE_DIR} +cd ${LOCAL_CLONE_DIR} + +wget -r --no-parent -A zip,whl "https://dist.apache.org/repos/dist/dev/beam/${RELEASE}/python" +cd "dist.apache.org/repos/dist/dev/beam/${RELEASE}/python/" +pip install twine +echo "Will upload the following files to PyPI:" +ls +echo "Are the files listed correct? [y|N]" +read confirmation +if [[ $confirmation != "y" ]]; then + echo "Exit without deploying artifacts to PyPI." + clean_up + exit +fi +twine upload * + +clean_up From 10732c7549a09015b97f18e80b2af69b0c8a4390 Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 10:41:09 -0400 Subject: [PATCH 089/151] Add pypi script to release guide. --- .../site/content/en/contribute/release-guide.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/website/www/site/content/en/contribute/release-guide.md b/website/www/site/content/en/contribute/release-guide.md index 7e199ae9d5ab..37e5b6bb67a6 100644 --- a/website/www/site/content/en/contribute/release-guide.md +++ b/website/www/site/content/en/contribute/release-guide.md @@ -1271,13 +1271,14 @@ please follow [the guide](https://help.github.com/articles/creating-a-personal-a ### Deploy Python artifacts to PyPI -1. Download everything from https://dist.apache.org/repos/dist/dev/beam/2.14.0/python/ ; -2. Keep only things that you see in https://pypi.org/project/apache-beam/#files , e.g. `.zip`, `.whl`, - delete the `.asc`, `.sha512`; -3. Upload the new release `twine upload *` from the directory with the `.zip` and `.whl` files; - -[Installing twine](https://packaging.python.org/tutorials/packaging-projects/#uploading-the-distribution-archives): `pip install twine`. You can install twine under [virtualenv](https://virtualenv.pypa.io/en/latest/) if preferred. - +* Script: [deploy_pypi.sh](https://github.com/apache/beam/blob/master/release/src/main/scripts/deploy_pypi.sh) +* Usage +``` +./beam/release/src/main/scripts/deploy_pypi.sh +``` +* Verify that the files at https://pypi.org/project/apache-beam/#files are correct. +All wheels should be published, in addition to the zip of the release source. +(Signatures and hashes do _not_ need to be uploaded.) ### Deploy source release to dist.apache.org From ec7278b935769b2ebed4b2ef27b55169cea28551 Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 08:15:11 -0700 Subject: [PATCH 090/151] [BEAM-10108] Update Flink versions in publish_docker_images.sh. --- release/src/main/scripts/publish_docker_images.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/release/src/main/scripts/publish_docker_images.sh b/release/src/main/scripts/publish_docker_images.sh index 1fb646313861..7575107ebf11 100755 --- a/release/src/main/scripts/publish_docker_images.sh +++ b/release/src/main/scripts/publish_docker_images.sh @@ -28,7 +28,7 @@ DOCKER_IMAGE_DEFAULT_REPO_ROOT=apache DOCKER_IMAGE_DEFAULT_REPO_PREFIX=beam_ PYTHON_VER=("python2.7" "python3.5" "python3.6" "python3.7") -FLINK_VER=("1.7" "1.8" "1.9") +FLINK_VER=("1.8" "1.9" "1.10") echo "Publish SDK docker images to Docker Hub." From 5129587b16064c9b11903de895306ce630a4ddbb Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 11:34:14 -0400 Subject: [PATCH 091/151] Add release date. --- website/www/site/content/en/get-started/downloads.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/website/www/site/content/en/get-started/downloads.md b/website/www/site/content/en/get-started/downloads.md index 14ae4d683162..a9575e4c73ff 100644 --- a/website/www/site/content/en/get-started/downloads.md +++ b/website/www/site/content/en/get-started/downloads.md @@ -87,7 +87,7 @@ versions denoted `0.x.y`. ## Releases -### 2.21.0 (2020-05-xx) +### 2.21.0 (2020-05-27) Official [source code download](http://www.apache.org/dyn/closer.cgi/beam/2.21.0/apache-beam-2.21.0-source-release.zip). [SHA-512](https://downloads.apache.org/beam/2.21.0/apache-beam-2.21.0-source-release.zip.sha512). [signature](https://downloads.apache.org/beam/2.21.0/apache-beam-2.21.0-source-release.zip.asc). @@ -248,4 +248,3 @@ Official [source code download](https://archive.apache.org/dist/beam/2.0.0/apach [signature](https://archive.apache.org/dist/beam/2.0.0/apache-beam-2.0.0-source-release.zip.asc). [Release notes](https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12319527&version=12339746). - From ff8430ea42b51a35e7316be6cb1c14150dca0afc Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 11:35:59 -0400 Subject: [PATCH 092/151] Add release date. --- CHANGES.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGES.md b/CHANGES.md index c55967a18bfb..1191ab8d2f35 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -75,7 +75,7 @@ * Fixed X (Java/Python) ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). -# [2.21.0] - 2020-05-xx +# [2.21.0] - 2020-05-27 ## Highlights From c5b11834414b6bce01bef05659d5d0770368ee2b Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 11:36:11 -0400 Subject: [PATCH 093/151] Add release date. --- website/www/site/content/en/blog/beam-2.21.0.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/www/site/content/en/blog/beam-2.21.0.md b/website/www/site/content/en/blog/beam-2.21.0.md index 286d71b6a20b..d46f432e3d7f 100644 --- a/website/www/site/content/en/blog/beam-2.21.0.md +++ b/website/www/site/content/en/blog/beam-2.21.0.md @@ -1,6 +1,6 @@ --- title: "Apache Beam 2.21.0" -date: 2020-05-xx 00:00:01 -0800 +date: 2020-05-27 00:00:01 -0800 categories: - blog authors: From e0f858f852a8b7ab7ede6c0d5e55d4653ea59ccd Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 11:36:29 -0400 Subject: [PATCH 094/151] Remove HTML comment (causes formatting issues) --- website/www/site/content/en/blog/beam-2.21.0.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/www/site/content/en/blog/beam-2.21.0.md b/website/www/site/content/en/blog/beam-2.21.0.md index d46f432e3d7f..734642148d48 100644 --- a/website/www/site/content/en/blog/beam-2.21.0.md +++ b/website/www/site/content/en/blog/beam-2.21.0.md @@ -19,7 +19,7 @@ limitations under the License. --> We are happy to present the new 2.21.0 release of Beam. This release includes both improvements and new functionality. -See the [download page](/get-started/downloads/#xxxx-xxxx) for this release. +See the [download page](/get-started/downloads/#xxxx-xxxx) for this release. For more information on changes in 2.21.0, check out the [detailed release notes](https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12319527&version=12347143). From 5b6e84fa380f1586bdd7ec1e8200e43ecc827f6e Mon Sep 17 00:00:00 2001 From: Steven Niemitz Date: Wed, 27 May 2020 11:52:52 -0400 Subject: [PATCH 095/151] Add a flag to tune the size of the grouping tables used by the dataflow workers (#11811) --- .../dataflow/worker/PartialGroupByKeyParDoFns.java | 10 ++++++++-- .../worker/util/common/worker/GroupingTables.java | 10 ++++++---- .../apache/beam/sdk/options/SdkHarnessOptions.java | 14 ++++++++++++++ .../beam/fn/harness/PrecombineGroupingTable.java | 13 +++++++------ 4 files changed, 35 insertions(+), 12 deletions(-) diff --git a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/PartialGroupByKeyParDoFns.java b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/PartialGroupByKeyParDoFns.java index ffb617053ce1..86df406613de 100644 --- a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/PartialGroupByKeyParDoFns.java +++ b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/PartialGroupByKeyParDoFns.java @@ -39,6 +39,7 @@ import org.apache.beam.sdk.coders.Coder; import org.apache.beam.sdk.coders.KvCoder; import org.apache.beam.sdk.options.PipelineOptions; +import org.apache.beam.sdk.options.SdkHarnessOptions; import org.apache.beam.sdk.options.StreamingOptions; import org.apache.beam.sdk.state.BagState; import org.apache.beam.sdk.transforms.windowing.BoundedWindow; @@ -97,6 +98,9 @@ static ParDoFn create( Receiver receiver, @Nullable StepContext stepContext) throws Exception { + long maxSizeBytes = + options.as(SdkHarnessOptions.class).getGroupingTableMaxSizeMb() * (1024L * 1024L); + Coder keyCoder = inputElementCoder.getKeyCoder(); Coder valueCoder = inputElementCoder.getValueCoder(); if (combineFn == null) { @@ -108,7 +112,8 @@ static ParDoFn create( PairInfo.create(), new CoderSizeEstimator<>(WindowedValue.getValueOnlyCoder(keyCoder)), new CoderSizeEstimator<>(inputCoder), - 0.001 /*sizeEstimatorSampleRate*/); + 0.001, /*sizeEstimatorSampleRate*/ + maxSizeBytes /*maxSizeBytes*/); return new SimplePartialGroupByKeyParDoFn<>(groupingTable, receiver); } else { GroupingTables.Combiner, InputT, AccumT, ?> valueCombiner = @@ -122,7 +127,8 @@ static ParDoFn create( valueCombiner, new CoderSizeEstimator<>(WindowedValue.getValueOnlyCoder(keyCoder)), new CoderSizeEstimator<>(combineFn.getAccumulatorCoder()), - 0.001 /*sizeEstimatorSampleRate*/); + 0.001, /*sizeEstimatorSampleRate*/ + maxSizeBytes /*maxSizeBytes*/); if (sideInputReader.isEmpty()) { return new SimplePartialGroupByKeyParDoFn<>(groupingTable, receiver); } else if (options.as(StreamingOptions.class).isStreaming()) { diff --git a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/util/common/worker/GroupingTables.java b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/util/common/worker/GroupingTables.java index d1ab37856546..ddccbf75b188 100644 --- a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/util/common/worker/GroupingTables.java +++ b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/util/common/worker/GroupingTables.java @@ -59,9 +59,10 @@ public static GroupingTable> bufferingAndSampling( PairInfo pairInfo, SizeEstimator keySizer, SizeEstimator valueSizer, - double sizeEstimatorSampleRate) { + double sizeEstimatorSampleRate, + long maxSizeBytes) { return new BufferingGroupingTable<>( - DEFAULT_MAX_GROUPING_TABLE_BYTES, + maxSizeBytes, groupingKeyCreator, pairInfo, new SamplingSizeEstimator<>(keySizer, sizeEstimatorSampleRate, 1.0), @@ -94,9 +95,10 @@ public static GroupingTable combiningAndS Combiner combineFn, SizeEstimator keySizer, SizeEstimator accumulatorSizer, - double sizeEstimatorSampleRate) { + double sizeEstimatorSampleRate, + long maxSizeBytes) { return new CombiningGroupingTable<>( - DEFAULT_MAX_GROUPING_TABLE_BYTES, + maxSizeBytes, groupingKeyCreator, pairInfo, combineFn, diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/options/SdkHarnessOptions.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/options/SdkHarnessOptions.java index c5ad12a3b4c8..5f1508168d45 100644 --- a/sdks/java/core/src/main/java/org/apache/beam/sdk/options/SdkHarnessOptions.java +++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/options/SdkHarnessOptions.java @@ -82,6 +82,20 @@ enum LogLevel { void setSdkHarnessLogLevelOverrides(SdkHarnessLogLevelOverrides value); + /** + * Size (in MB) of each grouping table used to pre-combine elements. If unset, defaults to 100 MB. + * + *

    CAUTION: If set too large, workers may run into OOM conditions more easily, each worker may + * have many grouping tables in-memory concurrently. + */ + @Description( + "The size (in MB) of the grouping tables used to pre-combine elements before " + + "shuffling. Larger values may reduce the amount of data shuffled.") + @Default.Integer(100) + int getGroupingTableMaxSizeMb(); + + void setGroupingTableMaxSizeMb(int value); + /** * Defines a log level override for a specific class, package, or name. * diff --git a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/PrecombineGroupingTable.java b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/PrecombineGroupingTable.java index 48a55bf3e8ae..515f0644c2ef 100644 --- a/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/PrecombineGroupingTable.java +++ b/sdks/java/harness/src/main/java/org/apache/beam/fn/harness/PrecombineGroupingTable.java @@ -27,6 +27,7 @@ import org.apache.beam.runners.core.SideInputReader; import org.apache.beam.sdk.coders.Coder; import org.apache.beam.sdk.options.PipelineOptions; +import org.apache.beam.sdk.options.SdkHarnessOptions; import org.apache.beam.sdk.transforms.Combine.CombineFn; import org.apache.beam.sdk.transforms.windowing.BoundedWindow; import org.apache.beam.sdk.util.WindowedValue; @@ -40,6 +41,10 @@ /** Static utility methods that provide {@link GroupingTable} implementations. */ public class PrecombineGroupingTable implements GroupingTable { + private static long getGroupingTableSizeBytes(PipelineOptions options) { + return options.as(SdkHarnessOptions.class).getGroupingTableMaxSizeMb() * 1024L * 1024L; + } + /** Returns a {@link GroupingTable} that combines inputs into a accumulator. */ public static GroupingTable, InputT, AccumT> combining( PipelineOptions options, @@ -50,7 +55,7 @@ public static GroupingTable, InputT, AccumT new ValueCombiner<>( GlobalCombineFnRunners.create(combineFn), NullSideInputReader.empty(), options); return new PrecombineGroupingTable<>( - DEFAULT_MAX_GROUPING_TABLE_BYTES, + getGroupingTableSizeBytes(options), new WindowingCoderGroupingKeyCreator<>(keyCoder), WindowedPairInfo.create(), valueCombiner, @@ -73,7 +78,7 @@ GroupingTable, InputT, AccumT> combiningAndSampling( new ValueCombiner<>( GlobalCombineFnRunners.create(combineFn), NullSideInputReader.empty(), options); return new PrecombineGroupingTable<>( - DEFAULT_MAX_GROUPING_TABLE_BYTES, + getGroupingTableSizeBytes(options), new WindowingCoderGroupingKeyCreator<>(keyCoder), WindowedPairInfo.create(), valueCombiner, @@ -255,10 +260,6 @@ public OutputT extract(WindowedValue windowedKey, AccumT accumulator) { } } - // By default, how many bytes we allow the grouping table to consume before - // it has to be flushed. - private static final long DEFAULT_MAX_GROUPING_TABLE_BYTES = 100_000_000L; - // How many bytes a word in the JVM has. private static final int BYTES_PER_JVM_WORD = getBytesPerJvmWord(); /** From 1ec86e737422c3a9b3f2ed7201397eded3524d96 Mon Sep 17 00:00:00 2001 From: Ahmet Altay Date: Wed, 27 May 2020 10:50:11 -0700 Subject: [PATCH 096/151] Add Pub/Sub Lite to in progress IOs --- website/www/site/content/en/documentation/io/built-in.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/website/www/site/content/en/documentation/io/built-in.md b/website/www/site/content/en/documentation/io/built-in.md index ba72908a885f..e40884e1e798 100644 --- a/website/www/site/content/en/documentation/io/built-in.md +++ b/website/www/site/content/en/documentation/io/built-in.md @@ -61,6 +61,10 @@ This table contains I/O transforms that are currently planned or in-progress. St Neo4jJava BEAM-1857 + + Pub/Sub LiteJava + BEAM-10114 + RestIOJava BEAM-1946 From 9939a8f99ea0b45035a0969bda48f62f7e17f874 Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 16:32:14 -0400 Subject: [PATCH 097/151] Move 2.20 download addresses to archive. --- website/www/site/content/en/get-started/downloads.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/website/www/site/content/en/get-started/downloads.md b/website/www/site/content/en/get-started/downloads.md index 14ae4d683162..a1697abb6fa3 100644 --- a/website/www/site/content/en/get-started/downloads.md +++ b/website/www/site/content/en/get-started/downloads.md @@ -95,9 +95,9 @@ Official [source code download](http://www.apache.org/dyn/closer.cgi/beam/2.21.0 [Release notes](https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12319527&version=12347143). ### 2.20.0 (2020-04-15) -Official [source code download](http://www.apache.org/dyn/closer.cgi/beam/2.20.0/apache-beam-2.20.0-source-release.zip). -[SHA-512](https://downloads.apache.org/beam/2.20.0/apache-beam-2.20.0-source-release.zip.sha512). -[signature](https://downloads.apache.org/beam/2.20.0/apache-beam-2.20.0-source-release.zip.asc). +Official [source code download](https://archive.apache.org/dist/beam/2.20.0/apache-beam-2.20.0-source-release.zip). +[SHA-512](https://archive.apache.org/dist/beam/2.20.0/apache-beam-2.20.0-source-release.zip.sha512). +[signature](https://archive.apache.org/dist/beam/2.20.0/apache-beam-2.20.0-source-release.zip.asc). [Release notes](https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12319527&version=12346780). From 00736f34913fa94051e818b37f43a3f588539c3d Mon Sep 17 00:00:00 2001 From: Pablo Estrada Date: Wed, 27 May 2020 14:06:41 -0700 Subject: [PATCH 098/151] [BEAM-10098] Enabling javadoc export for RabbitMqIO and KuduIO --- sdks/java/io/kudu/build.gradle | 2 +- sdks/java/io/rabbitmq/build.gradle | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/sdks/java/io/kudu/build.gradle b/sdks/java/io/kudu/build.gradle index 0090e13336e0..cda962d4d6ee 100644 --- a/sdks/java/io/kudu/build.gradle +++ b/sdks/java/io/kudu/build.gradle @@ -17,7 +17,7 @@ */ plugins { id 'org.apache.beam.module' } -applyJavaNature(exportJavadoc: false, automaticModuleName: 'org.apache.beam.sdk.io.kudu') +applyJavaNature(automaticModuleName: 'org.apache.beam.sdk.io.kudu') provideIntegrationTestingDependencies() enableJavaPerformanceTesting() diff --git a/sdks/java/io/rabbitmq/build.gradle b/sdks/java/io/rabbitmq/build.gradle index a5f1055cce95..83cf7c4591ab 100644 --- a/sdks/java/io/rabbitmq/build.gradle +++ b/sdks/java/io/rabbitmq/build.gradle @@ -17,7 +17,7 @@ */ plugins { id 'org.apache.beam.module' } -applyJavaNature(exportJavadoc: false, automaticModuleName: 'org.apache.beam.sdk.io.rabbitmq') +applyJavaNature(automaticModuleName: 'org.apache.beam.sdk.io.rabbitmq') description = "Apache Beam :: SDKs :: Java :: IO :: RabbitMQ" ext.summary = "IO to read and write to a RabbitMQ broker." From eae2113d43f206e263dd2e6bff3cb19b95f5b81e Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 17:26:02 -0400 Subject: [PATCH 099/151] Improve log messages in release scripts. --- release/src/main/scripts/cut_release_branch.sh | 9 +++++---- release/src/main/scripts/deploy_pypi.sh | 7 ++++--- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/release/src/main/scripts/cut_release_branch.sh b/release/src/main/scripts/cut_release_branch.sh index b3bdc832ea71..6d0f91379708 100755 --- a/release/src/main/scripts/cut_release_branch.sh +++ b/release/src/main/scripts/cut_release_branch.sh @@ -24,12 +24,12 @@ set -e function clean_up(){ - echo "Do you want to clean local clone repo? [y|N]" + echo "Do you want to clean local clone repo ${LOCAL_CLONE_DIR}? [y|N]" read confirmation if [[ $confirmation = "y" ]]; then cd ~ rm -rf ${LOCAL_CLONE_DIR} - echo "Clean up local repo." + echo "Cleaned up local repo." fi } @@ -73,6 +73,7 @@ echo "===============================================================" cd ~ if [[ -d ${LOCAL_CLONE_DIR} ]]; then + echo "Deleting existing local clone repo ${LOCAL_CLONE_DIR}." rm -rf ${LOCAL_CLONE_DIR} fi mkdir ${LOCAL_CLONE_DIR} @@ -101,7 +102,7 @@ echo "===============================================================" echo "Please make sure all changes above are expected. Do you confirm to commit?: [y|N]" read confirmation if [[ $confirmation != "y" ]]; then - echo "Exit without committing any changes on master branch." + echo "Exiting without committing any changes on master branch." clean_up exit fi @@ -136,7 +137,7 @@ echo "===============================================================" echo "Please make sure all changes above are expected. Do you confirm to commit?: [y|N]" read confirmation if [[ $confirmation != "y" ]]; then - echo "Exit without committing any changes on release branch." + echo "Exiting without committing any changes on release branch." clean_up exit fi diff --git a/release/src/main/scripts/deploy_pypi.sh b/release/src/main/scripts/deploy_pypi.sh index c6b3dcd5056f..5be84aa596e7 100755 --- a/release/src/main/scripts/deploy_pypi.sh +++ b/release/src/main/scripts/deploy_pypi.sh @@ -21,12 +21,12 @@ set -e function clean_up(){ - echo "Do you want to clean local clone repo? [y|N]" + echo "Do you want to clean local clone repo ${LOCAL_CLONE_DIR}? [y|N]" read confirmation if [[ $confirmation = "y" ]]; then cd ~ rm -rf ${LOCAL_CLONE_DIR} - echo "Clean up local repo." + echo "Cleaned up local repo." fi } @@ -35,6 +35,7 @@ read RELEASE LOCAL_CLONE_DIR="beam_release_${RELEASE}" cd ~ if [[ -d ${LOCAL_CLONE_DIR} ]]; then + echo "Deleting existing local clone repo ${LOCAL_CLONE_DIR}." rm -rf ${LOCAL_CLONE_DIR} fi mkdir ${LOCAL_CLONE_DIR} @@ -48,7 +49,7 @@ ls echo "Are the files listed correct? [y|N]" read confirmation if [[ $confirmation != "y" ]]; then - echo "Exit without deploying artifacts to PyPI." + echo "Exiting without deploying artifacts to PyPI." clean_up exit fi From b6100fd017c43f6a9e10307574ece718a152943b Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 17:30:37 -0400 Subject: [PATCH 100/151] Install twine in virtual env. --- release/src/main/scripts/deploy_pypi.sh | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/release/src/main/scripts/deploy_pypi.sh b/release/src/main/scripts/deploy_pypi.sh index 5be84aa596e7..daeb342a621e 100755 --- a/release/src/main/scripts/deploy_pypi.sh +++ b/release/src/main/scripts/deploy_pypi.sh @@ -41,9 +41,12 @@ fi mkdir ${LOCAL_CLONE_DIR} cd ${LOCAL_CLONE_DIR} +virtualenv deploy_pypi_env +source ./deploy_pypi_env/bin/activate +pip install twine + wget -r --no-parent -A zip,whl "https://dist.apache.org/repos/dist/dev/beam/${RELEASE}/python" cd "dist.apache.org/repos/dist/dev/beam/${RELEASE}/python/" -pip install twine echo "Will upload the following files to PyPI:" ls echo "Are the files listed correct? [y|N]" From 0e7447419e5568081601156a998f0151aeec7891 Mon Sep 17 00:00:00 2001 From: Brian Hulette Date: Wed, 27 May 2020 14:52:21 -0700 Subject: [PATCH 101/151] remove as_cloud_object override --- sdks/python/apache_beam/coders/row_coder.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/sdks/python/apache_beam/coders/row_coder.py b/sdks/python/apache_beam/coders/row_coder.py index 7012a56cb374..03114976c78e 100644 --- a/sdks/python/apache_beam/coders/row_coder.py +++ b/sdks/python/apache_beam/coders/row_coder.py @@ -67,9 +67,6 @@ def is_deterministic(self): def to_type_hint(self): return named_tuple_from_schema(self.schema) - def as_cloud_object(self, coders_context=None): - raise NotImplementedError("as_cloud_object not supported for RowCoder") - def __hash__(self): return hash(self.schema.SerializeToString()) From eb59a848ce519e8186750f95b2cda02bc52c683b Mon Sep 17 00:00:00 2001 From: Kamil Gabryjelski Date: Thu, 28 May 2020 00:11:56 +0200 Subject: [PATCH 102/151] Merge pull request #11796 from [BEAM-10003] Use local code for building code samples on website * Use code samples from local files instead of fetching from github * Update markdown files to use code_sample shortcode * Change script name in gradle and package.json * Update documentation * Remove empty line * Synchronize with latest changes * Update comment for code_sample --- website/.gitignore | 2 +- website/CONTRIBUTE.md | 10 +- website/build.gradle | 10 +- ...ithub_samples.sh => build_code_samples.sh} | 12 ++- website/www/package.json | 2 +- .../io/built-in/google-bigquery.md | 50 +++++----- .../documentation/io/developing-io-python.md | 12 +-- .../en/documentation/patterns/bigqueryio.md | 4 +- .../documentation/patterns/custom-windows.md | 12 +-- .../documentation/patterns/file-processing.md | 10 +- .../patterns/pipeline-options.md | 6 +- .../en/documentation/patterns/side-inputs.md | 6 +- .../en/documentation/programming-guide.md | 94 +++++++++---------- .../documentation/sdks/python-type-safety.md | 22 ++--- .../transforms/python/elementwise/filter.md | 24 ++--- .../transforms/python/elementwise/flatmap.md | 36 +++---- .../transforms/python/elementwise/keys.md | 4 +- .../transforms/python/elementwise/kvswap.md | 4 +- .../transforms/python/elementwise/map.md | 32 +++---- .../transforms/python/elementwise/pardo.md | 12 +-- .../python/elementwise/partition.md | 12 +-- .../transforms/python/elementwise/regex.md | 36 +++---- .../transforms/python/elementwise/tostring.md | 12 +-- .../transforms/python/elementwise/values.md | 4 +- .../python/elementwise/withtimestamps.md | 16 ++-- .../en/get-started/mobile-gaming-example.md | 44 ++++----- .../en/get-started/wordcount-example.md | 24 ++--- .../site/layouts/shortcodes/code_sample.html | 23 +++++ .../layouts/shortcodes/github_sample.html | 15 --- 29 files changed, 280 insertions(+), 270 deletions(-) rename website/www/{build_github_samples.sh => build_code_samples.sh} (75%) create mode 100644 website/www/site/layouts/shortcodes/code_sample.html delete mode 100644 website/www/site/layouts/shortcodes/github_sample.html diff --git a/website/.gitignore b/website/.gitignore index 8191c0750dc0..bbed591c748a 100644 --- a/website/.gitignore +++ b/website/.gitignore @@ -16,7 +16,7 @@ content/ www/node_modules www/dist www/site/resources -www/site/github_samples +www/site/code_samples www/site/_config_branch_repo.toml www/yarn-error.log !www/site/content diff --git a/website/CONTRIBUTE.md b/website/CONTRIBUTE.md index 555fd2a3026e..5176af95dedf 100644 --- a/website/CONTRIBUTE.md +++ b/website/CONTRIBUTE.md @@ -66,7 +66,7 @@ www/ │ │ └── js │   └── themes │ └── docsy -├── build_github_samples.sh +├── build_code_samples.sh ├── check-links.sh # links checker └── package.json ``` @@ -252,20 +252,20 @@ A table markdown here. {{< /table >}} ``` -### Github sample +### Code sample -To retrieve a piece of code in github. +To retrieve a piece of code from Beam project. Usage: ``` -{{< github_sample "/path/to/file" selected_tag >}} +{{< code_sample "path/to/file" selected_tag >}} ``` Example: ``` -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/user_score.py" extract_and_sum_score >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/user_score.py" extract_and_sum_score >}} ``` ### Others diff --git a/website/build.gradle b/website/build.gradle index b5988d8e2b42..7f8e7f69342b 100644 --- a/website/build.gradle +++ b/website/build.gradle @@ -104,16 +104,16 @@ task installDependencies(type: Exec) { "${->startDockerContainer.containerId()}", 'yarn', 'install' } -// Run build_github_samples.sh to fetch github content -// which is used by github_sample shortcodes to inject snippets into codeblocks -task buildGithubSamples(type: Exec) { +// Run build_code_samples.sh to fetch Beam project content +// which is used by code_sample shortcodes to inject snippets into codeblocks +task buildCodeSamples(type: Exec) { commandLine 'docker', 'exec', '--workdir', "$dockerSourceDir", - "${->startDockerContainer.containerId()}", 'yarn', 'build_github_samples' + "${->startDockerContainer.containerId()}", 'yarn', 'build_code_samples' } task setupDockerContainer(type: Exec) { dependsOn startDockerContainer - finalizedBy initGitSubmodules, installDependencies, buildGithubSamples + finalizedBy initGitSubmodules, installDependencies, buildCodeSamples ext.containerId = { return startDockerContainer.containerId() } diff --git a/website/www/build_github_samples.sh b/website/www/build_code_samples.sh similarity index 75% rename from website/www/build_github_samples.sh rename to website/www/build_code_samples.sh index b47e7d1286cf..a42ba444324b 100755 --- a/website/www/build_github_samples.sh +++ b/website/www/build_code_samples.sh @@ -23,19 +23,21 @@ pushd "${MY_DIR}" &>/dev/null || exit 1 echo "Working directory: ${MY_DIR}" -DIST_DIR=${1:-"./site/github_samples"} +PROJECT_ROOT_REL_PATH=../.. + +DIST_DIR=${1:-"./site/code_samples"} echo "Dist directory: ${DIST_DIR}" CONTENT_DIR=${2:-"./site/content"} -mapfile -t github_urls < <(grep -rh "{{< github_sample" "${CONTENT_DIR}" | sed -e 's/^.*"\(.*\)".*$/\1/g' | sort | uniq | sed 's/\/blob\//\//g' | xargs -n 1 echo) +mapfile -t code_sample_uris < <(grep -rh "{{< code_sample" "${CONTENT_DIR}" | sed -e 's/^.*"\(.*\)".*$/\1/g' | sort | uniq | xargs -n 1 echo) mkdir -pv "${DIST_DIR}" -for url in "${github_urls[@]}" +for uri in "${code_sample_uris[@]}" do - fileName=$(echo "$url" | sed -e 's/\//_/g') - curl -o "$DIST_DIR"/"$fileName" "https://raw.githubusercontent.com$url" + fileName=$(echo "$uri" | sed -e 's/\//_/g') + cp "$PROJECT_ROOT_REL_PATH"/"$uri" "$DIST_DIR"/"$fileName" done popd &>/dev/null || exit 1 diff --git a/website/www/package.json b/website/www/package.json index a5b1cbea637d..3b3a2b2e4de7 100644 --- a/website/www/package.json +++ b/website/www/package.json @@ -5,7 +5,7 @@ "repository": "apache/beam", "license": "MIT", "scripts": { - "build_github_samples": "./build_github_samples.sh", + "build_code_samples": "./build_code_samples.sh", "develop": "cd site && hugo server", "build": "cross-env HUGO_ENV=production hugo -d ../dist -s site -v", "start": "hugo -d ../dist -s site -vw" diff --git a/website/www/site/content/en/documentation/io/built-in/google-bigquery.md b/website/www/site/content/en/documentation/io/built-in/google-bigquery.md index d549f5569fed..16fa33e41819 100644 --- a/website/www/site/content/en/documentation/io/built-in/google-bigquery.md +++ b/website/www/site/content/en/documentation/io/built-in/google-bigquery.md @@ -103,11 +103,11 @@ To specify a table with a string, use the format table name. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryTableSpec >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryTableSpec >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_table_spec >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_table_spec >}} {{< /highlight >}} You can also omit `project_id` and use the `[dataset_id].[table_id]` format. If @@ -120,11 +120,11 @@ you omit the project ID, Beam uses the default project ID from your {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryTableSpecWithoutProject >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryTableSpecWithoutProject >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_table_spec_without_project >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_table_spec_without_project >}} {{< /highlight >}} #### Using a TableReference @@ -133,11 +133,11 @@ To specify a table with a `TableReference`, create a new `TableReference` using the three parts of the BigQuery table name. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryTableSpecObject >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryTableSpecObject >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_table_spec_object >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_table_spec_object >}} {{< /highlight >}} @@ -173,11 +173,11 @@ shows the correct format for data types used when reading from and writing to BigQuery: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryDataTypes >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryDataTypes >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_data_types >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_data_types >}} {{< /highlight >}} @@ -276,11 +276,11 @@ The following code reads an entire table that contains weather station data and then extracts the `max_temperature` column. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryReadTable >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryReadTable >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_read_table >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_read_table >}} {{< /highlight >}} @@ -300,22 +300,22 @@ If you don't want to read an entire table, you can supply a query string to The following code uses a SQL query to only read the `max_temperature` column. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryReadQuery >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryReadQuery >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_read_query >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_read_query >}} {{< /highlight >}} You can also use BigQuery's standard SQL dialect with a query string, as shown in the following example: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryReadQueryStdSQL >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryReadQueryStdSQL >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_read_query_std_sql >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_read_query_std_sql >}} {{< /highlight >}} ### Using the BigQuery Storage API {#storage-api} @@ -546,11 +546,11 @@ The following example code shows how to create a `TableSchema` for a table with two fields (source and quote) of type string. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQuerySchemaObject >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQuerySchemaObject >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_schema_object >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_schema_object >}} {{< /highlight >}} @@ -591,11 +591,11 @@ The following example shows how to use a string to specify the same table schema as the previous example. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQuerySchemaJson >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQuerySchemaJson >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_schema >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_schema >}} {{< /highlight >}} @@ -680,11 +680,11 @@ collection. The following examples use this `PCollection` that contains quotes. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryWriteInput >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryWriteInput >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_write_input >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_write_input >}} {{< /highlight >}} @@ -704,11 +704,11 @@ creates a table if needed; if the table already exists, it will be replaced. {{< /paragraph >}} {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryWriteTable >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryWriteTable >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_write >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_bigqueryio_write >}} {{< /highlight >}} @@ -723,7 +723,7 @@ be replaced. {{< /paragraph >}} {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryWriteFunction >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryWriteFunction >}} {{< /highlight >}} {{< paragraph class="language-java" >}} @@ -774,7 +774,7 @@ different table for each year. {{< /paragraph >}} {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryWriteDynamicDestinations >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryWriteDynamicDestinations >}} {{< /highlight >}} {{< highlight py >}} @@ -810,7 +810,7 @@ This example generates one partition per day. {{< /paragraph >}} {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryTimePartitioning >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryTimePartitioning >}} {{< /highlight >}} {{< highlight py >}} diff --git a/website/www/site/content/en/documentation/io/developing-io-python.md b/website/www/site/content/en/documentation/io/developing-io-python.md index 3e581e01dd13..47b3ed075714 100644 --- a/website/www/site/content/en/documentation/io/developing-io-python.md +++ b/website/www/site/content/en/documentation/io/developing-io-python.md @@ -183,13 +183,13 @@ See [AvroSource](https://github.com/apache/beam/blob/master/sdks/python/apache_b The following example, `CountingSource`, demonstrates an implementation of `BoundedSource` and uses the SDK-provided `RangeTracker` called `OffsetRangeTracker`. {{< highlight >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_source_new_source >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_source_new_source >}} {{< /highlight >}} To read data from the source in your pipeline, use the `Read` transform: {{< highlight >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_source_use_new_source >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_source_use_new_source >}} {{< /highlight >}} **Note:** When you create a source that end-users are going to use, we @@ -262,23 +262,23 @@ to `_CountingSource`. Then, create the wrapper `PTransform`, called `ReadFromCountingSource`: {{< highlight >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_source_new_ptransform >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_source_new_ptransform >}} {{< /highlight >}} Finally, read from the source: {{< highlight >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_source_use_ptransform >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_source_use_ptransform >}} {{< /highlight >}} For the sink, rename `SimpleKVSink` to `_SimpleKVSink`. Then, create the wrapper `PTransform`, called `WriteToKVSink`: {{< highlight >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_sink_new_ptransform >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_sink_new_ptransform >}} {{< /highlight >}} Finally, write to the sink: {{< highlight >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_sink_use_ptransform >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_custom_sink_use_ptransform >}} {{< /highlight >}} diff --git a/website/www/site/content/en/documentation/patterns/bigqueryio.md b/website/www/site/content/en/documentation/patterns/bigqueryio.md index 49393b873b41..1206c5deace6 100644 --- a/website/www/site/content/en/documentation/patterns/bigqueryio.md +++ b/website/www/site/content/en/documentation/patterns/bigqueryio.md @@ -38,9 +38,9 @@ In the result tuple you can access `FailedRows` to access the failed inserts. {{< /paragraph >}} {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryIODeadLetter >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" BigQueryIODeadLetter >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" BigQueryIODeadLetter >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" BigQueryIODeadLetter >}} {{< /highlight >}} diff --git a/website/www/site/content/en/documentation/patterns/custom-windows.md b/website/www/site/content/en/documentation/patterns/custom-windows.md index 22b5b285435d..23e83c46ada8 100644 --- a/website/www/site/content/en/documentation/patterns/custom-windows.md +++ b/website/www/site/content/en/documentation/patterns/custom-windows.md @@ -27,7 +27,7 @@ You can modify the [`assignWindows`](https://beam.apache.org/releases/javadoc/cu Access the `assignWindows` function through `WindowFn.AssignContext.element()`. The original, fixed-duration `assignWindows` function is: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CustomSessionWindow1 >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CustomSessionWindow1 >}} {{< /highlight >}} ### Creating data-driven gaps @@ -38,13 +38,13 @@ To create data-driven gaps, add the following snippets to the `assignWindows` fu For example, the following function assigns each element to a window between the timestamp and `gapDuration`: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CustomSessionWindow3 >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CustomSessionWindow3 >}} {{< /highlight >}} Then, set the `gapDuration` field in a windowing function: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CustomSessionWindow2 >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CustomSessionWindow2 >}} {{< /highlight >}} ### Windowing messages into sessions @@ -53,13 +53,13 @@ After creating data-driven gaps, you can window incoming data into the new, cust First, set the session length to the gap duration: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CustomSessionWindow4 >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CustomSessionWindow4 >}} {{< /highlight >}} Lastly, window data into sessions in your pipeline: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CustomSessionWindow6 >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CustomSessionWindow6 >}} {{< /highlight >}} ### Example data and windows @@ -103,4 +103,4 @@ user=user-1, score=9, window=[2019-05-26T14:30:33.276Z..2019-05-26T14:30:41.849Z user=user-2, score=10, window=[2019-05-26T14:30:37.357Z..2019-05-26T14:30:47.357Z) ``` -With dynamic sessions, User #2 gets different scores. The third messages arrives seven seconds after the second message, so it's grouped into a different session. The large, 18-point session is split into two 9-point sessions. \ No newline at end of file +With dynamic sessions, User #2 gets different scores. The third messages arrives seven seconds after the second message, so it's grouped into a different session. The large, 18-point session is split into two 9-point sessions. diff --git a/website/www/site/content/en/documentation/patterns/file-processing.md b/website/www/site/content/en/documentation/patterns/file-processing.md index f119cd34da0a..d5d53dca558c 100644 --- a/website/www/site/content/en/documentation/patterns/file-processing.md +++ b/website/www/site/content/en/documentation/patterns/file-processing.md @@ -36,7 +36,7 @@ Use the [`FileIO`](https://beam.apache.org/releases/javadoc/current/org/apache/b {{< /paragraph >}} {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" FileProcessPatternProcessNewFilesSnip1 >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" FileProcessPatternProcessNewFilesSnip1 >}} {{< /highlight >}} {{< paragraph class="language-java" >}} @@ -44,7 +44,7 @@ The [`TextIO`](https://beam.apache.org/releases/javadoc/current/org/apache/beam/ {{< /paragraph >}} {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" FileProcessPatternProcessNewFilesSnip2 >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" FileProcessPatternProcessNewFilesSnip2 >}} {{< /highlight >}} {{< paragraph class="language-java" >}} @@ -98,9 +98,9 @@ To read filenames in a pipeline job: {{< /paragraph >}} {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" FileProcessPatternAccessMetadataSnip1 >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" FileProcessPatternAccessMetadataSnip1 >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" FileProcessPatternAccessMetadataSnip1 >}} -{{< /highlight >}} \ No newline at end of file +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" FileProcessPatternAccessMetadataSnip1 >}} +{{< /highlight >}} diff --git a/website/www/site/content/en/documentation/patterns/pipeline-options.md b/website/www/site/content/en/documentation/patterns/pipeline-options.md index 5bd379ea02f2..6cd1a7d14712 100644 --- a/website/www/site/content/en/documentation/patterns/pipeline-options.md +++ b/website/www/site/content/en/documentation/patterns/pipeline-options.md @@ -28,9 +28,9 @@ Use the `ValueProvider` interface to access runtime parameters after completing You can use the `ValueProvider` interface to pass runtime parameters to your pipeline, but you can only log the parameters from within the the Beam DAG. A solution is to add a pipeline [branch](/documentation/programming-guide/#applying-transforms) with a `DoFn` that processes a placeholder value and then logs the runtime parameters: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" AccessingValueProviderInfoAfterRunSnip1 >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" AccessingValueProviderInfoAfterRunSnip1 >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" AccessingValueProviderInfoAfterRunSnip1 >}} -{{< /highlight >}} \ No newline at end of file +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" AccessingValueProviderInfoAfterRunSnip1 >}} +{{< /highlight >}} diff --git a/website/www/site/content/en/documentation/patterns/side-inputs.md b/website/www/site/content/en/documentation/patterns/side-inputs.md index 06cd2e6b247d..5d60acc20568 100644 --- a/website/www/site/content/en/documentation/patterns/side-inputs.md +++ b/website/www/site/content/en/documentation/patterns/side-inputs.md @@ -42,7 +42,7 @@ The global window side input triggers on processing time, so the main pipeline n For instance, the following code sample uses a `Map` to create a `DoFn`. The `Map` becomes a `View.asSingleton` side input that’s rebuilt on each counter tick. The side input updates every 5 seconds in order to demonstrate the workflow. In a real-world scenario, the side input would typically update every few hours or once per day. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" SideInputPatternSlowUpdateGlobalWindowSnip1 >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" SideInputPatternSlowUpdateGlobalWindowSnip1 >}} {{< /highlight >}} {{< highlight py >}} @@ -70,9 +70,9 @@ PCollection element. 1. Apply the side input. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" PeriodicallyUpdatingSideInputs >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" PeriodicallyUpdatingSideInputs >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" SideInputSlowUpdateSnip1 >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" SideInputSlowUpdateSnip1 >}} {{< /highlight >}} diff --git a/website/www/site/content/en/documentation/programming-guide.md b/website/www/site/content/en/documentation/programming-guide.md index 5f18e2ef0202..82bd0534633e 100644 --- a/website/www/site/content/en/documentation/programming-guide.md +++ b/website/www/site/content/en/documentation/programming-guide.md @@ -122,7 +122,7 @@ Pipeline p = Pipeline.create(options); {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" pipelines_constructing_creating >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" pipelines_constructing_creating >}} {{< /highlight >}} {{< highlight go >}} @@ -157,7 +157,7 @@ PipelineOptions options = {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" pipelines_constructing_creating >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" pipelines_constructing_creating >}} {{< /highlight >}} {{< highlight go >}} @@ -199,7 +199,7 @@ public interface MyOptions extends PipelineOptions { {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" pipeline_options_define_custom >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" pipeline_options_define_custom >}} {{< /highlight >}} {{< highlight go >}} @@ -229,7 +229,7 @@ public interface MyOptions extends PipelineOptions { {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" pipeline_options_define_custom_with_help_and_default >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" pipeline_options_define_custom_with_help_and_default >}} {{< /highlight >}} {{< highlight go >}} @@ -316,7 +316,7 @@ public static void main(String[] args) { {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" pipelines_constructing_reading >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" pipelines_constructing_reading >}} {{< /highlight >}} {{< highlight go >}} @@ -369,7 +369,7 @@ public static void main(String[] args) { {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_pcollection >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_pcollection >}} {{< /highlight >}} ### 3.2. PCollection characteristics {#pcollection-characteristics} @@ -631,8 +631,8 @@ PCollection wordLengths = words.apply( words = ... # The DoFn to perform on each element in the input PCollection. -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_pardo >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_apply >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_pardo >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_apply >}} {{< /highlight >}} {{< highlight go >}} @@ -708,7 +708,7 @@ static class ComputeWordLengthFn extends DoFn { {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_pardo >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_pardo >}} {{< /highlight >}} {{< paragraph class="language-java" >}} @@ -771,7 +771,7 @@ words = ... # Apply a lambda function to the PCollection words. # Save the result as the PCollection word_lengths. -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_using_flatmap >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_using_flatmap >}} {{< /highlight >}} {{< highlight go >}} @@ -810,7 +810,7 @@ words = ... # Apply a Map with a lambda function to the PCollection words. # Save the result as the PCollection word_lengths. -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_using_map >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_using_map >}} {{< /highlight >}} {{< paragraph class="language-java" >}} @@ -966,22 +966,22 @@ data contains names and phone numbers. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/test/java/org/apache/beam/examples/snippets/SnippetsTest.java" CoGroupByKeyTupleInputs >}} +{{< code_sample "examples/java/src/test/java/org/apache/beam/examples/snippets/SnippetsTest.java" CoGroupByKeyTupleInputs >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_group_by_key_cogroupbykey_tuple_inputs >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_group_by_key_cogroupbykey_tuple_inputs >}} {{< /highlight >}} After `CoGroupByKey`, the resulting data contains all data associated with each unique key from any of the input collections. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/test/java/org/apache/beam/examples/snippets/SnippetsTest.java" CoGroupByKeyTupleOutputs >}} +{{< code_sample "examples/java/src/test/java/org/apache/beam/examples/snippets/SnippetsTest.java" CoGroupByKeyTupleOutputs >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_group_by_key_cogroupbykey_tuple_outputs >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_group_by_key_cogroupbykey_tuple_outputs >}} {{< /highlight >}} The following code example joins the two `PCollection`s with `CoGroupByKey`, @@ -989,21 +989,21 @@ followed by a `ParDo` to consume the result. Then, the code uses tags to look up and format data from each collection. {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CoGroupByKeyTuple >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/snippets/Snippets.java" CoGroupByKeyTuple >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_group_by_key_cogroupbykey_tuple >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_group_by_key_cogroupbykey_tuple >}} {{< /highlight >}} The formatted data looks like this: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/test/java/org/apache/beam/examples/snippets/SnippetsTest.java" CoGroupByKeyTupleFormattedOutputs >}} +{{< code_sample "examples/java/src/test/java/org/apache/beam/examples/snippets/SnippetsTest.java" CoGroupByKeyTupleFormattedOutputs >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_group_by_key_cogroupbykey_tuple_formatted_outputs >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_group_by_key_cogroupbykey_tuple_formatted_outputs >}} {{< /highlight >}} #### 4.2.4. Combine {#combine} @@ -1048,7 +1048,7 @@ public static class SumInts implements SerializableFunction, I {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" combine_bounded_sum >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" combine_bounded_sum >}} {{< /highlight >}} ##### 4.2.4.2. Advanced combinations using CombineFn {#advanced-combines} @@ -1121,7 +1121,7 @@ public class AverageFn extends CombineFn { {{< highlight py >}} pc = ... -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" combine_custom_average_define >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" combine_custom_average_define >}} {{< /highlight >}} ##### 4.2.4.3. Combining a PCollection into a single value {#combining-pcollection} @@ -1145,7 +1145,7 @@ PCollection sum = pc.apply( # The resulting PCollection, called result, contains one value: the sum of all # the elements in the input PCollection. pc = ... -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" combine_custom_average_execute >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" combine_custom_average_execute >}} {{< /highlight >}} ##### 4.2.4.4. Combine and global windowing {#combine-global-windowing} @@ -1229,7 +1229,7 @@ PCollection> avgAccuracyPerPlayer = # PCollection is grouped by key and the numeric values associated with each key # are averaged into a float. player_accuracies = ... -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" combine_per_key >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" combine_per_key >}} {{< /highlight >}} #### 4.2.5. Flatten {#flatten} @@ -1258,7 +1258,7 @@ PCollection merged = collections.apply(Flatten.pCollections()); {{< highlight py >}} # Flatten takes a tuple of PCollection objects. # Returns a single PCollection that contains all of the elements in the PCollection objects in that tuple. -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_multiple_pcollections_flatten >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_multiple_pcollections_flatten >}} {{< /highlight >}} ##### 4.2.5.1. Data encoding in merged collections {#data-encoding-merged-collections} @@ -1321,10 +1321,10 @@ PCollection fortiethPercentile = studentsByPercentile.get(4); # Provide an int value with the desired number of result partitions, and a partitioning function (partition_fn in this example). # Returns a tuple of PCollection objects containing each of the resulting partitions as individual PCollection objects. students = ... -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_multiple_pcollections_partition >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_multiple_pcollections_partition >}} # You can extract each partition from the tuple of PCollection objects as follows: -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_multiple_pcollections_partition_40th >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_multiple_pcollections_partition_40th >}} {{< /highlight >}} ### 4.3. Requirements for writing user code for Beam transforms {#requirements-for-writing-user-code-for-beam-transforms} @@ -1448,12 +1448,12 @@ determined by the input data, or depend on a different branch of your pipeline. # of the actual elements of pcoll being passed into each process invocation. In this example, side inputs are # passed to a FlatMap transform as extra arguments and consumed by filter_using_length. words = ... -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_side_input >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_side_input >}} # We can also pass side inputs to a ParDo transform, which will get passed to its process method. # The first two arguments for the process method would be self and element. -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_side_input_dofn >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_side_input_dofn >}} ... {{< /highlight >}} @@ -1550,12 +1550,12 @@ together. # with_outputs are attributes on the returned DoOutputsTuple object. The tags give access to the # corresponding output PCollections. -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_with_tagged_outputs >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_with_tagged_outputs >}} # The result is also iterable, ordered in the same order that the tags were passed to with_outputs(), # the main tag (if specified) first. -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_with_tagged_outputs_iter >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_with_tagged_outputs_iter >}} {{< /highlight >}} #### 4.5.2. Emitting to multiple outputs in your DoFn {#multiple-outputs-dofn} @@ -1588,12 +1588,12 @@ together. # using the pvalue.OutputValue wrapper class. # Based on the previous example, this shows the DoFn emitting to the main output and two additional outputs. -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_emitting_values_on_tagged_outputs >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_emitting_values_on_tagged_outputs >}} # Producing multiple outputs is also available in Map and FlatMap. # Here is an example that uses FlatMap and shows that the tags do not need to be specified ahead of time. -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_with_undeclared_outputs >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_pardo_with_undeclared_outputs >}} {{< /highlight >}} #### 4.5.3. Accessing additional parameters in your DoFn {#other-dofn-parameters} @@ -1839,7 +1839,7 @@ transform's intermediate data changes type multiple times. {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" pipeline_monitoring_composite >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" pipeline_monitoring_composite >}} {{< /highlight >}} #### 4.6.2. Creating a composite transform {#composite-transform-creation} @@ -1867,7 +1867,7 @@ The following code sample shows how to declare a `PTransform` that accepts a {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_composite_transform >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_composite_transform >}} {{< /highlight >}} Within your `PTransform` subclass, you'll need to override the `expand` method. @@ -1891,7 +1891,7 @@ The following code sample shows how to override `expand` for the {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_composite_transform >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_composite_transform >}} {{< /highlight >}} As long as you override the `expand` method in your `PTransform` subclass to @@ -1969,7 +1969,7 @@ p.apply("ReadFromText", {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_pipelineio_read >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_pipelineio_read >}} {{< /highlight >}} To read data from disparate sources into a single `PCollection`, read each one @@ -1994,7 +1994,7 @@ records.apply("WriteToText", {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" model_pipelineio_write >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" model_pipelineio_write >}} {{< /highlight >}} ### 5.4. Beam-provided I/O transforms {#provided-io-transforms} @@ -3660,7 +3660,7 @@ into fixed windows, each 60 seconds in length: {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" setting_fixed_windows >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" setting_fixed_windows >}} {{< /highlight >}} #### 8.3.2. Sliding time windows {#using-sliding-time-windows} @@ -3676,7 +3676,7 @@ begins every five seconds: {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" setting_sliding_windows >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" setting_sliding_windows >}} {{< /highlight >}} #### 8.3.3. Session windows {#using-session-windows} @@ -3692,7 +3692,7 @@ least 10 minutes (600 seconds): {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" setting_session_windows >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" setting_session_windows >}} {{< /highlight >}} Note that the sessions are per-key — each key in the collection will have its @@ -3711,7 +3711,7 @@ a single global window for a `PCollection`: {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" setting_global_window >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" setting_global_window >}} {{< /highlight >}} ### 8.4. Watermarks and late data {#watermarks-and-late-data} @@ -3822,7 +3822,7 @@ with a `DoFn` to attach the timestamps to each element in your `PCollection`. {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" setting_timestamp >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" setting_timestamp >}} {{< /highlight >}} ## 9. Triggers {#triggers} @@ -3911,7 +3911,7 @@ firings: {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_early_late_triggers >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_early_late_triggers >}} {{< /highlight >}} #### 9.1.1. Default trigger {#default-trigger} @@ -3988,7 +3988,7 @@ sets the window's **accumulation mode**. {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_setting_trigger >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_setting_trigger >}} {{< /highlight >}} #### 9.4.1. Window accumulation modes {#window-accumulation-modes} @@ -4155,7 +4155,7 @@ example trigger code fires on the following conditions: {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_composite_triggers >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_composite_triggers >}} {{< /highlight >}} #### 9.5.3. Other composite triggers {#other-composite-triggers} @@ -4171,7 +4171,7 @@ elements, or after a minute. {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" model_other_composite_triggers >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" model_other_composite_triggers >}} {{< /highlight >}} ## 10. Metrics {#metrics} @@ -4876,4 +4876,4 @@ perUser.apply(ParDo.of(new DoFn, OutputT>() { isTimerSetState.clear(); } })); -{{< /highlight >}} \ No newline at end of file +{{< /highlight >}} diff --git a/website/www/site/content/en/documentation/sdks/python-type-safety.md b/website/www/site/content/en/documentation/sdks/python-type-safety.md index 5147664ba94a..4b966db084c4 100644 --- a/website/www/site/content/en/documentation/sdks/python-type-safety.md +++ b/website/www/site/content/en/documentation/sdks/python-type-safety.md @@ -45,13 +45,13 @@ Introducing type hints for the `PTransforms` you define allows you to catch pote Consider the following example, in which `numbers` is a `PCollection` of `str` values: {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_missing_define_numbers >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_missing_define_numbers >}} {{< /highlight >}} The code then applies a `Filter` transform to the `numbers` collection with a callable that retrieves the even numbers. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_missing_apply >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_missing_apply >}} {{< /highlight >}} When you call `p.run()`, this code generates an error when trying to execute this transform because `Filter` expects a `PCollection` of integers, but is given a `PCollection` of strings instead. @@ -87,7 +87,7 @@ Annotations are currently supported on: The following code declares an `int` input and a `str` output type hint on the `to_id` transform, using annotations on `my_fn`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test_py3.py" type_hints_map_annotations >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test_py3.py" type_hints_map_annotations >}} {{< /highlight >}} The following code declares `int` input and output type hints on `filter_evens`, using annotations on `FilterEvensDoFn.process`. @@ -97,7 +97,7 @@ It is an error to have a non-iterable return type annotation for these functions Other supported iterable types include: `Iterator`, `Generator`, `Tuple`, `List`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test_py3.py" type_hints_do_fn_annotations >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test_py3.py" type_hints_do_fn_annotations >}} {{< /highlight >}} The following code declares `int` input and output type hints on `double_evens`, using annotations on `FilterEvensDoubleDoFn.process`. @@ -105,7 +105,7 @@ Since `process` returns a `list` or `None`, the output type is annotated as `Opt Beam will also remove the outer `Optional` and (as above) the outer iterable of the return type, only on the `DoFn.process` method and functions passed to `FlatMap`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test_py3.py" type_hints_do_fn_annotations_optional >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test_py3.py" type_hints_do_fn_annotations_optional >}} {{< /highlight >}} ### Declaring Type Hints Inline @@ -113,7 +113,7 @@ Beam will also remove the outer `Optional` and (as above) the outer iterable of To specify type hints inline, use the methods `with_input_types` and `with_output_types`. The following example code declares an input type hint inline: {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_takes >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_takes >}} {{< /highlight >}} When you apply the Filter transform to the numbers collection in the example above, you'll be able to catch the error during pipeline construction. @@ -125,7 +125,7 @@ To specify type hints as properties of a `DoFn` or `PTransform`, use the decorat The following code declares an `int` type hint on `FilterEvensDoFn`, using the decorator `@with_input_types()`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_do_fn >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_do_fn >}} {{< /highlight >}} Decorators receive an arbitrary number of positional and/or keyword arguments, typically interpreted in the context of the function they're wrapping. Generally the first argument is a type hint for the main input, and additional arguments are type hints for side inputs. @@ -147,7 +147,7 @@ The following code specifies an input type hint that asserts the generic type `T If the input to `MyTransform` is of type `str`, Beam will infer the output type to be `Tuple[int, str]`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_transform >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_transform >}} {{< /highlight >}} ## Kinds of Type Hints @@ -200,13 +200,13 @@ In addition to using type hints for type checking at pipeline construction, you For example, the following pipeline emits elements of the wrong type. Depending on the runner implementation, its execution may or may not fail at runtime. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_runtime_off >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_runtime_off >}} {{< /highlight >}} However, if you enable runtime type checking, the code is guaranteed to fail at runtime. To enable runtime type checking, set the pipeline option `runtime_type_check` to `True`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_runtime_on >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_runtime_on >}} {{< /highlight >}} Note that because runtime type checks are done for each `PCollection` element, enabling this feature may incur a significant performance penalty. It is therefore recommended that runtime type checks are disabled for production pipelines. @@ -230,5 +230,5 @@ For example, suppose you have a `PCollection` of key-value pairs whose keys are The following code shows the example `Player` class and how to define a `Coder` for it. When you use type hints, Beam infers which `Coders` to use, using `beam.coders.registry`. The following code registers `PlayerCoder` as a coder for the `Player` class. In the example, the input type declared for `CombinePerKey` is `Tuple[Player, int]`. In this case, Beam infers that the `Coder` objects to use are `TupleCoder`, `PlayerCoder`, and `IntCoder`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_deterministic_key >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets_test.py" type_hints_deterministic_key >}} {{< /highlight >}} diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/filter.md b/website/www/site/content/en/documentation/transforms/python/elementwise/filter.md index 5d29149ba285..6a157f169452 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/filter.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/filter.md @@ -37,7 +37,7 @@ Then, we apply `Filter` in multiple ways to filter out produce by their duration We define a function `is_perennial` which returns `True` if the element's duration equals `'perennial'`, and `False` otherwise. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_function >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_function >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -45,7 +45,7 @@ Output `PCollection` after `Filter`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" perennials >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" perennials >}} {{< /highlight >}} {{< buttons-code-snippet @@ -57,7 +57,7 @@ Output `PCollection` after `Filter`: We can also use lambda functions to simplify **Example 1**. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_lambda >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_lambda >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -65,7 +65,7 @@ Output `PCollection` after `Filter`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" perennials >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" perennials >}} {{< /highlight >}} {{< buttons-code-snippet @@ -80,7 +80,7 @@ They are passed as additional positional arguments or keyword arguments to the f In this example, `has_duration` takes `plant` and `duration` as arguments. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_multiple_arguments >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_multiple_arguments >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -88,7 +88,7 @@ Output `PCollection` after `Filter`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" perennials >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" perennials >}} {{< /highlight >}} {{< buttons-code-snippet @@ -104,7 +104,7 @@ In this example, we pass a `PCollection` the value `'perennial'` as a singleton. We then use that value to filter out perennials. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_side_inputs_singleton >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_side_inputs_singleton >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -112,7 +112,7 @@ Output `PCollection` after `Filter`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" perennials >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" perennials >}} {{< /highlight >}} {{< buttons-code-snippet @@ -126,7 +126,7 @@ This accesses elements lazily as they are needed, so it is possible to iterate over large `PCollection`s that won't fit into memory. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_side_inputs_iter >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_side_inputs_iter >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -134,7 +134,7 @@ Output `PCollection` after `Filter`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" valid_plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" valid_plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -152,7 +152,7 @@ Note that all the elements of the `PCollection` must fit into memory for this. If the `PCollection` won't fit into memory, use `beam.pvalue.AsIter(pcollection)` instead. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_side_inputs_dict >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter.py" filter_side_inputs_dict >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -160,7 +160,7 @@ Output `PCollection` after `Filter`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" perennials >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/filter_test.py" perennials >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/flatmap.md b/website/www/site/content/en/documentation/transforms/python/elementwise/flatmap.md index 5fbdad6d88cf..872805b38637 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/flatmap.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/flatmap.md @@ -38,7 +38,7 @@ We use the function `str.split` which takes a single `str` element and outputs a This pipeline splits the input element using whitespaces, creating a list of zero or more elements. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_simple >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_simple >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -46,7 +46,7 @@ Output `PCollection` after `FlatMap`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -58,7 +58,7 @@ Output `PCollection` after `FlatMap`: We define a function `split_words` which splits an input `str` element using the delimiter `','` and outputs a `list` of `str`s. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_function >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_function >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -66,7 +66,7 @@ Output `PCollection` after `FlatMap`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} {{< /highlight >}} @@ -81,7 +81,7 @@ Each input element is already an `iterable`, where each element is what we want We use a lambda function that returns the same input element it received. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_lambda >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_lambda >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -89,7 +89,7 @@ Output `PCollection` after `FlatMap`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -103,7 +103,7 @@ We use a generator to iterate over the input list and yield each of the elements Each yielded result in the generator is an element in the resulting `PCollection`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_generator >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_generator >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -111,7 +111,7 @@ Output `PCollection` after `FlatMap`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -124,7 +124,7 @@ If your `PCollection` consists of `(key, value)` pairs, you can use `FlatMapTuple` to unpack them into different function arguments. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_tuple >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_tuple >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -132,7 +132,7 @@ Output `PCollection` after `FlatMapTuple`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -147,7 +147,7 @@ They are passed as additional positional arguments or keyword arguments to the f In this example, `split_words` takes `text` and `delimiter` as arguments. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_multiple_arguments >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_multiple_arguments >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -155,7 +155,7 @@ Output `PCollection` after `FlatMap`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -171,7 +171,7 @@ In this example, we pass a `PCollection` the value `','` as a singleton. We then use that value as the delimiter for the `str.split` method. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_side_inputs_singleton >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_side_inputs_singleton >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -179,7 +179,7 @@ Output `PCollection` after `FlatMap`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -193,7 +193,7 @@ This accesses elements lazily as they are needed, so it is possible to iterate over large `PCollection`s that won't fit into memory. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_side_inputs_iter >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_side_inputs_iter >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -201,7 +201,7 @@ Output `PCollection` after `FlatMap`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" valid_plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" valid_plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -219,7 +219,7 @@ Note that all the elements of the `PCollection` must fit into memory for this. If the `PCollection` won't fit into memory, use `beam.pvalue.AsIter(pcollection)` instead. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_side_inputs_dict >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap.py" flatmap_side_inputs_dict >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -227,7 +227,7 @@ Output `PCollection` after `FlatMap`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" valid_plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/flatmap_test.py" valid_plants >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/keys.md b/website/www/site/content/en/documentation/transforms/python/elementwise/keys.md index 013e36e7a504..65b4cba33266 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/keys.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/keys.md @@ -29,7 +29,7 @@ In the following example, we create a pipeline with a `PCollection` of key-value Then, we apply `Keys` to extract the keys and discard the values. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/keys.py" keys >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/keys.py" keys >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -37,7 +37,7 @@ Output `PCollection` after `Keys`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/keys_test.py" icons >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/keys_test.py" icons >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/kvswap.md b/website/www/site/content/en/documentation/transforms/python/elementwise/kvswap.md index 298cbaaf37ea..0bfe13df1baa 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/kvswap.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/kvswap.md @@ -30,7 +30,7 @@ In the following example, we create a pipeline with a `PCollection` of key-value Then, we apply `KvSwap` to swap the keys and values. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/kvswap.py" kvswap >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/kvswap.py" kvswap >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -38,7 +38,7 @@ Output `PCollection` after `KvSwap`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/kvswap_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/kvswap_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/map.md b/website/www/site/content/en/documentation/transforms/python/elementwise/map.md index 0a0c31ff6e69..f3036fea0c5b 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/map.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/map.md @@ -36,7 +36,7 @@ We use the function `str.strip` which takes a single `str` element and outputs a It strips the input element's whitespaces, including newlines and tabs. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_simple >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_simple >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -44,7 +44,7 @@ Output `PCollection` after `Map`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -56,7 +56,7 @@ Output `PCollection` after `Map`: We define a function `strip_header_and_newline` which strips any `'#'`, `' '`, and `'\n'` characters from each element. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_function >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_function >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -64,7 +64,7 @@ Output `PCollection` after `Map`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -76,7 +76,7 @@ Output `PCollection` after `Map`: We can also use lambda functions to simplify **Example 2**. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_lambda >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_lambda >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -84,7 +84,7 @@ Output `PCollection` after `Map`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -99,7 +99,7 @@ They are passed as additional positional arguments or keyword arguments to the f In this example, `strip` takes `text` and `chars` as arguments. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_multiple_arguments >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_multiple_arguments >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -107,7 +107,7 @@ Output `PCollection` after `Map`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -120,7 +120,7 @@ If your `PCollection` consists of `(key, value)` pairs, you can use `MapTuple` to unpack them into different function arguments. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_tuple >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_tuple >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -128,7 +128,7 @@ Output `PCollection` after `MapTuple`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -144,7 +144,7 @@ In this example, we pass a `PCollection` the value `'# \n'` as a singleton. We then use that value as the characters for the `str.strip` method. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_side_inputs_singleton >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_side_inputs_singleton >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -152,7 +152,7 @@ Output `PCollection` after `Map`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -166,7 +166,7 @@ This accesses elements lazily as they are needed, so it is possible to iterate over large `PCollection`s that won't fit into memory. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_side_inputs_iter >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_side_inputs_iter >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -174,7 +174,7 @@ Output `PCollection` after `Map`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -192,7 +192,7 @@ Note that all the elements of the `PCollection` must fit into memory for this. If the `PCollection` won't fit into memory, use `beam.pvalue.AsIter(pcollection)` instead. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_side_inputs_dict >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map.py" map_side_inputs_dict >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -200,7 +200,7 @@ Output `PCollection` after `Map`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plant_details >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/map_test.py" plant_details >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/pardo.md b/website/www/site/content/en/documentation/transforms/python/elementwise/pardo.md index c0514693954a..cd10cdeae67a 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/pardo.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/pardo.md @@ -42,7 +42,7 @@ The `process` method is called once per element, and it can yield zero or more output elements. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo.py" pardo_dofn >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo.py" pardo_dofn >}} {{}} {{< paragraph class="notebook-skip" >}} @@ -50,7 +50,7 @@ Output `PCollection` after `ParDo`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -71,7 +71,7 @@ In this example, we add new parameters to the `process` method to bind parameter object. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo.py" pardo_dofn_params >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo.py" pardo_dofn_params >}} {{}} {{< paragraph class="notebook-skip" >}} @@ -79,7 +79,7 @@ In this example, we add new parameters to the `process` method to bind parameter {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo_test.py" dofn_params >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo_test.py" dofn_params >}} {{< /highlight >}} {{< buttons-code-snippet @@ -132,7 +132,7 @@ starts and finishes with `start_bundle` and `finish_bundle`. For example, if the worker crashes, `teardown` might not be called. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo.py" pardo_dofn_methods >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo.py" pardo_dofn_methods >}} {{}} {{< paragraph class="notebook-skip" >}} @@ -140,7 +140,7 @@ starts and finishes with `start_bundle` and `finish_bundle`. {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo_test.py" results >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/pardo_test.py" results >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/partition.md b/website/www/site/content/en/documentation/transforms/python/elementwise/partition.md index 5034086cd763..72f6aa0502bd 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/partition.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/partition.md @@ -47,7 +47,7 @@ In the following example, we have a known list of durations. We partition the `PCollection` into one `PCollection` for every duration type. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition.py" partition_function >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition.py" partition_function >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -55,7 +55,7 @@ Output `PCollection`s: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition_test.py" partitions >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition_test.py" partitions >}} {{< /highlight >}} {{< buttons-code-snippet @@ -67,7 +67,7 @@ Output `PCollection`s: We can also use lambda functions to simplify **Example 1**. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition.py" partition_lambda >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition.py" partition_lambda >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -75,7 +75,7 @@ Output `PCollection`s: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition_test.py" partitions >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition_test.py" partitions >}} {{< /highlight >}} {{< buttons-code-snippet @@ -115,7 +115,7 @@ This `split_dataset` function is generic enough to support any number of partiti You might want to adapt the bucket assignment to use a more appropriate or randomized hash for your dataset. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition.py" partition_multiple_arguments >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition.py" partition_multiple_arguments >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -123,7 +123,7 @@ Output `PCollection`s: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition_test.py" train_test >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/partition_test.py" train_test >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/regex.md b/website/www/site/content/en/documentation/transforms/python/elementwise/regex.md index 3374f4c25d48..2e55c1589257 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/regex.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/regex.md @@ -62,7 +62,7 @@ To start matching at any point instead of the beginning of the string, use [`Regex.find(regex)`](#example-4-regex-find). {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_matches >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_matches >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -70,7 +70,7 @@ Output `PCollection` after `Regex.matches`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_matches >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_matches >}} {{< /highlight >}} {{< buttons-code-snippet @@ -91,7 +91,7 @@ To start matching at any point instead of the beginning of the string, use [`Regex.find_all(regex, group=Regex.ALL, outputEmpty=False)`](#example-5-regex-find-all). {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_all_matches >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_all_matches >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -99,7 +99,7 @@ Output `PCollection` after `Regex.all_matches`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_all_matches >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_all_matches >}} {{< /highlight >}} {{< buttons-code-snippet @@ -121,7 +121,7 @@ To start matching at any point instead of the beginning of the string, use [`Regex.find_kv(regex, keyGroup)`](#example-6-regex-find-as-key-value-pairs). {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_matches_kv >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_matches_kv >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -129,7 +129,7 @@ Output `PCollection` after `Regex.matches_kv`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_matches_kv >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_matches_kv >}} {{< /highlight >}} {{< buttons-code-snippet @@ -151,7 +151,7 @@ If you need to match from the start only, consider using [`Regex.matches(regex)`](#example-1-regex-match). {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_find >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_find >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -159,7 +159,7 @@ Output `PCollection` after `Regex.find`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_matches >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_matches >}} {{< /highlight >}} {{< buttons-code-snippet @@ -181,7 +181,7 @@ If you need to match all groups from the start only, consider using [`Regex.all_matches(regex)`](#example-2-regex-match-with-all-groups). {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_find_all >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_find_all >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -189,7 +189,7 @@ Output `PCollection` after `Regex.find_all`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_find_all >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_find_all >}} {{< /highlight >}} {{< buttons-code-snippet @@ -212,7 +212,7 @@ If you need to match as key-value pairs from the start only, consider using [`Regex.matches_kv(regex)`](#example-3-regex-match-into-key-value-pairs). {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_find_kv >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_find_kv >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -220,7 +220,7 @@ Output `PCollection` after `Regex.find_kv`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_find_kv >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_find_kv >}} {{< /highlight >}} {{< buttons-code-snippet @@ -235,7 +235,7 @@ You can also use on the `replacement`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_replace_all >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_replace_all >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -243,7 +243,7 @@ Output `PCollection` after `Regex.replace_all`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_replace_all >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_replace_all >}} {{< /highlight >}} {{< buttons-code-snippet @@ -258,7 +258,7 @@ You can also use on the `replacement`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_replace_first >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_replace_first >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -266,7 +266,7 @@ Output `PCollection` after `Regex.replace_first`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_replace_first >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_replace_first >}} {{< /highlight >}} {{< buttons-code-snippet @@ -279,7 +279,7 @@ Output `PCollection` after `Regex.replace_first`: The argument `outputEmpty` is set to `False` by default, but can be set to `True` to keep empty items in the output list. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_split >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex.py" regex_split >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -287,7 +287,7 @@ Output `PCollection` after `Regex.split`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_split >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/regex_test.py" plants_split >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/tostring.md b/website/www/site/content/en/documentation/transforms/python/elementwise/tostring.md index 292825c41ba7..61a2070fd388 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/tostring.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/tostring.md @@ -36,7 +36,7 @@ The following example converts a `(key, value)` pair into a string delimited by You can specify a different delimiter using the `delimiter` argument. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring.py" tostring_kvs >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring.py" tostring_kvs >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -44,7 +44,7 @@ Output `PCollection` after `ToString`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet @@ -57,7 +57,7 @@ The following example converts a dictionary into a string. The string output will be equivalent to `str(element)`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring.py" tostring_element >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring.py" tostring_element >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -65,7 +65,7 @@ Output `PCollection` after `ToString`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring_test.py" plant_lists >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring_test.py" plant_lists >}} {{< /highlight >}} {{< buttons-code-snippet @@ -80,7 +80,7 @@ You can specify a different delimiter using the `delimiter` argument. The string output will be equivalent to `iterable.join(delimiter)`. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring.py" tostring_iterables >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring.py" tostring_iterables >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -88,7 +88,7 @@ Output `PCollection` after `ToString`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring_test.py" plants_csv >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/tostring_test.py" plants_csv >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/values.md b/website/www/site/content/en/documentation/transforms/python/elementwise/values.md index b1179596da93..11e54a4fdbc7 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/values.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/values.md @@ -29,7 +29,7 @@ In the following example, we create a pipeline with a `PCollection` of key-value Then, we apply `Values` to extract the values and discard the keys. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/values.py" values >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/values.py" values >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -37,7 +37,7 @@ Output `PCollection` after `Values`: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/values_test.py" plants >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/values_test.py" plants >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/documentation/transforms/python/elementwise/withtimestamps.md b/website/www/site/content/en/documentation/transforms/python/elementwise/withtimestamps.md index 3a1c6fd9a10b..3cc037217b3f 100644 --- a/website/www/site/content/en/documentation/transforms/python/elementwise/withtimestamps.md +++ b/website/www/site/content/en/documentation/transforms/python/elementwise/withtimestamps.md @@ -34,7 +34,7 @@ The elements themselves often already contain a timestamp field. in the form of seconds. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps.py" withtimestamps_event_time >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps.py" withtimestamps_event_time >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -42,7 +42,7 @@ Output `PCollection` after getting the timestamps: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps_test.py" plant_timestamps >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps_test.py" plant_timestamps >}} {{< /highlight >}} {{< buttons-code-snippet @@ -57,7 +57,7 @@ For more information on time formatting options, see [`time.strftime`](https://docs.python.org/3/library/time.html#time.strftime). {{< highlight >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps.py" time_tuple2unix_time >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps.py" time_tuple2unix_time >}} {{< /highlight >}} To convert from a @@ -66,7 +66,7 @@ to `unix_time` you can use convert it to a `time.struct_time` first with [`datetime.timetuple`](https://docs.python.org/3/library/datetime.html#datetime.datetime.timetuple). {{< highlight >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps.py" datetime2unix_time >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps.py" datetime2unix_time >}} {{< /highlight >}} ### Example 2: Timestamp by logical clock @@ -76,7 +76,7 @@ If each element has a chronological number, these numbers can be used as a These numbers have to be converted to a *"seconds"* equivalent, which can be especially important depending on your windowing and late data rules. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps.py" withtimestamps_logical_clock >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps.py" withtimestamps_logical_clock >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -84,7 +84,7 @@ Output `PCollection` after getting the timestamps: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps_test.py" plant_events >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps_test.py" plant_events >}} {{< /highlight >}} {{< buttons-code-snippet @@ -100,7 +100,7 @@ Workers might have time deltas, so using this method is not a reliable way to do By using processing time, there is no way of knowing if data is arriving late because the timestamp is attached when the element *enters* into the pipeline. {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps.py" withtimestamps_processing_time >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps.py" withtimestamps_processing_time >}} {{< /highlight >}} {{< paragraph class="notebook-skip" >}} @@ -108,7 +108,7 @@ Output `PCollection` after getting the timestamps: {{< /paragraph >}} {{< highlight class="notebook-skip" >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps_test.py" plant_processing_times >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/transforms/elementwise/withtimestamps_test.py" plant_processing_times >}} {{< /highlight >}} {{< buttons-code-snippet diff --git a/website/www/site/content/en/get-started/mobile-gaming-example.md b/website/www/site/content/en/get-started/mobile-gaming-example.md index 9054f5373e10..6a976c56f42f 100644 --- a/website/www/site/content/en/get-started/mobile-gaming-example.md +++ b/website/www/site/content/en/get-started/mobile-gaming-example.md @@ -101,11 +101,11 @@ This example uses batch processing, and the diagram's Y axis represents processi After reading the score events from the input file, the pipeline groups all of those user/score pairs together and sums the score values into one total value per unique user. `UserScore` encapsulates the core logic for that step as the [user-defined composite transform](/documentation/programming-guide/#composite-transforms) `ExtractAndSumScore`: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/UserScore.java" DocInclude_USExtractXform >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/UserScore.java" DocInclude_USExtractXform >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/user_score.py" extract_and_sum_score >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/user_score.py" extract_and_sum_score >}} {{< /highlight >}} `ExtractAndSumScore` is written to be more general, in that you can pass in the field by which you want to group the data (in the case of our game, by unique user or unique team). This means we can re-use `ExtractAndSumScore` in other pipelines that group score data by team, for example. @@ -113,11 +113,11 @@ After reading the score events from the input file, the pipeline groups all of t Here's the main method of `UserScore`, showing how we apply all three steps of the pipeline: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/UserScore.java" DocInclude_USMain >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/UserScore.java" DocInclude_USMain >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/user_score.py" main >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/user_score.py" main >}} {{< /highlight >}} ### Limitations @@ -186,11 +186,11 @@ Beam's windowing feature uses the [intrinsic timestamp information](/documentati The following code shows this: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/HourlyTeamScore.java" DocInclude_HTSAddTsAndWindow >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/HourlyTeamScore.java" DocInclude_HTSAddTsAndWindow >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/hourly_team_score.py" add_timestamp_and_window >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/hourly_team_score.py" add_timestamp_and_window >}} {{< /highlight >}} Notice that the transforms the pipeline uses to specify the windowing are distinct from the actual data processing transforms (such as `ExtractAndSumScores`). This functionality provides you some flexibility in designing your Beam pipeline, in that you can run existing transforms over datasets with different windowing characteristics. @@ -206,11 +206,11 @@ It also lets the pipeline include relevant **late data**—data events with vali The following code shows how `HourlyTeamScore` uses the `Filter` transform to filter events that occur either before or after the relevant analysis period: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/HourlyTeamScore.java" DocInclude_HTSFilters >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/HourlyTeamScore.java" DocInclude_HTSFilters >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/hourly_team_score.py" filter_by_time_range >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/hourly_team_score.py" filter_by_time_range >}} {{< /highlight >}} #### Calculating Score Per Team, Per Window @@ -218,11 +218,11 @@ The following code shows how `HourlyTeamScore` uses the `Filter` transform to fi `HourlyTeamScore` uses the same `ExtractAndSumScores` transform as the `UserScore` pipeline, but passes a different key (team, as opposed to user). Also, because the pipeline applies `ExtractAndSumScores` _after_ applying fixed-time 1-hour windowing to the input data, the data gets grouped by both team _and_ window. You can see the full sequence of transforms in `HourlyTeamScore`'s main method: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/HourlyTeamScore.java" DocInclude_HTSMain >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/HourlyTeamScore.java" DocInclude_HTSMain >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/hourly_team_score.py" main >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/hourly_team_score.py" main >}} {{< /highlight >}} ### Limitations @@ -279,11 +279,11 @@ As processing time advances and more scores are processed, the trigger outputs t The following code example shows how `LeaderBoard` sets the processing time trigger to output the data for user scores: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/LeaderBoard.java" DocInclude_ProcTimeTrigger >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/LeaderBoard.java" DocInclude_ProcTimeTrigger >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/leader_board.py" processing_time_trigger >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/leader_board.py" processing_time_trigger >}} {{< /highlight >}} `LeaderBoard` sets the [window accumulation mode](/documentation/programming-guide/#window-accumulation-modes) to accumulate window panes as the trigger fires. This accumulation mode is set by invoking `.accumulatingFiredPanes` using `accumulation_mode=trigger.AccumulationMode.ACCUMULATING` when setting the trigger, and causes the pipeline to accumulate the previously emitted data together with any new data that's arrived since the last trigger fire. This ensures that `LeaderBoard` is a running sum for the user scores, rather than a collection of individual sums. @@ -313,11 +313,11 @@ Data arriving above the solid watermark line is _late data_ — this is a score The following code example shows how `LeaderBoard` applies fixed-time windowing with the appropriate triggers to have our pipeline perform the calculations we want: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/LeaderBoard.java" DocInclude_WindowAndTrigger >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/LeaderBoard.java" DocInclude_WindowAndTrigger >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/leader_board.py" window_and_trigger >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/leader_board.py" window_and_trigger >}} {{< /highlight >}} Taken together, these processing strategies let us address the latency and completeness issues present in the `UserScore` and `HourlyTeamScore` pipelines, while still using the same basic transforms to process the data—as a matter of fact, both calculations still use the same `ExtractAndSumScore` transform that we used in both the `UserScore` and `HourlyTeamScore` pipelines. @@ -356,21 +356,21 @@ Since the average depends on the pipeline data, we need to calculate it, and the The following code example shows the composite transform that handles abuse detection. The transform uses the `Sum.integersPerKey` transform to sum all scores per user, and then the `Mean.globally` transform to determine the average score for all users. Once that's been calculated (as a `PCollectionView` singleton), we can pass it to the filtering `ParDo` using `.withSideInputs`: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/GameStats.java" DocInclude_AbuseDetect >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/GameStats.java" DocInclude_AbuseDetect >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/game_stats.py" abuse_detect >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/game_stats.py" abuse_detect >}} {{< /highlight >}} The abuse-detection transform generates a view of users supected to be spambots. Later in the pipeline, we use that view to filter out any such users when we calculate the team score per hour, again by using the side input mechanism. The following code example shows where we insert the spam filter, between windowing the scores into fixed windows and extracting the team scores: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/GameStats.java" DocInclude_FilterAndCalc >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/GameStats.java" DocInclude_FilterAndCalc >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/game_stats.py" filter_and_calc >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/game_stats.py" filter_and_calc >}} {{< /highlight >}} #### Analyzing Usage Patterns @@ -390,21 +390,21 @@ between instances are.* We can use the session-windowed data to determine the average length of uninterrupted play time for all of our users, as well as the total score they achieve during each session. We can do this in the code by first applying session windows, summing the score per user and session, and then using a transform to calculate the length of each individual session: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/GameStats.java" DocInclude_SessionCalc >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/GameStats.java" DocInclude_SessionCalc >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/game_stats.py" session_calc >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/game_stats.py" session_calc >}} {{< /highlight >}} This gives us a set of user sessions, each with an attached duration. We can then calculate the _average_ session length by re-windowing the data into fixed time windows, and then calculating the average for all sessions that end in each hour: {{< highlight java >}} -{{< github_sample "/apache/beam/blob/master/examples/java/src/main/java/org/apache/beam/examples/complete/game/GameStats.java" DocInclude_Rewindow >}} +{{< code_sample "examples/java/src/main/java/org/apache/beam/examples/complete/game/GameStats.java" DocInclude_Rewindow >}} {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/game/game_stats.py" rewindow >}} +{{< code_sample "sdks/python/apache_beam/examples/complete/game/game_stats.py" rewindow >}} {{< /highlight >}} We can use the resulting information to find, for example, what times of day our users are playing the longest, or which stretches of the day are more likely to see shorter play sessions. diff --git a/website/www/site/content/en/get-started/wordcount-example.md b/website/www/site/content/en/get-started/wordcount-example.md index 58ae28507e34..08e447912fc6 100644 --- a/website/www/site/content/en/get-started/wordcount-example.md +++ b/website/www/site/content/en/get-started/wordcount-example.md @@ -123,7 +123,7 @@ sections, we will specify the pipeline's runner. {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_options >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_options >}} {{< /highlight >}} {{< paragraph class="language-java language-py" >}} @@ -143,7 +143,7 @@ Pipeline p = Pipeline.create(options); {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_create >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_create >}} {{< /highlight >}} {{< highlight go >}} @@ -179,7 +179,7 @@ p.apply(TextIO.read().from("gs://apache-beam-samples/shakespeare/*")) {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_read >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_read >}} {{< /highlight >}} {{< highlight go >}} @@ -204,7 +204,7 @@ lines := textio.Read(s, "gs://apache-beam-samples/shakespeare/*") {{< highlight py >}} # The Flatmap transform is a simplified version of ParDo. -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_pardo >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_pardo >}} {{< /highlight >}} {{< highlight go >}} @@ -231,7 +231,7 @@ words := beam.ParDo(s, func(line string, emit func(string)) { {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_count >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_count >}} {{< /highlight >}} {{< highlight go >}} @@ -253,7 +253,7 @@ counted := stats.Count(s, words) {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_map >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_map >}} {{< /highlight >}} {{< highlight go >}} @@ -272,7 +272,7 @@ formatted := beam.ParDo(s, func(w string, c int) string { {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_write >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_write >}} {{< /highlight >}} {{< highlight go >}} @@ -304,7 +304,7 @@ p.run().waitUntilFinish(); {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_run >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_minimal_run >}} {{< /highlight >}} {{< highlight go >}} @@ -534,7 +534,7 @@ static class ExtractWordsFn extends DoFn { {{< highlight py >}} # In this example, the DoFns are defined as classes: -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_wordcount_dofn >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_wordcount_dofn >}} {{< /highlight >}} {{< highlight go >}} @@ -603,7 +603,7 @@ public static void main(String[] args) throws IOException { {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_wordcount_composite >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_wordcount_composite >}} {{< /highlight >}} {{< highlight go >}} @@ -652,7 +652,7 @@ public static void main(String[] args) { {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_wordcount_options >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" examples_wordcount_wordcount_options >}} {{< /highlight >}} {{< highlight go >}} @@ -862,7 +862,7 @@ public class DebuggingWordCount { {{< /highlight >}} {{< highlight py >}} -{{< github_sample "/apache/beam/blob/master/sdks/python/apache_beam/examples/snippets/snippets.py" example_wordcount_debugging_logging >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" example_wordcount_debugging_logging >}} {{< /highlight >}} {{< highlight go >}} diff --git a/website/www/site/layouts/shortcodes/code_sample.html b/website/www/site/layouts/shortcodes/code_sample.html new file mode 100644 index 000000000000..4a94cc2e5346 --- /dev/null +++ b/website/www/site/layouts/shortcodes/code_sample.html @@ -0,0 +1,23 @@ +{{/* + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + http://www.apache.org/licenses/LICENSE-2.0 + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. See accompanying LICENSE file. +*/}} +{{/* + This shortcode is used to fetch a piece of code with tags from Beam code. + In setupDockerContainer stage of build process, we run build_code_samples.sh script, which + copies Beam project files from which we take code snippets to website/www/site/code_samples + directory. We do that because Hugo can't access files which are outside of its project tree + (Hugo's root is the directory that contains config.toml). When copying, we name this files + according to convention path_to_file_filename.extension in order to avoid name conflicts. + .Get 0 references an argument passed to code_sample shortcode which is a path to file with + code snippet. So if we pass path/to/file/filename.py to code_sample, $path variable will + have value code_samples/path_to_file_filename.py which Hugo can access. + There should be no breaklines here to make sure the string results do not get impacts of newlines. +*/}}{{ $tag := .Get 1 }}{{ $path := printf "code_samples/%s" (replaceRE "/" "_" (.Get 0)) }}{{ $data := readFile $path }}{{ $matchRegex := printf "%s%s%s%s%s" "\\[START " $tag "]\n[\\s\\S]*?\n.*\\[END " $tag "]" }}{{ $match := index (findRE $matchRegex $data) 0 }}{{ $lines := split $match "\n" }}{{ $lineCount := len $lines }}{{ $cleanedLines := $lines | first (sub $lineCount 1) | last (sub $lineCount 2) }}{{ $firstLine := index $cleanedLines 0 }}{{ $numberOfWhitespaces := index (findRE "^\\s*" $firstLine) 0 | len }}{{ $unindentRegex := printf "%s%d%s" "^\\s{" $numberOfWhitespaces "}" }}{{ $unindentedLines := apply $cleanedLines "replaceRE" $unindentRegex "" "." }}{{ $result := delimit $unindentedLines "\n" }}{{ print $result }} diff --git a/website/www/site/layouts/shortcodes/github_sample.html b/website/www/site/layouts/shortcodes/github_sample.html deleted file mode 100644 index db9fe9319687..000000000000 --- a/website/www/site/layouts/shortcodes/github_sample.html +++ /dev/null @@ -1,15 +0,0 @@ -{{/* - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - http://www.apache.org/licenses/LICENSE-2.0 - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. See accompanying LICENSE file. -*/}} -{{/* - This shortcode is used to fetch a piece of code with tags from GitHub. - There should be no breaklines here to make sure the string results do not get impacts of newlines. -*/}}{{ $tag := .Get 1 }}{{ $path := replaceRE "/blob/" "/" (.Get 0) }}{{ $path := printf "github_samples/%s" (replaceRE "/" "_" $path) }}{{ $data := readFile $path }}{{ $matchRegex := printf "%s%s%s%s%s" "\\[START " $tag "]\n[\\s\\S]*?\n.*\\[END " $tag "]" }}{{ $match := index (findRE $matchRegex $data) 0 }}{{ $lines := split $match "\n" }}{{ $lineCount := len $lines }}{{ $cleanedLines := $lines | first (sub $lineCount 1) | last (sub $lineCount 2) }}{{ $firstLine := index $cleanedLines 0 }}{{ $numberOfWhitespaces := index (findRE "^\\s*" $firstLine) 0 | len }}{{ $unindentRegex := printf "%s%d%s" "^\\s{" $numberOfWhitespaces "}" }}{{ $unindentedLines := apply $cleanedLines "replaceRE" $unindentRegex "" "." }}{{ $result := delimit $unindentedLines "\n" }}{{ print $result }} From 4817e843ad8e5aa8a8831a0fc0e2c5f10b0ab76f Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Wed, 27 May 2020 18:49:37 -0400 Subject: [PATCH 103/151] [BEAM-9971] Do not use context classloader. (#11784) * [BEAM-9971] Do not use context classloader. * Add TODO(BEAM-10109). --- .../beam/runners/core/construction/NativeTransforms.java | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/NativeTransforms.java b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/NativeTransforms.java index 730a5ca561f5..9ea47a10835b 100644 --- a/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/NativeTransforms.java +++ b/runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/NativeTransforms.java @@ -46,7 +46,10 @@ public class NativeTransforms { * Returns true if an only if the Runner understands this transform and can handle it directly. */ public static boolean isNative(RunnerApi.PTransform pTransform) { - Iterator matchers = ServiceLoader.load(IsNativeTransform.class).iterator(); + // TODO(BEAM-10109) Use default (context) classloader. + Iterator matchers = + ServiceLoader.load(IsNativeTransform.class, NativeTransforms.class.getClassLoader()) + .iterator(); while (matchers.hasNext()) { if (matchers.next().test(pTransform)) { return true; From d17259491a666b0bf7e11b4f5001f8d747aa06cc Mon Sep 17 00:00:00 2001 From: Chamikara Jayalath Date: Wed, 27 May 2020 18:21:45 -0700 Subject: [PATCH 104/151] Enables proto holders for testing runner API. Without this x-lang can be broken for some execution paths where this property get enabled automatically. --- sdks/python/apache_beam/pipeline.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/sdks/python/apache_beam/pipeline.py b/sdks/python/apache_beam/pipeline.py index d1380c6294b7..9d1b02c53e01 100644 --- a/sdks/python/apache_beam/pipeline.py +++ b/sdks/python/apache_beam/pipeline.py @@ -509,7 +509,8 @@ def run(self, test_runner_api='AUTO'): return Pipeline.from_runner_api( self.to_runner_api(use_fake_coders=True), self.runner, - self._options).run(False) + self._options, + allow_proto_holders=True).run(False) if self._options.view_as(TypeOptions).runtime_type_check: from apache_beam.typehints import typecheck From 05882606bc638698ebc8e16a978d184b3f7ba5fe Mon Sep 17 00:00:00 2001 From: Rui Wang Date: Wed, 27 May 2020 20:54:57 -0700 Subject: [PATCH 105/151] [BEAM-9363] Support TUMBLE aggregation (#11807) * [BEAM-9363] Support TUMBLE aggregation. --- .../impl/rel/BeamTableFunctionScanRel.java | 37 +++++++++++++++---- .../sql/zetasql/ZetaSQLDialectSpecTest.java | 25 +++++++++++++ 2 files changed, 54 insertions(+), 8 deletions(-) diff --git a/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/rel/BeamTableFunctionScanRel.java b/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/rel/BeamTableFunctionScanRel.java index 74d6ccae41e4..6381fd96b787 100644 --- a/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/rel/BeamTableFunctionScanRel.java +++ b/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/rel/BeamTableFunctionScanRel.java @@ -29,8 +29,11 @@ import org.apache.beam.sdk.transforms.DoFn; import org.apache.beam.sdk.transforms.PTransform; import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.transforms.WithTimestamps; import org.apache.beam.sdk.transforms.windowing.FixedWindows; import org.apache.beam.sdk.transforms.windowing.IntervalWindow; +import org.apache.beam.sdk.transforms.windowing.Window; +import org.apache.beam.sdk.transforms.windowing.WindowFn; import org.apache.beam.sdk.values.PCollection; import org.apache.beam.sdk.values.PCollectionList; import org.apache.beam.sdk.values.Row; @@ -99,14 +102,32 @@ public PCollection expand(PCollectionList input) { RexInputRef wmCol = (RexInputRef) call.getOperands().get(1); PCollection upstream = input.get(0); Schema outputSchema = CalciteUtils.toSchema(getRowType()); - return upstream - .apply( - ParDo.of( - new FixedWindowDoFn( - FixedWindows.of(durationParameter(call.getOperands().get(2))), - wmCol.getIndex(), - outputSchema))) - .setRowSchema(outputSchema); + FixedWindows windowFn = FixedWindows.of(durationParameter(call.getOperands().get(2))); + PCollection streamWithWindowMetadata = + upstream + .apply(ParDo.of(new FixedWindowDoFn(windowFn, wmCol.getIndex(), outputSchema))) + .setRowSchema(outputSchema); + + PCollection windowedStream = + assignTimestampsAndWindow( + streamWithWindowMetadata, wmCol.getIndex(), (WindowFn) windowFn); + + return windowedStream; + } + + /** Extract timestamps from the windowFieldIndex, then window into windowFns. */ + private PCollection assignTimestampsAndWindow( + PCollection upstream, int windowFieldIndex, WindowFn windowFn) { + PCollection windowedStream; + windowedStream = + upstream + .apply( + "assignEventTimestamp", + WithTimestamps.of(row -> row.getDateTime(windowFieldIndex).toInstant()) + .withAllowedTimestampSkew(new Duration(Long.MAX_VALUE))) + .setCoder(upstream.getCoder()) + .apply(Window.into(windowFn)); + return windowedStream; } } diff --git a/sdks/java/extensions/sql/zetasql/src/test/java/org/apache/beam/sdk/extensions/sql/zetasql/ZetaSQLDialectSpecTest.java b/sdks/java/extensions/sql/zetasql/src/test/java/org/apache/beam/sdk/extensions/sql/zetasql/ZetaSQLDialectSpecTest.java index 8385c706315a..c6aa39b1ef37 100644 --- a/sdks/java/extensions/sql/zetasql/src/test/java/org/apache/beam/sdk/extensions/sql/zetasql/ZetaSQLDialectSpecTest.java +++ b/sdks/java/extensions/sql/zetasql/src/test/java/org/apache/beam/sdk/extensions/sql/zetasql/ZetaSQLDialectSpecTest.java @@ -4780,6 +4780,31 @@ public void testTumbleAsTVF() { pipeline.run().waitUntilFinish(Duration.standardMinutes(PIPELINE_EXECUTION_WAITTIME_MINUTES)); } + @Test + public void testTVFTumbleAggregation() { + String sql = + "SELECT COUNT(*) as field_count, " + + "window_start " + + "FROM TUMBLE((select * from KeyValue), descriptor(ts), 'INTERVAL 1 SECOND') " + + "GROUP BY window_start"; + ZetaSQLQueryPlanner zetaSQLQueryPlanner = new ZetaSQLQueryPlanner(config); + BeamRelNode beamRelNode = zetaSQLQueryPlanner.convertToBeamRel(sql); + + PCollection stream = BeamSqlRelUtils.toPCollection(pipeline, beamRelNode); + + final Schema schema = + Schema.builder().addInt64Field("field_count").addDateTimeField("window_start").build(); + PAssert.that(stream) + .containsInAnyOrder( + Row.withSchema(schema) + .addValues(1L, new DateTime(2018, 7, 1, 21, 26, 7, ISOChronology.getInstanceUTC())) + .build(), + Row.withSchema(schema) + .addValues(1L, new DateTime(2018, 7, 1, 21, 26, 6, ISOChronology.getInstanceUTC())) + .build()); + pipeline.run().waitUntilFinish(Duration.standardMinutes(PIPELINE_EXECUTION_WAITTIME_MINUTES)); + } + @Test public void testIsNullTrueFalse() { String sql = From d71ee351e84f83c29b8d0759c9dcde0b477f161a Mon Sep 17 00:00:00 2001 From: Alexey Romanenko Date: Thu, 28 May 2020 13:31:15 +0200 Subject: [PATCH 106/151] [BEAM-9916] Fixed some IO Urls on website --- website/www/site/data/io_matrix.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/website/www/site/data/io_matrix.yaml b/website/www/site/data/io_matrix.yaml index f1e4c962f0e0..3ce5a4f864ec 100644 --- a/website/www/site/data/io_matrix.yaml +++ b/website/www/site/data/io_matrix.yaml @@ -61,13 +61,13 @@ categories: implementations: - language: java name: org.apache.beam.sdk.io.xml.XmlIO - url: https://beam.apache.org/releases/javadoc/2.3.0/org/apache/beam/sdk/io/xml/XmlIO.html + url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/xml/XmlIO.html - transform: TikaIO description: Transforms for parsing arbitrary files using [Apache Tika](https://tika.apache.org/). implementations: - language: java name: org.apache.beam.sdk.io.tika.TikaIO - url: https://beam.apache.org/releases/javadoc/2.3.0/org/apache/beam/sdk/io/tika/TikaIO.html + url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/tika/TikaIO.html - transform: ParquetIO description: IO for reading from and writing to [Parquet](https://parquet.apache.org/) files. docs: /documentation/io/built-in/parquet/ @@ -365,13 +365,13 @@ categories: implementations: - language: py name: apache_beam.io.flink.flink_streaming_impulse_source - url: https://beam.apache.org/releases/pydoc/2.20.0/apache_beam.io.flink.flink_streaming_impulse_source.html + url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.flink.flink_streaming_impulse_source.html - transform: GenerateSequence description: Generates a bounded or unbounded stream of integers. implementations: - language: java name: org.apache.beam.sdk.io.GenerateSequence - url: https://beam.apache.org/releases/javadoc/2.20.0/org/apache/beam/sdk/io/GenerateSequence.html + url: https://beam.apache.org/releases/javadoc/current/org/apache/beam/sdk/io/GenerateSequence.html - language: py name: apache_beam.io.external.generate_sequence.GenerateSequence - url: https://beam.apache.org/releases/pydoc/2.20.0/apache_beam.io.external.generate_sequence.html + url: https://beam.apache.org/releases/pydoc/current/apache_beam.io.external.generate_sequence.html From 972c331f12b74efbe127cf8e1befe9b5de8b292f Mon Sep 17 00:00:00 2001 From: Steven Niemitz Date: Thu, 28 May 2020 12:17:23 -0400 Subject: [PATCH 107/151] Avoid re-encoding value state cells each commit (#11823) --- .../worker/WindmillStateInternals.java | 20 ++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/WindmillStateInternals.java b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/WindmillStateInternals.java index a3619ab9bfab..964245b43715 100644 --- a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/WindmillStateInternals.java +++ b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/WindmillStateInternals.java @@ -345,6 +345,8 @@ private static class WindmillValue extends SimpleWindmillState implements Val private boolean modified = false; /** Whether the in memory value is the true value. */ private boolean valueIsKnown = false; + /** The size of the encoded value */ + private long cachedSize = -1; private T value; @@ -382,6 +384,9 @@ public WindmillValue readLater() { @Override public T read() { try (Closeable scope = scopedReadState()) { + if (!valueIsKnown) { + cachedSize = -1; + } value = getFuture().get(); valueIsKnown = true; return value; @@ -397,6 +402,7 @@ public T read() { public void write(T value) { modified = true; valueIsKnown = true; + cachedSize = -1; this.value = value; } @@ -410,14 +416,18 @@ protected WorkItemCommitRequest persistDirectly(WindmillStateCache.ForKey cache) return WorkItemCommitRequest.newBuilder().buildPartial(); } - ByteString.Output stream = ByteString.newOutput(); - if (value != null) { - coder.encode(value, stream, Coder.Context.OUTER); + ByteString encoded = null; + if (cachedSize == -1 || modified) { + ByteString.Output stream = ByteString.newOutput(); + if (value != null) { + coder.encode(value, stream, Coder.Context.OUTER); + } + encoded = stream.toByteString(); + cachedSize = encoded.size(); } - ByteString encoded = stream.toByteString(); // Place in cache to avoid a future read. - cache.put(namespace, address, this, encoded.size()); + cache.put(namespace, address, this, cachedSize); if (!modified) { // The value was read, but never written or cleared. From b843bfc1a277d4cd54fb811f7eb1f622af25c8cb Mon Sep 17 00:00:00 2001 From: steve Date: Thu, 28 May 2020 13:03:03 -0400 Subject: [PATCH 108/151] [BEAM-9964] Move workerCacheMb to a user-visible place --- .../options/DataflowPipelineDebugOptions.java | 12 ++++++++++++ .../options/DataflowWorkerHarnessOptions.java | 12 ------------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/options/DataflowPipelineDebugOptions.java b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/options/DataflowPipelineDebugOptions.java index e81ab43fbb40..9a63e00ba13a 100644 --- a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/options/DataflowPipelineDebugOptions.java +++ b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/options/DataflowPipelineDebugOptions.java @@ -192,6 +192,18 @@ public Dataflow create(PipelineOptions options) { void setDumpHeapOnOOM(boolean dumpHeapBeforeExit); + /** + * The size of the worker's in-memory cache, in megabytes. + * + *

    Currently, this cache is used for storing read values of side inputs. as well as the state + * for streaming jobs. + */ + @Description("The size of the worker's in-memory cache, in megabytes.") + @Default.Integer(100) + Integer getWorkerCacheMb(); + + void setWorkerCacheMb(Integer value); + /** * CAUTION: This option implies dumpHeapOnOOM, and has similar caveats. Specifically, heap dumps * can of comparable size to the default boot disk. Consider increasing the boot disk size before diff --git a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/options/DataflowWorkerHarnessOptions.java b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/options/DataflowWorkerHarnessOptions.java index 3f37c74929fb..596b26dc05b8 100644 --- a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/options/DataflowWorkerHarnessOptions.java +++ b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/options/DataflowWorkerHarnessOptions.java @@ -17,7 +17,6 @@ */ package org.apache.beam.runners.dataflow.options; -import org.apache.beam.sdk.options.Default; import org.apache.beam.sdk.options.Description; import org.apache.beam.sdk.options.Hidden; @@ -41,15 +40,4 @@ public interface DataflowWorkerHarnessOptions extends DataflowPipelineOptions { String getJobId(); void setJobId(String value); - - /** - * The size of the worker's in-memory cache, in megabytes. - * - *

    Currently, this cache is used for storing read values of side inputs. - */ - @Description("The size of the worker's in-memory cache, in megabytes.") - @Default.Integer(100) - Integer getWorkerCacheMb(); - - void setWorkerCacheMb(Integer value); } From 47ea1123c4d1bcac8333e884e713cba65d472c88 Mon Sep 17 00:00:00 2001 From: brucearctor <5032356+brucearctor@users.noreply.github.com> Date: Thu, 28 May 2020 13:05:41 -0700 Subject: [PATCH 109/151] [BEAM-9679] Flatten Kata for Go (#11806) --- .../Flatten/Flatten/cmd/main.go | 45 +++++++ .../go/Core Transforms/Flatten/Flatten/go.mod | 28 ++++ .../go/Core Transforms/Flatten/Flatten/go.sum | 123 ++++++++++++++++++ .../Flatten/Flatten/pkg/task/task.go | 22 ++++ .../Flatten/Flatten/task-info.yaml | 31 +++++ .../Core Transforms/Flatten/Flatten/task.md | 38 ++++++ .../Flatten/Flatten/test/task_test.go | 47 +++++++ .../Core Transforms/Flatten/lesson-info.yaml | 21 +++ .../go/Core Transforms/section-info.yaml | 1 + 9 files changed, 356 insertions(+) create mode 100644 learning/katas/go/Core Transforms/Flatten/Flatten/cmd/main.go create mode 100644 learning/katas/go/Core Transforms/Flatten/Flatten/go.mod create mode 100644 learning/katas/go/Core Transforms/Flatten/Flatten/go.sum create mode 100644 learning/katas/go/Core Transforms/Flatten/Flatten/pkg/task/task.go create mode 100644 learning/katas/go/Core Transforms/Flatten/Flatten/task-info.yaml create mode 100644 learning/katas/go/Core Transforms/Flatten/Flatten/task.md create mode 100644 learning/katas/go/Core Transforms/Flatten/Flatten/test/task_test.go create mode 100644 learning/katas/go/Core Transforms/Flatten/lesson-info.yaml diff --git a/learning/katas/go/Core Transforms/Flatten/Flatten/cmd/main.go b/learning/katas/go/Core Transforms/Flatten/Flatten/cmd/main.go new file mode 100644 index 000000000000..486287241144 --- /dev/null +++ b/learning/katas/go/Core Transforms/Flatten/Flatten/cmd/main.go @@ -0,0 +1,45 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package main + +import ( + "github.com/apache/beam/sdks/go/pkg/beam" + "github.com/apache/beam/sdks/go/pkg/beam/log" + "github.com/apache/beam/sdks/go/pkg/beam/x/beamx" + "github.com/apache/beam/sdks/go/pkg/beam/x/debug" + "context" + "flatten/pkg/task" +) + +func main() { + ctx := context.Background() + + p, s := beam.NewPipelineWithRoot() + + aWords := beam.Create(s, "apple", "ant", "arrow") + bWords := beam.Create(s, "ball", "book", "bow") + + + output := task.ApplyTransform(s, aWords, bWords) + + debug.Print(s, output) + + err := beamx.Run(ctx, p) + + if err != nil { + log.Exitf(context.Background(), "Failed to execute job: %v", err) + } +} diff --git a/learning/katas/go/Core Transforms/Flatten/Flatten/go.mod b/learning/katas/go/Core Transforms/Flatten/Flatten/go.mod new file mode 100644 index 000000000000..d0ed83857607 --- /dev/null +++ b/learning/katas/go/Core Transforms/Flatten/Flatten/go.mod @@ -0,0 +1,28 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +module flatten + +go 1.13 + +require ( + github.com/apache/beam v2.20.0+incompatible + github.com/golang/protobuf v1.4.0 // indirect + github.com/google/go-cmp v0.4.0 + github.com/googleapis/gax-go v2.0.2+incompatible // indirect + go.opencensus.io v0.22.3 // indirect + google.golang.org/api v0.22.0 // indirect + google.golang.org/grpc v1.28.1 // indirect +) diff --git a/learning/katas/go/Core Transforms/Flatten/Flatten/go.sum b/learning/katas/go/Core Transforms/Flatten/Flatten/go.sum new file mode 100644 index 000000000000..15ecb7727e03 --- /dev/null +++ b/learning/katas/go/Core Transforms/Flatten/Flatten/go.sum @@ -0,0 +1,123 @@ +cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= +cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= +cloud.google.com/go v0.38.0 h1:ROfEUZz+Gh5pa62DJWXSaonyu3StP6EA6lPEXPI6mCo= +cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU= +github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= +github.com/apache/beam v2.20.0+incompatible h1:YzP/+VyAnYdu4Wjh5EkBz3vUjVdE7vUPEZ6xijCJ2sk= +github.com/apache/beam v2.20.0+incompatible/go.mod h1:/8NX3Qi8vGstDLLaeaU7+lzVEu/ACaQhYjeefzQ0y1o= +github.com/census-instrumentation/opencensus-proto v0.2.1/go.mod h1:f6KPmirojxKA12rnyqOA5BBL4O983OfeGPqjHWSTneU= +github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw= +github.com/cncf/udpa/go v0.0.0-20191209042840-269d4d468f6f/go.mod 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Transforms/Flatten/Flatten/pkg/task/task.go @@ -0,0 +1,22 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package task + +import "github.com/apache/beam/sdks/go/pkg/beam" + +func ApplyTransform(s beam.Scope, aInputs beam.PCollection, bInputs beam.PCollection) beam.PCollection { + return beam.Flatten(s, aInputs, bInputs) +} \ No newline at end of file diff --git a/learning/katas/go/Core Transforms/Flatten/Flatten/task-info.yaml b/learning/katas/go/Core Transforms/Flatten/Flatten/task-info.yaml new file mode 100644 index 000000000000..4f9e9b55403f --- /dev/null +++ b/learning/katas/go/Core Transforms/Flatten/Flatten/task-info.yaml @@ -0,0 +1,31 @@ +# Licensed to the Apache Software Foundation (ASF) under one or more +# contributor license agreements. See the NOTICE file distributed with +# this work for additional information regarding copyright ownership. +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +type: edu +files: +- name: go.sum + visible: false +- name: test/task_test.go + visible: false +- name: cmd/main.go + visible: true +- name: go.mod + visible: false +- name: pkg/task/task.go + visible: true + placeholders: + - offset: 972 + length: 33 + placeholder_text: TODO() diff --git a/learning/katas/go/Core Transforms/Flatten/Flatten/task.md b/learning/katas/go/Core Transforms/Flatten/Flatten/task.md new file mode 100644 index 000000000000..d1d8a42fb929 --- /dev/null +++ b/learning/katas/go/Core Transforms/Flatten/Flatten/task.md @@ -0,0 +1,38 @@ + + +Flatten +------- + +Flatten is a Beam transform for PCollection objects that store the same data type. Flatten merges +multiple PCollection objects into a single logical PCollection. + +**Kata:** Implement a +[Flatten](https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam#Flatten) +transform that merges two PCollection of words into a single PCollection. + +

    + Refer to + Flatten to solve this problem. +
    + +
    + Refer to the Beam Programming Guide + + "Flatten" section for more information. +
    \ No newline at end of file diff --git a/learning/katas/go/Core Transforms/Flatten/Flatten/test/task_test.go b/learning/katas/go/Core Transforms/Flatten/Flatten/test/task_test.go new file mode 100644 index 000000000000..2615e31f64df --- /dev/null +++ b/learning/katas/go/Core Transforms/Flatten/Flatten/test/task_test.go @@ -0,0 +1,47 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package test + +import ( + "flatten/pkg/task" + "github.com/apache/beam/sdks/go/pkg/beam" + "github.com/apache/beam/sdks/go/pkg/beam/testing/passert" + "github.com/apache/beam/sdks/go/pkg/beam/testing/ptest" + "testing" +) + +func TestApplyTransform(t *testing.T) { + p, s := beam.NewPipelineWithRoot() + tests := []struct { + aWords beam.PCollection + bWords beam.PCollection + want []interface{} + }{ + { + aWords: beam.Create(s, "apple", "ant", "arrow"), + bWords: beam.Create(s, "ball", "book", "bow"), + want: []interface{}{"apple", "ant", "arrow", "ball", "book", "bow"}, + }, + } + for _, tt := range tests { + got := task.ApplyTransform(s, tt.aWords, tt.bWords) + passert.Equals(s, got, tt.want...) + if err := ptest.Run(p); err != nil { + t.Error(err) + } + } +} + diff --git a/learning/katas/go/Core Transforms/Flatten/lesson-info.yaml b/learning/katas/go/Core Transforms/Flatten/lesson-info.yaml new file mode 100644 index 000000000000..e68515874b96 --- /dev/null +++ b/learning/katas/go/Core Transforms/Flatten/lesson-info.yaml @@ -0,0 +1,21 @@ +# +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. +# + +content: +- Flatten \ No newline at end of file diff --git a/learning/katas/go/Core Transforms/section-info.yaml b/learning/katas/go/Core Transforms/section-info.yaml index 8ea49eb04ce4..3fe207041313 100644 --- a/learning/katas/go/Core Transforms/section-info.yaml +++ b/learning/katas/go/Core Transforms/section-info.yaml @@ -20,3 +20,4 @@ content: - Map - GroupByKey +- Flatten \ No newline at end of file From 018e889829e300ab9f321da7e0010ff0011a73b1 Mon Sep 17 00:00:00 2001 From: Robert Burke Date: Thu, 28 May 2020 13:29:07 -0700 Subject: [PATCH 110/151] [BEAM-9220] Go Dataflow jobs to use runner v2 (#11207) --- sdks/go/pkg/beam/runners/dataflow/dataflow.go | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/sdks/go/pkg/beam/runners/dataflow/dataflow.go b/sdks/go/pkg/beam/runners/dataflow/dataflow.go index 8681ceb05e25..920731338b13 100644 --- a/sdks/go/pkg/beam/runners/dataflow/dataflow.go +++ b/sdks/go/pkg/beam/runners/dataflow/dataflow.go @@ -24,6 +24,7 @@ import ( "fmt" "io" "path" + "strings" "sync/atomic" "time" @@ -127,6 +128,17 @@ func Execute(ctx context.Context, p *beam.Pipeline) error { hooks.SerializeHooksToOptions() experiments := jobopts.GetExperiments() + // Always use runner v2, unless set already. + var v2set bool + for _, e := range experiments { + if strings.Contains(e, "use_runner_v2") || strings.Contains(e, "use_unified_worker") { + v2set = true + break + } + } + if !v2set { + experiments = append(experiments, "use_unified_worker") + } if *minCPUPlatform != "" { experiments = append(experiments, fmt.Sprintf("min_cpu_platform=%v", *minCPUPlatform)) } From d68f7f23171eecb71c4b5438f8f1be1dbc21345c Mon Sep 17 00:00:00 2001 From: Robert Bradshaw Date: Thu, 28 May 2020 14:19:39 -0700 Subject: [PATCH 111/151] Update multi-language roadmap status. --- .../content/en/roadmap/connectors-multi-sdk.md | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/website/www/site/content/en/roadmap/connectors-multi-sdk.md b/website/www/site/content/en/roadmap/connectors-multi-sdk.md index e00d6e424fe1..d632c09f0967 100644 --- a/website/www/site/content/en/roadmap/connectors-multi-sdk.md +++ b/website/www/site/content/en/roadmap/connectors-multi-sdk.md @@ -25,7 +25,7 @@ efforts. See [Beam portability framework roadmap](https://beam.apache.org/roadma # Cross-language transforms -_Last updated on November 2019._ +_Last updated on May 2020._ As an added benefit of Beam portability effort, we are able to utilize Beam transforms across SDKs. This has many benefits. @@ -33,7 +33,7 @@ As an added benefit of Beam portability effort, we are able to utilize Beam tran + Beam pipelines written using Python and Go SDKs will be able to utilize the vast selection of connectors that are currently implemented for Java SDK. + Java SDK will be able to utilize connectors for systems that only offer a Python API. + Go SDK, will be able to utilize connectors currently available for Java and Python SDKs. -* Ease of developing and maintaining Beam transforms - in general, with cross-language transforms, Beam transform authors will be able to implement new Beam transforms using a +* Ease of developing and maintaining Beam transforms - in general, with cross-language transforms, Beam transform authors will be able to implement new Beam transforms using a language of choice and utilize these transforms from other languages reducing the maintenance and support overheads. * [Beam SQL](https://beam.apache.org/documentation/dsls/sql/overview/), that is currently only available to Java SDK, will become available to Python and Go SDKs. * [Beam TFX transforms](https://www.tensorflow.org/tfx/transform/get_started), that are currently only available to Beam Python SDK pipelines will become available to Java and Go SDKs. @@ -48,9 +48,9 @@ Work related to developing/updating the cross-language transforms API for Java/P * Basic API for Java SDK - completed * Basic API for Python SDK - completed -* Basic API for Go SDK - Not started +* Basic API for Go SDK - In progress * Basic cross-language transform expansion service for Java and Python SDKs - completed -* Artifact staging - In progress - [email thread](https://lists.apache.org/thread.html/6fcee7047f53cf1c0636fb65367ef70842016d57effe2e5795c4137d@%3Cdev.beam.apache.org%3E), [doc](https://docs.google.com/document/d/1XaiNekAY2sptuQRIXpjGAyaYdSc-wlJ-VKjl04c8N48/edit#heading=h.900gc947qrw8) +* Artifact staging - mostly completed - [email thread](https://lists.apache.org/thread.html/6fcee7047f53cf1c0636fb65367ef70842016d57effe2e5795c4137d@%3Cdev.beam.apache.org%3E), [doc](https://docs.google.com/document/d/1XaiNekAY2sptuQRIXpjGAyaYdSc-wlJ-VKjl04c8N48/edit#heading=h.900gc947qrw8) ### Support for Flink runner @@ -62,27 +62,29 @@ Work related to making cross-language transforms available for Flink runner. Work related to making cross-language transforms available for Dataflow runner. -* Basic support for executing cross-language transforms on Dataflow runner +* Basic support for executing cross-language transforms on Dataflow runner + This work requires updates to Dataflow service's job submission and job execution logic. This is currently being developed at Google. ### Support for Direct runner Work related to making cross-language transforms available on Direct runner -* Basic support for executing cross-language transforms on portable Direct runner - Not started +* Basic support for executing cross-language transforms on Pyton Direct runner - completed +* Basic support for executing cross-language transforms on Java Direct runner - Not started ### Connector/transform support Ongoing and planned work related to making existing connectors/transforms available to other SDKs through the cross-language transforms framework. -* Java KafkIO - In progress - [BEAM-7029](https://issues.apache.org/jira/browse/BEAM-7029) +* Java KafkIO - completed - [BEAM-7029](https://issues.apache.org/jira/browse/BEAM-7029) * Java PubSubIO - In progress - [BEAM-7738](https://issues.apache.org/jira/browse/BEAM-7738) +* Java SQL - completed - [BEAM-8603](https://issues.apache.org/jira/browse/BEAM-8603) ### Portable Beam schema Portable Beam schema support will provide a generalized mechanism for serializing and transferring data across language boundaries which will be extremely useful for pipelines that employ cross-language transforms. -* Make row coder a standard coder and implement in python - In progress - [BEAM-7886](https://issues.apache.org/jira/browse/BEAM-7886) +* Make row coder a standard coder and implement in python - completed - [BEAM-7886](https://issues.apache.org/jira/browse/BEAM-7886) ### Integration/Performance testing From a5e642aa01f867e8c84df4a813767355eee60af4 Mon Sep 17 00:00:00 2001 From: Daniel Oliveira Date: Thu, 21 May 2020 19:55:04 -0700 Subject: [PATCH 112/151] [BEAM-9935] Respect allowed split points and fraction in Go. Adds code to more closely align with the implementations of splitting in Python and Java. Note that not all cases are implemented. There is no measurement of sub-element progress yet, nor is there sub-element (SDF) splitting yet. --- .../pkg/beam/core/runtime/exec/datasource.go | 105 +++++++++++--- .../beam/core/runtime/exec/datasource_test.go | 135 +++++++++++++++++- sdks/go/pkg/beam/core/runtime/exec/plan.go | 6 +- .../pkg/beam/core/runtime/harness/harness.go | 6 +- 4 files changed, 226 insertions(+), 26 deletions(-) diff --git a/sdks/go/pkg/beam/core/runtime/exec/datasource.go b/sdks/go/pkg/beam/core/runtime/exec/datasource.go index ccc4a09acb50..f9e9a943cba8 100644 --- a/sdks/go/pkg/beam/core/runtime/exec/datasource.go +++ b/sdks/go/pkg/beam/core/runtime/exec/datasource.go @@ -20,6 +20,7 @@ import ( "fmt" "io" "math" + "sort" "sync" "time" @@ -266,33 +267,95 @@ func (n *DataSource) Progress() ProgressReportSnapshot { return ProgressReportSnapshot{PID: n.outputPID, ID: n.SID.PtransformID, Name: n.Name, Count: c} } -// Split takes a sorted set of potential split indices, selects and actuates -// split on an appropriate split index, and returns the selected split index -// if successful. Returns an error when unable to split. -func (n *DataSource) Split(splits []int64, frac float64) (int64, error) { - if splits == nil { - return 0, fmt.Errorf("failed to split: requested splits were empty") - } +// Split takes a sorted set of potential split indices and a fraction of the +// remainder to split at, selects and actuates a split on an appropriate split +// index, and returns the selected split index if successful or an error when +// unsuccessful. +// +// The bufSize param specifies the estimated number of elements that will be +// sent to this DataSource, and is used to be able to perform accurate splits +// even if the DataSource has not yet received all its elements. A bufSize of +// 0 or less indicates that its unknown, and so uses the current known size. +func (n *DataSource) Split(splits []int64, frac float64, bufSize int64) (int64, error) { if n == nil { return 0, fmt.Errorf("failed to split at requested splits: {%v}, DataSource not initialized", splits) } + if frac > 1.0 { + frac = 1.0 + } else if frac < 0.0 { + frac = 0.0 + } + n.mu.Lock() - c := n.index - // Find the smallest split index that we haven't yet processed, and set - // the promised split index to this value. - for _, s := range splits { - // // Never split on the first element, or the current element. - if s > 0 && s > c && s <= n.splitIdx { - n.splitIdx = s - fs := n.splitIdx - n.mu.Unlock() - return fs, nil - } + // Size to split within is the minimum of bufSize or splitIdx so we avoid + // including elements we already know won't be processed. + if bufSize <= 0 || n.splitIdx < bufSize { + bufSize = n.splitIdx + } + s, err := splitHelper(n.index, bufSize, splits, frac) + if err != nil { + n.mu.Unlock() + return 0, err } + n.splitIdx = s + fs := n.splitIdx n.mu.Unlock() - // If we can't find a suitable split index from the requested choices, - // return an error. - return 0, fmt.Errorf("failed to split at requested splits: {%v}, DataSource at index: %v", splits, c) + return fs, nil +} + +// splitHelper is a helper function that finds a split point in a range. +// currIdx and splitIdx should match the DataSource's index and splitIdx fields, +// and represent the start and end of the splittable range respectively. splits +// is an optional slice of valid split indices, and if nil then all indices are +// considered valid split points. frac must be between [0, 1], and represents +// a fraction of the remaining work that the split point aims to be as close +// as possible to. +func splitHelper(currIdx, splitIdx int64, splits []int64, frac float64) (int64, error) { + // Get split index from fraction. Find the closest index to the fraction of + // the remainder. + var start int64 = 0 + if currIdx > start { + start = currIdx + } + // This is the first valid split index, since we should never split at 0 or + // at the current element. + safeStart := start + 1 + // The remainder starts at our actual progress (i.e. start), but our final + // split index has to be >= our safeStart. + fracIdx := start + int64(math.Round(frac*float64(splitIdx-start))) + if fracIdx < safeStart { + fracIdx = safeStart + } + if splits == nil { + // All split points are valid so just split at fraction. + return fracIdx, nil + } else { + // Find the closest unprocessed split point to our fraction. + sort.Slice(splits, func(i, j int) bool { return splits[i] < splits[j] }) + var prevDiff int64 = math.MaxInt64 + var bestS int64 = -1 + for _, s := range splits { + if s >= safeStart && s <= splitIdx { + diff := intAbs(fracIdx - s) + if diff <= prevDiff { + prevDiff = diff + bestS = s + } else { + break // Stop early if the difference starts increasing. + } + } + } + if bestS != -1 { + return bestS, nil + } + } + return 0, fmt.Errorf("failed to split DataSource (at index: %v) at requested splits: {%v}", currIdx, splits) +} + +// intAbs implements absolute value for integers via Two's Complement. +func intAbs(n int64) int64 { + y := n >> 63 // y ← x ⟫ 63 + return (n ^ y) - y // (x ⨁ y) - y } type concatReStream struct { diff --git a/sdks/go/pkg/beam/core/runtime/exec/datasource_test.go b/sdks/go/pkg/beam/core/runtime/exec/datasource_test.go index 1ce493cd1d8f..c0ff1a941ecc 100644 --- a/sdks/go/pkg/beam/core/runtime/exec/datasource_test.go +++ b/sdks/go/pkg/beam/core/runtime/exec/datasource_test.go @@ -341,7 +341,7 @@ func TestDataSource_Split(t *testing.T) { <-blockedCh // Validate that we do not split on the element we're blocking on index. // The first valid split is at test.splitIdx. - if splitIdx, err := source.Split([]int64{0, 1, 2, 3, 4, 5}, -1); err != nil { + if splitIdx, err := source.Split([]int64{0, 1, 2, 3, 4, 5}, -1, 0); err != nil { t.Errorf("error in Split: %v", err) } else if got, want := splitIdx, test.splitIdx; got != want { t.Errorf("error in Split: got splitIdx = %v, want %v ", got, want) @@ -371,6 +371,57 @@ func TestDataSource_Split(t *testing.T) { } }) + // Test that the bufSize param can be used to affect the split range. + t.Run("bufSize", func(t *testing.T) { + test := struct { + splitPts []int64 + frac float64 + bufSize int64 + splitIdx int64 + expected []interface{} + }{ + // splitIdx defaults to the max int64, so if bufSize is respected + // the closest splitPt is 3, otherwise it'll be 5000. + splitPts: []int64{3, 5000}, + frac: 0.5, + bufSize: 10, + splitIdx: 3, + expected: elements[:3], + } + + source, out, pr := initSourceTest("bufSize") + p, err := NewPlan("a", []Unit{out, source}) + if err != nil { + t.Fatalf("failed to construct plan: %v", err) + } + dc := DataContext{Data: &TestDataManager{R: pr}} + ctx := context.Background() + + // StartBundle resets the source, so no splits can be actuated before then, + // which means we need to actuate the plan manually, and insert the split request + // after StartBundle. + for i, root := range p.units { + if err := root.Up(ctx); err != nil { + t.Fatalf("error in root[%d].Up: %v", i, err) + } + } + p.status = Active + + runOnRoots(ctx, t, p, "StartBundle", func(root Root, ctx context.Context) error { return root.StartBundle(ctx, "1", dc) }) + + // SDK never splits on 0, so check that every test. + sp := SplitPoints{Splits: test.splitPts, Frac: test.frac, BufSize: test.bufSize} + if splitIdx, err := p.Split(sp); err != nil { + t.Fatalf("error in Split: %v", err) + } else if got, want := splitIdx, test.splitIdx; got != want { + t.Fatalf("error in Split: got splitIdx = %v, want %v ", got, want) + } + runOnRoots(ctx, t, p, "Process", Root.Process) + runOnRoots(ctx, t, p, "FinishBundle", Root.FinishBundle) + + validateSource(t, out, source, makeValues(test.expected...)) + }) + // Test expects splitting errors, but for processing to be successful. t.Run("errors", func(t *testing.T) { source, out, pr := initSourceTest("noSplitsUntilStarted") @@ -410,15 +461,93 @@ func TestDataSource_Split(t *testing.T) { t.Run("sanity_errors", func(t *testing.T) { var source *DataSource - if _, err := source.Split([]int64{0}, -1); err == nil { + if _, err := source.Split([]int64{0}, -1, 0); err == nil { t.Fatal("expected error splitting nil *DataSource") } - if _, err := source.Split(nil, -1); err == nil { + if _, err := source.Split(nil, -1, 0); err == nil { t.Fatal("expected error splitting nil desired splits") } }) } +// TestSplitHelper tests the underlying split logic to confirm that various +// cases produce expected split points. +func TestSplitHelper(t *testing.T) { + // Test splits at various fractions. + t.Run("SimpleSplits", func(t *testing.T) { + tests := []struct { + curr, size int64 + frac float64 + want int64 + }{ + // Split as close to the beginning as possible. + {curr: 0, size: 16, frac: 0, want: 1}, + // The closest split is at 4, even when just above or below it. + {curr: 0, size: 16, frac: 0.24, want: 4}, + {curr: 0, size: 16, frac: 0.25, want: 4}, + {curr: 0, size: 16, frac: 0.26, want: 4}, + // Split the *remainder* in half. + {curr: 0, size: 16, frac: 0.5, want: 8}, + {curr: 2, size: 16, frac: 0.5, want: 9}, + {curr: 6, size: 16, frac: 0.5, want: 11}, + } + for _, test := range tests { + test := test + t.Run(fmt.Sprintf("(%v of [%v, %v])", test.frac, test.curr, test.size), func(t *testing.T) { + got, err := splitHelper(test.curr, test.size, nil, test.frac) + if err != nil { + t.Errorf("error in splitHelper: %v", err) + } else if got != test.want { + t.Errorf("incorrect split point: got: %v, want: %v", got, test.want) + } + }) + } + }) + + // Test splits with allowed split points. + t.Run("WithAllowedSplits", func(t *testing.T) { + tests := []struct { + curr, size int64 + splits []int64 + frac float64 + want int64 + err bool // True if test should cause a failure. + }{ + // The desired split point is at 4. + {curr: 0, size: 16, splits: []int64{2, 3, 4, 5}, frac: 0.25, want: 4}, + // If we can't split at 4, choose the closest possible split point. + {curr: 0, size: 16, splits: []int64{2, 3, 5}, frac: 0.25, want: 5}, + {curr: 0, size: 16, splits: []int64{2, 3, 6}, frac: 0.25, want: 3}, + // Also test the case where all possible split points lie above or + // below the desired split point. + {curr: 0, size: 16, splits: []int64{5, 6, 7}, frac: 0.25, want: 5}, + {curr: 0, size: 16, splits: []int64{1, 2, 3}, frac: 0.25, want: 3}, + // We have progressed beyond all possible split points, so can't split. + {curr: 5, size: 16, splits: []int64{1, 2, 3}, frac: 0.25, err: true}, + } + for _, test := range tests { + test := test + t.Run(fmt.Sprintf("(%v of [%v, %v], splits = %v)", test.frac, test.curr, test.size, test.splits), func(t *testing.T) { + got, err := splitHelper(test.curr, test.size, test.splits, test.frac) + if test.err { + if err == nil { + t.Errorf("splitHelper should have errored, instead got: %v", got) + } + } else { + if err != nil { + t.Errorf("error in splitHelper: %v", err) + } else if got != test.want { + t.Errorf("incorrect split point: got: %v, want: %v", got, test.want) + } + } + }) + } + }) + + // TODO(BEAM-9935): Add SDF and element progress splitting tests from Java + // and Python once those features are added. +} + func runOnRoots(ctx context.Context, t *testing.T, p *Plan, name string, mthd func(Root, context.Context) error) { t.Helper() for i, root := range p.roots { diff --git a/sdks/go/pkg/beam/core/runtime/exec/plan.go b/sdks/go/pkg/beam/core/runtime/exec/plan.go index fde9e7c78fa0..2f07f3c3dbaf 100644 --- a/sdks/go/pkg/beam/core/runtime/exec/plan.go +++ b/sdks/go/pkg/beam/core/runtime/exec/plan.go @@ -198,6 +198,10 @@ type SplitPoints struct { // Splits is a list of desired split indices. Splits []int64 Frac float64 + + // Estimated total number of elements (including unsent) for the source. + // A zero value indicates unknown, instead use locally known size. + BufSize int64 } // Split takes a set of potential split indexes, and if successful returns @@ -206,7 +210,7 @@ type SplitPoints struct { // Returns an error when unable to split. func (p *Plan) Split(s SplitPoints) (int64, error) { if p.source != nil { - return p.source.Split(s.Splits, s.Frac) + return p.source.Split(s.Splits, s.Frac, s.BufSize) } return 0, fmt.Errorf("failed to split at requested splits: {%v}, Source not initialized", s) } diff --git a/sdks/go/pkg/beam/core/runtime/harness/harness.go b/sdks/go/pkg/beam/core/runtime/harness/harness.go index 26cd02e7b036..44099210d049 100644 --- a/sdks/go/pkg/beam/core/runtime/harness/harness.go +++ b/sdks/go/pkg/beam/core/runtime/harness/harness.go @@ -310,7 +310,11 @@ func (c *control) handleInstruction(ctx context.Context, req *fnpb.InstructionRe if ds == nil { return fail(ctx, instID, "failed to split: desired splits for root of %v was empty.", ref) } - split, err := plan.Split(exec.SplitPoints{Splits: ds.GetAllowedSplitPoints(), Frac: ds.GetFractionOfRemainder()}) + split, err := plan.Split(exec.SplitPoints{ + Splits: ds.GetAllowedSplitPoints(), + Frac: ds.GetFractionOfRemainder(), + BufSize: ds.GetEstimatedInputElements(), + }) if err != nil { return fail(ctx, instID, "unable to split %v: %v", ref, err) From 775ad8edbb95244b03e56e2bd0bbf20b11eba22d Mon Sep 17 00:00:00 2001 From: Udi Meiri Date: Thu, 28 May 2020 15:14:36 -0700 Subject: [PATCH 113/151] [BEAM-8280] Blog post: Python typing changes (#11070) * [BEAM-8280] Blog post: Python typing changes Co-authored-by: Chad Dombrova * Added excerpt and reworked sidebar. * Rename file to match new style and update headers More cleanup * More fixes, blog with dates in the future don't appear so I changed the date today. * Also update link to blog post * Update date to today Co-authored-by: Chad Dombrova --- CHANGES.md | 2 +- .../www/site/content/en/blog/python-typing.md | 136 ++++++++++++++++++ website/www/site/data/authors.yml | 3 + 3 files changed, 140 insertions(+), 1 deletion(-) create mode 100644 website/www/site/content/en/blog/python-typing.md diff --git a/CHANGES.md b/CHANGES.md index affe1e068786..d3e706515ae5 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -108,7 +108,7 @@ for example usage. More details will be in [Ensuring Python Type Safety](https://beam.apache.org/documentation/sdks/python-type-safety/) and an upcoming - [blog post](https://beam.apache.org/blog/python/typing/2020/03/06/python-typing.html). + [blog post](https://beam.apache.org/blog/python-typing/index.html). * Java SDK: Introducing the concept of options in Beam Schema’s. These options add extra context to fields and schemas. This replaces the current Beam metadata that is present diff --git a/website/www/site/content/en/blog/python-typing.md b/website/www/site/content/en/blog/python-typing.md new file mode 100644 index 000000000000..7982c19fe9e4 --- /dev/null +++ b/website/www/site/content/en/blog/python-typing.md @@ -0,0 +1,136 @@ +--- +layout: post +title: "Python SDK Typing Changes" +date: 2020-05-28 00:00:01 -0800 +categories: + - blog + - python + - typing +authors: + - chadrik + - udim +--- + + +Beam Python has recently increased its support and integration of Python 3 type +annotations for improved code clarity and type correctness checks. +Read on to find out what's new. + + + +Python supports type annotations on functions (PEP 484). Static type checkers, +such as mypy, are used to verify adherence to these types. +For example: +``` +def f(v: int) -> int: + return v[0] +``` +Running mypy on the above code will give the error: +`Value of type "int" is not indexable`. + +We've recently made changes to Beam in 2 areas: + +Adding type annotations throughout Beam. Type annotations make a large and +sophisticated codebase like Beam easier to comprehend and navigate in your +favorite IDE. + +Second, we've added support for Python 3 type annotations. This allows SDK +users to specify a DoFn's type hints in one place. +We've also expanded Beam's support of `typing` module types. + +For more background see: +[Ensuring Python Type Safety](https://beam.apache.org/documentation/sdks/python-type-safety/). + +# Beam Is Typed + +In tandem with the new type annotation support within DoFns, we've invested a +great deal of time adding type annotations to the Beam python code itself. +With this in place, we have begun using mypy, a static type +checker, as part of Beam's code review process, which ensures higher quality +contributions and fewer bugs. +The added context and insight that type annotations add throughout Beam is +useful for all Beam developers, contributors and end users alike, but +it is especially beneficial for developers who are new to the project. +If you use an IDE that understands type annotations, it will provide richer +type completions and warnings than before. +You'll also be able to use your IDE to inspect the types of Beam functions and +transforms to better understand how they work, which will ease your own +development. +Finally, once Beam is fully annotated, end users will be able to benefit from +the use of static type analysis on their own pipelines and custom transforms. + +# New Ways to Annotate + +## Python 3 Syntax Annotations + +Coming in Beam 2.21 (BEAM-8280), you will be able to use Python annotation +syntax to specify input and output types. + +For example, this new form: +``` +class MyDoFn(beam.DoFn): + def process(self, element: int) -> typing.Text: + yield str(element) +``` +is equivalent to this: +``` +@apache_beam.typehints.with_input_types(int) +@apache_beam.typehints.with_output_types(typing.Text) +class MyDoFn(beam.DoFn): + def process(self, element): + yield str(element) +``` + +One of the advantages of the new form is that you may already be using it +in tandem with a static type checker such as mypy, thus getting additional +runtime type checking for free. + +This feature will be enabled by default, and there will be 2 mechanisms in +place to disable it: +1. Calling `apache_beam.typehints.disable_type_annotations()` before pipeline +construction will disable the new feature completely. +1. Decorating a function with `@apache_beam.typehints.no_annotations` will +tell Beam to ignore annotations for it. + +Uses of Beam's `with_input_type`, `with_output_type` methods and decorators will +still work and take precedence over annotations. + +### Sidebar + +You might ask: couldn't we use mypy to type check Beam pipelines? +There are several reasons why this is not the case. +- Pipelines are constructed at runtime and may depend on information that is +only known at that time, such as a config file or database table schema. +- PCollections don't have the necessary type information, so mypy sees them as +effectively containing any element type. +This may change in in the future. +- Transforms using lambdas (ex: `beam.Map(lambda x: (1, x)`) cannot be +annotated properly using PEP 484. +However, Beam does a best-effort attempt to analyze the output type +from the bytecode. + +## Typing Module Support + +Python's [typing](https://docs.python.org/3/library/typing.html) module defines +types used in type annotations. This is what we call "native" types. +While Beam has its own typing types, it also supports native types. +While both Beam and native types are supported, for new code we encourage using +native typing types. Native types have as these are supported by additional tools. + +While working on Python 3 annotations syntax support, we've also discovered and +fixed issues with native type support. There may still be bugs and unsupported +native types. Please +[let us know](https://beam.apache.org/community/contact-us/) if you encounter +issues. diff --git a/website/www/site/data/authors.yml b/website/www/site/data/authors.yml index 8a111a688cec..376cfdbaa62b 100644 --- a/website/www/site/data/authors.yml +++ b/website/www/site/data/authors.yml @@ -30,6 +30,9 @@ anton: ccy: name: Charles Chen email: ccy@apache.org +chadrik: + name: Chad Dombrova + email: chadrik@apache.org chamikara: name: Chamikara Jayalath email: chamikara@apache.org From e7abbdbf7ebd56c14b7ecf4831b70bf08218d0b3 Mon Sep 17 00:00:00 2001 From: Robert Bradshaw Date: Thu, 28 May 2020 15:58:01 -0700 Subject: [PATCH 114/151] Update website/www/site/content/en/roadmap/connectors-multi-sdk.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Ismaël Mejía --- website/www/site/content/en/roadmap/connectors-multi-sdk.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/website/www/site/content/en/roadmap/connectors-multi-sdk.md b/website/www/site/content/en/roadmap/connectors-multi-sdk.md index d632c09f0967..55d11fd73d32 100644 --- a/website/www/site/content/en/roadmap/connectors-multi-sdk.md +++ b/website/www/site/content/en/roadmap/connectors-multi-sdk.md @@ -76,7 +76,7 @@ Work related to making cross-language transforms available on Direct runner Ongoing and planned work related to making existing connectors/transforms available to other SDKs through the cross-language transforms framework. -* Java KafkIO - completed - [BEAM-7029](https://issues.apache.org/jira/browse/BEAM-7029) +* Java KafkaIO - completed - [BEAM-7029](https://issues.apache.org/jira/browse/BEAM-7029) * Java PubSubIO - In progress - [BEAM-7738](https://issues.apache.org/jira/browse/BEAM-7738) * Java SQL - completed - [BEAM-8603](https://issues.apache.org/jira/browse/BEAM-8603) @@ -96,4 +96,3 @@ Work related to adding documenting on cross-language transforms to Beam Website. * Document cross-language transforms API for Java/Python - Not started * Document API for making existing transforms available as cross-language transforms for Java/Python - Not started - From 9e5dd68bb951cf8c7faaf15d4e5852b0fe6963d2 Mon Sep 17 00:00:00 2001 From: Heejong Lee Date: Fri, 22 May 2020 02:13:45 -0700 Subject: [PATCH 115/151] [BEAM-10125] adding cross-language KafkaIO integration test --- .../io/external/xlang_kafkaio_it_test.py | 141 ++++++++++++++++++ 1 file changed, 141 insertions(+) create mode 100644 sdks/python/apache_beam/io/external/xlang_kafkaio_it_test.py diff --git a/sdks/python/apache_beam/io/external/xlang_kafkaio_it_test.py b/sdks/python/apache_beam/io/external/xlang_kafkaio_it_test.py new file mode 100644 index 000000000000..7dbbf837748d --- /dev/null +++ b/sdks/python/apache_beam/io/external/xlang_kafkaio_it_test.py @@ -0,0 +1,141 @@ +# +# Licensed to the Apache Software Foundation (ASF) under one or more +# contributor license agreements. See the NOTICE file distributed with +# this work for additional information regarding copyright ownership. +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +"""Integration test for Python cross-language pipelines for Java KafkaIO.""" + +from __future__ import absolute_import + +import contextlib +import logging +import os +import socket +import subprocess +import time +import typing +import unittest + +import apache_beam as beam +from apache_beam.io.external.kafka import ReadFromKafka +from apache_beam.io.external.kafka import WriteToKafka +from apache_beam.metrics import Metrics +from apache_beam.options.pipeline_options import PipelineOptions +from apache_beam.testing.test_pipeline import TestPipeline + + +class CrossLanguageKafkaIO(object): + def __init__(self, bootstrap_servers, topic, expansion_service=None): + self.bootstrap_servers = bootstrap_servers + self.topic = topic + self.expansion_service = expansion_service + self.sum_counter = Metrics.counter('source', 'elements_sum') + + def build_write_pipeline(self, pipeline): + _ = ( + pipeline + | 'Impulse' >> beam.Impulse() + | 'Generate' >> beam.FlatMap(lambda x: range(1000)) # pylint: disable=range-builtin-not-iterating + | 'Reshuffle' >> beam.Reshuffle() + | 'MakeKV' >> beam.Map(lambda x: + (b'', str(x).encode())).with_output_types( + typing.Tuple[bytes, bytes]) + | 'WriteToKafka' >> WriteToKafka( + producer_config={'bootstrap.servers': self.bootstrap_servers}, + topic=self.topic, + expansion_service=self.expansion_service)) + + def build_read_pipeline(self, pipeline): + _ = ( + pipeline + | 'ReadFromKafka' >> ReadFromKafka( + consumer_config={ + 'bootstrap.servers': self.bootstrap_servers, + 'auto.offset.reset': 'earliest' + }, + topics=[self.topic], + expansion_service=self.expansion_service) + | 'Windowing' >> beam.WindowInto( + beam.window.FixedWindows(300), + trigger=beam.transforms.trigger.AfterProcessingTime(60), + accumulation_mode=beam.transforms.trigger.AccumulationMode. + DISCARDING) + | 'DecodingValue' >> beam.Map(lambda elem: int(elem[1].decode())) + | 'CombineGlobally' >> beam.CombineGlobally(sum).without_defaults() + | 'SetSumCounter' >> beam.Map(self.sum_counter.inc)) + + def run_xlang_kafkaio(self, pipeline): + self.build_write_pipeline(pipeline) + self.build_read_pipeline(pipeline) + pipeline.run(False) + + +@unittest.skipUnless( + os.environ.get('LOCAL_KAFKA_JAR'), + "LOCAL_KAFKA_JAR environment var is not provided.") +class CrossLanguageKafkaIOTest(unittest.TestCase): + def get_open_port(self): + s = None + try: + s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) + except: # pylint: disable=bare-except + # Above call will fail for nodes that only support IPv6. + s = socket.socket(socket.AF_INET6, socket.SOCK_STREAM) + s.bind(('localhost', 0)) + s.listen(1) + port = s.getsockname()[1] + s.close() + return port + + @contextlib.contextmanager + def local_kafka_service(self, local_kafka_jar_file): + kafka_port = str(self.get_open_port()) + zookeeper_port = str(self.get_open_port()) + kafka_server = None + try: + kafka_server = subprocess.Popen( + ['java', '-jar', local_kafka_jar_file, kafka_port, zookeeper_port]) + time.sleep(3) + yield kafka_port + finally: + if kafka_server: + kafka_server.kill() + + def get_options(self): + options = PipelineOptions([ + '--runner', + 'FlinkRunner', + '--parallelism', + '2', + '--experiment', + 'beam_fn_api' + ]) + return options + + def test_kafkaio_write(self): + local_kafka_jar = os.environ.get('LOCAL_KAFKA_JAR') + with self.local_kafka_service(local_kafka_jar) as kafka_port: + options = self.get_options() + p = TestPipeline(options=options) + p.not_use_test_runner_api = True + CrossLanguageKafkaIO('localhost:%s' % kafka_port, + 'xlang_kafkaio_test').build_write_pipeline(p) + job = p.run() + job.wait_until_finish() + + +if __name__ == '__main__': + logging.getLogger().setLevel(logging.INFO) + unittest.main() From 6dc08a4fb361b19a3353e9bd93563bc1120723df Mon Sep 17 00:00:00 2001 From: David Moravek Date: Fri, 29 May 2020 17:41:32 +0200 Subject: [PATCH 116/151] [BEAM-8608] Chain DoFns in Flink batch runner when possible. --- .../beam/runners/flink/FlinkCapabilities.java | 34 ++++ .../beam/runners/flink/FlinkCapabilities.java | 34 ++++ .../flink/FlinkBatchTransformTranslators.java | 21 ++- .../functions/FlinkDoFnFunction.java | 156 ++++++++++++------ .../functions/FlinkStatefulDoFnFunction.java | 7 +- 5 files changed, 193 insertions(+), 59 deletions(-) create mode 100644 runners/flink/1.10/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java create mode 100644 runners/flink/1.8/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java diff --git a/runners/flink/1.10/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java b/runners/flink/1.10/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java new file mode 100644 index 000000000000..aabdc977e995 --- /dev/null +++ b/runners/flink/1.10/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java @@ -0,0 +1,34 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.runners.flink; + +/** Handle different capabilities between flink versions. */ +public class FlinkCapabilities { + + /** + * Support for outputting elements in close method of chained drivers. + * + *

    {@see } for more + * details. + * + * @return True if feature is supported. + */ + public static boolean supportsOutputInTearDown() { + return true; + } +} diff --git a/runners/flink/1.8/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java b/runners/flink/1.8/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java new file mode 100644 index 000000000000..02586e38a262 --- /dev/null +++ b/runners/flink/1.8/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java @@ -0,0 +1,34 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.runners.flink; + +/** Handle different capabilities between flink versions. */ +public class FlinkCapabilities { + + /** + * Support for outputting elements in close method of chained drivers. + * + *

    {@see } for more + * details. + * + * @return True if feature is supported. + */ + public static boolean supportsOutputInTearDown() { + return false; + } +} diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java index 4254a0604c78..9ddf5049dc01 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java @@ -240,7 +240,7 @@ public void translateNode( PTransform>, PCollection>>> transform, FlinkBatchTranslationContext context) { - // for now, this is copied from the Combine.PerKey translater. Once we have the new runner API + // for now, this is copied from the Combine.PerKey translator. Once we have the new runner API // we can replace GroupByKey by a Combine.PerKey with the Concatenate CombineFn DataSet>> inputDataSet = @@ -527,11 +527,12 @@ public void translateNode( Map, PValue> outputs = context.getOutputs(transform); - TupleTag mainOutputTag; + final TupleTag mainOutputTag; DoFnSchemaInformation doFnSchemaInformation; Map> sideInputMapping; try { - mainOutputTag = ParDoTranslation.getMainOutputTag(context.getCurrentTransform()); + mainOutputTag = + (TupleTag) ParDoTranslation.getMainOutputTag(context.getCurrentTransform()); } catch (IOException e) { throw new RuntimeException(e); } @@ -638,8 +639,8 @@ public void translateNode( outputDataSet = new GroupReduceOperator(grouping, typeInformation, doFnWrapper, fullName); } else { - FlinkDoFnFunction doFnWrapper = - new FlinkDoFnFunction( + final FlinkDoFnFunction doFnWrapper = + new FlinkDoFnFunction<>( doFn, fullName, windowingStrategy, @@ -652,8 +653,14 @@ public void translateNode( doFnSchemaInformation, sideInputMapping); - outputDataSet = - new MapPartitionOperator<>(inputDataSet, typeInformation, doFnWrapper, fullName); + if (FlinkCapabilities.supportsOutputInTearDown()) { + outputDataSet = + new FlatMapOperator<>(inputDataSet, typeInformation, doFnWrapper, fullName); + } else { + // This can be removed once we drop support for 1.9 and 1.10 versions. + outputDataSet = + new MapPartitionOperator<>(inputDataSet, typeInformation, doFnWrapper, fullName); + } } transformSideInputs(sideInputs, outputDataSet, context); diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkDoFnFunction.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkDoFnFunction.java index a34d840e7417..7a77c8d8ddfe 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkDoFnFunction.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkDoFnFunction.java @@ -19,7 +19,9 @@ import java.util.List; import java.util.Map; +import java.util.Objects; import java.util.Optional; +import javax.annotation.Nullable; import org.apache.beam.runners.core.DoFnRunner; import org.apache.beam.runners.core.DoFnRunners; import org.apache.beam.runners.core.construction.SerializablePipelineOptions; @@ -40,7 +42,9 @@ import org.apache.beam.sdk.values.TupleTag; import org.apache.beam.sdk.values.WindowingStrategy; import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Lists; -import org.apache.flink.api.common.functions.RichMapPartitionFunction; +import org.apache.flink.api.common.functions.AbstractRichFunction; +import org.apache.flink.api.common.functions.FlatMapFunction; +import org.apache.flink.api.common.functions.MapPartitionFunction; import org.apache.flink.api.common.functions.RuntimeContext; import org.apache.flink.configuration.Configuration; import org.apache.flink.util.Collector; @@ -53,8 +57,9 @@ * all outputs with the output number. Afterwards a filter will filter out those elements that are * not to be in a specific output. */ -public class FlinkDoFnFunction - extends RichMapPartitionFunction, WindowedValue> { +public class FlinkDoFnFunction extends AbstractRichFunction + implements FlatMapFunction, WindowedValue>, + MapPartitionFunction, WindowedValue> { private final SerializablePipelineOptions serializedOptions; @@ -71,9 +76,14 @@ public class FlinkDoFnFunction private final DoFnSchemaInformation doFnSchemaInformation; private final Map> sideInputMapping; + private transient CollectorAware collectorAware; private transient DoFnInvoker doFnInvoker; + private transient DoFnRunner doFnRunner; private transient FlinkMetricContainer metricContainer; + private boolean bundleStarted = false; + private boolean exceptionThrownInFlatMap = false; + public FlinkDoFnFunction( DoFn doFn, String stepName, @@ -100,22 +110,49 @@ public FlinkDoFnFunction( this.sideInputMapping = sideInputMapping; } + @Override + public void flatMap(WindowedValue value, Collector> out) { + try { + if (!bundleStarted) { + bundleStarted = true; + doFnRunner.startBundle(); + } + collectorAware.setCollector(out); + doFnRunner.processElement(value); + } catch (Exception e) { + exceptionThrownInFlatMap = true; + throw e; + } + } + @Override public void mapPartition( - Iterable> values, Collector> out) - throws Exception { + Iterable> values, Collector> out) { + for (WindowedValue value : values) { + flatMap(value, out); + } + } - RuntimeContext runtimeContext = getRuntimeContext(); + @Override + public void open(Configuration parameters) { + // Note that the SerializablePipelineOptions already initialize FileSystems in the readObject() + // deserialization method. However, this is a hack, and we want to properly initialize the + // options where they are needed. + FileSystems.setDefaultPipelineOptions(serializedOptions.get()); + doFnInvoker = DoFnInvokers.tryInvokeSetupFor(doFn); + metricContainer = new FlinkMetricContainer(getRuntimeContext()); - DoFnRunners.OutputManager outputManager; + // setup DoFnRunner + final RuntimeContext runtimeContext = getRuntimeContext(); + final DoFnRunners.OutputManager outputManager; if (outputMap.size() == 1) { - outputManager = new FlinkDoFnFunction.DoFnOutputManager(out); + outputManager = new DoFnOutputManager(); } else { // it has some additional outputs - outputManager = new FlinkDoFnFunction.MultiDoFnOutputManager((Collector) out, outputMap); + outputManager = new MultiDoFnOutputManager(outputMap); } - List> additionalOutputTags = Lists.newArrayList(outputMap.keySet()); + final List> additionalOutputTags = Lists.newArrayList(outputMap.keySet()); DoFnRunner doFnRunner = DoFnRunners.simpleRunner( @@ -132,79 +169,100 @@ public void mapPartition( doFnSchemaInformation, sideInputMapping); - FlinkPipelineOptions pipelineOptions = serializedOptions.get().as(FlinkPipelineOptions.class); - if (!pipelineOptions.getDisableMetrics()) { + if (!serializedOptions.get().as(FlinkPipelineOptions.class).getDisableMetrics()) { doFnRunner = new DoFnRunnerWithMetricsUpdate<>(stepName, doFnRunner, metricContainer); } - doFnRunner.startBundle(); - - for (WindowedValue value : values) { - doFnRunner.processElement(value); - } - - doFnRunner.finishBundle(); - } - - @Override - public void open(Configuration parameters) { - // Note that the SerializablePipelineOptions already initialize FileSystems in the readObject() - // deserialization method. However, this is a hack, and we want to properly initialize the - // options where they are needed. - FileSystems.setDefaultPipelineOptions(serializedOptions.get()); - doFnInvoker = DoFnInvokers.tryInvokeSetupFor(doFn); - metricContainer = new FlinkMetricContainer(getRuntimeContext()); + this.collectorAware = (CollectorAware) outputManager; + this.doFnRunner = doFnRunner; } @Override public void close() throws Exception { + Exception suppressed = null; + try { + if (bundleStarted && !exceptionThrownInFlatMap) { + doFnRunner.finishBundle(); + } + } catch (Exception e) { + // Suppress exception, so we can properly teardown DoFn. + suppressed = e; + } try { metricContainer.registerMetricsForPipelineResult(); Optional.ofNullable(doFnInvoker).ifPresent(DoFnInvoker::invokeTeardown); + if (suppressed != null) { + throw suppressed; + } } finally { Workarounds.deleteStaticCaches(); } } - static class DoFnOutputManager implements DoFnRunners.OutputManager { + interface CollectorAware { + + void setCollector(Collector> collector); + } + + static class DoFnOutputManager implements DoFnRunners.OutputManager, CollectorAware { + + @Nullable private Collector> collector; - private Collector collector; + DoFnOutputManager() { + this(null); + } - DoFnOutputManager(Collector collector) { + DoFnOutputManager(@Nullable Collector> collector) { this.collector = collector; } @Override - @SuppressWarnings("unchecked") + public void setCollector(Collector> collector) { + this.collector = Objects.requireNonNull(collector); + } + + @Override public void output(TupleTag tag, WindowedValue output) { - collector.collect( - WindowedValue.of( - new RawUnionValue(0 /* single output */, output.getValue()), - output.getTimestamp(), - output.getWindows(), - output.getPane())); + Objects.requireNonNull(collector) + .collect( + WindowedValue.of( + new RawUnionValue(0 /* single output */, output.getValue()), + output.getTimestamp(), + output.getWindows(), + output.getPane())); } } - static class MultiDoFnOutputManager implements DoFnRunners.OutputManager { + static class MultiDoFnOutputManager implements DoFnRunners.OutputManager, CollectorAware { - private Collector> collector; - private Map, Integer> outputMap; + @Nullable private Collector> collector; + private final Map, Integer> outputMap; + + MultiDoFnOutputManager(Map, Integer> outputMap) { + this.outputMap = outputMap; + } MultiDoFnOutputManager( - Collector> collector, Map, Integer> outputMap) { + @Nullable Collector> collector, + Map, Integer> outputMap) { this.collector = collector; this.outputMap = outputMap; } + @Override + public void setCollector(Collector> collector) { + this.collector = Objects.requireNonNull(collector); + } + @Override public void output(TupleTag tag, WindowedValue output) { - collector.collect( - WindowedValue.of( - new RawUnionValue(outputMap.get(tag), output.getValue()), - output.getTimestamp(), - output.getWindows(), - output.getPane())); + Objects.requireNonNull(collector) + .collect( + WindowedValue.of( + new RawUnionValue(outputMap.get(tag), output.getValue()), + output.getTimestamp(), + output.getWindows(), + output.getPane())); } } } diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkStatefulDoFnFunction.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkStatefulDoFnFunction.java index 1dc13fe2686d..fdc0df297ddf 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkStatefulDoFnFunction.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkStatefulDoFnFunction.java @@ -42,6 +42,7 @@ import org.apache.beam.sdk.transforms.DoFn; import org.apache.beam.sdk.transforms.DoFnSchemaInformation; import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.transforms.join.RawUnionValue; import org.apache.beam.sdk.transforms.reflect.DoFnInvoker; import org.apache.beam.sdk.transforms.reflect.DoFnInvokers; import org.apache.beam.sdk.transforms.windowing.BoundedWindow; @@ -59,7 +60,7 @@ /** A {@link RichGroupReduceFunction} for stateful {@link ParDo} in Flink Batch Runner. */ public class FlinkStatefulDoFnFunction - extends RichGroupReduceFunction>, WindowedValue> { + extends RichGroupReduceFunction>, WindowedValue> { private final DoFn, OutputT> dofn; private String stepName; @@ -104,7 +105,7 @@ public FlinkStatefulDoFnFunction( @Override public void reduce( - Iterable>> values, Collector> out) + Iterable>> values, Collector> out) throws Exception { RuntimeContext runtimeContext = getRuntimeContext(); @@ -113,7 +114,7 @@ public void reduce( outputManager = new FlinkDoFnFunction.DoFnOutputManager(out); } else { // it has some additional Outputs - outputManager = new FlinkDoFnFunction.MultiDoFnOutputManager((Collector) out, outputMap); + outputManager = new FlinkDoFnFunction.MultiDoFnOutputManager(out, outputMap); } final Iterator>> iterator = values.iterator(); From 7978c0fe04385358c6816b79d6a2fcda9a858df0 Mon Sep 17 00:00:00 2001 From: Heejong Lee Date: Fri, 29 May 2020 08:49:15 -0700 Subject: [PATCH 117/151] [BEAM-10078] uniquify Dataflow specific jars when staging (#11814) * [BEAM-10078] uniquify Dataflow specific jars when staging * add comments and logging --- .../runners/dataflow/util/PackageUtil.java | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/util/PackageUtil.java b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/util/PackageUtil.java index 72139931edfd..036d2dbf059f 100644 --- a/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/util/PackageUtil.java +++ b/runners/google-cloud-dataflow-java/src/main/java/org/apache/beam/runners/dataflow/util/PackageUtil.java @@ -397,10 +397,27 @@ public static PackageAttributes forFileToStage( String.format("Non-existent file to stage: %s", file.getAbsolutePath())); } checkState(!file.isDirectory(), "Source file must not be a directory."); + String target; + // Dataflow worker jar and windmill binary can be overridden by providing files with + // predefined file names. Normally, we can use the artifact file name as same as + // the last component of GCS object resource path. However, we need special handling + // for those predefined names since they also need to be unique even in the same + // staging directory. + switch (dest) { + case "dataflow-worker.jar": + case "windmill_main": + target = + Environments.createStagingFileName( + file, Files.asByteSource(file).hash(Hashing.sha256())); + LOG.info("Staging custom {} as {}", dest, target); + break; + default: + target = dest; + } DataflowPackage destination = new DataflowPackage(); String resourcePath = FileSystems.matchNewResource(stagingPath, true) - .resolve(dest, StandardResolveOptions.RESOLVE_FILE) + .resolve(target, StandardResolveOptions.RESOLVE_FILE) .toString(); destination.setLocation(resourcePath); destination.setName(dest); From fc941a02fd2ad1e77dd4db2ce4c298bbc2a206b6 Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Fri, 29 May 2020 12:50:48 -0400 Subject: [PATCH 118/151] =?UTF-8?q?[BEAM-10107]=20Remove=20outdated=20inst?= =?UTF-8?q?ructions=20for=20website=20updates=20in=20rele=E2=80=A6=20(#118?= =?UTF-8?q?52)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [BEAM-10107] Remove outdated instructions for website updates in release guide. * Replace outdated example PR. * Add example PR for beam-site and remove redundant instructions. --- .../content/en/contribute/release-guide.md | 31 +++++-------------- 1 file changed, 8 insertions(+), 23 deletions(-) diff --git a/website/www/site/content/en/contribute/release-guide.md b/website/www/site/content/en/contribute/release-guide.md index 1ecc1368e801..441a2167901e 100644 --- a/website/www/site/content/en/contribute/release-guide.md +++ b/website/www/site/content/en/contribute/release-guide.md @@ -618,10 +618,6 @@ For this step, we recommend you using automation script to create a RC, but you - Please follow the [user guide](https://github.com/apache/beam-wheels#user-guide) to build python wheels. - Once all python wheels have been staged to GCS, please run [./sign_hash_python_wheels.sh](https://github.com/apache/beam/blob/master/release/src/main/scripts/sign_hash_python_wheels.sh), which copies the wheels along with signatures and hashes to [dist.apache.org](https://dist.apache.org/repos/dist/dev/beam/). - 1. Update Beam website ([example](https://github.com/apache/beam/pull/11727)) - 1. Update release version in `website/www/site/config.toml`. - 1. Add new release in `website/www/site/content/en/get-started/downloads.md`. - 1. Update `website/www/site/static/.htaccess` to redirect to the new version. ********** @@ -674,26 +670,17 @@ to the Beam website, usually within an hour. **PR 1: apache/beam-site** This pull request is against the `apache/beam-site` repo, on the `release-docs` -branch. - -* Add the new Javadoc to [SDK API Reference page](https://beam.apache.org/releases/javadoc/) page, as follows: - * Unpack the Maven artifact `org.apache.beam:beam-sdks-java-javadoc` into some temporary location. Call this `${JAVADOC_TMP}`. - * Copy the generated Javadoc into the website repository: `cp -r ${JAVADOC_TMP} javadoc/${RELEASE}`. -* Add the new Pydoc to [SDK API Reference page](https://beam.apache.org/releases/pydoc/) page, as follows: - * Copy the generated Pydoc into the website repository: `cp -r ${PYDOC_ROOT} pydoc/${RELEASE}`. - * Remove `.doctrees` directory. -* Stage files using: `git add --all javadoc/ pydoc/`. +branch ([example](https://github.com/apache/beam-site/pull/603)). +It is created by `build_release_candidate.sh` (see above). **PR 2: apache/beam** -This pull request is against the `apache/beam` repo, on the `master` branch. +This pull request is against the `apache/beam` repo, on the `master` branch ([example](https://github.com/apache/beam/pull/11727)). -* Update the `release_latest` version flag in `/website/_config.yml`, and list - the new release in `/website/src/get-started/downloads.md`, linking to the - source code download and the Release Notes in JIRA. -* Update the `RedirectMatch` rule in - [/website/src/.htaccess](https://github.com/apache/beam/blob/master/website/src/.htaccess) - to point to the new release. See file history for examples. +* Update release version in `website/www/site/config.toml`. +* Add new release in `website/www/site/content/en/get-started/downloads.md`. + * Download links will not work until the release is finalized. +* Update `website/www/site/static/.htaccess` to redirect to the new version. ### Blog post @@ -1141,12 +1128,10 @@ All wheels should be published, in addition to the zip of the release source. Copy the source release from the `dev` repository to the `release` repository at `dist.apache.org` using Subversion. -Move last release artifacts from `dist.apache.org` to `archive.apache.org` using Subversion. Then update download address for last release version, [example PR](https://github.com/apache/beam-site/pull/478). +Move last release artifacts from `dist.apache.org` to `archive.apache.org` using Subversion. Make sure to change these links on the website ([example](https://github.com/apache/beam/pull/11727)). __NOTE__: Only PMC members have permissions to do it, ping [dev@](mailto:dev@beam.apache.org) for assitance; -Make sure the download address for last release version is upldaed, [example PR](https://github.com/apache/beam-site/pull/478). - ### Deploy SDK docker images to DockerHub * Script: [publish_docker_images.sh](https://github.com/apache/beam/blob/master/release/src/main/scripts/publish_docker_images.sh) * Usage From 193e54c3e2f0fffa8d92dfed998800ea86cec073 Mon Sep 17 00:00:00 2001 From: Damon Douglas Date: Fri, 29 May 2020 10:53:57 -0700 Subject: [PATCH 119/151] [BEAM-9679] Add a CoGroupByKey lesson to the Core Transforms section (#11803) * Add a CoGroupByKey lesson to the Core Transforms section --- .../CoGroupByKey/CoGroupByKey/cmd/main.go | 44 +++ .../CoGroupByKey/CoGroupByKey/go.mod | 26 ++ .../CoGroupByKey/CoGroupByKey/go.sum | 314 ++++++++++++++++++ .../CoGroupByKey/pkg/task/task.go | 52 +++ .../CoGroupByKey/CoGroupByKey/task-info.yaml | 35 ++ .../CoGroupByKey/task-remote-info.yaml | 2 + .../CoGroupByKey/CoGroupByKey/task.md | 104 ++++++ .../CoGroupByKey/test/task_test.go | 55 +++ .../CoGroupByKey/lesson-info.yaml | 21 ++ .../CoGroupByKey/lesson-remote-info.yaml | 3 + .../Flatten/Flatten/task-remote-info.yaml | 2 + .../Flatten/lesson-remote-info.yaml | 3 + .../Map/ParDo OneToMany/go.mod | 3 +- .../Map/ParDo OneToMany/go.sum | 5 +- .../Map/ParDo OneToMany/task-remote-info.yaml | 2 +- .../Core Transforms/Map/ParDo Struct/go.mod | 3 +- .../Core Transforms/Map/ParDo Struct/go.sum | 5 +- .../Map/ParDo Struct/task-remote-info.yaml | 2 +- .../katas/go/Core Transforms/Map/ParDo/go.mod | 3 +- .../katas/go/Core Transforms/Map/ParDo/go.sum | 5 +- .../Map/ParDo/task-remote-info.yaml | 2 +- .../go/Core Transforms/section-info.yaml | 3 +- .../Hello Beam/Hello Beam Test/go.mod | 2 +- .../Hello Beam Test/task-remote-info.yaml | 2 +- .../Introduction/Hello Beam/Hello Beam/go.mod | 2 +- .../Hello Beam/task-remote-info.yaml | 2 +- learning/katas/go/course-remote-info.yaml | 2 +- 27 files changed, 683 insertions(+), 21 deletions(-) create mode 100644 learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/cmd/main.go create mode 100644 learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/go.mod create mode 100644 learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/go.sum create mode 100644 learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/pkg/task/task.go create mode 100644 learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task-info.yaml create mode 100644 learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task-remote-info.yaml create mode 100644 learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task.md create mode 100644 learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/test/task_test.go create mode 100644 learning/katas/go/Core Transforms/CoGroupByKey/lesson-info.yaml create mode 100644 learning/katas/go/Core Transforms/CoGroupByKey/lesson-remote-info.yaml create mode 100644 learning/katas/go/Core Transforms/Flatten/Flatten/task-remote-info.yaml create mode 100644 learning/katas/go/Core Transforms/Flatten/lesson-remote-info.yaml diff --git a/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/cmd/main.go b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/cmd/main.go new file mode 100644 index 000000000000..ee11b3b65a5e --- /dev/null +++ b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/cmd/main.go @@ -0,0 +1,44 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package main + +import ( + "cogroupbykey/pkg/task" + "context" + "github.com/apache/beam/sdks/go/pkg/beam" + "github.com/apache/beam/sdks/go/pkg/beam/log" + "github.com/apache/beam/sdks/go/pkg/beam/x/beamx" + "github.com/apache/beam/sdks/go/pkg/beam/x/debug" +) + +func main() { + ctx := context.Background() + + p, s := beam.NewPipelineWithRoot() + + fruits := beam.Create(s.Scope("Fruits"), "apple", "banana", "cherry") + countries := beam.Create(s.Scope("Countries"), "australia", "brazil", "canada") + + output := task.ApplyTransform(s, fruits, countries) + + debug.Print(s, output) + + err := beamx.Run(ctx, p) + + if err != nil { + log.Exitf(ctx, "Failed to execute job: %v", err) + } +} diff --git a/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/go.mod b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/go.mod new file mode 100644 index 000000000000..c0c99f3de73b --- /dev/null +++ b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/go.mod @@ -0,0 +1,26 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +module cogroupbykey + +go 1.14 + +require ( + github.com/apache/beam v2.20.0+incompatible + github.com/golang/protobuf v1.4.2 // indirect + github.com/google/go-cmp v0.4.1 // indirect + google.golang.org/api v0.25.0 // indirect + google.golang.org/grpc v1.29.1 // indirect +) diff --git a/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/go.sum b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/go.sum new file mode 100644 index 000000000000..92a428884f45 --- /dev/null +++ b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/go.sum @@ -0,0 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h1:sXmLre5bzIR6ypkjXCDI3jHPssRhc8KD/Ome589sc3U= +honnef.co/go/tools v0.0.1-2020.1.3/go.mod h1:X/FiERA/W4tHapMX5mGpAtMSVEeEUOyHaw9vFzvIQ3k= +rsc.io/binaryregexp v0.2.0/go.mod h1:qTv7/COck+e2FymRvadv62gMdZztPaShugOCi3I+8D8= +rsc.io/quote/v3 v3.1.0/go.mod h1:yEA65RcK8LyAZtP9Kv3t0HmxON59tX3rD+tICJqUlj0= +rsc.io/sampler v1.3.0/go.mod h1:T1hPZKmBbMNahiBKFy5HrXp6adAjACjK9JXDnKaTXpA= diff --git a/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/pkg/task/task.go b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/pkg/task/task.go new file mode 100644 index 000000000000..c498b3585a1d --- /dev/null +++ b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/pkg/task/task.go @@ -0,0 +1,52 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package task + +import ( + "fmt" + "github.com/apache/beam/sdks/go/pkg/beam" +) + +func ApplyTransform(s beam.Scope, fruits beam.PCollection, countries beam.PCollection) beam.PCollection { + fruitsKV := beam.ParDo(s, func(word string) (string, string) { + return string(word[0]), word + }, fruits) + + countriesKV := beam.ParDo(s, func(word string) (string, string) { + return string(word[0]), word + }, countries) + + grouped := beam.CoGroupByKey(s, fruitsKV, countriesKV) + return beam.ParDo(s, func(key string, fruitsIter func(*string) bool, countriesIter func(*string) bool, emit func(string)) { + wa := &WordsAlphabet{ + Alphabet: key, + } + fruitsIter(&wa.Fruit) + countriesIter(&wa.Country) + emit(wa.String()) + }, grouped) +} + +type WordsAlphabet struct { + Alphabet string + Fruit string + Country string +} + +func (wa *WordsAlphabet) String() string { + return fmt.Sprintf("WordsAlphabet%+v", *wa) +} + diff --git a/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task-info.yaml b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task-info.yaml new file mode 100644 index 000000000000..2aa604763256 --- /dev/null +++ b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task-info.yaml @@ -0,0 +1,35 @@ +# +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. +# + +type: edu +files: +- name: test/task_test.go + visible: false +- name: cmd/main.go + visible: true +- name: go.mod + visible: false +- name: pkg/task/task.go + visible: true + placeholders: + - offset: 978 + length: 533 + placeholder_text: TODO() +- name: go.sum + visible: false diff --git a/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task-remote-info.yaml b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task-remote-info.yaml new file mode 100644 index 000000000000..6846e3ac7a55 --- /dev/null +++ b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task-remote-info.yaml @@ -0,0 +1,2 @@ +id: 1342650 +update_date: Thu, 28 May 2020 22:33:24 UTC diff --git a/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task.md b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task.md new file mode 100644 index 000000000000..9d2868abc44c --- /dev/null +++ b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/task.md @@ -0,0 +1,104 @@ + + +# CoGroupByKey + +CoGroupByKey performs a relational join of two or more key/value PCollections that have the same +key type. + +**Kata:** Implement a [beam.CoGroupByKey](https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam#CoGroupByKey) +transform that join words by the first alphabetical letter, and then produces the string representation of the +WordsAlphabet model. + +

    + Refer to + beam.CoGroupByKey + to solve this problem. +
    + +
    + Refer to the Beam Programming Guide + + "CoGroupByKey" section for more information. +
    + +
    + Think of this problem in three stages. First, create key/value pairs of PCollections called KV + for fruits and countries, pairing the first character with the word. Next, apply CoGroupByKey to the KVs + followed by a ParDo. +
    + +
    + In the last lesson we learned how to make key/value PCollections called KV. Now we have + two to make from fruits and countries. + + To return as a KV, you can return two values from your DoFn. The first return value represents the Key, and + the second return value represents the Value. An example is shown below. + +``` +func doFn(element string) (string, string) { + key := string(element[0]) + value := element + return key, value +} +``` +
    + +
    + In the last lesson we learned that + + beam.GroupByKey takes a single KV. + beam.CoGroupByKey + takes more than one KV. +
    + +
    + Our final step in this problem requires a + beam.ParDo + with a DoFn that's different than what we've seen in previous lessons. In the previous step we should + have a PCollection acquired from CoGroupByKey. A ParDo for that PCollection expects a DoFn that looks + like the following. + + ``` + func doFn(key string, iterA func(*string) bool, iterB func(*string) bool, emit func(string)){ + ... + } + ``` + + Each `func(*string) bool` parameter above corresponds to each of the PCollection KVs that we provided to CoGroupByKey. + + `func(*string)` returns true if there is a value available when the pipeline invokes your doFn. + + Note that it takes a `*string` instead of a `string`. In Go, this means that to acquire its value, we need to + do this. + +``` + var v string + iterA(&v) + // do something with v +``` + + Not necessary for this task, though if you expected multiple values per key, you would do something like this. +``` + var v string + for iterA(&v) { + // do something with v + } +``` +
    diff --git a/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/test/task_test.go b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/test/task_test.go new file mode 100644 index 000000000000..90a5912ebe22 --- /dev/null +++ b/learning/katas/go/Core Transforms/CoGroupByKey/CoGroupByKey/test/task_test.go @@ -0,0 +1,55 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package task + +import ( + "cogroupbykey/pkg/task" + "github.com/apache/beam/sdks/go/pkg/beam" + "github.com/apache/beam/sdks/go/pkg/beam/testing/passert" + "github.com/apache/beam/sdks/go/pkg/beam/testing/ptest" + "testing" +) + +func TestApplyTransform(t *testing.T) { + p, s := beam.NewPipelineWithRoot() + type args struct { + fruits beam.PCollection + countries beam.PCollection + } + tests := []struct { + args args + want []interface{} + }{ + { + args: args{ + fruits: beam.Create(s.Scope("Fruits"), "apple", "banana", "cherry"), + countries: beam.Create(s.Scope("Countries"), "australia", "brazil", "canada"), + }, + want: []interface{}{ + "WordsAlphabet{Alphabet:a Fruit:apple Country:australia}", + "WordsAlphabet{Alphabet:b Fruit:banana Country:brazil}", + "WordsAlphabet{Alphabet:c Fruit:cherry Country:canada}", + }, + }, + } + for _, tt := range tests { + got := task.ApplyTransform(s, tt.args.fruits, tt.args.countries) + passert.Equals(s, got, tt.want...) + if err := ptest.Run(p); err != nil { + t.Error(err) + } + } +} diff --git a/learning/katas/go/Core Transforms/CoGroupByKey/lesson-info.yaml b/learning/katas/go/Core Transforms/CoGroupByKey/lesson-info.yaml new file mode 100644 index 000000000000..273c0771cccf --- /dev/null +++ b/learning/katas/go/Core Transforms/CoGroupByKey/lesson-info.yaml @@ -0,0 +1,21 @@ +# +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. +# + +content: +- CoGroupByKey diff --git a/learning/katas/go/Core Transforms/CoGroupByKey/lesson-remote-info.yaml b/learning/katas/go/Core Transforms/CoGroupByKey/lesson-remote-info.yaml new file mode 100644 index 000000000000..548d0f7247dc --- /dev/null +++ b/learning/katas/go/Core Transforms/CoGroupByKey/lesson-remote-info.yaml @@ -0,0 +1,3 @@ +id: 361640 +update_date: Thu, 28 May 2020 22:33:20 UTC +unit: 346169 diff --git a/learning/katas/go/Core Transforms/Flatten/Flatten/task-remote-info.yaml b/learning/katas/go/Core Transforms/Flatten/Flatten/task-remote-info.yaml new file mode 100644 index 000000000000..6d24d40ec8c0 --- /dev/null +++ b/learning/katas/go/Core Transforms/Flatten/Flatten/task-remote-info.yaml @@ -0,0 +1,2 @@ +id: 1342651 +update_date: Thu, 28 May 2020 22:33:30 UTC diff --git a/learning/katas/go/Core Transforms/Flatten/lesson-remote-info.yaml b/learning/katas/go/Core Transforms/Flatten/lesson-remote-info.yaml new file mode 100644 index 000000000000..f7ed569d95fa --- /dev/null +++ b/learning/katas/go/Core Transforms/Flatten/lesson-remote-info.yaml @@ -0,0 +1,3 @@ +id: 361641 +update_date: Thu, 28 May 2020 22:33:26 UTC +unit: 346170 diff --git a/learning/katas/go/Core Transforms/Map/ParDo OneToMany/go.mod b/learning/katas/go/Core Transforms/Map/ParDo OneToMany/go.mod index 64758068e63d..89da9b4bcbf4 100644 --- a/learning/katas/go/Core Transforms/Map/ParDo OneToMany/go.mod +++ b/learning/katas/go/Core Transforms/Map/ParDo OneToMany/go.mod @@ -15,12 +15,11 @@ module pardo_onetomany -go 1.13 +go 1.14 require ( github.com/apache/beam v2.20.0+incompatible github.com/golang/protobuf v1.4.0 // indirect - github.com/googleapis/gax-go v2.0.2+incompatible // indirect go.opencensus.io v0.22.3 // indirect google.golang.org/api v0.22.0 // indirect google.golang.org/grpc v1.28.1 // indirect diff --git a/learning/katas/go/Core Transforms/Map/ParDo OneToMany/go.sum b/learning/katas/go/Core Transforms/Map/ParDo OneToMany/go.sum index 66ee82f3d108..709c1101db07 100644 --- a/learning/katas/go/Core Transforms/Map/ParDo OneToMany/go.sum +++ b/learning/katas/go/Core Transforms/Map/ParDo OneToMany/go.sum @@ -35,10 +35,9 @@ github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMyw github.com/google/go-cmp v0.3.1/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= github.com/google/go-cmp v0.4.0 h1:xsAVV57WRhGj6kEIi8ReJzQlHHqcBYCElAvkovg3B/4= github.com/google/go-cmp v0.4.0/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= +github.com/google/martian v2.1.0+incompatible h1:/CP5g8u/VJHijgedC/Legn3BAbAaWPgecwXBIDzw5no= github.com/google/martian v2.1.0+incompatible/go.mod h1:9I4somxYTbIHy5NJKHRl3wXiIaQGbYVAs8BPL6v8lEs= github.com/google/pprof v0.0.0-20181206194817-3ea8567a2e57/go.mod h1:zfwlbNMJ+OItoe0UupaVj+oy1omPYYDuagoSzA8v9mc= -github.com/googleapis/gax-go v2.0.2+incompatible h1:silFMLAnr330+NRuag/VjIGF7TLp/LBrV2CJKFLWEww= -github.com/googleapis/gax-go v2.0.2+incompatible/go.mod h1:SFVmujtThgffbyetf+mdk2eWhX2bMyUtNHzFKcPA9HY= github.com/googleapis/gax-go/v2 v2.0.4/go.mod h1:0Wqv26UfaUD9n4G6kQubkQ+KchISgw+vpHVxEJEs9eg= github.com/googleapis/gax-go/v2 v2.0.5 h1:sjZBwGj9Jlw33ImPtvFviGYvseOtDM7hkSKB7+Tv3SM= github.com/googleapis/gax-go/v2 v2.0.5/go.mod h1:DWXyrwAJ9X0FpwwEdw+IPEYBICEFu5mhpdKc/us6bOk= @@ -82,6 +81,7 @@ golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5h golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a h1:1BGLXjeY4akVXGgbC9HugT3Jv3hCI0z56oJR5vAMgBU= golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20190502145724-3ef323f4f1fd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20190507160741-ecd444e8653b h1:ag/x1USPSsqHud38I9BAC88qdNLDHHtQ4mlgQIZPPNA= golang.org/x/sys v0.0.0-20190507160741-ecd444e8653b/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/text v0.3.0 h1:g61tztE5qeGQ89tm6NTjjM9VPIm088od1l6aSorWRWg= golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= @@ -102,6 +102,7 @@ google.golang.org/api v0.22.0 h1:J1Pl9P2lnmYFSJvgs70DKELqHNh8CNWXPbud4njEE2s= google.golang.org/api v0.22.0/go.mod h1:BwFmGc8tA3vsd7r/7kR8DY7iEEGSU04BFxCo5jP/sfE= google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM= google.golang.org/appengine v1.4.0/go.mod h1:xpcJRLb0r/rnEns0DIKYYv+WjYCduHsrkT7/EB5XEv4= +google.golang.org/appengine v1.5.0 h1:KxkO13IPW4Lslp2bz+KHP2E3gtFlrIGNThxkZQ3g+4c= google.golang.org/appengine v1.5.0/go.mod h1:xpcJRLb0r/rnEns0DIKYYv+WjYCduHsrkT7/EB5XEv4= google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc= google.golang.org/genproto v0.0.0-20190307195333-5fe7a883aa19/go.mod h1:VzzqZJRnGkLBvHegQrXjBqPurQTc5/KpmUdxsrq26oE= diff --git a/learning/katas/go/Core Transforms/Map/ParDo OneToMany/task-remote-info.yaml b/learning/katas/go/Core Transforms/Map/ParDo OneToMany/task-remote-info.yaml index 8e0e17b2c09f..6b6405a4ad16 100644 --- a/learning/katas/go/Core Transforms/Map/ParDo OneToMany/task-remote-info.yaml +++ b/learning/katas/go/Core Transforms/Map/ParDo OneToMany/task-remote-info.yaml @@ -1,2 +1,2 @@ id: 1289189 -update_date: Wed, 20 May 2020 06:15:28 UTC +update_date: Thu, 28 May 2020 22:33:42 UTC diff --git a/learning/katas/go/Core Transforms/Map/ParDo Struct/go.mod b/learning/katas/go/Core Transforms/Map/ParDo Struct/go.mod index 0c0fddeae56e..7b5d3a2e31f7 100644 --- a/learning/katas/go/Core Transforms/Map/ParDo Struct/go.mod +++ b/learning/katas/go/Core Transforms/Map/ParDo Struct/go.mod @@ -15,12 +15,11 @@ module mapelements -go 1.13 +go 1.14 require ( github.com/apache/beam v2.20.0+incompatible github.com/golang/protobuf v1.4.0 // indirect - github.com/googleapis/gax-go v2.0.2+incompatible // indirect go.opencensus.io v0.22.3 // indirect google.golang.org/api v0.22.0 // indirect google.golang.org/grpc v1.28.1 // indirect diff --git a/learning/katas/go/Core Transforms/Map/ParDo Struct/go.sum b/learning/katas/go/Core Transforms/Map/ParDo Struct/go.sum index 66ee82f3d108..709c1101db07 100644 --- a/learning/katas/go/Core Transforms/Map/ParDo Struct/go.sum +++ b/learning/katas/go/Core Transforms/Map/ParDo Struct/go.sum @@ -35,10 +35,9 @@ github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMyw github.com/google/go-cmp v0.3.1/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= github.com/google/go-cmp v0.4.0 h1:xsAVV57WRhGj6kEIi8ReJzQlHHqcBYCElAvkovg3B/4= github.com/google/go-cmp v0.4.0/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= +github.com/google/martian v2.1.0+incompatible h1:/CP5g8u/VJHijgedC/Legn3BAbAaWPgecwXBIDzw5no= github.com/google/martian v2.1.0+incompatible/go.mod h1:9I4somxYTbIHy5NJKHRl3wXiIaQGbYVAs8BPL6v8lEs= github.com/google/pprof v0.0.0-20181206194817-3ea8567a2e57/go.mod h1:zfwlbNMJ+OItoe0UupaVj+oy1omPYYDuagoSzA8v9mc= -github.com/googleapis/gax-go v2.0.2+incompatible h1:silFMLAnr330+NRuag/VjIGF7TLp/LBrV2CJKFLWEww= -github.com/googleapis/gax-go v2.0.2+incompatible/go.mod h1:SFVmujtThgffbyetf+mdk2eWhX2bMyUtNHzFKcPA9HY= github.com/googleapis/gax-go/v2 v2.0.4/go.mod h1:0Wqv26UfaUD9n4G6kQubkQ+KchISgw+vpHVxEJEs9eg= github.com/googleapis/gax-go/v2 v2.0.5 h1:sjZBwGj9Jlw33ImPtvFviGYvseOtDM7hkSKB7+Tv3SM= github.com/googleapis/gax-go/v2 v2.0.5/go.mod h1:DWXyrwAJ9X0FpwwEdw+IPEYBICEFu5mhpdKc/us6bOk= @@ -82,6 +81,7 @@ golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5h golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a h1:1BGLXjeY4akVXGgbC9HugT3Jv3hCI0z56oJR5vAMgBU= golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20190502145724-3ef323f4f1fd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20190507160741-ecd444e8653b h1:ag/x1USPSsqHud38I9BAC88qdNLDHHtQ4mlgQIZPPNA= golang.org/x/sys v0.0.0-20190507160741-ecd444e8653b/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/text v0.3.0 h1:g61tztE5qeGQ89tm6NTjjM9VPIm088od1l6aSorWRWg= golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= @@ -102,6 +102,7 @@ google.golang.org/api v0.22.0 h1:J1Pl9P2lnmYFSJvgs70DKELqHNh8CNWXPbud4njEE2s= google.golang.org/api v0.22.0/go.mod h1:BwFmGc8tA3vsd7r/7kR8DY7iEEGSU04BFxCo5jP/sfE= google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM= google.golang.org/appengine v1.4.0/go.mod h1:xpcJRLb0r/rnEns0DIKYYv+WjYCduHsrkT7/EB5XEv4= +google.golang.org/appengine v1.5.0 h1:KxkO13IPW4Lslp2bz+KHP2E3gtFlrIGNThxkZQ3g+4c= google.golang.org/appengine v1.5.0/go.mod h1:xpcJRLb0r/rnEns0DIKYYv+WjYCduHsrkT7/EB5XEv4= google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc= google.golang.org/genproto v0.0.0-20190307195333-5fe7a883aa19/go.mod h1:VzzqZJRnGkLBvHegQrXjBqPurQTc5/KpmUdxsrq26oE= diff --git a/learning/katas/go/Core Transforms/Map/ParDo Struct/task-remote-info.yaml b/learning/katas/go/Core Transforms/Map/ParDo Struct/task-remote-info.yaml index 5ca73c7400f6..368c38dad01a 100644 --- a/learning/katas/go/Core Transforms/Map/ParDo Struct/task-remote-info.yaml +++ b/learning/katas/go/Core Transforms/Map/ParDo Struct/task-remote-info.yaml @@ -1,2 +1,2 @@ id: 1289190 -update_date: Wed, 20 May 2020 06:15:31 UTC +update_date: Thu, 28 May 2020 22:33:45 UTC diff --git a/learning/katas/go/Core Transforms/Map/ParDo/go.mod b/learning/katas/go/Core Transforms/Map/ParDo/go.mod index da50fd0795d4..4393de855643 100644 --- a/learning/katas/go/Core Transforms/Map/ParDo/go.mod +++ b/learning/katas/go/Core Transforms/Map/ParDo/go.mod @@ -15,12 +15,11 @@ module pardo -go 1.13 +go 1.14 require ( github.com/apache/beam v2.20.0+incompatible github.com/golang/protobuf v1.4.0 // indirect - github.com/googleapis/gax-go v2.0.2+incompatible // indirect go.opencensus.io v0.22.3 // indirect google.golang.org/api v0.21.0 // indirect google.golang.org/grpc v1.28.1 // indirect diff --git a/learning/katas/go/Core Transforms/Map/ParDo/go.sum b/learning/katas/go/Core Transforms/Map/ParDo/go.sum index 22b190304fca..395e4a1ba737 100644 --- a/learning/katas/go/Core Transforms/Map/ParDo/go.sum +++ b/learning/katas/go/Core Transforms/Map/ParDo/go.sum @@ -35,10 +35,9 @@ github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMyw github.com/google/go-cmp v0.3.1/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= github.com/google/go-cmp v0.4.0 h1:xsAVV57WRhGj6kEIi8ReJzQlHHqcBYCElAvkovg3B/4= github.com/google/go-cmp v0.4.0/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= +github.com/google/martian v2.1.0+incompatible h1:/CP5g8u/VJHijgedC/Legn3BAbAaWPgecwXBIDzw5no= github.com/google/martian v2.1.0+incompatible/go.mod h1:9I4somxYTbIHy5NJKHRl3wXiIaQGbYVAs8BPL6v8lEs= github.com/google/pprof v0.0.0-20181206194817-3ea8567a2e57/go.mod h1:zfwlbNMJ+OItoe0UupaVj+oy1omPYYDuagoSzA8v9mc= -github.com/googleapis/gax-go v2.0.2+incompatible h1:silFMLAnr330+NRuag/VjIGF7TLp/LBrV2CJKFLWEww= -github.com/googleapis/gax-go v2.0.2+incompatible/go.mod h1:SFVmujtThgffbyetf+mdk2eWhX2bMyUtNHzFKcPA9HY= github.com/googleapis/gax-go/v2 v2.0.4/go.mod h1:0Wqv26UfaUD9n4G6kQubkQ+KchISgw+vpHVxEJEs9eg= github.com/googleapis/gax-go/v2 v2.0.5 h1:sjZBwGj9Jlw33ImPtvFviGYvseOtDM7hkSKB7+Tv3SM= github.com/googleapis/gax-go/v2 v2.0.5/go.mod h1:DWXyrwAJ9X0FpwwEdw+IPEYBICEFu5mhpdKc/us6bOk= @@ -82,6 +81,7 @@ golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5h golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a h1:1BGLXjeY4akVXGgbC9HugT3Jv3hCI0z56oJR5vAMgBU= golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20190502145724-3ef323f4f1fd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20190507160741-ecd444e8653b h1:ag/x1USPSsqHud38I9BAC88qdNLDHHtQ4mlgQIZPPNA= golang.org/x/sys v0.0.0-20190507160741-ecd444e8653b/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/text v0.3.0 h1:g61tztE5qeGQ89tm6NTjjM9VPIm088od1l6aSorWRWg= golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= @@ -102,6 +102,7 @@ google.golang.org/api v0.21.0 h1:zS+Q/CJJnVlXpXQVIz+lH0ZT2lBuT2ac7XD8Y/3w6hY= google.golang.org/api v0.21.0/go.mod h1:BwFmGc8tA3vsd7r/7kR8DY7iEEGSU04BFxCo5jP/sfE= google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM= google.golang.org/appengine v1.4.0/go.mod h1:xpcJRLb0r/rnEns0DIKYYv+WjYCduHsrkT7/EB5XEv4= +google.golang.org/appengine v1.5.0 h1:KxkO13IPW4Lslp2bz+KHP2E3gtFlrIGNThxkZQ3g+4c= google.golang.org/appengine v1.5.0/go.mod h1:xpcJRLb0r/rnEns0DIKYYv+WjYCduHsrkT7/EB5XEv4= google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc= google.golang.org/genproto v0.0.0-20190307195333-5fe7a883aa19/go.mod h1:VzzqZJRnGkLBvHegQrXjBqPurQTc5/KpmUdxsrq26oE= diff --git a/learning/katas/go/Core Transforms/Map/ParDo/task-remote-info.yaml b/learning/katas/go/Core Transforms/Map/ParDo/task-remote-info.yaml index c5aaaae2a15f..42e50eda6d25 100644 --- a/learning/katas/go/Core Transforms/Map/ParDo/task-remote-info.yaml +++ b/learning/katas/go/Core Transforms/Map/ParDo/task-remote-info.yaml @@ -1,2 +1,2 @@ id: 1289188 -update_date: Wed, 20 May 2020 06:15:25 UTC +update_date: Thu, 28 May 2020 22:33:39 UTC diff --git a/learning/katas/go/Core Transforms/section-info.yaml b/learning/katas/go/Core Transforms/section-info.yaml index 3fe207041313..d228f9a30d38 100644 --- a/learning/katas/go/Core Transforms/section-info.yaml +++ b/learning/katas/go/Core Transforms/section-info.yaml @@ -20,4 +20,5 @@ content: - Map - GroupByKey -- Flatten \ No newline at end of file +- CoGroupByKey +- Flatten diff --git a/learning/katas/go/Introduction/Hello Beam/Hello Beam Test/go.mod b/learning/katas/go/Introduction/Hello Beam/Hello Beam Test/go.mod index 6cf809a0c9b5..696bd8f55c03 100644 --- a/learning/katas/go/Introduction/Hello Beam/Hello Beam Test/go.mod +++ b/learning/katas/go/Introduction/Hello Beam/Hello Beam Test/go.mod @@ -15,7 +15,7 @@ module hello_beam_test -go 1.13 +go 1.14 require ( github.com/apache/beam v2.19.0+incompatible diff --git a/learning/katas/go/Introduction/Hello Beam/Hello Beam Test/task-remote-info.yaml b/learning/katas/go/Introduction/Hello Beam/Hello Beam Test/task-remote-info.yaml index a75da50ff181..eaf8e5387bd1 100644 --- a/learning/katas/go/Introduction/Hello Beam/Hello Beam Test/task-remote-info.yaml +++ b/learning/katas/go/Introduction/Hello Beam/Hello Beam Test/task-remote-info.yaml @@ -1,2 +1,2 @@ id: 1236832 -update_date: Tue, 05 May 2020 02:02:03 UTC +update_date: Thu, 28 May 2020 22:33:36 UTC diff --git a/learning/katas/go/Introduction/Hello Beam/Hello Beam/go.mod b/learning/katas/go/Introduction/Hello Beam/Hello Beam/go.mod index 13bb5997a52f..233fe5c13c7e 100644 --- a/learning/katas/go/Introduction/Hello Beam/Hello Beam/go.mod +++ b/learning/katas/go/Introduction/Hello Beam/Hello Beam/go.mod @@ -15,7 +15,7 @@ module hello_beam -go 1.13 +go 1.14 require ( github.com/apache/beam v2.19.0+incompatible diff --git a/learning/katas/go/Introduction/Hello Beam/Hello Beam/task-remote-info.yaml b/learning/katas/go/Introduction/Hello Beam/Hello Beam/task-remote-info.yaml index 46551fb4c9fd..7f138de415ba 100644 --- a/learning/katas/go/Introduction/Hello Beam/Hello Beam/task-remote-info.yaml +++ b/learning/katas/go/Introduction/Hello Beam/Hello Beam/task-remote-info.yaml @@ -1,2 +1,2 @@ id: 1236831 -update_date: Wed, 20 May 2020 06:15:22 UTC +update_date: Thu, 28 May 2020 22:33:33 UTC diff --git a/learning/katas/go/course-remote-info.yaml b/learning/katas/go/course-remote-info.yaml index 2651d8336da7..b875f83687ed 100644 --- a/learning/katas/go/course-remote-info.yaml +++ b/learning/katas/go/course-remote-info.yaml @@ -1,2 +1,2 @@ id: 70387 -update_date: Tue, 05 May 2020 02:02:55 UTC +update_date: Wed, 20 May 2020 06:16:18 UTC From 1bcb551a7b212989b08a518b5c8ebdf52d11775e Mon Sep 17 00:00:00 2001 From: Robert Burke Date: Fri, 29 May 2020 10:54:53 -0700 Subject: [PATCH 120/151] [BEAM-10110] Propagate ids for custom coders. (#11832) * [BEAM-10110] Propagate ids for custom coders. * [BEAM-10110] In coder strings, use ids if present. --- sdks/go/pkg/beam/core/graph/coder/coder.go | 17 +++++++++++++++-- sdks/go/pkg/beam/core/runtime/graphx/coder.go | 3 +++ .../go/pkg/beam/core/runtime/graphx/dataflow.go | 16 ++++++++++------ 3 files changed, 28 insertions(+), 8 deletions(-) diff --git a/sdks/go/pkg/beam/core/graph/coder/coder.go b/sdks/go/pkg/beam/core/graph/coder/coder.go index 61ebdc6f3d37..2ba07d72c882 100644 --- a/sdks/go/pkg/beam/core/graph/coder/coder.go +++ b/sdks/go/pkg/beam/core/graph/coder/coder.go @@ -45,6 +45,8 @@ type CustomCoder struct { // Dec is the decoding function: []byte -> T. It may optionally take a // reflect.Type parameter and return an error as well. Dec *funcx.Fn + + ID string // (optional) This coder's ID if translated from a pipeline proto. } // TODO(herohde) 5/16/2017: do we want/need to allow user coders that follow the @@ -76,7 +78,10 @@ func (c *CustomCoder) Equals(o *CustomCoder) bool { } func (c *CustomCoder) String() string { - return fmt.Sprintf("%v[%v]", c.Type, c.Name) + if c.ID == "" { + return fmt.Sprintf("%v[%v]", c.Type, c.Name) + } + return fmt.Sprintf("%v[%v;%v]", c.Type, c.Name, c.ID) } // Type signatures of encode/decode for verification. @@ -187,6 +192,8 @@ type Coder struct { Components []*Coder // WindowedValue, KV, CoGBK Custom *CustomCoder // Custom Window *WindowCoder // WindowedValue + + ID string // (optional) This coder's ID if translated from a pipeline proto. } // Equals returns true iff the two coders are equal. It assumes that @@ -224,10 +231,16 @@ func (c *Coder) String() string { return "$" } if c.Custom != nil { - return c.Custom.String() + if c.ID == "" { + return c.Custom.String() + } + return fmt.Sprintf("%v;%v", c.Custom, c.ID) } ret := fmt.Sprintf("%v", c.Kind) + if c.ID != "" { + ret = fmt.Sprintf("%v;%v", c.Kind, c.ID) + } if len(c.Components) > 0 { var args []string for _, elm := range c.Components { diff --git a/sdks/go/pkg/beam/core/runtime/graphx/coder.go b/sdks/go/pkg/beam/core/runtime/graphx/coder.go index b00581f0c367..212ad3b78d4c 100644 --- a/sdks/go/pkg/beam/core/runtime/graphx/coder.go +++ b/sdks/go/pkg/beam/core/runtime/graphx/coder.go @@ -106,6 +106,7 @@ func NewCoderUnmarshaller(m map[string]*pb.Coder) *CoderUnmarshaller { } } +// Coders unmarshals a list of coder ids. func (b *CoderUnmarshaller) Coders(ids []string) ([]*coder.Coder, error) { coders := make([]*coder.Coder, len(ids)) for i, id := range ids { @@ -133,6 +134,7 @@ func (b *CoderUnmarshaller) Coder(id string) (*coder.Coder, error) { if err != nil { return nil, errors.WithContextf(err, "unmarshalling coder %v", id) } + ret.ID = id b.coders[id] = ret return ret, nil @@ -256,6 +258,7 @@ func (b *CoderUnmarshaller) makeCoder(c *pb.Coder) (*coder.Coder, error) { if err != nil { return nil, err } + custom.ID = components[0] t := typex.New(custom.Type) return &coder.Coder{Kind: coder.Custom, T: t, Custom: custom}, nil diff --git a/sdks/go/pkg/beam/core/runtime/graphx/dataflow.go b/sdks/go/pkg/beam/core/runtime/graphx/dataflow.go index da6d9b520e77..364a849962cb 100644 --- a/sdks/go/pkg/beam/core/runtime/graphx/dataflow.go +++ b/sdks/go/pkg/beam/core/runtime/graphx/dataflow.go @@ -29,11 +29,12 @@ import ( // CoderRef defines the (structured) Coder in serializable form. It is // an artifact of the CloudObject encoding. type CoderRef struct { - Type string `json:"@type,omitempty"` - Components []*CoderRef `json:"component_encodings,omitempty"` - IsWrapper bool `json:"is_wrapper,omitempty"` - IsPairLike bool `json:"is_pair_like,omitempty"` - IsStreamLike bool `json:"is_stream_like,omitempty"` + Type string `json:"@type,omitempty"` + Components []*CoderRef `json:"component_encodings,omitempty"` + IsWrapper bool `json:"is_wrapper,omitempty"` + IsPairLike bool `json:"is_pair_like,omitempty"` + IsStreamLike bool `json:"is_stream_like,omitempty"` + PipelineProtoCoderID string `json:"pipeline_proto_coder_id,omitempty"` } // Exported types are used for translation lookup. @@ -92,7 +93,10 @@ func EncodeCoderRef(c *coder.Coder) (*CoderRef, error) { if err != nil { return nil, err } - return &CoderRef{Type: lengthPrefixType, Components: []*CoderRef{{Type: data}}}, nil + return &CoderRef{ + Type: lengthPrefixType, + Components: []*CoderRef{{Type: data, PipelineProtoCoderID: c.Custom.ID}}, + }, nil case coder.KV: if len(c.Components) != 2 { From 05df70322217db17c03e00eca97b330fb9b1eef1 Mon Sep 17 00:00:00 2001 From: Kyle Weaver Date: Fri, 29 May 2020 14:19:00 -0400 Subject: [PATCH 121/151] [BEAM-10154] Remove stray version number. --- website/www/site/content/en/documentation/dsls/sql/overview.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/www/site/content/en/documentation/dsls/sql/overview.md b/website/www/site/content/en/documentation/dsls/sql/overview.md index fc89197ef884..f91037b3e9da 100644 --- a/website/www/site/content/en/documentation/dsls/sql/overview.md +++ b/website/www/site/content/en/documentation/dsls/sql/overview.md @@ -38,7 +38,7 @@ There are two additional concepts you need to know to use SQL in your pipeline: - [SqlTransform](https://beam.apache.org/releases/javadoc/{{< param release_latest >}}/index.html?org/apache/beam/sdk/extensions/sql/SqlTransform.html): the interface for creating `PTransforms` from SQL queries. - [Row](https://beam.apache.org/releases/javadoc/{{< param release_latest >}}/index.html?org/apache/beam/sdk/values/Row.html): the type of elements that Beam SQL operates on. A `PCollection` plays the role of a table. -{{< param release_latest >}} + ## Walkthrough The [SQL pipeline walkthrough](/documentation/dsls/sql/walkthrough) works through how to use Beam SQL with example code. From 21848c63978892ea2b021529da270ababc6fffb2 Mon Sep 17 00:00:00 2001 From: Sam Rohde Date: Fri, 1 May 2020 14:04:31 -0700 Subject: [PATCH 122/151] Moves apply_WriteToBigQuery to override This will throw an exception in the case that there is a consumer for the WriteToBigQuery that will be replaced. This is because the replacement write outputs a PDone instead of a dict. Change-Id: If782bf1276da3ae739b7d44dad9bea4c12e875f5 --- .../runners/dataflow/dataflow_runner.py | 40 +----- .../runners/dataflow/dataflow_runner_test.py | 61 ++++++++ .../runners/dataflow/ptransform_overrides.py | 136 ++++++++++++++++++ 3 files changed, 200 insertions(+), 37 deletions(-) diff --git a/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py b/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py index 4cddd3318a82..063dd6ec893a 100644 --- a/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py +++ b/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py @@ -26,7 +26,6 @@ from __future__ import division import base64 -import json import logging import os import subprocess @@ -464,6 +463,9 @@ def run_pipeline(self, pipeline, options): # any added PTransforms. pipeline.replace_all(DataflowRunner._PTRANSFORM_OVERRIDES) + from apache_beam.runners.dataflow.ptransform_overrides import WriteToBigQueryPTransformOverride + pipeline.replace_all([WriteToBigQueryPTransformOverride(pipeline, options)]) + if (apiclient._use_fnapi(options) and not apiclient._use_unified_worker(options)): pipeline.replace_all(DataflowRunner._JRH_PTRANSFORM_OVERRIDES) @@ -805,42 +807,6 @@ def run_Flatten(self, transform_node, options): PropertyNames.OUTPUT_NAME: PropertyNames.OUT }]) - def apply_WriteToBigQuery(self, transform, pcoll, options): - # Make sure this is the WriteToBigQuery class that we expected, and that - # users did not specifically request the new BQ sink by passing experiment - # flag. - - # TODO(BEAM-6928): Remove this function for release 2.14.0. - experiments = options.view_as(DebugOptions).experiments or [] - from apache_beam.runners.dataflow.internal import apiclient - use_fnapi = apiclient._use_fnapi(options) - if (not isinstance(transform, beam.io.WriteToBigQuery) or use_fnapi or - 'use_beam_bq_sink' in experiments): - return self.apply_PTransform(transform, pcoll, options) - if transform.schema == beam.io.gcp.bigquery.SCHEMA_AUTODETECT: - raise RuntimeError( - 'Schema auto-detection is not supported on the native sink') - standard_options = options.view_as(StandardOptions) - if standard_options.streaming: - if (transform.write_disposition == - beam.io.BigQueryDisposition.WRITE_TRUNCATE): - raise RuntimeError('Can not use write truncation mode in streaming') - return self.apply_PTransform(transform, pcoll, options) - else: - from apache_beam.io.gcp.bigquery_tools import parse_table_schema_from_json - schema = None - if transform.schema: - schema = parse_table_schema_from_json(json.dumps(transform.schema)) - return pcoll | 'WriteToBigQuery' >> beam.io.Write( - beam.io.BigQuerySink( - transform.table_reference.tableId, - transform.table_reference.datasetId, - transform.table_reference.projectId, - schema, - transform.create_disposition, - transform.write_disposition, - kms_key=transform.kms_key)) - # TODO(srohde): Remove this after internal usages have been removed. def apply_GroupByKey(self, transform, pcoll, options): return transform.expand(pcoll) diff --git a/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py b/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py index 16ea3362661a..4d0f116fbc48 100644 --- a/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py +++ b/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py @@ -752,6 +752,67 @@ def test_gbk_translation(self): self.assertEqual( gbk_step[u'properties']['output_info'], expected_output_info) + def test_write_bigquery_translation(self): + runner = DataflowRunner() + + with beam.Pipeline(runner=runner, + options=PipelineOptions(self.default_properties)) as p: + # pylint: disable=expression-not-assigned + p | beam.Create([1]) | beam.io.WriteToBigQuery('some.table') + + job_dict = json.loads(str(runner.job)) + + expected_step = { + "kind": "ParallelWrite", + "name": "s2", + "properties": { + "create_disposition": "CREATE_IF_NEEDED", + "dataset": "some", + "display_data": [], + "encoding": { + "@type": "kind:windowed_value", + "component_encodings": [{ + "component_encodings": [], + "pipeline_proto_coder_id": "ref_Coder_RowAsDictJsonCoder_4" + }, { + "@type": "kind:global_window" + }], + "is_wrapper": True + }, + "format": "bigquery", + "parallel_input": { + "@type": "OutputReference", + "output_name": "out", + "step_name": "s1" + }, + "table": "table", + "user_name": "WriteToBigQuery/Write/NativeWrite", + "write_disposition": "WRITE_APPEND" + } + } + job_dict = json.loads(str(runner.job)) + write_step = [ + s for s in job_dict[u'steps'] + if s[u'properties'][u'user_name'].startswith('WriteToBigQuery') + ][0] + + # Delete the @type field because in this case it is a hash which may change + # depending on the pickling version. + step_encoding = write_step[u'properties'][u'encoding'] + del step_encoding[u'component_encodings'][0][u'@type'] + self.assertEqual(expected_step, write_step) + + def test_write_bigquery_failed_translation(self): + """Tests that WriteToBigQuery cannot have any consumers if replaced.""" + runner = DataflowRunner() + + with self.assertRaises(ValueError): + with beam.Pipeline(runner=runner, + options=PipelineOptions(self.default_properties)) as p: + # pylint: disable=expression-not-assigned + out = p | beam.Create([1]) | beam.io.WriteToBigQuery('some.table') + out['FailedRows'] | 'MyTransform' >> beam.Map(lambda _: _) + class CustomMergingWindowFn(window.WindowFn): def assign(self, assign_context): diff --git a/sdks/python/apache_beam/runners/dataflow/ptransform_overrides.py b/sdks/python/apache_beam/runners/dataflow/ptransform_overrides.py index 9d6e5d35467f..75b1db0b6341 100644 --- a/sdks/python/apache_beam/runners/dataflow/ptransform_overrides.py +++ b/sdks/python/apache_beam/runners/dataflow/ptransform_overrides.py @@ -21,6 +21,8 @@ from __future__ import absolute_import +from apache_beam.options.pipeline_options import DebugOptions +from apache_beam.options.pipeline_options import StandardOptions from apache_beam.pipeline import PTransformOverride @@ -184,3 +186,137 @@ def expand(self, pbegin): # will choose the incorrect coder for this transform. return Read(ptransform.source).with_output_types( ptransform.source.coder.to_type_hint()) + + +class WriteToBigQueryPTransformOverride(PTransformOverride): + def __init__(self, pipeline, options): + super(WriteToBigQueryPTransformOverride, self).__init__() + self.options = options + self.outputs = [] + + self._check_bq_outputs(pipeline) + + def _check_bq_outputs(self, pipeline): + """Checks that there are no consumers if the transform will be replaced. + + The WriteToBigQuery replacement is the native BigQuerySink which has an + output of a PDone. The original transform, however, returns a dict. The user + may be inadvertantly using the dict output which will have no side-effects + or fail pipeline construction esoterically. This checks the outputs and + gives a user-friendsly error. + """ + # Imported here to avoid circular dependencies. + # pylint: disable=wrong-import-order, wrong-import-position + from apache_beam.pipeline import PipelineVisitor + from apache_beam.io import WriteToBigQuery + + # First, retrieve all the outpts from all the WriteToBigQuery transforms + # that will be replaced. Later, we will use these to make sure no one + # consumes these. + class GetWriteToBqOutputsVisitor(PipelineVisitor): + def __init__(self, matches): + self.matches = matches + self.outputs = set() + + def enter_composite_transform(self, transform_node): + # Only add outputs that are going to be replaced. + if self.matches(transform_node): + self.outputs.update(set(transform_node.outputs.values())) + + outputs_visitor = GetWriteToBqOutputsVisitor(self.matches) + pipeline.visit(outputs_visitor) + + # Finally, verify that there are no consumers to the previously found + # outputs. + class VerifyWriteToBqOutputsVisitor(PipelineVisitor): + def __init__(self, outputs): + self.outputs = outputs + + def enter_composite_transform(self, transform_node): + self.visit_transform(transform_node) + + def visit_transform(self, transform_node): + if [o for o in self.outputs if o in transform_node.inputs]: + raise ValueError( + 'WriteToBigQuery was being replaced with the native ' + 'BigQuerySink, but the transform "{}" has an input which will be ' + 'replaced with a PDone. To fix, please remove all transforms ' + 'that read from any WriteToBigQuery transforms.'.format( + transform_node.full_label)) + + pipeline.visit(VerifyWriteToBqOutputsVisitor(outputs_visitor.outputs)) + + def matches(self, applied_ptransform): + # Imported here to avoid circular dependencies. + # pylint: disable=wrong-import-order, wrong-import-position + from apache_beam import io + from apache_beam.runners.dataflow.internal import apiclient + + transform = applied_ptransform.transform + if (not isinstance(transform, io.WriteToBigQuery) or + getattr(transform, 'override', False)): + return False + + use_fnapi = apiclient._use_fnapi(self.options) + experiments = self.options.view_as(DebugOptions).experiments or [] + if (use_fnapi or 'use_beam_bq_sink' in experiments): + return False + + if transform.schema == io.gcp.bigquery.SCHEMA_AUTODETECT: + raise RuntimeError( + 'Schema auto-detection is not supported on the native sink') + + # The replacement is only valid for Batch. + standard_options = self.options.view_as(StandardOptions) + if standard_options.streaming: + if transform.write_disposition == io.BigQueryDisposition.WRITE_TRUNCATE: + raise RuntimeError('Can not use write truncation mode in streaming') + return False + + self.outputs = list(applied_ptransform.outputs.keys()) + return True + + def get_replacement_transform(self, ptransform): + # Imported here to avoid circular dependencies. + # pylint: disable=wrong-import-order, wrong-import-position + from apache_beam import io + + class WriteToBigQuery(io.WriteToBigQuery): + override = True + + def __init__(self, transform, outputs): + self.transform = transform + self.outputs = outputs + + def __getattr__(self, name): + """Returns the given attribute from the parent. + + This allows this transform to act like a WriteToBigQuery transform + without having to construct a new WriteToBigQuery transform. + """ + return self.transform.__getattribute__(name) + + def expand(self, pcoll): + from apache_beam.io.gcp.bigquery_tools import parse_table_schema_from_json + import json + + schema = None + if self.schema: + schema = parse_table_schema_from_json(json.dumps(self.schema)) + + out = pcoll | io.Write( + io.BigQuerySink( + self.table_reference.tableId, + self.table_reference.datasetId, + self.table_reference.projectId, + schema, + self.create_disposition, + self.write_disposition, + kms_key=self.kms_key)) + + # The WriteToBigQuery can have different outputs depending on if it's + # Batch or Streaming. This retrieved the output keys from the node and + # is replacing them here to be consistent. + return {key: out for key in self.outputs} + + return WriteToBigQuery(ptransform, self.outputs) From 12878fce8a096fd4d4f82d8cc6a2f9343f92b35b Mon Sep 17 00:00:00 2001 From: Brian Hulette Date: Fri, 29 May 2020 11:56:38 -0700 Subject: [PATCH 123/151] [BEAM-10121] Python RowCoder doesn't support nested structs (#11841) * Rename TEST_CASE * Add support for nested structs --- sdks/python/apache_beam/coders/row_coder.py | 2 ++ .../apache_beam/coders/row_coder_test.py | 22 +++++++++++++------ 2 files changed, 17 insertions(+), 7 deletions(-) diff --git a/sdks/python/apache_beam/coders/row_coder.py b/sdks/python/apache_beam/coders/row_coder.py index 03114976c78e..8c41891d0d8a 100644 --- a/sdks/python/apache_beam/coders/row_coder.py +++ b/sdks/python/apache_beam/coders/row_coder.py @@ -103,6 +103,8 @@ def coder_from_type(field_type): elif type_info == "array_type": return IterableCoder( RowCoder.coder_from_type(field_type.array_type.element_type)) + elif type_info == "row_type": + return RowCoder(field_type.row_type.schema) # The Java SDK supports several more types, but the coders are not yet # standard, and are not implemented in Python. diff --git a/sdks/python/apache_beam/coders/row_coder_test.py b/sdks/python/apache_beam/coders/row_coder_test.py index 0ffd98338190..8eb7ee26dcfb 100644 --- a/sdks/python/apache_beam/coders/row_coder_test.py +++ b/sdks/python/apache_beam/coders/row_coder_test.py @@ -49,9 +49,9 @@ class RowCoderTest(unittest.TestCase): - TEST_CASE = Person("Jon Snow", 23, None, ["crow", "wildling"]) - TEST_CASES = [ - TEST_CASE, + JON_SNOW = Person("Jon Snow", 23, None, ["crow", "wildling"]) + PEOPLE = [ + JON_SNOW, Person("Daenerys Targaryen", 25, "Westeros", ["Mother of Dragons"]), Person("Michael Bluth", 30, None, []) ] @@ -60,7 +60,7 @@ def test_create_row_coder_from_named_tuple(self): expected_coder = RowCoder(typing_to_runner_api(Person).row_type.schema) real_coder = coders_registry.get_coder(Person) - for test_case in self.TEST_CASES: + for test_case in self.PEOPLE: self.assertEqual( expected_coder.encode(test_case), real_coder.encode(test_case)) @@ -90,7 +90,7 @@ def test_create_row_coder_from_schema(self): ]) coder = RowCoder(schema) - for test_case in self.TEST_CASES: + for test_case in self.PEOPLE: self.assertEqual(test_case, coder.decode(coder.encode(test_case))) @unittest.skip( @@ -182,9 +182,17 @@ def test_row_coder_in_pipeine(self): with TestPipeline() as p: res = ( p - | beam.Create(self.TEST_CASES) + | beam.Create(self.PEOPLE) | beam.Filter(lambda person: person.name == "Jon Snow")) - assert_that(res, equal_to([self.TEST_CASE])) + assert_that(res, equal_to([self.JON_SNOW])) + + def test_row_coder_nested_struct(self): + Pair = typing.NamedTuple('Pair', [('left', Person), ('right', Person)]) + + value = Pair(self.PEOPLE[0], self.PEOPLE[1]) + coder = RowCoder(typing_to_runner_api(Pair).row_type.schema) + + self.assertEqual(value, coder.decode(coder.encode(value))) if __name__ == "__main__": From b365680881dd82f1ea905eb24ab428372b8b930b Mon Sep 17 00:00:00 2001 From: Sam Rohde Date: Fri, 29 May 2020 12:02:58 -0700 Subject: [PATCH 124/151] Skip test if py=3.8 see BEAM-9754 Change-Id: Ifb2480e9d208d2bcf643c0edaf730fc2479a50fb --- .../apache_beam/runners/dataflow/dataflow_runner_test.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py b/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py index 4d0f116fbc48..36e222d90b19 100644 --- a/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py +++ b/sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py @@ -752,6 +752,9 @@ def test_gbk_translation(self): self.assertEqual( gbk_step[u'properties']['output_info'], expected_output_info) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_write_bigquery_translation(self): runner = DataflowRunner() @@ -802,6 +805,9 @@ def test_write_bigquery_translation(self): del step_encoding[u'component_encodings'][0][u'@type'] self.assertEqual(expected_step, write_step) + @unittest.skipIf( + sys.version_info.minor == 8, + 'Doesn\'t work on Python 3.8, see: BEAM-9754') def test_write_bigquery_failed_translation(self): """Tests that WriteToBigQuery cannot have any consumers if replaced.""" runner = DataflowRunner() From d87fc525e820f78c4546f3f0f5bd5218e3ce323f Mon Sep 17 00:00:00 2001 From: Robert Bradshaw Date: Fri, 29 May 2020 12:24:48 -0700 Subject: [PATCH 125/151] [BEAM-7746] Fix type errors and enable checks for apache_beam.dataframe.* (#11632) --- sdks/python/apache_beam/dataframe/convert.py | 41 +++++++++++++------ sdks/python/apache_beam/dataframe/doctests.py | 5 ++- .../apache_beam/dataframe/frame_base.py | 3 +- .../apache_beam/dataframe/transforms.py | 26 ++++++++++-- sdks/python/mypy.ini | 3 -- 5 files changed, 57 insertions(+), 21 deletions(-) diff --git a/sdks/python/apache_beam/dataframe/convert.py b/sdks/python/apache_beam/dataframe/convert.py index c55fa9efa20c..f0c5824b27f1 100644 --- a/sdks/python/apache_beam/dataframe/convert.py +++ b/sdks/python/apache_beam/dataframe/convert.py @@ -17,12 +17,21 @@ from __future__ import absolute_import import inspect +from typing import TYPE_CHECKING +from typing import Any +from typing import Dict +from typing import Tuple +from typing import Union from apache_beam import pvalue from apache_beam.dataframe import expressions from apache_beam.dataframe import frame_base from apache_beam.dataframe import transforms +if TYPE_CHECKING: + # pylint: disable=ungrouped-imports + import pandas + # TODO: Or should this be called as_dataframe? def to_dataframe( @@ -49,9 +58,9 @@ def to_dataframe( # TODO: Or should this be called from_dataframe? def to_pcollection( - *dataframes, # type: Tuple[frame_base.DeferredFrame] + *dataframes, # type: frame_base.DeferredFrame **kwargs): - # type: (...) -> Union[pvalue.PCollection, Tuple[pvalue.PCollection]] + # type: (...) -> Union[pvalue.PCollection, Tuple[pvalue.PCollection, ...]] """Converts one or more deferred dataframe-like objects back to a PCollection. @@ -67,18 +76,23 @@ def to_pcollection( if label is None: # Attempt to come up with a reasonable, stable label by retrieving the name # of these variables in the calling context. - previous_frame = inspect.currentframe().f_back + current_frame = inspect.currentframe() + if current_frame is None: + label = 'ToDataframe(...)' + + else: + previous_frame = current_frame.f_back - def name(obj): - for key, value in previous_frame.f_locals.items(): - if obj is value: - return key - for key, value in previous_frame.f_globals.items(): - if obj is value: - return key - return '...' + def name(obj): + for key, value in previous_frame.f_locals.items(): + if obj is value: + return key + for key, value in previous_frame.f_globals.items(): + if obj is value: + return key + return '...' - label = 'ToDataframe(%s)' % ', '.join(name(e) for e in dataframes) + label = 'ToDataframe(%s)' % ', '.join(name(e) for e in dataframes) def extract_input(placeholder): if not isinstance(placeholder._reference, pvalue.PCollection): @@ -91,7 +105,8 @@ def extract_input(placeholder): results = {p: extract_input(p) for p in placeholders } | label >> transforms._DataframeExpressionsTransform( - dict((ix, df._expr) for ix, df in enumerate(dataframes))) + dict((ix, df._expr) for ix, df in enumerate( + dataframes))) # type: Dict[Any, pvalue.PCollection] if len(results) == 1 and not always_return_tuple: return results[0] else: diff --git a/sdks/python/apache_beam/dataframe/doctests.py b/sdks/python/apache_beam/dataframe/doctests.py index a81494438037..030a58d101e7 100644 --- a/sdks/python/apache_beam/dataframe/doctests.py +++ b/sdks/python/apache_beam/dataframe/doctests.py @@ -43,6 +43,9 @@ import contextlib import doctest import re +from typing import Any +from typing import Dict +from typing import List import numpy as np import pandas as pd @@ -136,7 +139,7 @@ class _InMemoryResultRecorder(object): """ # Class-level value to survive pickling. - _ALL_RESULTS = {} + _ALL_RESULTS = {} # type: Dict[str, List[Any]] def __init__(self): self._id = id(self) diff --git a/sdks/python/apache_beam/dataframe/frame_base.py b/sdks/python/apache_beam/dataframe/frame_base.py index 275d2b99e275..61b399a8811a 100644 --- a/sdks/python/apache_beam/dataframe/frame_base.py +++ b/sdks/python/apache_beam/dataframe/frame_base.py @@ -17,6 +17,7 @@ from __future__ import absolute_import import inspect +from typing import Dict import pandas as pd @@ -25,7 +26,7 @@ class DeferredFrame(object): - _pandas_type_map = {} + _pandas_type_map = {} # type: Dict[type, type] def __init__(self, expr): self._expr = expr diff --git a/sdks/python/apache_beam/dataframe/transforms.py b/sdks/python/apache_beam/dataframe/transforms.py index 31b62f1405fb..8c8943d73245 100644 --- a/sdks/python/apache_beam/dataframe/transforms.py +++ b/sdks/python/apache_beam/dataframe/transforms.py @@ -16,6 +16,15 @@ from __future__ import absolute_import +from typing import TYPE_CHECKING +from typing import Any +from typing import Dict +from typing import List +from typing import Mapping +from typing import Tuple +from typing import TypeVar +from typing import Union + import pandas as pd import apache_beam as beam @@ -23,6 +32,12 @@ from apache_beam.dataframe import expressions from apache_beam.dataframe import frames # pylint: disable=unused-import +if TYPE_CHECKING: + # pylint: disable=ungrouped-imports + from apache_beam.pvalue import PCollection + +T = TypeVar('T') + class DataframeTransform(transforms.PTransform): """A PTransform for applying function that takes and returns dataframes @@ -82,8 +97,8 @@ def expand(self, inputs): def _apply_deferred_ops( self, - inputs, # type: Dict[PlaceholderExpr, PCollection] - outputs, # type: Dict[Any, Expression] + inputs, # type: Dict[expressions.Expression, PCollection] + outputs, # type: Dict[Any, expressions.Expression] ): # -> Dict[Any, PCollection] """Construct a Beam graph that evaluates a set of expressions on a set of input PCollections. @@ -248,7 +263,12 @@ def _dict_union(dicts): return result -def _flatten(valueish, root=()): +def _flatten( + valueish, # type: Union[T, List[T], Tuple[T], Dict[Any, T]] + root=(), # type: Tuple[Any, ...] + ): + # type: (...) -> Mapping[Tuple[Any, ...], T] + """Given a nested structure of dicts, tuples, and lists, return a flat dictionary where the values are the leafs and the keys are the "paths" to these leaves. diff --git a/sdks/python/mypy.ini b/sdks/python/mypy.ini index 151eebf6b44b..1b24e6cd4ecd 100644 --- a/sdks/python/mypy.ini +++ b/sdks/python/mypy.ini @@ -67,9 +67,6 @@ ignore_errors = true [mypy-apache_beam.coders.*] ignore_errors = true -[mypy-apache_beam.dataframe.*] -ignore_errors = true - [mypy-apache_beam.io.*] ignore_errors = true From a0297da609956b429eaf5f34bea03df89b067022 Mon Sep 17 00:00:00 2001 From: Rajat Mittal Date: Sat, 30 May 2020 11:42:13 -0500 Subject: [PATCH 126/151] Update programming-guide.md --- website/www/site/content/en/documentation/programming-guide.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/www/site/content/en/documentation/programming-guide.md b/website/www/site/content/en/documentation/programming-guide.md index 82bd0534633e..067a3a33f826 100644 --- a/website/www/site/content/en/documentation/programming-guide.md +++ b/website/www/site/content/en/documentation/programming-guide.md @@ -2020,7 +2020,7 @@ Most structured records share some common characteristics: languages: int, long, string, etc. * Often a field type can be marked as optional (sometimes referred to as nullable) or required. -Oten records have a nested structure. A nested structure occurs when a field itself has subfields so the +Often records have a nested structure. A nested structure occurs when a field itself has subfields so the type of the field itself has a schema. Fields that are array or map types is also a common feature of these structured records. From 6598f10df293951f264ef9b94a7cf19ca47b180a Mon Sep 17 00:00:00 2001 From: Rajat Mittal Date: Sat, 30 May 2020 12:34:31 -0500 Subject: [PATCH 127/151] Update programming-guide.md --- .../site/content/en/documentation/programming-guide.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/website/www/site/content/en/documentation/programming-guide.md b/website/www/site/content/en/documentation/programming-guide.md index 067a3a33f826..a9f5f0962341 100644 --- a/website/www/site/content/en/documentation/programming-guide.md +++ b/website/www/site/content/en/documentation/programming-guide.md @@ -2655,7 +2655,7 @@ field as a top-level field. Both top-level and nested fields can be selected. Fo could select only the userId and streetAddress fields as follows {{< highlight java >}} -purchases.apply(Select.fieldNames("userId", shippingAddress.streetAddress")); +purchases.apply(Select.fieldNames("userId", "shippingAddress.streetAddress")); {{< /highlight >}} The resulting `PCollection` will have the following schema @@ -2683,7 +2683,7 @@ The resulting `PCollection` will have the following schema The same is true for wildcard selections. The following {{< highlight java >}} -purchases.apply(Select.fieldNames("userId", shippingAddress.*")); +purchases.apply(Select.fieldNames("userId", "shippingAddress.*")); {{< /highlight >}} Will result in the following schema @@ -2729,7 +2729,7 @@ top-level field in the resulting row. This means that if multiple fields are sel selected field will appear as its own array field. For example {{< highlight java >}} -purchases.apply(Select.fieldNames( "transactions.bank", transactions.purchaseAmount")); +purchases.apply(Select.fieldNames( "transactions.bank", "transactions.purchaseAmount")); {{< /highlight >}} Will result in the following schema @@ -2832,7 +2832,7 @@ The simplest usage of `Group` specifies no aggregations, in which case all input are grouped together into an `ITERABLE` field. For example {{< highlight java >}} -purchases.apply(Group.byFieldNames("userId", shippingAddress.streetAddress")); +purchases.apply(Group.byFieldNames("userId", "shippingAddress.streetAddress")); {{< /highlight >}} The output schema of this is: @@ -2863,7 +2863,7 @@ The names of the key and values fields in the output schema can be controlled us builders, as follows: {{< highlight java >}} -purchases.apply(Group.byFieldNames("userId", shippingAddress.streetAddress") +purchases.apply(Group.byFieldNames("userId", "shippingAddress.streetAddress") .withKeyField("userAndStreet") .withValueField("matchingPurchases")); {{< /highlight >}} From 36892965effd2f7298960a7beab74a78cc6c742b Mon Sep 17 00:00:00 2001 From: David Moravek Date: Mon, 1 Jun 2020 08:30:38 +0200 Subject: [PATCH 128/151] [BEAM-8608] Code review. Fix checkstyle. --- .../java/org/apache/beam/runners/flink/FlinkCapabilities.java | 4 ++-- .../java/org/apache/beam/runners/flink/FlinkCapabilities.java | 4 ++-- .../beam/runners/flink/FlinkBatchTransformTranslators.java | 4 ++-- .../java/build-tools/src/main/resources/beam/suppressions.xml | 1 + 4 files changed, 7 insertions(+), 6 deletions(-) diff --git a/runners/flink/1.10/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java b/runners/flink/1.10/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java index aabdc977e995..1b56c72946a9 100644 --- a/runners/flink/1.10/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java +++ b/runners/flink/1.10/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java @@ -23,12 +23,12 @@ public class FlinkCapabilities { /** * Support for outputting elements in close method of chained drivers. * - *

    {@see } for more + *

    {@see FLINK-14709} for more * details. * * @return True if feature is supported. */ - public static boolean supportsOutputInTearDown() { + public static boolean supportsOutputDuringClosing() { return true; } } diff --git a/runners/flink/1.8/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java b/runners/flink/1.8/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java index 02586e38a262..e1d2a44f9597 100644 --- a/runners/flink/1.8/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java +++ b/runners/flink/1.8/src/main/java/org/apache/beam/runners/flink/FlinkCapabilities.java @@ -23,12 +23,12 @@ public class FlinkCapabilities { /** * Support for outputting elements in close method of chained drivers. * - *

    {@see } for more + *

    {@see FLINK-14709} for more * details. * * @return True if feature is supported. */ - public static boolean supportsOutputInTearDown() { + public static boolean supportsOutputDuringClosing() { return false; } } diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java index 9ddf5049dc01..8e3b623850be 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java @@ -653,11 +653,11 @@ public void translateNode( doFnSchemaInformation, sideInputMapping); - if (FlinkCapabilities.supportsOutputInTearDown()) { + if (FlinkCapabilities.supportsOutputDuringClosing()) { outputDataSet = new FlatMapOperator<>(inputDataSet, typeInformation, doFnWrapper, fullName); } else { - // This can be removed once we drop support for 1.9 and 1.10 versions. + // This can be removed once we drop support for 1.8 and 1.9 versions. outputDataSet = new MapPartitionOperator<>(inputDataSet, typeInformation, doFnWrapper, fullName); } diff --git a/sdks/java/build-tools/src/main/resources/beam/suppressions.xml b/sdks/java/build-tools/src/main/resources/beam/suppressions.xml index fea30fb08615..751466f5a446 100644 --- a/sdks/java/build-tools/src/main/resources/beam/suppressions.xml +++ b/sdks/java/build-tools/src/main/resources/beam/suppressions.xml @@ -95,6 +95,7 @@ + From 1b1408540bb050d17491c71d77f98c403ae70236 Mon Sep 17 00:00:00 2001 From: Kamil Wasilewski Date: Mon, 1 Jun 2020 10:04:58 +0200 Subject: [PATCH 129/151] [BEAM-9421] Better documentation of output results from AnnotateText transform (#11776) --- .../apache_beam/examples/snippets/snippets.py | 91 ++++++++++ .../en/documentation/patterns/ai-platform.md | 159 ++++++++++++++++++ .../en/documentation/patterns/overview.md | 3 + .../section-menu/en/documentation.html | 27 +-- 4 files changed, 267 insertions(+), 13 deletions(-) create mode 100644 website/www/site/content/en/documentation/patterns/ai-platform.md diff --git a/sdks/python/apache_beam/examples/snippets/snippets.py b/sdks/python/apache_beam/examples/snippets/snippets.py index c2ca40117021..29d7577b9270 100644 --- a/sdks/python/apache_beam/examples/snippets/snippets.py +++ b/sdks/python/apache_beam/examples/snippets/snippets.py @@ -37,6 +37,7 @@ import argparse import base64 +import json from builtins import object from builtins import range from decimal import Decimal @@ -51,6 +52,13 @@ from apache_beam.testing.util import equal_to from apache_beam.transforms.core import PTransform +# Protect against environments where Google Cloud Natural Language client is +# not available. +try: + from apache_beam.ml.gcp import naturallanguageml as nlp +except ImportError: + nlp = None + # Quiet some pylint warnings that happen because of the somewhat special # format for the code snippets. # pylint:disable=invalid-name @@ -1520,3 +1528,86 @@ def bigqueryio_deadletter(): # [END BigQueryIODeadLetter] return result + + +def extract_sentiments(response): + # [START nlp_extract_sentiments] + return { + 'sentences': [{ + sentence.text.content: sentence.sentiment.score + } for sentence in response.sentences], + 'document_sentiment': response.document_sentiment.score, + } + # [END nlp_extract_sentiments] + + +def extract_entities(response): + # [START nlp_extract_entities] + return [{ + 'name': entity.name, + 'type': nlp.enums.Entity.Type(entity.type).name, + } for entity in response.entities] + # [END nlp_extract_entities] + + +def analyze_dependency_tree(response): + # [START analyze_dependency_tree] + from collections import defaultdict + adjacency_lists = [] + + index = 0 + for sentence in response.sentences: + adjacency_list = defaultdict(list) + sentence_begin = sentence.text.begin_offset + sentence_end = sentence_begin + len(sentence.text.content) - 1 + + while index < len(response.tokens) and \ + response.tokens[index].text.begin_offset <= sentence_end: + token = response.tokens[index] + head_token_index = token.dependency_edge.head_token_index + head_token_text = response.tokens[head_token_index].text.content + adjacency_list[head_token_text].append(token.text.content) + index += 1 + adjacency_lists.append(adjacency_list) + # [END analyze_dependency_tree] + + return adjacency_lists + + +def nlp_analyze_text(): + # [START nlp_analyze_text] + features = nlp.types.AnnotateTextRequest.Features( + extract_entities=True, + extract_document_sentiment=True, + extract_entity_sentiment=True, + extract_syntax=True, + ) + + with beam.Pipeline() as p: + responses = ( + p + | beam.Create([ + 'My experience so far has been fantastic! ' + 'I\'d really recommend this product.' + ]) + | beam.Map(lambda x: nlp.Document(x, type='PLAIN_TEXT')) + | nlp.AnnotateText(features)) + + _ = ( + responses + | beam.Map(extract_sentiments) + | 'Parse sentiments to JSON' >> beam.Map(json.dumps) + | 'Write sentiments' >> beam.io.WriteToText('sentiments.txt')) + + _ = ( + responses + | beam.Map(extract_entities) + | 'Parse entities to JSON' >> beam.Map(json.dumps) + | 'Write entities' >> beam.io.WriteToText('entities.txt')) + + _ = ( + responses + | beam.Map(analyze_dependency_tree) + | 'Parse adjacency list to JSON' >> beam.Map(json.dumps) + | 'Write adjacency list' >> beam.io.WriteToText('adjancency_list.txt')) + # [END nlp_analyze_text] diff --git a/website/www/site/content/en/documentation/patterns/ai-platform.md b/website/www/site/content/en/documentation/patterns/ai-platform.md new file mode 100644 index 000000000000..d5509679b26b --- /dev/null +++ b/website/www/site/content/en/documentation/patterns/ai-platform.md @@ -0,0 +1,159 @@ +--- +title: "AI Platform integration patterns" +--- + + +# AI Platform integration patterns + +This page describes common patterns in pipelines with Google Cloud AI Platform transforms. + +{{< language-switcher java py >}} + +## Analysing the structure and meaning of text + +This section shows how to use [Google Cloud Natural Language API](https://cloud.google.com/natural-language) to perform text analysis. + +Beam provides a PTransform called [AnnotateText](https://beam.apache.org/releases/pydoc/current/apache_beam.ml.gcp.naturallanguageml.html#apache_beam.ml.gcp.naturallanguageml.AnnotateText). The transform takes a PCollection of type [Document](https://beam.apache.org/releases/pydoc/current/apache_beam.ml.gcp.naturallanguageml.html#apache_beam.ml.gcp.naturallanguageml.Document). Each Document object contains various information about text. This includes the content, whether it is a plain text or HTML, an optional language hint and other settings. +`AnnotateText` produces response object of type `AnnotateTextResponse` returned from the API. `AnnotateTextResponse` is a protobuf message which contains a lot of attributes, some of which are complex structures. + +Here is an example of a pipeline that creates in-memory PCollection of strings, changes each string to Document object and invokes Natural Language API. Then, for each response object, a function is called to extract certain results of analysis. + +{{< highlight py >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" nlp_analyze_text >}} +{{< /highlight >}} + +{{< highlight java >}} +// Java examples will be available on Beam 2.23 release. +{{< /highlight >}} + + +### Extracting sentiments + +This is a part of response object returned from the API. Sentence-level sentiments can be found in `sentences` attribute. `sentences` behaves like a standard Python sequence, therefore all core language features (like iteration or slicing) will work. Overall sentiment can be found in `document_sentiment` attribute. + +``` +sentences { + text { + content: "My experience so far has been fantastic!" + } + sentiment { + magnitude: 0.8999999761581421 + score: 0.8999999761581421 + } +} +sentences { + text { + content: "I\'d really recommend this product." + begin_offset: 41 + } + sentiment { + magnitude: 0.8999999761581421 + score: 0.8999999761581421 + } +} + +...many lines omitted + +document_sentiment { + magnitude: 1.899999976158142 + score: 0.8999999761581421 +} +``` + +The function for extracting information about sentence-level and document-level sentiments is shown in the next code snippet. + +{{< highlight py >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" nlp_extract_sentiments >}} +{{< /highlight >}} + +{{< highlight java >}} +// Java examples will be available on Beam 2.23 release. +{{< /highlight >}} + +The snippet loops over `sentences` and, for each sentence, extracts the sentiment score. + +The output is: + +``` +{"sentences": [{"My experience so far has been fantastic!": 0.8999999761581421}, {"I'd really recommend this product.": 0.8999999761581421}], "document_sentiment": 0.8999999761581421} +``` + +### Extracting entities + +The next function inspects the response for entities and returns the names and the types of those entities. + +{{< highlight py >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" nlp_extract_entities >}} +{{< /highlight >}} + +{{< highlight java >}} +// Java examples will be available on Beam 2.23 release. +{{< /highlight >}} + +Entities can be found in `entities` attribute. Just like before, `entities` is a sequence, that's why list comprehension is a viable choice. The most tricky part is interpreting the types of entities. Natural Language API defines entity types as enum. In a response object, entity types are returned as integers. That's why a user has to instantiate `naturallanguageml.enums.Entity.Type` to access a human-readable name. + +The output is: + +``` +[{"name": "experience", "type": "OTHER"}, {"name": "product", "type": "CONSUMER_GOOD"}] +``` + +### Accessing sentence dependency tree + +The following code loops over the sentences and, for each sentence, builds an adjacency list that represents a dependency tree. For more information on what dependency tree is, see [Morphology & Dependency Trees](https://cloud.google.com/natural-language/docs/morphology#dependency_trees). + +{{< highlight py >}} +{{< code_sample "sdks/python/apache_beam/examples/snippets/snippets.py" analyze_dependency_tree >}} +{{< /highlight >}} + +{{< highlight java >}} +// Java examples will be available on Beam 2.23 release. +{{< /highlight >}} + +The output is below. For better readability, indexes are replaced by text which they refer to: + +``` +[ + { + "experience": [ + "My" + ], + "been": [ + "experience", + "far", + "has", + "been", + "fantastic", + "!" + ], + "far": [ + "so" + ] + }, + { + "recommend": [ + "I", + "'d", + "really", + "recommend", + "product", + "." + ], + "product": [ + "this" + ] + } +] +``` diff --git a/website/www/site/content/en/documentation/patterns/overview.md b/website/www/site/content/en/documentation/patterns/overview.md index 561c8f00187c..225ef8429d2b 100644 --- a/website/www/site/content/en/documentation/patterns/overview.md +++ b/website/www/site/content/en/documentation/patterns/overview.md @@ -38,6 +38,9 @@ Pipeline patterns demonstrate common Beam use cases. Pipeline patterns are based **BigQuery patterns** - Patterns for BigQueryIO * [Google BigQuery patterns](/documentation/patterns/bigqueryio/#google-bigquery-patterns) +**AI Platform integration patterns** - Patterns for using Google Cloud AI Platform transforms +* [Analysing the structure and meaning of text](/documentation/patterns/ai-platform/#analysing-the-structure-and-meaning-of-text) + ## Contributing a pattern To contribute a new pipeline pattern, create an issue with the [`pipeline-patterns` label](https://issues.apache.org/jira/browse/BEAM-7449?jql=labels%20%3D%20pipeline-patterns) and add details to the issue description. See [Get started contributing](/contribute/) for more information. diff --git a/website/www/site/layouts/partials/section-menu/en/documentation.html b/website/www/site/layouts/partials/section-menu/en/documentation.html index 68e541072281..b83774d34f06 100644 --- a/website/www/site/layouts/partials/section-menu/en/documentation.html +++ b/website/www/site/layouts/partials/section-menu/en/documentation.html @@ -174,17 +174,17 @@

  • @@ -212,7 +212,7 @@
    • - +
  • Java @@ -224,18 +224,18 @@
  • @@ -273,7 +273,7 @@
    • - + @@ -289,6 +289,7 @@
  • Custom I/O
  • Custom windows
  • BigQueryIO
    • +
  • AI Platform
    • From e9837feb508db7c2a2c1b2d1c8da1135caca3ecb Mon Sep 17 00:00:00 2001 From: Kamil Wasilewski Date: Mon, 1 Jun 2020 11:56:02 +0200 Subject: [PATCH 130/151] [BEAM-9421] Website section that describes getting predictions using AI Platform Prediciton (#11075) --- .../en/documentation/patterns/ai-platform.md | 57 +++++++++++++++++++ .../en/documentation/patterns/overview.md | 1 + 2 files changed, 58 insertions(+) diff --git a/website/www/site/content/en/documentation/patterns/ai-platform.md b/website/www/site/content/en/documentation/patterns/ai-platform.md index d5509679b26b..905f89584447 100644 --- a/website/www/site/content/en/documentation/patterns/ai-platform.md +++ b/website/www/site/content/en/documentation/patterns/ai-platform.md @@ -157,3 +157,60 @@ The output is below. For better readability, indexes are replaced by text which } ] ``` + +## Getting predictions + +This section shows how to use [Google Cloud AI Platform Prediction](https://cloud.google.com/ai-platform/prediction/docs/overview) to make predictions about new data from a cloud-hosted machine learning model. + +[tfx_bsl](https://github.com/tensorflow/tfx-bsl) is a library with a Beam PTransform called `RunInference`. `RunInference` is able to perform an inference that can use an external service endpoint for receiving data. When using a service endpoint, the transform takes a PCollection of type `tf.train.Example` and, for every batch of elements, sends a request to AI Platform Prediction. The size of a batch is automatically computed. For more details on how Beam finds the best batch size, refer to a docstring for [BatchElements](https://beam.apache.org/releases/pydoc/current/apache_beam.transforms.util.html?highlight=batchelements#apache_beam.transforms.util.BatchElements). Currently, the transform does not support using `tf.train.SequenceExample` as input, but the work is in progress. + + The transform produces a PCollection of type `PredictionLog`, which contains predictions. + +Before getting started, deploy a TensorFlow model to AI Platform Prediction. The cloud service manages the infrastructure needed to handle prediction requests in both efficient and scalable way. Do note that only TensorFlow models are supported by the transform. For more information, see [Exporting a SavedModel for prediction](https://cloud.google.com/ai-platform/prediction/docs/exporting-savedmodel-for-prediction). + +Once a machine learning model is deployed, prepare a list of instances to get predictions for. To send binary data, make sure that the name of an input ends in `_bytes`. This will base64-encode data before sending a request. + +### Example +Here is an example of a pipeline that reads input instances from the file, converts JSON objects to `tf.train.Example` objects and sends data to AI Platform Prediction. The content of a file can look like this: + +``` +{"input": "the quick brown"} +{"input": "la bruja le"} +``` + +The example creates `tf.train.BytesList` instances, thus it expects byte-like strings as input. However, other data types, like `tf.train.FloatList` and `tf.train.Int64List`, are also supported by the transform. + +Here is the code: + +{{< highlight py >}} +import json + +import apache_beam as beam + +import tensorflow as tf +from tfx_bsl.beam.run_inference import RunInference +from tfx_bsl.proto import model_spec_pb2 + +def convert_json_to_tf_example(json_obj): + samples = json.loads(json_obj) + for name, text in samples.items(): + value = tf.train.Feature(bytes_list=tf.train.BytesList( + value=[text.encode('utf-8')])) + feature = {name: value} + return tf.train.Example(features=tf.train.Features(feature=feature)) + +with beam.Pipeline() as p: + _ = (p + | beam.io.ReadFromText('gs://my-bucket/samples.json') + | beam.Map(convert_json_to_tf_example) + | RunInference( + model_spec_pb2.InferenceEndpoint( + model_endpoint_spec=model_spec_pb2.AIPlatformPredictionModelSpec( + project_id='my-project-id', + model_name='my-model-name', + version_name='my-model-version')))) +{{< /highlight >}} + +{{< highlight java >}} +// Getting predictions is not yet available for Java. [BEAM-9501] +{{< /highlight >}} diff --git a/website/www/site/content/en/documentation/patterns/overview.md b/website/www/site/content/en/documentation/patterns/overview.md index 225ef8429d2b..3bc682d2ab97 100644 --- a/website/www/site/content/en/documentation/patterns/overview.md +++ b/website/www/site/content/en/documentation/patterns/overview.md @@ -40,6 +40,7 @@ Pipeline patterns demonstrate common Beam use cases. Pipeline patterns are based **AI Platform integration patterns** - Patterns for using Google Cloud AI Platform transforms * [Analysing the structure and meaning of text](/documentation/patterns/ai-platform/#analysing-the-structure-and-meaning-of-text) +* [Getting predictions](/documentation/patterns/ai-platform/#getting-predictions) ## Contributing a pattern From a1031c8151ec117742a3d496309327d5c1a0b78e Mon Sep 17 00:00:00 2001 From: Piotr Szuberski Date: Mon, 1 Jun 2020 17:47:14 +0200 Subject: [PATCH 131/151] [BEAM-10162, BEAM-10163] Change PubSubIO and BigQueryIO job names; update README.md --- .test-infra/jenkins/README.md | 3 +++ .../jenkins/job_PerformanceTests_BigQueryIO_Python.groovy | 8 ++++---- .../jenkins/job_PerformanceTests_PubsubIO_Python.groovy | 4 ++-- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/.test-infra/jenkins/README.md b/.test-infra/jenkins/README.md index 18aaa40cf4fd..67c9e446f392 100644 --- a/.test-infra/jenkins/README.md +++ b/.test-infra/jenkins/README.md @@ -94,6 +94,8 @@ Beam Jenkins overview page: [link](https://builds.apache.org/view/A-D/view/Beam/ |------|------|-------------------|-------------| | beam_PerformanceTests_Analysis | [cron](https://builds.apache.org/job/beam_PerformanceTests_Analysis/) | `Run Performance Tests Analysis` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_Analysis/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_Analysis) | | beam_PerformanceTests_AvroIOIT | [cron](https://builds.apache.org/job/beam_PerformanceTests_AvroIOIT/), [hdfs_cron](https://builds.apache.org/job/beam_PerformanceTests_AvroIOIT_HDFS/) | `Run Java AvroIO Performance Test` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_AvroIOIT/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_AvroIOIT) [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_AvroIOIT_HDFS/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_AvroIOIT_HDFS) | +| beam_PerformanceTests_BiqQueryIO_Read_Python | [cron](https://builds.apache.org/job/beam_PerformanceTests_BiqQueryIO_Read_Python/) | `Run BigQueryIO Read Performance Test Python` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_BiqQueryIO_Read_Python/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_BiqQueryIO_Read_Python) | +| beam_PerformanceTests_BiqQueryIO_Write_Python_Batch | [cron](https://builds.apache.org/job/beam_PerformanceTests_BiqQueryIO_Write_Python_Batch/) | `Run BigQueryIO Write Performance Test Python Batch` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_BiqQueryIO_Write_Python_Batch/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_BiqQueryIO_Write_Python_Batch) | | beam_PerformanceTests_Compressed_TextIOIT | [cron](https://builds.apache.org/job/beam_PerformanceTests_Compressed_TextIOIT/), [hdfs_cron](https://builds.apache.org/job/beam_PerformanceTests_Compressed_TextIOIT_HDFS/) | `Run Java CompressedTextIO Performance Test` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_Compressed_TextIOIT/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_Compressed_TextIOIT) [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_Compressed_TextIOIT_HDFS/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_Compressed_TextIOIT_HDFS) | | beam_PerformanceTests_HadoopFormat | [cron](https://builds.apache.org/job/beam_PerformanceTests_HadoopFormat/) | `Run Java HadoopFormatIO Performance Test` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_HadoopFormat/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_HadoopFormat) | | beam_PerformanceTests_JDBC | [cron](https://builds.apache.org/job/beam_PerformanceTests_JDBC/) | `Run Java JdbcIO Performance Test` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_JDBC/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_JDBC) | @@ -101,6 +103,7 @@ Beam Jenkins overview page: [link](https://builds.apache.org/view/A-D/view/Beam/ | beam_PerformanceTests_ManyFiles_TextIOIT | [cron](https://builds.apache.org/job/beam_PerformanceTests_ManyFiles_TextIOIT/), [hdfs_cron](https://builds.apache.org/job/beam_PerformanceTests_ManyFiles_TextIOIT_HDFS/) | `Run Java ManyFilesTextIO Performance Test` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_ManyFiles_TextIOIT/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_ManyFiles_TextIOIT) [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_ManyFiles_TextIOIT_HDFS/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_ManyFiles_TextIOIT_HDFS) | | beam_PerformanceTests_MongoDBIOIT | [cron](https://builds.apache.org/job/beam_PerformanceTests_MongoDBIO_IT/) | `Run Java MongoDBIO Performance Test` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_MongoDBIO_IT/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_MongoDBIO_IT) | | beam_PerformanceTests_ParquetIOIT | [cron](https://builds.apache.org/job/beam_PerformanceTests_ParquetIOIT/), [hdfs_cron](https://builds.apache.org/job/beam_PerformanceTests_ParquetIOIT_HDFS/) | `Run Java ParquetIO Performance Test` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_ParquetIOIT/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_ParquetIOIT) [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_ParquetIOIT_HDFS/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_ParquetIOIT_HDFS) | +| beam_PerformanceTests_PubsubIOIT_Python_Streaming | [cron](https://builds.apache.org/job/beam_PerformanceTests_PubsubIOIT_Python_Streaming/) | `Run PubsubIO Performance Test Python` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_PubsubIOIT_Python_Streaming/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_PubsubIOIT_Python_Streaming) | | beam_PerformanceTests_Spark | [cron](https://builds.apache.org/job/beam_PerformanceTests_Spark/) | `Run Spark Performance Test` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_Spark/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_Spark) | | beam_PerformanceTests_TFRecordIOIT | [cron](https://builds.apache.org/job/beam_PerformanceTests_TFRecordIOIT/) | `Run Java TFRecordIO Performance Test` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_TFRecordIOIT/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_TFRecordIOIT) | | beam_PerformanceTests_TextIOIT | [cron](https://builds.apache.org/job/beam_PerformanceTests_TextIOIT/), [hdfs_cron](https://builds.apache.org/job/beam_PerformanceTests_TextIOIT_HDFS/) | `Run Java TextIO Performance Test` | [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_TextIOIT/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_TextIOIT) [![Build Status](https://builds.apache.org/job/beam_PerformanceTests_TextIOIT_HDFS/badge/icon)](https://builds.apache.org/job/beam_PerformanceTests_TextIOIT_HDFS) | diff --git a/.test-infra/jenkins/job_PerformanceTests_BigQueryIO_Python.groovy b/.test-infra/jenkins/job_PerformanceTests_BigQueryIO_Python.groovy index c8fcc6825344..56dc0c894192 100644 --- a/.test-infra/jenkins/job_PerformanceTests_BigQueryIO_Python.groovy +++ b/.test-infra/jenkins/job_PerformanceTests_BigQueryIO_Python.groovy @@ -82,7 +82,7 @@ def executeJob = { scope, testConfig -> } PhraseTriggeringPostCommitBuilder.postCommitJob( - 'beam_BiqQueryIO_Read_Performance_Test_Python', + 'beam_PerformanceTests_BiqQueryIO_Read_Python', 'Run BigQueryIO Read Performance Test Python', 'BigQueryIO Read Performance Test Python', this @@ -90,12 +90,12 @@ PhraseTriggeringPostCommitBuilder.postCommitJob( executeJob(delegate, bqio_read_test) } -CronJobBuilder.cronJob('beam_BiqQueryIO_Read_Performance_Test_Python', 'H 15 * * *', this) { +CronJobBuilder.cronJob('beam_PerformanceTests_BiqQueryIO_Read_Python', 'H 15 * * *', this) { executeJob(delegate, bqio_read_test) } PhraseTriggeringPostCommitBuilder.postCommitJob( - 'beam_BiqQueryIO_Write_Performance_Test_Python_Batch', + 'beam_PerformanceTests_BiqQueryIO_Write_Python_Batch', 'Run BigQueryIO Write Performance Test Python Batch', 'BigQueryIO Write Performance Test Python Batch', this @@ -103,6 +103,6 @@ PhraseTriggeringPostCommitBuilder.postCommitJob( executeJob(delegate, bqio_write_test) } -CronJobBuilder.cronJob('beam_BiqQueryIO_Write_Performance_Test_Python_Batch', 'H 15 * * *', this) { +CronJobBuilder.cronJob('beam_PerformanceTests_BiqQueryIO_Write_Python_Batch', 'H 15 * * *', this) { executeJob(delegate, bqio_write_test) } diff --git a/.test-infra/jenkins/job_PerformanceTests_PubsubIO_Python.groovy b/.test-infra/jenkins/job_PerformanceTests_PubsubIO_Python.groovy index 96361c007920..f08e53ec765d 100644 --- a/.test-infra/jenkins/job_PerformanceTests_PubsubIO_Python.groovy +++ b/.test-infra/jenkins/job_PerformanceTests_PubsubIO_Python.groovy @@ -62,7 +62,7 @@ def executeJob = { scope, testConfig -> } PhraseTriggeringPostCommitBuilder.postCommitJob( - 'beam_PubsubIO_Performance_Test_Python', + 'beam_PerformanceTests_PubsubIOIT_Python_Streaming', 'Run PubsubIO Performance Test Python', 'PubsubIO Performance Test Python', this @@ -70,6 +70,6 @@ PhraseTriggeringPostCommitBuilder.postCommitJob( executeJob(delegate, psio_test) } -CronJobBuilder.cronJob('beam_PubsubIO_Performance_Test_Python', 'H 15 * * *', this) { +CronJobBuilder.cronJob('beam_PerformanceTests_PubsubIOIT_Python_Streaming', 'H 15 * * *', this) { executeJob(delegate, psio_test) } From 194f981cca8de97a9380b39eec67a98b13bddc71 Mon Sep 17 00:00:00 2001 From: Robert Burke Date: Mon, 1 Jun 2020 08:49:37 -0700 Subject: [PATCH 132/151] [BEAM-10051] Scope instruction data. (#11864) * [BEAM-10051] Scope instruction data. --- .../pkg/beam/core/runtime/harness/datamgr.go | 128 ++++++++++++++---- .../beam/core/runtime/harness/datamgr_test.go | 73 ++++++++-- 2 files changed, 167 insertions(+), 34 deletions(-) diff --git a/sdks/go/pkg/beam/core/runtime/harness/datamgr.go b/sdks/go/pkg/beam/core/runtime/harness/datamgr.go index 3fb9401dd017..08e62f2233c3 100644 --- a/sdks/go/pkg/beam/core/runtime/harness/datamgr.go +++ b/sdks/go/pkg/beam/core/runtime/harness/datamgr.go @@ -38,8 +38,6 @@ type ScopedDataManager struct { mgr *DataChannelManager instID instructionID - // TODO(herohde) 7/20/2018: capture and force close open reads/writes. However, - // we would need the underlying Close to be idempotent or a separate method. closed bool mu sync.Mutex } @@ -82,9 +80,10 @@ func (s *ScopedDataManager) open(ctx context.Context, port exec.Port) (*DataChan // Close prevents new IO for this instruction. func (s *ScopedDataManager) Close() error { s.mu.Lock() + defer s.mu.Unlock() s.closed = true + s.mgr.closeInstruction(s.instID) s.mgr = nil - s.mu.Unlock() return nil } @@ -125,6 +124,14 @@ func (m *DataChannelManager) Open(ctx context.Context, port exec.Port) (*DataCha return ch, nil } +func (m *DataChannelManager) closeInstruction(instID instructionID) { + m.mu.Lock() + defer m.mu.Unlock() + for _, ch := range m.ports { + ch.removeInstruction(instID) + } +} + // clientID identifies a client of a connected channel. type clientID struct { ptransformID string @@ -148,8 +155,13 @@ type DataChannel struct { id string client dataClient - writers map[clientID]*dataWriter - readers map[clientID]*dataReader + writers map[instructionID]map[string]*dataWriter + readers map[instructionID]map[string]*dataReader + + // recently terminated instructions + endedInstructions map[instructionID]struct{} + rmQueue []instructionID + // readErr indicates a client.Recv error and is used to prevent new readers. readErr error @@ -178,11 +190,12 @@ func newDataChannel(ctx context.Context, port exec.Port) (*DataChannel, error) { func makeDataChannel(ctx context.Context, id string, client dataClient, cancelFn context.CancelFunc) *DataChannel { ret := &DataChannel{ - id: id, - client: client, - writers: make(map[clientID]*dataWriter), - readers: make(map[clientID]*dataReader), - cancelFn: cancelFn, + id: id, + client: client, + writers: make(map[instructionID]map[string]*dataWriter), + readers: make(map[instructionID]map[string]*dataReader), + endedInstructions: make(map[instructionID]struct{}), + cancelFn: cancelFn, } go ret.read(ctx) @@ -227,14 +240,16 @@ func (c *DataChannel) read(ctx context.Context) { // close the r.buf channels twice, or send on a closed channel. // Any other approach is racy, and may cause one of the above // panics. - for _, r := range c.readers { - log.Errorf(ctx, "DataChannel.read %v reader %v closing due to error on channel", c.id, r.id) - if !r.completed { - r.completed = true - r.err = err - close(r.buf) + for _, m := range c.readers { + for _, r := range m { + log.Errorf(ctx, "DataChannel.read %v reader %v closing due to error on channel", c.id, r.id) + if !r.completed { + r.completed = true + r.err = err + close(r.buf) + } + delete(cache, r.id) } - delete(cache, r.id) } c.terminateStreamOnError(err) c.mu.Unlock() @@ -319,31 +334,95 @@ func (r *errReader) Close() error { // makeReader creates a dataReader. It expects to be called while c.mu is held. func (c *DataChannel) makeReader(ctx context.Context, id clientID) *dataReader { - if r, ok := c.readers[id]; ok { + var m map[string]*dataReader + var ok bool + if m, ok = c.readers[id.instID]; !ok { + m = make(map[string]*dataReader) + c.readers[id.instID] = m + } + + if r, ok := m[id.ptransformID]; ok { return r } r := &dataReader{id: id, buf: make(chan []byte, bufElements), done: make(chan bool, 1), channel: c} - c.readers[id] = r + + // Just in case initial data for an instruction arrives *after* an instructon has ended. + // eg. it was blocked by another reader being slow, or the other instruction failed. + // So we provide a pre-completed reader, and do not cache it, as there's no further cleanup for it. + if _, ok := c.endedInstructions[id.instID]; ok { + r.completed = true + close(r.buf) + r.err = io.EOF // In case of any actual data readers, so they terminate without error. + return r + } + + m[id.ptransformID] = r return r } func (c *DataChannel) removeReader(id clientID) { c.mu.Lock() - delete(c.readers, id) + if m, ok := c.readers[id.instID]; ok { + delete(m, id.ptransformID) + } c.mu.Unlock() } +const endedInstructionCap = 32 + +// removeInstruction closes all readers and writers registered for the instruction +// and deletes this instruction from the channel's reader and writer maps. +func (c *DataChannel) removeInstruction(instID instructionID) { + c.mu.Lock() + + // We don't want to leak memory, so cap the endedInstructions list. + if len(c.rmQueue) >= endedInstructionCap { + toRemove := c.rmQueue[0] + c.rmQueue = c.rmQueue[1:] + delete(c.endedInstructions, toRemove) + } + c.endedInstructions[instID] = struct{}{} + c.rmQueue = append(c.rmQueue, instID) + + rs := c.readers[instID] + ws := c.writers[instID] + + // Prevent other users while we iterate. + delete(c.readers, instID) + delete(c.writers, instID) + c.mu.Unlock() + + // Close grabs the channel lock, so this must be outside the critical section. + for _, r := range rs { + r.Close() + } + for _, w := range ws { + w.Close() + } +} + func (c *DataChannel) makeWriter(ctx context.Context, id clientID) *dataWriter { c.mu.Lock() defer c.mu.Unlock() - if w, ok := c.writers[id]; ok { + var m map[string]*dataWriter + var ok bool + if m, ok = c.writers[id.instID]; !ok { + m = make(map[string]*dataWriter) + c.writers[id.instID] = m + } + + if w, ok := m[id.ptransformID]; ok { return w } + // We don't check for ended instructions for writers, as writers + // can only be created if an instruction is in scope, and aren't + // runner or user directed. + w := &dataWriter{ch: c, id: id} - c.writers[id] = w + m[id.ptransformID] = w return w } @@ -389,9 +468,6 @@ func (r *dataReader) Read(buf []byte) (int, error) { return n, nil } -// TODO(herohde) 7/20/2018: we should probably either not be tracking writers or -// make dataWriter threadsafe. Either case is likely a corruption generator. - type dataWriter struct { buf []byte @@ -431,7 +507,7 @@ func (w *dataWriter) Close() error { // Now acquire the locks since we're sending. w.ch.mu.Lock() defer w.ch.mu.Unlock() - delete(w.ch.writers, w.id) + delete(w.ch.writers[w.id.instID], w.id.ptransformID) msg := &fnpb.Elements{ Data: []*fnpb.Elements_Data{ { diff --git a/sdks/go/pkg/beam/core/runtime/harness/datamgr_test.go b/sdks/go/pkg/beam/core/runtime/harness/datamgr_test.go index 5601c3823fd4..31172e8a04b0 100644 --- a/sdks/go/pkg/beam/core/runtime/harness/datamgr_test.go +++ b/sdks/go/pkg/beam/core/runtime/harness/datamgr_test.go @@ -22,6 +22,7 @@ import ( "io/ioutil" "log" "strings" + "sync" "testing" "time" @@ -38,9 +39,14 @@ type fakeDataClient struct { calls int err error skipFirstError bool + + blocked sync.Mutex // Prevent data from being read by the gotourtinr. } func (f *fakeDataClient) Recv() (*fnpb.Elements, error) { + f.blocked.Lock() + defer f.blocked.Unlock() + f.calls++ data := []byte{1, 2, 3, 4, 1, 2, 3, 4} elemData := fnpb.Elements_Data{ @@ -130,6 +136,12 @@ func TestDataChannelTerminate_dataReader(t *testing.T) { // Set the 2nd Recv call to have an error. client.err = expectedError }, + }, { + name: "onInstructionEnd", + expectedError: io.EOF, + caseFn: func(t *testing.T, r io.ReadCloser, client *fakeDataClient, c *DataChannel) { + c.removeInstruction("inst_ref") + }, }, } for _, test := range tests { @@ -170,7 +182,46 @@ func TestDataChannelTerminate_dataReader(t *testing.T) { } }) } +} + +func TestDataChannelRemoveInstruction_dataAfterClose(t *testing.T) { + done := make(chan bool, 1) + client := &fakeDataClient{t: t, done: done} + client.blocked.Lock() + + ctx, cancelFn := context.WithCancel(context.Background()) + c := makeDataChannel(ctx, "id", client, cancelFn) + c.removeInstruction("inst_ref") + + client.blocked.Unlock() + + r := c.OpenRead(ctx, "ptr", "inst_ref") + + dr := r.(*dataReader) + if !dr.completed || dr.err != io.EOF { + t.Errorf("Expected a closed reader, but was still open: completed: %v, err: %v", dr.completed, dr.err) + } + n, err := r.Read(make([]byte, 4)) + if err != io.EOF { + t.Errorf("Unexpected error from read: %v, read %d bytes.", err, n) + } +} + +func TestDataChannelRemoveInstruction_limitInstructionCap(t *testing.T) { + done := make(chan bool, 1) + client := &fakeDataClient{t: t, done: done} + ctx, cancelFn := context.WithCancel(context.Background()) + c := makeDataChannel(ctx, "id", client, cancelFn) + + for i := 0; i < endedInstructionCap+10; i++ { + instID := instructionID(fmt.Sprintf("inst_ref%d", i)) + c.OpenRead(ctx, "ptr", instID) + c.removeInstruction(instID) + } + if got, want := len(c.endedInstructions), endedInstructionCap; got != want { + t.Errorf("unexpected len(endedInstructions) got %v, want %v,", got, want) + } } func TestDataChannelTerminate_Writes(t *testing.T) { @@ -179,27 +230,34 @@ func TestDataChannelTerminate_Writes(t *testing.T) { expectedError := fmt.Errorf("EXPECTED ERROR") + instID := instructionID("inst_ref") tests := []struct { name string - caseFn func(t *testing.T, w io.WriteCloser, client *fakeDataClient) error + caseFn func(t *testing.T, w io.WriteCloser, client *fakeDataClient, c *DataChannel) error }{ { name: "onClose_Flush", - caseFn: func(t *testing.T, w io.WriteCloser, client *fakeDataClient) error { + caseFn: func(t *testing.T, w io.WriteCloser, client *fakeDataClient, c *DataChannel) error { return w.Close() }, }, { name: "onClose_Sentinel", - caseFn: func(t *testing.T, w io.WriteCloser, client *fakeDataClient) error { + caseFn: func(t *testing.T, w io.WriteCloser, client *fakeDataClient, c *DataChannel) error { client.skipFirstError = true return w.Close() }, }, { name: "onWrite", - caseFn: func(t *testing.T, w io.WriteCloser, client *fakeDataClient) error { + caseFn: func(t *testing.T, w io.WriteCloser, client *fakeDataClient, c *DataChannel) error { _, err := w.Write([]byte{'d', 'o', 'n', 'e'}) return err }, + }, { + name: "onInstructionEnd", + caseFn: func(t *testing.T, w io.WriteCloser, client *fakeDataClient, c *DataChannel) error { + c.removeInstruction(instID) + return expectedError + }, }, } for _, test := range tests { @@ -209,7 +267,7 @@ func TestDataChannelTerminate_Writes(t *testing.T) { ctx, cancelFn := context.WithCancel(context.Background()) c := makeDataChannel(ctx, "id", client, cancelFn) - w := c.OpenWrite(ctx, "ptr", "inst_ref") + w := c.OpenWrite(ctx, "ptr", instID) msg := []byte{'b', 'y', 't', 'e'} var bufSize int @@ -221,7 +279,7 @@ func TestDataChannelTerminate_Writes(t *testing.T) { } } - err := test.caseFn(t, w, client) + err := test.caseFn(t, w, client, c) if got, want := err, expectedError; err == nil || !strings.Contains(err.Error(), expectedError.Error()) { t.Errorf("Unexpected error: got %v, want %v", got, want) @@ -229,7 +287,7 @@ func TestDataChannelTerminate_Writes(t *testing.T) { // Verify that new readers return the same error for writes after stream termination. // TODO(lostluck) 2019.11.26: use the the go 1.13 errors package to check this rather // than a strings.Contains check once testing infrastructure can use go 1.13. - if n, err := c.OpenWrite(ctx, "ptr", "inst_ref").Write(msg); err != nil && !strings.Contains(err.Error(), expectedError.Error()) { + if n, err := c.OpenWrite(ctx, "ptr", instID).Write(msg); err != nil && !strings.Contains(err.Error(), expectedError.Error()) { t.Errorf("Unexpected error from write: got %v, want, %v read %d bytes.", err, expectedError, n) } select { @@ -240,5 +298,4 @@ func TestDataChannelTerminate_Writes(t *testing.T) { } }) } - } From e0217d1efa00d37ef66db040d06da610ea9e8c99 Mon Sep 17 00:00:00 2001 From: Damon Douglas Date: Mon, 1 Jun 2020 08:50:22 -0700 Subject: [PATCH 133/151] [BEAM-9679] Add Combine/Simple Function to Core Transforms (#11866) --- .../Combine/Simple Function/cmd/main.go | 43 +++ .../Combine/Simple Function/go.mod | 27 ++ .../Combine/Simple Function/go.sum | 310 ++++++++++++++++++ .../Combine/Simple Function/pkg/task/task.go | 26 ++ .../Combine/Simple Function/task-info.yaml | 35 ++ .../Simple Function/task-remote-info.yaml | 2 + .../Combine/Simple Function/task.md | 43 +++ .../Combine/Simple Function/test/task_test.go | 44 +++ .../Core Transforms/Combine/lesson-info.yaml | 21 ++ .../Combine/lesson-remote-info.yaml | 3 + .../Flatten/lesson-remote-info.yaml | 2 +- .../go/Core Transforms/section-info.yaml | 1 + learning/katas/go/course-remote-info.yaml | 2 +- 13 files changed, 557 insertions(+), 2 deletions(-) create mode 100644 learning/katas/go/Core Transforms/Combine/Simple Function/cmd/main.go create mode 100644 learning/katas/go/Core Transforms/Combine/Simple Function/go.mod create mode 100644 learning/katas/go/Core Transforms/Combine/Simple Function/go.sum create mode 100644 learning/katas/go/Core Transforms/Combine/Simple Function/pkg/task/task.go create mode 100644 learning/katas/go/Core Transforms/Combine/Simple Function/task-info.yaml create mode 100644 learning/katas/go/Core Transforms/Combine/Simple Function/task-remote-info.yaml create mode 100644 learning/katas/go/Core Transforms/Combine/Simple Function/task.md create mode 100644 learning/katas/go/Core Transforms/Combine/Simple Function/test/task_test.go create mode 100644 learning/katas/go/Core Transforms/Combine/lesson-info.yaml create mode 100644 learning/katas/go/Core Transforms/Combine/lesson-remote-info.yaml diff --git a/learning/katas/go/Core Transforms/Combine/Simple Function/cmd/main.go b/learning/katas/go/Core Transforms/Combine/Simple Function/cmd/main.go new file mode 100644 index 000000000000..eb413972a7b2 --- /dev/null +++ b/learning/katas/go/Core Transforms/Combine/Simple Function/cmd/main.go @@ -0,0 +1,43 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package main + +import ( + "context" + "github.com/apache/beam/sdks/go/pkg/beam" + "github.com/apache/beam/sdks/go/pkg/beam/log" + "github.com/apache/beam/sdks/go/pkg/beam/x/beamx" + "github.com/apache/beam/sdks/go/pkg/beam/x/debug" + "simple_function/pkg/task" +) + +func main() { + ctx := context.Background() + + p, s := beam.NewPipelineWithRoot() + + input := beam.Create(s, 10, 30, 50, 70, 90) + + output := task.ApplyTransform(s, input) + + debug.Print(s, output) + + err := beamx.Run(ctx, p) + + if err != nil { + log.Exitf(context.Background(), "Failed to execute job: %v", err) + } +} diff --git a/learning/katas/go/Core Transforms/Combine/Simple Function/go.mod b/learning/katas/go/Core Transforms/Combine/Simple Function/go.mod new file mode 100644 index 000000000000..f8cdb28c1a10 --- /dev/null +++ b/learning/katas/go/Core Transforms/Combine/Simple Function/go.mod @@ -0,0 +1,27 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +module simple_function + +go 1.14 + +require ( + github.com/apache/beam v2.21.0+incompatible + github.com/golang/protobuf v1.4.2 // indirect + github.com/google/go-cmp v0.4.1 // indirect + github.com/googleapis/gax-go v1.0.3 // indirect + google.golang.org/api v0.25.0 // indirect + google.golang.org/grpc v1.29.1 // indirect +) diff --git a/learning/katas/go/Core Transforms/Combine/Simple Function/go.sum b/learning/katas/go/Core Transforms/Combine/Simple Function/go.sum new file mode 100644 index 000000000000..00ef75933562 --- /dev/null +++ b/learning/katas/go/Core 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h1:X/FiERA/W4tHapMX5mGpAtMSVEeEUOyHaw9vFzvIQ3k= +rsc.io/binaryregexp v0.2.0/go.mod h1:qTv7/COck+e2FymRvadv62gMdZztPaShugOCi3I+8D8= +rsc.io/quote/v3 v3.1.0/go.mod h1:yEA65RcK8LyAZtP9Kv3t0HmxON59tX3rD+tICJqUlj0= +rsc.io/sampler v1.3.0/go.mod h1:T1hPZKmBbMNahiBKFy5HrXp6adAjACjK9JXDnKaTXpA= diff --git a/learning/katas/go/Core Transforms/Combine/Simple Function/pkg/task/task.go b/learning/katas/go/Core Transforms/Combine/Simple Function/pkg/task/task.go new file mode 100644 index 000000000000..afe5abbfa164 --- /dev/null +++ b/learning/katas/go/Core Transforms/Combine/Simple Function/pkg/task/task.go @@ -0,0 +1,26 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package task + +import ( + "github.com/apache/beam/sdks/go/pkg/beam" +) + +func ApplyTransform(s beam.Scope, input beam.PCollection) beam.PCollection { + return beam.Combine(s, func(sum, elem int) int { + return sum + elem + }, input) +} diff --git a/learning/katas/go/Core Transforms/Combine/Simple Function/task-info.yaml b/learning/katas/go/Core Transforms/Combine/Simple Function/task-info.yaml new file mode 100644 index 000000000000..1b3b8e5fd670 --- /dev/null +++ b/learning/katas/go/Core Transforms/Combine/Simple Function/task-info.yaml @@ -0,0 +1,35 @@ +# +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. +# + +type: edu +files: +- name: test/task_test.go + visible: false +- name: cmd/main.go + visible: true +- name: go.mod + visible: false +- name: pkg/task/task.go + visible: true + placeholders: + - offset: 949 + length: 72 + placeholder_text: TODO() +- name: go.sum + visible: false diff --git a/learning/katas/go/Core Transforms/Combine/Simple Function/task-remote-info.yaml b/learning/katas/go/Core Transforms/Combine/Simple Function/task-remote-info.yaml new file mode 100644 index 000000000000..098280d38d3c --- /dev/null +++ b/learning/katas/go/Core Transforms/Combine/Simple Function/task-remote-info.yaml @@ -0,0 +1,2 @@ +id: 1347871 +update_date: Mon, 01 Jun 2020 14:35:52 UTC diff --git a/learning/katas/go/Core Transforms/Combine/Simple Function/task.md b/learning/katas/go/Core Transforms/Combine/Simple Function/task.md new file mode 100644 index 000000000000..ea0cc8c52760 --- /dev/null +++ b/learning/katas/go/Core Transforms/Combine/Simple Function/task.md @@ -0,0 +1,43 @@ + + +# Combine - Simple Function + +Combine is a Beam transform for combining collections of elements or values in your data. When you +apply a Combine transform, you must provide the function that contains the logic for combining the +elements or values. The combining function should be commutative and associative, as the function +is not necessarily invoked exactly once on all values with a given key. Because the input data +(including the value collection) may be distributed across multiple workers, the combining function +might be called multiple times to perform partial combining on subsets of the value collection. + +Simple combine operations, such as sums, can usually be implemented as a simple function. + +**Kata:** Implement the summation of numbers using +[beam.Combine](https://godoc.org/github.com/apache/beam/sdks/go/pkg/beam#Combine). + +
    + Implement a combine function compatible with the + + beam.Combine method that performs the summation of a PCollection<int>. +
    + +
    + Refer to the Beam Programming Guide + + "Simple combinations using simple functions" section for more information. +
    diff --git a/learning/katas/go/Core Transforms/Combine/Simple Function/test/task_test.go b/learning/katas/go/Core Transforms/Combine/Simple Function/test/task_test.go new file mode 100644 index 000000000000..2b0ff0c3bdda --- /dev/null +++ b/learning/katas/go/Core Transforms/Combine/Simple Function/test/task_test.go @@ -0,0 +1,44 @@ +// Licensed to the Apache Software Foundation (ASF) under one or more +// contributor license agreements. See the NOTICE file distributed with +// this work for additional information regarding copyright ownership. +// The ASF licenses this file to You under the Apache License, Version 2.0 +// (the "License"); you may not use this file except in compliance with +// the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package test + +import ( + "github.com/apache/beam/sdks/go/pkg/beam" + "github.com/apache/beam/sdks/go/pkg/beam/testing/passert" + "github.com/apache/beam/sdks/go/pkg/beam/testing/ptest" + "simple_function/pkg/task" + "testing" +) + +func TestApplyTransform(t *testing.T) { + p, s := beam.NewPipelineWithRoot() + tests := []struct { + input beam.PCollection + want []interface{} + }{ + { + input: beam.Create(s, 10, 30, 50, 70, 90), + want: []interface{}{250}, + }, + } + for _, tt := range tests { + got := task.ApplyTransform(s, tt.input) + passert.Equals(s, got, tt.want...) + if err := ptest.Run(p); err != nil { + t.Error(err) + } + } +} diff --git a/learning/katas/go/Core Transforms/Combine/lesson-info.yaml b/learning/katas/go/Core Transforms/Combine/lesson-info.yaml new file mode 100644 index 000000000000..698fc8cc2265 --- /dev/null +++ b/learning/katas/go/Core Transforms/Combine/lesson-info.yaml @@ -0,0 +1,21 @@ +# +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. +# + +content: +- Simple Function diff --git a/learning/katas/go/Core Transforms/Combine/lesson-remote-info.yaml b/learning/katas/go/Core Transforms/Combine/lesson-remote-info.yaml new file mode 100644 index 000000000000..3747bd27cf4d --- /dev/null +++ b/learning/katas/go/Core Transforms/Combine/lesson-remote-info.yaml @@ -0,0 +1,3 @@ +id: 362667 +update_date: Mon, 01 Jun 2020 14:35:48 UTC +unit: 347283 diff --git a/learning/katas/go/Core Transforms/Flatten/lesson-remote-info.yaml b/learning/katas/go/Core Transforms/Flatten/lesson-remote-info.yaml index f7ed569d95fa..a6b715b74dda 100644 --- a/learning/katas/go/Core Transforms/Flatten/lesson-remote-info.yaml +++ b/learning/katas/go/Core Transforms/Flatten/lesson-remote-info.yaml @@ -1,3 +1,3 @@ id: 361641 -update_date: Thu, 28 May 2020 22:33:26 UTC +update_date: Mon, 01 Jun 2020 14:35:55 UTC unit: 346170 diff --git a/learning/katas/go/Core Transforms/section-info.yaml b/learning/katas/go/Core Transforms/section-info.yaml index d228f9a30d38..8bde6d156bf8 100644 --- a/learning/katas/go/Core Transforms/section-info.yaml +++ b/learning/katas/go/Core Transforms/section-info.yaml @@ -21,4 +21,5 @@ content: - Map - GroupByKey - CoGroupByKey +- Combine - Flatten diff --git a/learning/katas/go/course-remote-info.yaml b/learning/katas/go/course-remote-info.yaml index b875f83687ed..ce7ead8cfc33 100644 --- a/learning/katas/go/course-remote-info.yaml +++ b/learning/katas/go/course-remote-info.yaml @@ -1,2 +1,2 @@ id: 70387 -update_date: Wed, 20 May 2020 06:16:18 UTC +update_date: Thu, 28 May 2020 22:34:30 UTC From 280e243dfe135ab7ed434022be78c22cdc46be8d Mon Sep 17 00:00:00 2001 From: Chamikara Jayalath Date: Mon, 1 Jun 2020 11:58:21 -0700 Subject: [PATCH 134/151] Updates CHANGES.md to include new I/Os for Beam 2.22.0. (#11879) * Update CHANGES.md * Update CHANGES.md --- CHANGES.md | 30 +++++++++++++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) diff --git a/CHANGES.md b/CHANGES.md index d3e706515ae5..0168d04216c6 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -47,7 +47,7 @@ * Fixed X (Java/Python) ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). --> -# [2.22.0] - Unreleased +# [2.23.0] - Unreleased ## Highlights @@ -61,6 +61,34 @@ ## New Features / Improvements +* X feature added (Java/Python) ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). + +## Breaking Changes + +* X behavior was changed ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). + +## Deprecations + +* X behavior is deprecated and will be removed in X versions ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). + +## Known Issues + +* Fixed X (Java/Python) ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). + +# [2.22.0] - Unreleased + +## Highlights + +* New highly anticipated feature X added to Python SDK ([BEAM-X](https://issues.apache.org/jira/browse/BEAM-X)). +* New highly anticipated feature Y added to Java SDK ([BEAM-Y](https://issues.apache.org/jira/browse/BEAM-Y)). + +## I/Os + +* Basic Kafka read/write support for DataflowRunner (Python) ([BEAM-8019](https://issues.apache.org/jira/browse/BEAM-8019)). +* Sources and sinks for Google Healthcare APIs (Java)([BEAM-9468](https://issues.apache.org/jira/browse/BEAM-9468)). + +## New Features / Improvements + * `--workerCacheMB` flag is supported in Dataflow streaming pipeline ([BEAM-9964](https://issues.apache.org/jira/browse/BEAM-9964)) * `--direct_num_workers=0` is supported for FnApi runner. It will set the number of threads/subprocesses to number of cores of the machine executing the pipeline ([BEAM-9443](https://issues.apache.org/jira/browse/BEAM-9443)). * Python SDK now has experimental support for SqlTransform ([BEAM-8603](https://issues.apache.org/jira/browse/BEAM-8603)). From 89fc35b87d5dc074d25d60a97bb96d71e04be283 Mon Sep 17 00:00:00 2001 From: Lukasz Cwik Date: Mon, 1 Jun 2020 15:16:19 -0700 Subject: [PATCH 135/151] [BEAM-10158] Use a shared unbounded thread pool within Beam Python. (#11867) * [BEAM-10158] Use a shared unbounded thread pool within Beam Python. * fixup! Fix lint errors * fixup! Address PR comments * fixup! fix lint --- .../runners/portability/artifact_service_test.py | 6 +++--- .../runners/portability/expansion_service_test.py | 4 ++-- .../portability/fn_api_runner/fn_runner.py | 4 ++-- .../portability/fn_api_runner/worker_handlers.py | 14 +++++++++----- .../runners/portability/local_job_service.py | 7 ++++--- .../runners/portability/portable_stager_test.py | 4 ++-- .../apache_beam/runners/worker/data_plane_test.py | 4 ++-- .../runners/worker/log_handler_test.py | 4 ++-- .../apache_beam/runners/worker/sdk_worker.py | 9 +++++---- .../apache_beam/runners/worker/sdk_worker_test.py | 4 ++-- .../runners/worker/worker_pool_main.py | 5 +++-- .../runners/worker/worker_status_test.py | 4 ++-- .../apache_beam/utils/thread_pool_executor.py | 13 +++++++++++++ .../utils/thread_pool_executor_test.py | 15 +++++++++++++++ 14 files changed, 66 insertions(+), 31 deletions(-) diff --git a/sdks/python/apache_beam/runners/portability/artifact_service_test.py b/sdks/python/apache_beam/runners/portability/artifact_service_test.py index 14993dcaabb1..6a6768ad6e0f 100644 --- a/sdks/python/apache_beam/runners/portability/artifact_service_test.py +++ b/sdks/python/apache_beam/runners/portability/artifact_service_test.py @@ -44,7 +44,7 @@ from apache_beam.portability.api import beam_runner_api_pb2 from apache_beam.runners.portability import artifact_service from apache_beam.utils import proto_utils -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor class AbstractArtifactServiceTest(unittest.TestCase): @@ -83,7 +83,7 @@ def test_basic(self): self._run_staging(self._service, self._service) def test_with_grpc(self): - server = grpc.server(UnboundedThreadPoolExecutor()) + server = grpc.server(thread_pool_executor.shared_unbounded_instance()) try: beam_artifact_api_pb2_grpc.add_LegacyArtifactStagingServiceServicer_to_server( self._service, server) @@ -225,7 +225,7 @@ def check(index): self._service, tokens[session(index)], name(index))) # pylint: disable=range-builtin-not-iterating - pool = UnboundedThreadPoolExecutor() + pool = thread_pool_executor.shared_unbounded_instance() sessions = set(pool.map(put, range(100))) tokens = dict(pool.map(commit, sessions)) # List forces materialization. diff --git a/sdks/python/apache_beam/runners/portability/expansion_service_test.py b/sdks/python/apache_beam/runners/portability/expansion_service_test.py index 6a7ab579c54d..a1b531db13be 100644 --- a/sdks/python/apache_beam/runners/portability/expansion_service_test.py +++ b/sdks/python/apache_beam/runners/portability/expansion_service_test.py @@ -36,7 +36,7 @@ from apache_beam.runners.portability import expansion_service from apache_beam.transforms import ptransform from apache_beam.transforms.external import ImplicitSchemaPayloadBuilder -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor # This script provides an expansion service and example ptransforms for running # external transform test cases. See external_test.py for details. @@ -296,7 +296,7 @@ def main(unused_argv): '-p', '--port', type=int, help='port on which to serve the job api') options = parser.parse_args() global server - server = grpc.server(UnboundedThreadPoolExecutor()) + server = grpc.server(thread_pool_executor.shared_unbounded_instance()) beam_expansion_api_pb2_grpc.add_ExpansionServiceServicer_to_server( expansion_service.ExpansionServiceServicer( PipelineOptions( diff --git a/sdks/python/apache_beam/runners/portability/fn_api_runner/fn_runner.py b/sdks/python/apache_beam/runners/portability/fn_api_runner/fn_runner.py index 58db57c9157f..c2147ce44182 100644 --- a/sdks/python/apache_beam/runners/portability/fn_api_runner/fn_runner.py +++ b/sdks/python/apache_beam/runners/portability/fn_api_runner/fn_runner.py @@ -64,7 +64,7 @@ from apache_beam.transforms import environments from apache_beam.utils import profiler from apache_beam.utils import proto_utils -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor if TYPE_CHECKING: from apache_beam.pipeline import Pipeline @@ -925,7 +925,7 @@ def execute(part_map_input_timers): expected_output_timers, dry_run) - with UnboundedThreadPoolExecutor() as executor: + with thread_pool_executor.shared_unbounded_instance() as executor: for result, split_result in executor.map(execute, zip(part_inputs, # pylint: disable=zip-builtin-not-iterating timer_inputs)): split_result_list += split_result diff --git a/sdks/python/apache_beam/runners/portability/fn_api_runner/worker_handlers.py b/sdks/python/apache_beam/runners/portability/fn_api_runner/worker_handlers.py index 6808b47823b4..6a276565f70b 100644 --- a/sdks/python/apache_beam/runners/portability/fn_api_runner/worker_handlers.py +++ b/sdks/python/apache_beam/runners/portability/fn_api_runner/worker_handlers.py @@ -63,7 +63,7 @@ from apache_beam.runners.worker.sdk_worker import _Future from apache_beam.runners.worker.statecache import StateCache from apache_beam.utils import proto_utils -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor # State caching is enabled in the fn_api_runner for testing, except for one # test which runs without state caching (FnApiRunnerTestWithDisabledCaching). @@ -441,7 +441,8 @@ def __init__(self, # type: (...) -> None self.state = state self.provision_info = provision_info - self.control_server = grpc.server(UnboundedThreadPoolExecutor()) + self.control_server = grpc.server( + thread_pool_executor.shared_unbounded_instance()) self.control_port = self.control_server.add_insecure_port('[::]:0') self.control_address = 'localhost:%s' % self.control_port @@ -451,11 +452,13 @@ def __init__(self, no_max_message_sizes = [("grpc.max_receive_message_length", -1), ("grpc.max_send_message_length", -1)] self.data_server = grpc.server( - UnboundedThreadPoolExecutor(), options=no_max_message_sizes) + thread_pool_executor.shared_unbounded_instance(), + options=no_max_message_sizes) self.data_port = self.data_server.add_insecure_port('[::]:0') self.state_server = grpc.server( - UnboundedThreadPoolExecutor(), options=no_max_message_sizes) + thread_pool_executor.shared_unbounded_instance(), + options=no_max_message_sizes) self.state_port = self.state_server.add_insecure_port('[::]:0') self.control_handler = BeamFnControlServicer(worker_manager) @@ -493,7 +496,8 @@ def __init__(self, GrpcStateServicer(state), self.state_server) self.logging_server = grpc.server( - UnboundedThreadPoolExecutor(), options=no_max_message_sizes) + thread_pool_executor.shared_unbounded_instance(), + options=no_max_message_sizes) self.logging_port = self.logging_server.add_insecure_port('[::]:0') beam_fn_api_pb2_grpc.add_BeamFnLoggingServicer_to_server( BasicLoggingService(), self.logging_server) diff --git a/sdks/python/apache_beam/runners/portability/local_job_service.py b/sdks/python/apache_beam/runners/portability/local_job_service.py index b99bfeb183ab..dcdc4425fcba 100644 --- a/sdks/python/apache_beam/runners/portability/local_job_service.py +++ b/sdks/python/apache_beam/runners/portability/local_job_service.py @@ -48,7 +48,7 @@ from apache_beam.runners.portability import artifact_service from apache_beam.runners.portability.fn_api_runner import fn_runner from apache_beam.runners.portability.fn_api_runner import worker_handlers -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor if TYPE_CHECKING: from google.protobuf import struct_pb2 # pylint: disable=ungrouped-imports @@ -141,7 +141,7 @@ def get_service_address(self): return 'localhost' def start_grpc_server(self, port=0): - self._server = grpc.server(UnboundedThreadPoolExecutor()) + self._server = grpc.server(thread_pool_executor.shared_unbounded_instance()) port = self._server.add_insecure_port( '%s:%d' % (self.get_bind_address(), port)) beam_job_api_pb2_grpc.add_JobServiceServicer_to_server(self, self._server) @@ -194,7 +194,8 @@ def __init__( self._worker_id = worker_id def run(self): - logging_server = grpc.server(UnboundedThreadPoolExecutor()) + logging_server = grpc.server( + thread_pool_executor.shared_unbounded_instance()) logging_port = logging_server.add_insecure_port('[::]:0') logging_server.start() logging_servicer = BeamFnLoggingServicer() diff --git a/sdks/python/apache_beam/runners/portability/portable_stager_test.py b/sdks/python/apache_beam/runners/portability/portable_stager_test.py index c7a8e1cfc674..44fb4986649e 100644 --- a/sdks/python/apache_beam/runners/portability/portable_stager_test.py +++ b/sdks/python/apache_beam/runners/portability/portable_stager_test.py @@ -36,7 +36,7 @@ from apache_beam.portability.api import beam_artifact_api_pb2 from apache_beam.portability.api import beam_artifact_api_pb2_grpc from apache_beam.runners.portability import portable_stager -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor class PortableStagerTest(unittest.TestCase): @@ -58,7 +58,7 @@ def _stage_files(self, files): describing the name of the artifacts in local temp folder and desired name in staging location. """ - server = grpc.server(UnboundedThreadPoolExecutor()) + server = grpc.server(thread_pool_executor.shared_unbounded_instance()) staging_service = TestLocalFileSystemLegacyArtifactStagingServiceServicer( self._remote_dir) beam_artifact_api_pb2_grpc.add_LegacyArtifactStagingServiceServicer_to_server( diff --git a/sdks/python/apache_beam/runners/worker/data_plane_test.py b/sdks/python/apache_beam/runners/worker/data_plane_test.py index a4922a55a3ca..4f09df350ba9 100644 --- a/sdks/python/apache_beam/runners/worker/data_plane_test.py +++ b/sdks/python/apache_beam/runners/worker/data_plane_test.py @@ -34,7 +34,7 @@ from apache_beam.runners.worker import data_plane from apache_beam.runners.worker.worker_id_interceptor import WorkerIdInterceptor from apache_beam.testing.util import timeout -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor class DataChannelTest(unittest.TestCase): @@ -56,7 +56,7 @@ def _grpc_data_channel_test(self, time_based_flush=False): data_channel_service = \ data_servicer.get_conn_by_worker_id(worker_id) - server = grpc.server(UnboundedThreadPoolExecutor()) + server = grpc.server(thread_pool_executor.shared_unbounded_instance()) beam_fn_api_pb2_grpc.add_BeamFnDataServicer_to_server(data_servicer, server) test_port = server.add_insecure_port('[::]:0') server.start() diff --git a/sdks/python/apache_beam/runners/worker/log_handler_test.py b/sdks/python/apache_beam/runners/worker/log_handler_test.py index 4d9291d99e68..80fe543e3335 100644 --- a/sdks/python/apache_beam/runners/worker/log_handler_test.py +++ b/sdks/python/apache_beam/runners/worker/log_handler_test.py @@ -32,7 +32,7 @@ from apache_beam.runners.common import NameContext from apache_beam.runners.worker import log_handler from apache_beam.runners.worker import statesampler -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor _LOGGER = logging.getLogger(__name__) @@ -52,7 +52,7 @@ def Logging(self, request_iterator, context): class FnApiLogRecordHandlerTest(unittest.TestCase): def setUp(self): self.test_logging_service = BeamFnLoggingServicer() - self.server = grpc.server(UnboundedThreadPoolExecutor()) + self.server = grpc.server(thread_pool_executor.shared_unbounded_instance()) beam_fn_api_pb2_grpc.add_BeamFnLoggingServicer_to_server( self.test_logging_service, self.server) self.test_port = self.server.add_insecure_port('[::]:0') diff --git a/sdks/python/apache_beam/runners/worker/sdk_worker.py b/sdks/python/apache_beam/runners/worker/sdk_worker.py index eed471d0bc7e..a58dd2facf21 100644 --- a/sdks/python/apache_beam/runners/worker/sdk_worker.py +++ b/sdks/python/apache_beam/runners/worker/sdk_worker.py @@ -64,7 +64,7 @@ from apache_beam.runners.worker.statecache import StateCache from apache_beam.runners.worker.worker_id_interceptor import WorkerIdInterceptor from apache_beam.runners.worker.worker_status import FnApiWorkerStatusHandler -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor if TYPE_CHECKING: from apache_beam.portability.api import endpoints_pb2 @@ -186,10 +186,11 @@ def __init__(self, else: self._status_handler = None - # TODO(BEAM-8998) use common UnboundedThreadPoolExecutor to process bundle - # progress once dataflow runner's excessive progress polling is removed. + # TODO(BEAM-8998) use common + # thread_pool_executor.shared_unbounded_instance() to process bundle + # progress once dataflow runner's excessive progress polling is removed. self._report_progress_executor = futures.ThreadPoolExecutor(max_workers=1) - self._worker_thread_pool = UnboundedThreadPoolExecutor() + self._worker_thread_pool = thread_pool_executor.shared_unbounded_instance() self._responses = queue.Queue( ) # type: queue.Queue[beam_fn_api_pb2.InstructionResponse] _LOGGER.info('Initializing SDKHarness with unbounded number of workers.') diff --git a/sdks/python/apache_beam/runners/worker/sdk_worker_test.py b/sdks/python/apache_beam/runners/worker/sdk_worker_test.py index a7c3bc394674..d9b808354f20 100644 --- a/sdks/python/apache_beam/runners/worker/sdk_worker_test.py +++ b/sdks/python/apache_beam/runners/worker/sdk_worker_test.py @@ -38,7 +38,7 @@ from apache_beam.portability.api import metrics_pb2 from apache_beam.runners.worker import sdk_worker from apache_beam.runners.worker import statecache -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor _LOGGER = logging.getLogger(__name__) @@ -102,7 +102,7 @@ def _check_fn_registration_multi_request(self, *args): test_controller = BeamFnControlServicer(requests) - server = grpc.server(UnboundedThreadPoolExecutor()) + server = grpc.server(thread_pool_executor.shared_unbounded_instance()) beam_fn_api_pb2_grpc.add_BeamFnControlServicer_to_server( test_controller, server) test_port = server.add_insecure_port("[::]:0") diff --git a/sdks/python/apache_beam/runners/worker/worker_pool_main.py b/sdks/python/apache_beam/runners/worker/worker_pool_main.py index b18961a391bd..f4a4728c373d 100644 --- a/sdks/python/apache_beam/runners/worker/worker_pool_main.py +++ b/sdks/python/apache_beam/runners/worker/worker_pool_main.py @@ -48,7 +48,7 @@ from apache_beam.portability.api import beam_fn_api_pb2 from apache_beam.portability.api import beam_fn_api_pb2_grpc from apache_beam.runners.worker import sdk_worker -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor _LOGGER = logging.getLogger(__name__) @@ -78,7 +78,8 @@ def start( container_executable=None # type: Optional[str] ): # type: (...) -> Tuple[str, grpc.Server] - worker_server = grpc.server(UnboundedThreadPoolExecutor()) + worker_server = grpc.server( + thread_pool_executor.shared_unbounded_instance()) worker_address = 'localhost:%s' % worker_server.add_insecure_port( '[::]:%s' % port) worker_pool = cls( diff --git a/sdks/python/apache_beam/runners/worker/worker_status_test.py b/sdks/python/apache_beam/runners/worker/worker_status_test.py index 0872de4787b0..fea0d7371288 100644 --- a/sdks/python/apache_beam/runners/worker/worker_status_test.py +++ b/sdks/python/apache_beam/runners/worker/worker_status_test.py @@ -28,7 +28,7 @@ from apache_beam.portability.api import beam_fn_api_pb2_grpc from apache_beam.runners.worker.worker_status import FnApiWorkerStatusHandler from apache_beam.testing.util import timeout -from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor +from apache_beam.utils import thread_pool_executor class BeamFnStatusServicer(beam_fn_api_pb2_grpc.BeamFnWorkerStatusServicer): @@ -52,7 +52,7 @@ class FnApiWorkerStatusHandlerTest(unittest.TestCase): def setUp(self): self.num_request = 3 self.test_status_service = BeamFnStatusServicer(self.num_request) - self.server = grpc.server(UnboundedThreadPoolExecutor()) + self.server = grpc.server(thread_pool_executor.shared_unbounded_instance()) beam_fn_api_pb2_grpc.add_BeamFnWorkerStatusServicer_to_server( self.test_status_service, self.server) self.test_port = self.server.add_insecure_port('[::]:0') diff --git a/sdks/python/apache_beam/utils/thread_pool_executor.py b/sdks/python/apache_beam/utils/thread_pool_executor.py index a5443ed5c4b2..c111b9aeff36 100644 --- a/sdks/python/apache_beam/utils/thread_pool_executor.py +++ b/sdks/python/apache_beam/utils/thread_pool_executor.py @@ -134,3 +134,16 @@ def shutdown(self, wait=True): if wait: for worker in self._workers: worker.join() + + +class _SharedUnboundedThreadPoolExecutor(UnboundedThreadPoolExecutor): + def shutdown(self, wait=True): + # Prevent shutting down the shared thread pool + pass + + +_SHARED_UNBOUNDED_THREAD_POOL_EXECUTOR = _SharedUnboundedThreadPoolExecutor() + + +def shared_unbounded_instance(): + return _SHARED_UNBOUNDED_THREAD_POOL_EXECUTOR diff --git a/sdks/python/apache_beam/utils/thread_pool_executor_test.py b/sdks/python/apache_beam/utils/thread_pool_executor_test.py index d9bbae41440b..b9251cad00a1 100644 --- a/sdks/python/apache_beam/utils/thread_pool_executor_test.py +++ b/sdks/python/apache_beam/utils/thread_pool_executor_test.py @@ -30,6 +30,7 @@ # patches unittest.TestCase to be python3 compatible import future.tests.base # pylint: disable=unused-import +from apache_beam.utils import thread_pool_executor from apache_beam.utils.thread_pool_executor import UnboundedThreadPoolExecutor @@ -111,6 +112,20 @@ def test_map(self): with self._lock: self.assertEqual(5, len(self._worker_idents)) + def test_shared_shutdown_does_nothing(self): + thread_pool_executor.shared_unbounded_instance().shutdown() + + futures = [] + with thread_pool_executor.shared_unbounded_instance() as executor: + for _ in range(0, 5): + futures.append(executor.submit(self.append_and_sleep, 0.01)) + + for future in futures: + future.result(timeout=10) + + with self._lock: + self.assertEqual(5, len(self._worker_idents)) + if __name__ == '__main__': unittest.main() From 54dccb0143035158685a31920e268f8ff87033e3 Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Mon, 1 Jun 2020 17:06:42 -0700 Subject: [PATCH 136/151] wip --- .../sdk/transforms/SerializableFunction.java | 3 +- .../beam/sdk/io/gcp/healthcare/FhirIO.java | 108 ++++++++++++------ .../gcp/healthcare/HealthcareApiClient.java | 5 +- .../healthcare/HttpHealthcareApiClient.java | 17 ++- .../sdk/io/gcp/healthcare/FhirIOTestUtil.java | 69 ++++++++++- .../sdk/io/gcp/healthcare/FhirIOWriteIT.java | 51 ++++----- 6 files changed, 183 insertions(+), 70 deletions(-) diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java index 3dbe893eef4e..cbd7d01d80fe 100644 --- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java +++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java @@ -18,6 +18,7 @@ package org.apache.beam.sdk.transforms; import com.fasterxml.jackson.core.JsonProcessingException; +import java.io.IOException; import java.io.Serializable; /** @@ -36,5 +37,5 @@ public interface SerializableFunction extends ProcessFunction, Serializable { /** Returns the result of invoking this function on the given input. */ @Override - OutputT apply(InputT input) throws JsonProcessingException; + OutputT apply(InputT input) throws IOException; } diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java index 8b6cae2cc336..19ece0754b9d 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java @@ -1419,7 +1419,8 @@ public void initClient() throws IOException { } @ProcessElement - public void create(ProcessContext context) { + public void create(ProcessContext context) + throws IOException { T input = context.element(); String body = formatBodyFunction.apply(input); String type = typeFunction.apply(input); @@ -1447,7 +1448,7 @@ public void create(ProcessContext context) { * @param fhirStore the fhir store * @return the update resources */ - public static UpdateResources update(ValueProvider fhirStore){ + public static UpdateResources update(ValueProvider fhirStore){ return new UpdateResources(fhirStore); } @@ -1458,19 +1459,28 @@ public static UpdateResources update(ValueProvider fhirStore){ * @param fhirStore the fhir store * @return the update resources */ - public static UpdateResources update(String fhirStore){ + public static UpdateResources update(String fhirStore){ return new UpdateResources(fhirStore); } /** * {@link PTransform} for Updating FHIR resources resources. * + * This transform assumes the input {@link PCollection} contains + * {@link KV} of resource name, value pairs and by default will call {@code .toString} to extract + * string values. + * However, the user can override this behavior by specifying a {@link SerializableFunction} with + * custom logic to extract the resource name and body from the {@link KV} in + * {@link UpdateResources#withResourceNameFunction(SerializableFunction)} and + * {@link UpdateResources#withFormatBodyFunction(SerializableFunction)} + * *

    https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/update */ - public static class UpdateResources extends PTransform, Write.Result> { - private final String fhirStore; + public static class UpdateResources extends PTransform, Write.Result> { + private final ValueProvider fhirStore; private SerializableFunction formatBodyFunction; private SerializableFunction resourceNameFunction; + private SerializableFunction etagFunction; public static final TupleTag UPDATE_RESULTS = new TupleTag() {}; private static final Logger LOG = LoggerFactory.getLogger(UpdateResources.class); @@ -1480,9 +1490,17 @@ public static class UpdateResources extends PTransform, Write. * @param fhirStore the fhir store */ UpdateResources(ValueProvider fhirStore) { - this.fhirStore = fhirStore.get(); + this.fhirStore = fhirStore; } + /** + * Instantiates a new Update resources. + * + * @param fhirStore the fhir store + */ + UpdateResources(String fhirStore) { + this.fhirStore = StaticValueProvider.of(fhirStore); + } /** * Add a {@link SerializableFunction} to extract a resource name from the input element. * @@ -1506,16 +1524,19 @@ public UpdateResources withFormatBodyFunction( this.formatBodyFunction = formatBodyFunction; return this; } - /** - * Instantiates a new Update resources. + * With ETag function update resources. * - * @param fhirStore the fhir store + * @param etagFunction ETag function + * @return the update resources */ - UpdateResources(String fhirStore) { - this.fhirStore = fhirStore; + public UpdateResources withETagFunction( + SerializableFunction etagFunction) { + this.etagFunction = etagFunction; + return this; } + @Override public FhirIO.Write.Result expand(PCollection input) { checkArgument( @@ -1527,7 +1548,7 @@ public FhirIO.Write.Result expand(PCollection input) { return Write.Result.in( input.getPipeline(), input - .apply(ParDo.of(new UpdateFn(fhirStore, formatBodyFunction, resourceNameFunction))) + .apply(ParDo.of(new UpdateFn(fhirStore, formatBodyFunction, resourceNameFunction, etagFunction))) .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } @@ -1536,17 +1557,20 @@ static class UpdateFn extends DoFn> { private Counter failedUpdates = Metrics.counter(UpdateFn.class, "failed-updates"); private transient HealthcareApiClient client; private final ObjectMapper mapper = new ObjectMapper(); - private final String fhirStore; + private final ValueProvider fhirStore; private SerializableFunction formatBodyFunction; private SerializableFunction resourceNameFunction; + private SerializableFunction etagFunction; UpdateFn( - String fhirStore, + ValueProvider fhirStore, SerializableFunction formatBodyFunction, - SerializableFunction resourceNameFunction) { + SerializableFunction resourceNameFunction, + @Nullable SerializableFunction etagFunction) { this.fhirStore = fhirStore; this.formatBodyFunction = formatBodyFunction; this.resourceNameFunction = resourceNameFunction; + this.etagFunction = etagFunction; } @Setup @@ -1555,14 +1579,19 @@ public void initClient() throws IOException { } @ProcessElement - public void update(ProcessContext context) { + public void update(ProcessContext context) + throws IOException { T input = context.element(); String body = formatBodyFunction.apply(input); try { // Validate that data was set to valid JSON. mapper.readTree(body); String resourceName = resourceNameFunction.apply(input); - HttpBody result = client.fhirUpdate(fhirStore, resourceName, body); + String etag = null; + if (etagFunction != null){ + etag = etagFunction.apply(input); + } + HttpBody result = client.fhirUpdate(fhirStore.get(), resourceName, body, etag); context.output(UPDATE_RESULTS, result.getData()); } catch (IOException | HealthcareHttpException e) { failedUpdates.inc(); @@ -1600,10 +1629,11 @@ public static ConditionalUpdate conditionalUpdate(String fhirStore){ *

    https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/conditionalUpdate */ public static class ConditionalUpdate extends PTransform, Write.Result> { - private final String fhirStore; + private final ValueProvider fhirStore; private SerializableFunction> searchParametersFunction; private SerializableFunction typeFunction; private SerializableFunction formatBodyFunction; + private SerializableFunction etagFunction; /** * Instantiates a new Conditional update. @@ -1611,9 +1641,19 @@ public static class ConditionalUpdate extends PTransform, Writ * @param fhirStore the fhir store */ ConditionalUpdate(ValueProvider fhirStore) { - this.fhirStore = fhirStore.get(); + this.fhirStore = fhirStore; + } + + /** + * Instantiates a new Conditional update. + * + * @param fhirStore the fhir store + */ + ConditionalUpdate(String fhirStore) { + this.fhirStore = StaticValueProvider.of(fhirStore); } + /** * With search parameters function conditional update. * @@ -1649,13 +1689,9 @@ public ConditionalUpdate withFormatBodyFunction( return this; } - /** - * Instantiates a new Conditional update. - * - * @param fhirStore the fhir store - */ - ConditionalUpdate(String fhirStore) { - this.fhirStore = fhirStore; + public ConditionalUpdate withEtagFunction(SerializableFunction etagFunction) { + this.etagFunction = etagFunction; + return this; } @Override @@ -1678,7 +1714,8 @@ public FhirIO.Write.Result expand(PCollection input) { .apply( ParDo.of( new ConditionalUpdateFn( - fhirStore, typeFunction, searchParametersFunction, formatBodyFunction))) + fhirStore, typeFunction, searchParametersFunction, formatBodyFunction, + etagFunction))) .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } @@ -1688,20 +1725,23 @@ static class ConditionalUpdateFn extends DoFn> { Metrics.counter(ConditionalUpdateFn.class, "failed-conditional-updates"); private transient HealthcareApiClient client; private final ObjectMapper mapper = new ObjectMapper(); - private final String fhirStore; + private final ValueProvider fhirStore; private SerializableFunction> searchParametersFunction; private SerializableFunction typeFunction; private SerializableFunction formatBodyFunction; + private SerializableFunction etagFunction; ConditionalUpdateFn( - String fhirStore, + ValueProvider fhirStore, SerializableFunction typeFunction, SerializableFunction> searchParametersFunction, - SerializableFunction formatBodyFunction) { + SerializableFunction formatBodyFunction, + @Nullable SerializableFunction etagFunction) { this.fhirStore = fhirStore; this.typeFunction = typeFunction; this.searchParametersFunction = searchParametersFunction; this.formatBodyFunction = formatBodyFunction; + this.etagFunction = etagFunction; } @Setup @@ -1710,7 +1750,7 @@ public void initClient() throws IOException { } @ProcessElement - public void conditionalUpdate(ProcessContext context) { + public void conditionalUpdate(ProcessContext context) throws IOException { T input = context.element(); String type = typeFunction.apply(input); String body = formatBodyFunction.apply(input); @@ -1718,7 +1758,11 @@ public void conditionalUpdate(ProcessContext context) { // Validate that data was set to valid JSON. mapper.readTree(body); Map searchParameters = searchParametersFunction.apply(input); - client.fhirConditionalUpdate(fhirStore, type, body, searchParameters); + String etag = null; + if (etagFunction != null){ + etag = etagFunction.apply(input); + } + client.fhirConditionalUpdate(fhirStore.get(), type, body, searchParameters, etag); } catch (IOException | HealthcareHttpException e) { failedConditionalUpdates.inc(); context.output(HealthcareIOError.of(body, e)); diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java index 8083356bfe0e..3f553f1c7ec7 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java @@ -157,10 +157,11 @@ HttpBody fhirConditionalUpdate( String fhirStore, String relativeResourceName, String resource, - Map searchParameters) + Map searchParameters, + @Nullable String etag) throws IOException, HealthcareHttpException; - HttpBody fhirUpdate(String fhirStore, String type, String resource) + HttpBody fhirUpdate(String fhirStore, String type, String resource, @Nullable String etag) throws IOException, HealthcareHttpException; /** diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java index 78c7bcbb3fcd..dbad6125dbc1 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java @@ -86,6 +86,7 @@ public class HttpHealthcareApiClient implements HealthcareApiClient, Serializabl private static final String FHIRSTORE_HEADER_CONTENT_TYPE = "application/fhir+json"; private static final String FHIRSTORE_HEADER_ACCEPT = "application/fhir+json; charset=utf-8"; private static final String FHIRSTORE_HEADER_ACCEPT_CHARSET = "utf-8"; + private static final String IF_MATCH_HEADER = "If-Match"; private static final Logger LOG = LoggerFactory.getLogger(HttpHealthcareApiClient.class); private transient CloudHealthcare client; public transient HttpClient httpClient; @@ -531,20 +532,32 @@ public HttpBody fhirCreate( @Override public HttpBody fhirConditionalUpdate( - String fhirStore, String type, String resource, Map searchParameters) + String fhirStore, String type, String resource, Map searchParameters, + @Nullable String etag) throws IOException, HealthcareHttpException { + Map headers = new HashMap<>(); + if (etag != null) { + headers.put(IF_MATCH_HEADER, etag); + } return executeFhirHttpRequest( FhirHttpRequest.of(fhirStore, resource) + .setHeaders(headers) .setPathSuffix("/" + type) .setParameters(searchParameters) .setMethod(Method.PUT)); } @Override - public HttpBody fhirUpdate(String fhirStore, String relativeResourceName, String resource) + public HttpBody fhirUpdate(String fhirStore, String relativeResourceName, String resource, + @Nullable String etag) throws IOException, HealthcareHttpException { + Map headers = new HashMap<>(); + if (etag != null) { + headers.put(IF_MATCH_HEADER, etag); + } return executeFhirHttpRequest( FhirHttpRequest.of(fhirStore, resource) + .setHeaders(headers) .setPathSuffix("/" + relativeResourceName) .setMethod(Method.PUT)); } diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java index 100c26efc0be..61af5fa8f50b 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java @@ -17,6 +17,7 @@ */ package org.apache.beam.sdk.io.gcp.healthcare; +import com.fasterxml.jackson.databind.ObjectMapper; import com.google.api.client.http.HttpHeaders; import com.google.api.client.http.HttpRequestInitializer; import com.google.api.client.http.javanet.NetHttpTransport; @@ -39,16 +40,52 @@ import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException; +import org.apache.beam.sdk.transforms.SerializableFunction; class FhirIOTestUtil { public static final String DEFAULT_TEMP_BUCKET = "temp-storage-for-healthcare-io-tests"; + + public static class ExtractIDSearchQuery implements + SerializableFunction { + private ObjectMapper mapper; + + ExtractIDSearchQuery(){ + mapper = new ObjectMapper(); + } + + @Override + public String apply(String resource) throws IOException { + Map map = mapper.readValue(resource.toString().getBytes(), Map.class); + String id = map.get("id"); + return String.format("_id=%s", id); + } + } + + public static class GetByKey implements + SerializableFunction { + private final String key; + private ObjectMapper mapper; + + public GetByKey(String key){ + this.key = key; + mapper = new ObjectMapper(); + } + + @Override + public String apply(String resource) throws IOException { + Map map = mapper.readValue(resource.getBytes(), Map.class); + return map.get(key); + } + } + // TODO read initial resources function. // TODO read update resources function. // TODO spot check resource update utility. - private static Stream readPrettyBundles(String version) { - ClassLoader classLoader = FhirIOTestUtil.class.getClassLoader(); - Path resourceDir = Paths.get("build", "resources", "test", version); + + private static Stream readAllTestResources(String subDir, String version ) { + Path resourceDir = Paths.get("build", "resources", "test", + subDir, version); String absolutePath = resourceDir.toFile().getAbsolutePath(); File dir = new File(absolutePath); File[] fhirJsons = dir.listFiles(); @@ -63,8 +100,15 @@ private static Stream readPrettyBundles(String version) { } }) .map(String::new); + + } + private static Stream readPrettyBundles(String version) { + return readAllTestResources("transactional_bundles", version); } + private static Stream readPrettyResources(String version) { + return readAllTestResources("resources", version); + } // Could generate more messages at scale using a tool like // https://synthetichealth.github.io/synthea/ if necessary chose not to avoid the dependency. static final List DSTU2_PRETTY_BUNDLES = @@ -84,6 +128,25 @@ private static Stream readPrettyBundles(String version) { BUNDLES = Collections.unmodifiableMap(m); } + // Could generate more messages at scale using a tool like + // https://synthetichealth.github.io/synthea/ if necessary chose not to avoid the dependency. + static final List DSTU2_PRETTY_RESOURCES = + readPrettyResources("DSTU2").collect(Collectors.toList()); + static final List STU3_PRETTY_RESOURCES = + readPrettyResources("STU3").collect(Collectors.toList()); + static final List R4_PRETTY_RESOURCES= + readPrettyResources("R4").collect(Collectors.toList()); + + static final Map> RESOURCES; + + static { + Map> m = new HashMap<>(); + m.put("DSTU2", DSTU2_PRETTY_RESOURCES); + m.put("STU3", STU3_PRETTY_RESOURCES); + m.put("R4", R4_PRETTY_RESOURCES); + RESOURCES = Collections.unmodifiableMap(m); + } + /** Populate the test resources into the FHIR store and returns a list of resource IDs. */ static void executeFhirBundles(HealthcareApiClient client, String fhirStore, List bundles) throws IOException, HealthcareHttpException { diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java index 8d46186c472b..4f127c050add 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java @@ -19,24 +19,27 @@ import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.BUNDLES; import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.DEFAULT_TEMP_BUCKET; +import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.RESOURCES; import static org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.HEALTHCARE_DATASET_TEMPLATE; import java.io.IOException; import java.security.SecureRandom; import java.util.Arrays; import java.util.Collection; -import java.util.HashMap; import com.fasterxml.jackson.databind.ObjectMapper; +import java.util.HashMap; import java.util.Map; import org.apache.beam.sdk.Pipeline; import org.apache.beam.sdk.extensions.gcp.options.GcpOptions; import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure; import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Write.Result; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.GetByKey; import org.apache.beam.sdk.options.PipelineOptionsFactory; import org.apache.beam.sdk.testing.PAssert; import org.apache.beam.sdk.testing.TestPipeline; -import org.apache.beam.sdk.transforms.Count; import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.WithKeys; +import org.apache.beam.sdk.values.KV; import org.junit.After; import org.junit.AfterClass; import org.junit.Before; @@ -139,24 +142,13 @@ public void testFhirIO_CreateResources() { (Result) pipeline .apply(Create.of(BUNDLES.get(version))) .apply(FhirIO.createResources(options.getFhirStore()) - .withTypeFunction((String resource) -> { - ObjectMapper mapper = new ObjectMapper(); - Map map = mapper.readValue(resource, Map.class); - return map.get("resourceType"); - - }) - .withIfNotExistFunction((String resource) -> { - ObjectMapper mapper = new ObjectMapper(); - Map map = mapper.readValue(resource, Map.class); - String id = map.get("id"); - return String.format("_id=%s", id); - }) - .withFormatBodyFunction((String x) -> x) + .withTypeFunction(new GetByKey("resourceType")) + .withIfNotExistFunction(new FhirIOTestUtil.ExtractIDSearchQuery()) + .withFormatBodyFunction(x -> x) ); - // TODO have a known number of pre-condition failed case and assert it appears in error queue - PAssert.thatSingleton(writeResult.getFailedBodies().apply(Count.globally())).isEqualTo(1L); + PAssert.that(writeResult.getFailedBodies()).empty(); pipeline.run().waitUntilFinish(); } @@ -164,14 +156,14 @@ public void testFhirIO_CreateResources() { @Test public void testFhirIO_Update() { // TODO write initial resources to FHIR - // use beam to perform updates FhirIO.Write.Result writeResult = (Result) pipeline - .apply(Create.of(BUNDLES.get(version))) - .apply(FhirIO.update(options.getFhirStore()) - .withFormatBodyFunction(x -> "{}") - .withResourceNameFunction(x -> "name") - ); + .apply("Create Test Resources", Create.of(RESOURCES.get(version))) + .apply("Extract ID keys", WithKeys.of(new GetByKey("id"))) + .apply("Update Resources", + FhirIO.>update(options.getFhirStore()) + .withResourceNameFunction(x -> x.getKey()) + .withFormatBodyFunction(x -> ((KV) x).getValue())); PAssert.that(writeResult.getFailedBodies()).empty(); @@ -184,13 +176,12 @@ public void testFhirIO_ConditionalUpdate() { // TODO write initial resources to FHIR FhirIO.Write.Result writeResult = (Result) pipeline - .apply(Create.of(BUNDLES.get(version))) - .apply(FhirIO.conditionalUpdate(options.getFhirStore()) - .withTypeFunction(x -> "patient") - .withFormatBodyFunction(x -> "{}") - .withSearchParametersFunction(x-> new HashMap()) - ); + .apply("Create Test Resources", Create.of(RESOURCES.get(version))) + .apply("Conditional Update Resources", + FhirIO.conditionalUpdate(options.getFhirStore()) + .withTypeFunction(x -> "patient") + .withFormatBodyFunction(x -> "{}") + .withSearchParametersFunction(x -> new HashMap<>())); // TODO spot check update results - // TODO have a known number of pre-condition failed case and assert it appears in error queue } } From 01c11e7211937bde3c238fe3639f9dfe7774d093 Mon Sep 17 00:00:00 2001 From: darshanj Date: Tue, 2 Jun 2020 11:54:54 +0800 Subject: [PATCH 137/151] [BEAM-9825] | Implement Intersect,Union,Except transforms (#11610) * [BEAM-9825] | Implement Intersect,Union,Except transforms --- .../org/apache/beam/sdk/transforms/Sets.java | 680 ++++++++++++++++++ .../apache/beam/sdk/transforms/SetsTest.java | 324 +++++++++ .../sql/impl/rel/BeamSetOperatorRelBase.java | 43 +- 3 files changed, 1027 insertions(+), 20 deletions(-) create mode 100644 sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Sets.java create mode 100644 sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/SetsTest.java diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Sets.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Sets.java new file mode 100644 index 000000000000..16a728167b24 --- /dev/null +++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Sets.java @@ -0,0 +1,680 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.transforms; + +import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkArgument; +import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkNotNull; + +import java.util.ArrayList; +import java.util.List; +import org.apache.beam.sdk.Pipeline; +import org.apache.beam.sdk.coders.Coder; +import org.apache.beam.sdk.transforms.join.CoGbkResult; +import org.apache.beam.sdk.transforms.join.CoGroupByKey; +import org.apache.beam.sdk.transforms.join.KeyedPCollectionTuple; +import org.apache.beam.sdk.transforms.windowing.Trigger; +import org.apache.beam.sdk.transforms.windowing.WindowFn; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.PCollectionList; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Iterables; + +/** + * The {@code PTransform}s that allow to compute different set functions across {@link + * PCollection}s. + * + *

    They come in two variants. 1. Between two {@link PCollection} 2. Between two or more {@link + * PCollection} in a {@link PCollectionList}. + * + *

    Following {@code PTransform}s follows SET DISTINCT semantics: intersectDistinct, + * expectDistinct, unionDistinct + * + *

    Following {@code PTransform}s follows SET ALL semantics: intersectAll, expectAll, unionAll + * + *

    For example, the following demonstrates intersectDistinct between two collections {@link + * PCollection}s. + * + * 

    {@code
+ * Pipeline p = ...;
+ *
+ * PCollection left = p.apply(Create.of("1", "2", "3", "3", "4", "5"));
+ * PCollection right = p.apply(Create.of("1", "3", "4", "4", "6"));
+ *
+ * PCollection results =
+ *     left.apply(SetFns.intersectDistinct(right)); // results will be PCollection containing: "1","3","4"
+ *
+ * }
    + * + *

    For example, the following demonstrates intersectDistinct between three collections {@link + * PCollection}s in a {@link PCollectionList}. + * + * 

    {@code
+ * Pipeline p = ...;
+ *
+ * PCollection first = p.apply(Create.of("1", "2", "3", "3", "4", "5"));
+ * PCollection second = p.apply(Create.of("1", "3", "4", "4", "6"));
+ * PCollection third = p.apply(Create.of("3", "4", "4"));
+ *
+ * // Following example will perform (first intersect second) intersect third.
+ * PCollection results =
+ *     PCollectionList.of(first).and(second).and(third)
+ *     .apply(SetFns.intersectDistinct()); // results will be PCollection containing: "3","4"
+ *
+ * }
    + */ +public class Sets { + + /** + * Returns a new {@code PTransform} transform that follows SET DISTINCT semantics to compute the + * intersection with provided {@code PCollection}. + * + *

    The argument should not be modified after this is called. + * + *

    The elements of the output {@link PCollection} will all distinct elements that present in + * both pipeline is constructed and provided {@link PCollection}. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}). Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the input {@code PCollection} + * + * 

    {@code
+   * Pipeline p = ...;
+   *
+   * PCollection left = p.apply(Create.of("1", "2", "3", "3", "4", "5"));
+   * PCollection right = p.apply(Create.of("1", "3", "4", "4", "6"));
+   *
+   * PCollection results =
+   *     left.apply(SetFns.intersectDistinct(right)); // results will be PCollection containing: "1","3","4"
+   *
+   * }
    + * + * @param the type of the elements in the input and output {@code PCollection}s. + */ + public static PTransform, PCollection> intersectDistinct( + PCollection rightCollection) { + checkNotNull(rightCollection, "rightCollection argument is null"); + return new SetImpl<>(rightCollection, intersectDistinct()); + } + + /** + * Returns a {@code PTransform} that takes a {@code PCollectionList>} and returns a + * {@code PCollection} containing the intersection of collections done in order for all + * collections in {@code PCollectionList}. + * + *

    Returns a new {@code PTransform} transform that follows SET DISTINCT semantics which takes a + * {@code PCollectionList>} and returns a {@code PCollection} containing the + * intersection of collections done in order for all collections in {@code PCollectionList}. + * + *

    The elements of the output {@link PCollection} will have all distinct elements that are + * present in both pipeline is constructed and next {@link PCollection} in the list and applied to + * all collections in order. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the first {@code PCollection} in {@code PCollectionList}. + * + * 

    {@code
+   * Pipeline p = ...;
+   *
+   * PCollection first = p.apply(Create.of("1", "2", "3", "3", "4", "5"));
+   * PCollection second = p.apply(Create.of("1", "3", "4", "4", "6"));
+   * PCollection third = p.apply(Create.of("3", "4", "4"));
+   *
+   * // Following example will perform (first intersect second) intersect third.
+   * PCollection results =
+   *     PCollectionList.of(first).and(second).and(third)
+   *     .apply(SetFns.intersectDistinct()); // results will be PCollection containing: "3","4"
+   *
+   * }
    + * + * @param the type of the elements in the input {@code PCollectionList} and output {@code + * PCollection}s. + */ + public static PTransform, PCollection> intersectDistinct() { + SerializableBiFunction intersectFn = + (numberOfElementsinLeft, numberOfElementsinRight) -> + (numberOfElementsinLeft > 0 && numberOfElementsinRight > 0) ? 1L : 0L; + return new SetImplCollections<>(intersectFn); + } + + /** + * Returns a new {@code PTransform} transform that follows SET ALL semantics to compute the + * intersection with provided {@code PCollection}. + * + *

    The argument should not be modified after this is called. + * + *

    The elements of the output {@link PCollection} which will follow INTESECT_ALL Semantics as + * follows: Given there are m elements on pipeline which is constructed {@link PCollection} (left) + * and n elements on in provided {@link PCollection} (right): - it will output MIN(m - n, 0) + * elements of left for all elements which are present in both left and right. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the input {@code PCollection} + * + * 

    {@code
+   * Pipeline p = ...;
+   *
+   * PCollection left = p.apply(Create.of("1", "1", "1", "2", "3", "3", "4", "5"));
+   * PCollection right = p.apply(Create.of("1", "1", "3", "4", "4", "6"));
+   *
+   * PCollection results =
+   *     left.apply(SetFns.intersectAll(right)); // results will be PCollection containing: "1","1","3","4"
+   * }
    + * + * @param the type of the elements in the input and output {@code PCollection}s. + */ + public static PTransform, PCollection> intersectAll( + PCollection rightCollection) { + checkNotNull(rightCollection, "rightCollection argument is null"); + return new SetImpl<>(rightCollection, intersectAll()); + } + + /** + * Returns a new {@code PTransform} transform that follows SET ALL semantics which takes a {@code + * PCollectionList>} and returns a {@code PCollection} containing the + * intersection all of collections done in order for all collections in {@code + * PCollectionList}. + * + *

    The elements of the output {@link PCollection} which will follow INTERSECT_ALL semantics. + * Output is calculated as follows: Given there are m elements on pipeline which is constructed + * {@link PCollection} (left) and n elements on in provided {@link PCollection} (right): - it will + * output MIN(m - n, 0) elements of left for all elements which are present in both left and + * right. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the first {@code PCollection} in {@code PCollectionList}. + * + * 

    {@code
+   * Pipeline p = ...;
+   * PCollection first = p.apply(Create.of("1", "1", "1", "2", "3", "3", "4", "5"));
+   * PCollection second = p.apply(Create.of("1", "1", "3", "4", "4", "6"));
+   * PCollection third = p.apply(Create.of("1", "5"));
+   *
+   * // Following example will perform (first intersect second) intersect third.
+   * PCollection results =
+   *     PCollectionList.of(first).and(second).and(third)
+   *     .apply(SetFns.intersectAll()); // results will be PCollection containing: "1"
+   *
+   * }
    + * + * @param the type of the elements in the input {@code PCollectionList} and output {@code + * PCollection}s. + */ + public static PTransform, PCollection> intersectAll() { + return new SetImplCollections<>(Math::min); + } + + /** + * Returns a new {@code PTransform} transform that follows SET DISTINCT semantics to compute the + * difference (except) with provided {@code PCollection}. + * + *

    The argument should not be modified after this is called. + * + *

    The elements of the output {@link PCollection} will all distinct elements that present in + * pipeline is constructed but not present in provided {@link PCollection}. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the input {@code PCollection} + * + * 

    {@code
+   * Pipeline p = ...;
+   *
+   * PCollection left = p.apply(Create.of("1", "1", "1", "2", "3", "3","4", "5"));
+   * PCollection right = p.apply(Create.of("1", "1", "3", "4", "4", "6"));
+   *
+   * PCollection results =
+   *     left.apply(SetFns.exceptDistinct(right)); // results will be PCollection containing: "2","5"
+   * }
    + * + * @param the type of the elements in the input and output {@code PCollection}s. + */ + public static PTransform, PCollection> exceptDistinct( + PCollection rightCollection) { + checkNotNull(rightCollection, "rightCollection argument is null"); + return new SetImpl<>(rightCollection, exceptDistinct()); + } + + /** + * Returns a {@code PTransform} that takes a {@code PCollectionList>} and returns a + * {@code PCollection} containing the difference (except) of collections done in order for all + * collections in {@code PCollectionList}. + * + *

    Returns a new {@code PTransform} transform that follows SET DISTINCT semantics which takes a + * {@code PCollectionList>} and returns a {@code PCollection} containing the + * difference (except) of collections done in order for all collections in {@code + * PCollectionList}. + * + *

    The elements of the output {@link PCollection} will have all distinct elements that are + * present in pipeline is constructed but not present in next {@link PCollection} in the list and + * applied to all collections in order. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the first {@code PCollection} in {@code PCollectionList}. + * + * 

    {@code
+   * Pipeline p = ...;
+   * PCollection first = p.apply(Create.of("1", "1", "1", "2", "3", "3", "4", "5"));
+   * PCollection second = p.apply(Create.of("1", "1", "3", "4", "4", "6"));
+   *
+   * PCollection third = p.apply(Create.of("1", "2", "2"));
+   *
+   * // Following example will perform (first intersect second) intersect third.
+   * PCollection results =
+   *     PCollectionList.of(first).and(second).and(third)
+   *     .apply(SetFns.exceptDistinct()); // results will be PCollection containing: "5"
+   *
+   * }
    + * + * @param the type of the elements in the input {@code PCollectionList} and output {@code + * PCollection}s. + */ + public static PTransform, PCollection> exceptDistinct() { + SerializableBiFunction exceptFn = + (numberOfElementsinLeft, numberOfElementsinRight) -> + numberOfElementsinLeft > 0 && numberOfElementsinRight == 0 ? 1L : 0L; + return new SetImplCollections<>(exceptFn); + } + + /** + * Returns a new {@code PTransform} transform that follows SET ALL semantics to compute the + * difference all (exceptAll) with provided {@code PCollection}. + * + *

    The argument should not be modified after this is called. + * + *

    The elements of the output {@link PCollection} which will follow EXCEPT_ALL Semantics as + * follows: Given there are m elements on pipeline which is constructed {@link PCollection} (left) + * and n elements on in provided {@link PCollection} (right): - it will output m elements of left + * for all elements which are present in left but not in right. - it will output MAX(m - n, 0) + * elements of left for all elements which are present in both left and right. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the input {@code PCollection} + * + * 

    {@code
+   * Pipeline p = ...;
+   *
+   * PCollection left = p.apply(Create.of("1", "1", "1", "2", "3", "3", "3", "4", "5"));
+   * PCollection right = p.apply(Create.of("1", "3", "4", "4", "6"));
+   *
+   * PCollection results =
+   *     left.apply(SetFns.exceptAll(right)); // results will be PCollection containing: "1","1","2","3","3","5"
+   * }
    + * + * @param the type of the elements in the input and output {@code PCollection}s. + */ + public static PTransform, PCollection> exceptAll( + PCollection rightCollection) { + checkNotNull(rightCollection, "rightCollection argument is null"); + return new SetImpl<>(rightCollection, exceptAll()); + } + + /** + * Returns a new {@code PTransform} transform that follows SET ALL semantics which takes a {@code + * PCollectionList>} and returns a {@code PCollection} containing the difference + * all (exceptAll) of collections done in order for all collections in {@code PCollectionList}. + * + *

    The elements of the output {@link PCollection} which will follow EXCEPT_ALL semantics. + * Output is calculated as follows: Given there are m elements on pipeline which is constructed + * {@link PCollection} (left) and n elements on in provided {@link PCollection} (right): - it will + * output m elements of left for all elements which are present in left but not in right. - it + * will output MAX(m - n, 0) elements of left for all elements which are present in both left and + * right. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the first {@code PCollection} in {@code PCollectionList}. + * + * 

    {@code
+   * Pipeline p = ...;
+   * PCollection first = p.apply(Create.of("1", "1", "1", "2", "3", "3", "3", "4", "5"));
+   * PCollection second = p.apply(Create.of("1", "3", "4", "4", "6"));
+   * PCollection third = p.apply(Create.of("1", "5"));
+   *
+   * // Following example will perform (first intersect second) intersect third.
+   * PCollection results =
+   *     PCollectionList.of(first).and(second).and(third)
+   *     .apply(SetFns.exceptAll()); // results will be PCollection containing: "1","2","3","3"
+   *
+   * }
    + * + * @param the type of the elements in the input {@code PCollectionList} and output {@code + * PCollection}s. + */ + public static PTransform, PCollection> exceptAll() { + SerializableBiFunction exceptFn = + (numberOfElementsinLeft, numberOfElementsinRight) -> + Math.max(numberOfElementsinLeft - numberOfElementsinRight, 0L); + return new SetImplCollections<>(exceptFn); + } + + /** + * Returns a new {@code PTransform} transform that follows SET DISTINCT semantics to compute the + * union with provided {@code PCollection}. + * + *

    The argument should not be modified after this is called. + * + *

    The elements of the output {@link PCollection} will all distinct elements that present in + * pipeline is constructed or present in provided {@link PCollection}. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the input {@code PCollection} + * + * 

    {@code
+   * Pipeline p = ...;
+   *
+   * PCollection left = p.apply(Create.of("1", "1", "2"));
+   * PCollection right = p.apply(Create.of("1", "3", "4", "4"));
+   *
+   * PCollection results =
+   *     left.apply(SetFns.unionDistinct(right)); // results will be PCollection containing: "1","2","3","4"
+   * }
    + * + * @param the type of the elements in the input and output {@code PCollection}s. + */ + public static PTransform, PCollection> unionDistinct( + PCollection rightCollection) { + checkNotNull(rightCollection, "rightCollection argument is null"); + return new SetImpl<>(rightCollection, unionDistinct()); + } + + /** + * Returns a new {@code PTransform} transform that follows SET DISTINCT semantics which takes a + * {@code PCollectionList>} and returns a {@code PCollection} containing the + * union of collections done in order for all collections in {@code PCollectionList}. + * + *

    The elements of the output {@link PCollection} will have all distinct elements that are + * present in pipeline is constructed or present in next {@link PCollection} in the list and + * applied to all collections in order. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the first {@code PCollection} in {@code PCollectionList}. + * + * 

    {@code
+   * Pipeline p = ...;
+   * PCollection first = p.apply(Create.of("1", "1", "2"));
+   * PCollection second = p.apply(Create.of("1", "3", "4", "4"));
+   *
+   * PCollection third = p.apply(Create.of("1", "5"));
+   *
+   * // Following example will perform (first intersect second) intersect third.
+   * PCollection results =
+   *     PCollectionList.of(first).and(second).and(third)
+   *     .apply(SetFns.unionDistinct()); // results will be PCollection containing: "1","2","3","4","5"
+   *
+   * }
    + * + * @param the type of the elements in the input {@code PCollectionList} and output {@code + * PCollection}s. + */ + public static PTransform, PCollection> unionDistinct() { + SerializableBiFunction unionFn = + (numberOfElementsinLeft, numberOfElementsinRight) -> 1L; + return new SetImplCollections<>(unionFn); + } + + /** + * Returns a new {@code PTransform} transform that follows SET ALL semantics to compute the + * unionAll with provided {@code PCollection}. + * + *

    The argument should not be modified after this is called. + * + *

    The elements of the output {@link PCollection} which will follow UNION_ALL semantics as + * follows: Given there are m elements on pipeline which is constructed {@link PCollection} (left) + * and n elements on in provided {@link PCollection} (right): - it will output m elements of left + * and m elements of right. + * + *

    Note that this transform requires that the {@code Coder} of the all {@code PCollection} + * to be deterministic (see {@link Coder#verifyDeterministic()}). If the collection {@code Coder} + * is not deterministic, an exception is thrown at pipeline construction time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the input {@code PCollection} + * + * 

    {@code
+   * Pipeline p = ...;
+   *
+   * PCollection left = p.apply(Create.of("1", "1", "2"));
+   * PCollection right = p.apply(Create.of("1", "3", "4", "4"));
+   *
+   * PCollection results =
+   *     left.apply(SetFns.unionAll(right)); // results will be PCollection containing: "1","1","1","2","3","4","4"
+   * }
    + * + * @param the type of the elements in the input and output {@code PCollection}s. + */ + public static PTransform, PCollection> unionAll( + PCollection rightCollection) { + checkNotNull(rightCollection, "rightCollection argument is null"); + return new SetImpl<>(rightCollection, unionAll()); + } + + /** + * Returns a new {@code PTransform} transform that follows SET ALL semantics which takes a {@code + * PCollectionList>} and returns a {@code PCollection} containing the unionAll + * of collections done in order for all collections in {@code PCollectionList}. + * + *

    The elements of the output {@link PCollection} which will follow UNION_ALL semantics. Output + * is calculated as follows: Given there are m elements on pipeline which is constructed {@link + * PCollection} (left) and n elements on in provided {@link PCollection} (right): - it will output + * m elements of left and m elements of right. + * + *

    Note that this transform requires that the {@code Coder} of the all inputs {@code + * PCollection} to be deterministic (see {@link Coder#verifyDeterministic()}). If the + * collection {@code Coder} is not deterministic, an exception is thrown at pipeline construction + * time. + * + *

    All inputs must have equal {@link WindowFn}s and compatible triggers (see {@link + * Trigger#isCompatible(Trigger)}).Triggers with multiple firings may lead to nondeterministic + * results since the this {@code PTransform} is only computed over each individual firing. + * + *

    By default, the output {@code PCollection} encodes its elements using the same {@code + * Coder} as that of the first {@code PCollection} in {@code PCollectionList}. + * + * 

    {@code
+   * Pipeline p = ...;
+   * PCollection first = p.apply(Create.of("1", "1", "2"));
+   * PCollection second = p.apply(Create.of("1", "3", "4", "4"));
+   * PCollection third = p.apply(Create.of("1", "5"));
+   *
+   * // Following example will perform (first intersect second) intersect third.
+   * PCollection results =
+   *     PCollectionList.of(first).and(second).and(third)
+   *     .apply(SetFns.unionAll()); // results will be PCollection containing: "1","1","1","1","2","3","4","4","5"
+   *
+   * }
    + * + * @param the type of the elements in the input {@code PCollectionList} and output {@code + * PCollection}s. + */ + public static Flatten.PCollections unionAll() { + return Flatten.pCollections(); + } + + private static class SetImpl extends PTransform, PCollection> { + + private final transient PCollection rightCollection; + private final PTransform, PCollection> listTransformFn; + + private SetImpl( + PCollection rightCollection, + PTransform, PCollection> listTransformFn) { + this.rightCollection = rightCollection; + this.listTransformFn = listTransformFn; + } + + @Override + public PCollection expand(PCollection leftCollection) { + return PCollectionList.of(leftCollection).and(rightCollection).apply(listTransformFn); + } + } + + private static class SetImplCollections + extends PTransform, PCollection> { + + private final SerializableBiFunction fn; + + private SetImplCollections(SerializableBiFunction fn) { + this.fn = fn; + } + + @Override + public PCollection expand(PCollectionList input) { + List> all = input.getAll(); + MapElements> elementToVoid = + MapElements.via( + new SimpleFunction>() { + @Override + public KV apply(T element) { + return KV.of(element, null); + } + }); + + checkArgument(all.size() > 1, "must have at least two input to a PCollectionList"); + + PCollection first = all.get(0); + Pipeline pipeline = first.getPipeline(); + String firstName = first.getName(); + + List> allTags = new ArrayList<>(); + KeyedPCollectionTuple keyedPCollectionTuple = KeyedPCollectionTuple.empty(pipeline); + + for (PCollection col : all) { + TupleTag tag = new TupleTag<>(); + + PCollection> kvOfElementAndVoid = + col.apply("PrepareKVs" + col.getName(), elementToVoid); + + allTags.add(tag); + keyedPCollectionTuple = keyedPCollectionTuple.and(tag, kvOfElementAndVoid); + } + + PCollection> coGbkResults = + keyedPCollectionTuple.apply("CBKAll" + firstName, CoGroupByKey.create()); + + // TODO: lift combiners through the CoGBK. + PCollection results = + coGbkResults.apply( + "FilterSetElement" + firstName, + ParDo.of( + new DoFn, T>() { + + @ProcessElement + public void processElement(ProcessContext c) { + KV elementGroups = c.element(); + CoGbkResult value = elementGroups.getValue(); + T element = elementGroups.getKey(); + + long numberOfOutputs = Iterables.size(value.getAll(allTags.get(0))); + List> tail = allTags.subList(1, allTags.size()); + + for (TupleTag tag : tail) { + long nextSize = Iterables.size(value.getAll(tag)); + numberOfOutputs = fn.apply(numberOfOutputs, nextSize); + } + for (long i = 0L; i < numberOfOutputs; i++) { + c.output(element); + } + } + })); + + return results.setCoder(first.getCoder()); + } + } +} diff --git a/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/SetsTest.java b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/SetsTest.java new file mode 100644 index 000000000000..ed07a65b0219 --- /dev/null +++ b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/SetsTest.java @@ -0,0 +1,324 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.transforms; + +import static junit.framework.TestCase.assertEquals; + +import java.util.Arrays; +import org.apache.beam.sdk.schemas.Schema; +import org.apache.beam.sdk.testing.NeedsRunner; +import org.apache.beam.sdk.testing.PAssert; +import org.apache.beam.sdk.testing.TestPipeline; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.PCollectionList; +import org.apache.beam.sdk.values.Row; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Iterables; +import org.junit.Before; +import org.junit.Rule; +import org.junit.Test; +import org.junit.experimental.categories.Category; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +@RunWith(JUnit4.class) +public class SetsTest { + + @Rule public final TestPipeline p = TestPipeline.create(); + + Schema schema = Schema.builder().addStringField("alphabet").build(); + + static PCollection first; + static PCollection second; + static PCollection firstRows; + static PCollection secondRows; + + private Iterable toRows(String... values) { + return Iterables.transform( + Arrays.asList(values), (elem) -> Row.withSchema(schema).addValues(elem).build()); + } + + @Before + public void setup() { + final String[] firstData = {"a", "a", "a", "b", "b", "c", "d", "d", "g", "g", "h", "h"}; + final String[] secondData = {"a", "a", "b", "b", "b", "c", "d", "d", "e", "e", "f", "f"}; + + first = p.apply("first", Create.of(Arrays.asList(firstData))); + second = p.apply("second", Create.of(Arrays.asList(secondData))); + + firstRows = p.apply("firstRows", Create.of(toRows(firstData)).withRowSchema(schema)); + secondRows = p.apply("secondRows", Create.of(toRows(secondData)).withRowSchema(schema)); + } + + @Test + @Category(NeedsRunner.class) + public void testIntersection() { + PAssert.that(first.apply("strings", Sets.intersectDistinct(second))) + .containsInAnyOrder("a", "b", "c", "d"); + + PCollection results = firstRows.apply("rows", Sets.intersectDistinct(secondRows)); + + PAssert.that(results).containsInAnyOrder(toRows("a", "b", "c", "d")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testIntersectionCollectionList() { + + PCollection third = p.apply("third", Create.of(Arrays.asList("b", "b", "c", "f"))); + PCollection thirdRows = p.apply("thirdRows", Create.of(toRows("b", "b", "c", "f"))); + + PAssert.that( + PCollectionList.of(first) + .and(second) + .and(third) + .apply("stringsCols", Sets.intersectDistinct())) + .containsInAnyOrder("b", "c"); + + PCollection results = + PCollectionList.of(firstRows) + .and(secondRows) + .and(thirdRows) + .apply("rowCols", Sets.intersectDistinct()); + + PAssert.that(results).containsInAnyOrder(toRows("b", "c")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testIntersectionAll() { + + PAssert.that(first.apply("strings", Sets.intersectAll(second))) + .containsInAnyOrder("a", "a", "b", "b", "c", "d", "d"); + + PCollection results = firstRows.apply("rows", Sets.intersectAll(secondRows)); + + PAssert.that(results).containsInAnyOrder(toRows("a", "a", "b", "b", "c", "d", "d")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testIntersectionAllCollectionList() { + PCollection third = p.apply("third", Create.of(Arrays.asList("a", "b", "f"))); + PCollection thirdRows = p.apply("thirdRows", Create.of(toRows("a", "b", "f"))); + + PAssert.that( + PCollectionList.of(first) + .and(second) + .and(third) + .apply("stringsCols", Sets.intersectAll())) + .containsInAnyOrder("a", "b"); + + PCollection results = + PCollectionList.of(firstRows) + .and(secondRows) + .and(thirdRows) + .apply("rowCols", Sets.intersectAll()); + + PAssert.that(results).containsInAnyOrder(toRows("a", "b")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testExcept() { + + PAssert.that(first.apply("strings", Sets.exceptDistinct(second))).containsInAnyOrder("g", "h"); + + PCollection results = firstRows.apply("rows", Sets.exceptDistinct(secondRows)); + + PAssert.that(results).containsInAnyOrder(toRows("g", "h")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testExceptCollectionList() { + PCollection third = p.apply("third", Create.of(Arrays.asList("a", "b", "b", "g", "g"))); + PCollection thirdRows = p.apply("thirdRows", Create.of(toRows("a", "b", "b", "g", "g"))); + + PAssert.that( + PCollectionList.of(first) + .and(second) + .and(third) + .apply("stringsCols", Sets.exceptDistinct())) + .containsInAnyOrder("h"); + + PCollection results = + PCollectionList.of(firstRows) + .and(secondRows) + .and(thirdRows) + .apply("rowCols", Sets.exceptDistinct()); + + PAssert.that(results).containsInAnyOrder(toRows("h")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testExceptAll() { + + PAssert.that(first.apply("strings", Sets.exceptAll(second))) + .containsInAnyOrder("a", "g", "g", "h", "h"); + + PCollection results = firstRows.apply("rows", Sets.exceptAll(secondRows)); + + PAssert.that(results).containsInAnyOrder(toRows("a", "g", "g", "h", "h")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testExceptAllCollectionList() { + PCollection third = p.apply("third", Create.of(Arrays.asList("a", "b", "b", "g", "f"))); + PCollection thirdRows = p.apply("thirdRows", Create.of(toRows("a", "b", "b", "g"))); + + PAssert.that( + PCollectionList.of(first).and(second).and(third).apply("stringsCols", Sets.exceptAll())) + .containsInAnyOrder("g", "h", "h"); + + PCollection results = + PCollectionList.of(firstRows) + .and(secondRows) + .and(thirdRows) + .apply("rowCols", Sets.exceptAll()); + + PAssert.that(results).containsInAnyOrder(toRows("g", "h", "h")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testUnion() { + + PAssert.that(first.apply("strings", Sets.unionDistinct(second))) + .containsInAnyOrder("a", "b", "c", "d", "e", "f", "g", "h"); + + PCollection results = firstRows.apply("rows", Sets.unionDistinct(secondRows)); + + PAssert.that(results).containsInAnyOrder(toRows("a", "b", "c", "d", "e", "f", "g", "h")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testUnionCollectionList() { + PCollection third = p.apply("third", Create.of(Arrays.asList("a", "k", "k"))); + PCollection thirdRows = p.apply("thirdRows", Create.of(toRows("a", "k", "k"))); + + PAssert.that( + PCollectionList.of(first) + .and(second) + .and(third) + .apply("stringsCols", Sets.unionDistinct())) + .containsInAnyOrder("a", "b", "c", "d", "e", "f", "g", "h", "k"); + + PCollection results = + PCollectionList.of(firstRows) + .and(secondRows) + .and(thirdRows) + .apply("rowCols", Sets.unionDistinct()); + + PAssert.that(results).containsInAnyOrder(toRows("a", "b", "c", "d", "e", "f", "g", "h", "k")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testUnionAll() { + + PAssert.that(first.apply("strings", Sets.unionAll(second))) + .containsInAnyOrder( + "a", "a", "a", "a", "a", "b", "b", "b", "b", "b", "c", "c", "d", "d", "d", "d", "e", + "e", "f", "f", "g", "g", "h", "h"); + + PCollection results = firstRows.apply("rows", Sets.unionAll(secondRows)); + + PAssert.that(results) + .containsInAnyOrder( + toRows( + "a", "a", "a", "a", "a", "b", "b", "b", "b", "b", "c", "c", "d", "d", "d", "d", "e", + "e", "f", "f", "g", "g", "h", "h")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } + + @Test + @Category(NeedsRunner.class) + public void testUnionAllCollections() { + + PCollection third = p.apply("third", Create.of(Arrays.asList("a", "b", "b", "k", "k"))); + PCollection thirdRows = p.apply("thirdRows", Create.of(toRows("a", "b", "b", "k", "k"))); + + PAssert.that( + PCollectionList.of(first).and(second).and(third).apply("stringsCols", Sets.unionAll())) + .containsInAnyOrder( + "a", "a", "a", "a", "a", "a", "b", "b", "b", "b", "b", "b", "b", "c", "c", "d", "d", + "d", "d", "e", "e", "f", "f", "g", "g", "h", "h", "k", "k"); + + PCollection results = + PCollectionList.of(firstRows) + .and(secondRows) + .and(thirdRows) + .apply("rowCols", Sets.unionAll()); + + PAssert.that(results) + .containsInAnyOrder( + toRows( + "a", "a", "a", "a", "a", "a", "b", "b", "b", "b", "b", "b", "b", "c", "c", "d", "d", + "d", "d", "e", "e", "f", "f", "g", "g", "h", "h", "k", "k")); + + assertEquals(schema, results.getSchema()); + + p.run(); + } +} diff --git a/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/rel/BeamSetOperatorRelBase.java b/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/rel/BeamSetOperatorRelBase.java index ab76a7b897a9..bdc5f4c1bffa 100644 --- a/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/rel/BeamSetOperatorRelBase.java +++ b/sdks/java/extensions/sql/src/main/java/org/apache/beam/sdk/extensions/sql/impl/rel/BeamSetOperatorRelBase.java @@ -20,15 +20,11 @@ import static org.apache.beam.vendor.calcite.v1_20_0.com.google.common.base.Preconditions.checkArgument; import java.io.Serializable; -import org.apache.beam.sdk.extensions.sql.impl.transform.BeamSetOperatorsTransforms; -import org.apache.beam.sdk.schemas.transforms.CoGroup; -import org.apache.beam.sdk.schemas.transforms.CoGroup.By; import org.apache.beam.sdk.transforms.PTransform; -import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.transforms.Sets; import org.apache.beam.sdk.transforms.windowing.WindowFn; import org.apache.beam.sdk.values.PCollection; import org.apache.beam.sdk.values.PCollectionList; -import org.apache.beam.sdk.values.PCollectionTuple; import org.apache.beam.sdk.values.Row; /** @@ -75,20 +71,27 @@ public PCollection expand(PCollectionList inputs) { + rightWindow); } - // TODO: We may want to preaggregate the counts first using Group instead of calling CoGroup and - // measuring the - // iterable size. If on average there are duplicates in the input, this will be faster. - final String lhsTag = "lhs"; - final String rhsTag = "rhs"; - PCollection joined = - PCollectionTuple.of(lhsTag, leftRows, rhsTag, rightRows) - .apply("CoGroup", CoGroup.join(By.fieldNames("*"))); - return joined - .apply( - "FilterResults", - ParDo.of( - new BeamSetOperatorsTransforms.SetOperatorFilteringDoFn( - lhsTag, rhsTag, opType, all))) - .setRowSchema(joined.getSchema().getField("key").getType().getRowSchema()); + switch (opType) { + case UNION: + if (all) { + return leftRows.apply(Sets.unionAll(rightRows)); + } else { + return leftRows.apply(Sets.unionDistinct(rightRows)); + } + case INTERSECT: + if (all) { + return leftRows.apply(Sets.intersectAll(rightRows)); + } else { + return leftRows.apply(Sets.intersectDistinct(rightRows)); + } + case MINUS: + if (all) { + return leftRows.apply(Sets.exceptAll(rightRows)); + } else { + return leftRows.apply(Sets.exceptDistinct(rightRows)); + } + default: + throw new IllegalStateException("Unexpected set operation value: " + opType); + } } } From b6ca2aba5a0141eed5bed29a9948e2c65874254f Mon Sep 17 00:00:00 2001 From: Michal Walenia <32354134+mwalenia@users.noreply.github.com> Date: Tue, 2 Jun 2020 08:56:14 +0200 Subject: [PATCH 138/151] [BEAM-9723] Add DLP integration transforms (#11566) [BEAM-9723] Add Google Cloud DLP integration transforms. * DLPDeidentifyText * DLPReidentifyText * DLPInspectText are now available. --- CHANGES.md | 4 + sdks/java/extensions/ml/build.gradle | 15 +- .../sdk/extensions/ml/BatchRequestForDLP.java | 113 +++++++ .../sdk/extensions/ml/DLPDeidentifyText.java | 282 +++++++++++++++++ .../sdk/extensions/ml/DLPInspectText.java | 240 +++++++++++++++ .../sdk/extensions/ml/DLPReidentifyText.java | 286 ++++++++++++++++++ .../sdk/extensions/ml/MapStringToDlpRow.java | 59 ++++ .../extensions/ml/BatchRequestForDlpTest.java | 63 ++++ .../extensions/ml/DLPDeidentifyTextTest.java | 101 +++++++ .../sdk/extensions/ml/DLPInspectTextTest.java | 101 +++++++ .../extensions/ml/DLPReidentifyTextTest.java | 101 +++++++ .../extensions/ml/DLPTextOperationsIT.java | 159 ++++++++++ .../extensions/ml/MapStringToDlpRowTest.java | 69 +++++ 13 files changed, 1591 insertions(+), 2 deletions(-) create mode 100644 sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/BatchRequestForDLP.java create mode 100644 sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPDeidentifyText.java create mode 100644 sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPInspectText.java create mode 100644 sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPReidentifyText.java create mode 100644 sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/MapStringToDlpRow.java create mode 100644 sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/BatchRequestForDlpTest.java create mode 100644 sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPDeidentifyTextTest.java create mode 100644 sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPInspectTextTest.java create mode 100644 sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPReidentifyTextTest.java create mode 100644 sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPTextOperationsIT.java create mode 100644 sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/MapStringToDlpRowTest.java diff --git a/CHANGES.md b/CHANGES.md index 0168d04216c6..d00b9c7fa1e9 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -93,6 +93,10 @@ * `--direct_num_workers=0` is supported for FnApi runner. It will set the number of threads/subprocesses to number of cores of the machine executing the pipeline ([BEAM-9443](https://issues.apache.org/jira/browse/BEAM-9443)). * Python SDK now has experimental support for SqlTransform ([BEAM-8603](https://issues.apache.org/jira/browse/BEAM-8603)). * Add OnWindowExpiration method to Stateful DoFn ([BEAM-1589](https://issues.apache.org/jira/browse/BEAM-1589)). +* Added PTransforms for Google Cloud DLP (Data Loss Prevention) services integration ([BEAM-9723](https://issues.apache.org/jira/browse/BEAM-9723)): + * Inspection of data, + * Deidentification of data, + * Reidentification of data. * Add a more complete I/O support matrix in the documentation site ([BEAM-9916](https://issues.apache.org/jira/browse/BEAM-9916)). * Upgrade Sphinx to 3.0.3 for building PyDoc. diff --git a/sdks/java/extensions/ml/build.gradle b/sdks/java/extensions/ml/build.gradle index 1f61c6a6da4a..c5e1ed3905fc 100644 --- a/sdks/java/extensions/ml/build.gradle +++ b/sdks/java/extensions/ml/build.gradle @@ -1,3 +1,5 @@ +import groovy.json.JsonOutput + /* * * * Licensed to the Apache Software Foundation (ASF) under one @@ -19,7 +21,7 @@ */ plugins { id 'org.apache.beam.module' } -applyJavaNature(automaticModuleName: 'org.apache.beam.sdk.extensions.protobuf') +applyJavaNature(automaticModuleName: 'org.apache.beam.sdk.extensions.ml') description = 'Apache Beam :: SDKs :: Java :: Extensions :: ML' @@ -27,16 +29,25 @@ dependencies { compile project(path: ":sdks:java:core", configuration: "shadow") compile project(":sdks:java:expansion-service") compile 'com.google.cloud:google-cloud-video-intelligence:1.2.0' + compile 'com.google.cloud:google-cloud-dlp:1.1.4' compile 'com.google.cloud:google-cloud-language:1.99.4' + provided library.java.junit + testCompile project(path: ':sdks:java:core', configuration: 'shadowTest') testCompile project(path: ':sdks:java:core', configuration: 'shadowTest') testCompile library.java.mockito_core testCompile 'com.google.cloud:google-cloud-video-intelligence:1.2.0' + testCompile 'com.google.cloud:google-cloud-dlp:1.1.4' + testCompile project(path: ":sdks:java:extensions:google-cloud-platform-core", configuration: "testRuntime") testCompile 'com.google.cloud:google-cloud-language:1.99.4' - testCompile library.java.junit testRuntimeOnly project(path: ":runners:direct-java", configuration: "shadow") testRuntimeOnly project(":runners:google-cloud-dataflow-java") } project.test { + def gcpProject = project.findProperty("gcpProject") ?: 'apache-beam-testing' include "**/**IT.class" + def pipelineOptions = [ + "--project=${gcpProject}" + ] + systemProperty "beamTestPipelineOptions", JsonOutput.toJson(pipelineOptions) } diff --git a/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/BatchRequestForDLP.java b/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/BatchRequestForDLP.java new file mode 100644 index 000000000000..aabac4e0fcda --- /dev/null +++ b/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/BatchRequestForDLP.java @@ -0,0 +1,113 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import com.google.privacy.dlp.v2.Table; +import java.util.ArrayList; +import java.util.List; +import java.util.concurrent.atomic.AtomicInteger; +import org.apache.beam.sdk.annotations.Experimental; +import org.apache.beam.sdk.metrics.Counter; +import org.apache.beam.sdk.metrics.Metrics; +import org.apache.beam.sdk.state.BagState; +import org.apache.beam.sdk.state.StateSpec; +import org.apache.beam.sdk.state.StateSpecs; +import org.apache.beam.sdk.state.TimeDomain; +import org.apache.beam.sdk.state.Timer; +import org.apache.beam.sdk.state.TimerSpec; +import org.apache.beam.sdk.state.TimerSpecs; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.windowing.BoundedWindow; +import org.apache.beam.sdk.values.KV; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** Batches input rows to reduce number of requests sent to Cloud DLP service. */ +@Experimental +class BatchRequestForDLP extends DoFn, KV>> { + public static final Logger LOG = LoggerFactory.getLogger(BatchRequestForDLP.class); + + private final Counter numberOfRowsBagged = + Metrics.counter(BatchRequestForDLP.class, "numberOfRowsBagged"); + + private final Integer batchSizeBytes; + + @StateId("elementsBag") + private final StateSpec>> elementsBag = StateSpecs.bag(); + + @TimerId("eventTimer") + private final TimerSpec eventTimer = TimerSpecs.timer(TimeDomain.EVENT_TIME); + + /** + * Constructs the batching DoFn. + * + * @param batchSize Desired batch size in bytes. + */ + public BatchRequestForDLP(Integer batchSize) { + this.batchSizeBytes = batchSize; + } + + @ProcessElement + public void process( + @Element KV element, + @StateId("elementsBag") BagState> elementsBag, + @TimerId("eventTimer") Timer eventTimer, + BoundedWindow w) { + elementsBag.add(element); + eventTimer.set(w.maxTimestamp()); + } + + /** + * Outputs the elements buffered in the elementsBag in batches of desired size. + * + * @param elementsBag element buffer. + * @param output Batched input elements. + */ + @OnTimer("eventTimer") + public void onTimer( + @StateId("elementsBag") BagState> elementsBag, + OutputReceiver>> output) { + if (elementsBag.read().iterator().hasNext()) { + String key = elementsBag.read().iterator().next().getKey(); + AtomicInteger bufferSize = new AtomicInteger(); + List rows = new ArrayList<>(); + elementsBag + .read() + .forEach( + element -> { + int elementSize = element.getValue().getSerializedSize(); + boolean clearBuffer = bufferSize.intValue() + elementSize > batchSizeBytes; + if (clearBuffer) { + LOG.debug( + "Clear buffer of {} bytes, Key {}", bufferSize.intValue(), element.getKey()); + numberOfRowsBagged.inc(rows.size()); + output.output(KV.of(element.getKey(), rows)); + rows.clear(); + bufferSize.set(0); + } + rows.add(element.getValue()); + bufferSize.getAndAdd(element.getValue().getSerializedSize()); + }); + if (!rows.isEmpty()) { + LOG.debug("Outputting remaining {} rows.", rows.size()); + numberOfRowsBagged.inc(rows.size()); + output.output(KV.of(key, rows)); + } + } + } +} diff --git a/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPDeidentifyText.java b/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPDeidentifyText.java new file mode 100644 index 000000000000..0502950c70f6 --- /dev/null +++ b/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPDeidentifyText.java @@ -0,0 +1,282 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import com.google.auto.value.AutoValue; +import com.google.cloud.dlp.v2.DlpServiceClient; +import com.google.privacy.dlp.v2.ContentItem; +import com.google.privacy.dlp.v2.DeidentifyConfig; +import com.google.privacy.dlp.v2.DeidentifyContentRequest; +import com.google.privacy.dlp.v2.DeidentifyContentResponse; +import com.google.privacy.dlp.v2.FieldId; +import com.google.privacy.dlp.v2.InspectConfig; +import com.google.privacy.dlp.v2.ProjectName; +import com.google.privacy.dlp.v2.Table; +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; +import java.util.stream.Collectors; +import javax.annotation.Nullable; +import org.apache.beam.sdk.annotations.Experimental; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.PCollectionView; + +/** + * A {@link PTransform} connecting to Cloud DLP (https://cloud.google.com/dlp/docs/libraries) and + * deidentifying text according to provided settings. The transform supports both columnar delimited + * input data (eg. CSV) and unstructured input. + * + *

    If the headerColumns property is set and a sideinput with table headers is added to the + * PTransform, delimiter also should be set, else the results will be incorrect. If headerColumns is + * neither set nor passed as side input, input is assumed to be unstructured. + * + *

    Either deidentifyTemplateName (String) or deidentifyConfig {@link DeidentifyConfig} need to be + * set. inspectTemplateName and inspectConfig ({@link InspectConfig} are optional. + * + *

    Batch size defines how big are batches sent to DLP at once in bytes. + * + *

    The transform consumes {@link KV} of {@link String}s (assumed to be filename as key and + * contents as value) and outputs {@link KV} of {@link String} (eg. filename) and {@link + * DeidentifyContentResponse}, which will contain {@link Table} of results for the user to consume. + */ +@Experimental +@AutoValue +public abstract class DLPDeidentifyText + extends PTransform< + PCollection>, PCollection>> { + + public static final Integer DLP_PAYLOAD_LIMIT_BYTES = 524000; + + /** @return Template name for data inspection. */ + @Nullable + public abstract String getInspectTemplateName(); + + /** @return Template name for data deidentification. */ + @Nullable + public abstract String getDeidentifyTemplateName(); + + /** + * @return Configuration object for data inspection. If present, supersedes the template settings. + */ + @Nullable + public abstract InspectConfig getInspectConfig(); + + /** @return Configuration object for deidentification. If present, supersedes the template. */ + @Nullable + public abstract DeidentifyConfig getDeidentifyConfig(); + + /** @return List of column names if the input KV value is a delimited row. */ + @Nullable + public abstract PCollectionView> getHeaderColumns(); + + /** @return Delimiter to be used when splitting values from input strings into columns. */ + @Nullable + public abstract String getColumnDelimiter(); + + /** @return Size of input elements batch to be sent to Cloud DLP service in one request. */ + public abstract Integer getBatchSizeBytes(); + + /** @return ID of Google Cloud project to be used when deidentifying data. */ + public abstract String getProjectId(); + + @AutoValue.Builder + public abstract static class Builder { + /** @param inspectTemplateName Template name for data inspection. */ + public abstract Builder setInspectTemplateName(String inspectTemplateName); + + /** @param headerColumns List of column names if the input KV value is a delimited row. */ + public abstract Builder setHeaderColumns(PCollectionView> headerColumns); + + /** + * @param delimiter Delimiter to be used when splitting values from input strings into columns. + */ + public abstract Builder setColumnDelimiter(String delimiter); + + /** + * @param batchSize Size of input elements batch to be sent to Cloud DLP service in one request. + */ + public abstract Builder setBatchSizeBytes(Integer batchSize); + + /** @param projectId ID of Google Cloud project to be used when deidentifying data. */ + public abstract Builder setProjectId(String projectId); + + /** @param deidentifyTemplateName Template name for data deidentification. */ + public abstract Builder setDeidentifyTemplateName(String deidentifyTemplateName); + + /** + * @param inspectConfig Configuration object for data inspection. If present, supersedes the + * template settings. + */ + public abstract Builder setInspectConfig(InspectConfig inspectConfig); + + /** + * @param deidentifyConfig Configuration object for data deidentification. If present, + * supersedes the template settings. + */ + public abstract Builder setDeidentifyConfig(DeidentifyConfig deidentifyConfig); + + abstract DLPDeidentifyText autoBuild(); + + public DLPDeidentifyText build() { + DLPDeidentifyText dlpDeidentifyText = autoBuild(); + if (dlpDeidentifyText.getDeidentifyConfig() == null + && dlpDeidentifyText.getDeidentifyTemplateName() == null) { + throw new IllegalArgumentException( + "Either deidentifyConfig or deidentifyTemplateName need to be set!"); + } + if (dlpDeidentifyText.getBatchSizeBytes() > DLP_PAYLOAD_LIMIT_BYTES) { + throw new IllegalArgumentException( + String.format( + "Batch size is too large! It should be smaller or equal than %d.", + DLP_PAYLOAD_LIMIT_BYTES)); + } + if (dlpDeidentifyText.getColumnDelimiter() == null + && dlpDeidentifyText.getHeaderColumns() != null) { + throw new IllegalArgumentException( + "Column delimiter should be set if headers are present."); + } + if (dlpDeidentifyText.getHeaderColumns() == null + && dlpDeidentifyText.getColumnDelimiter() != null) { + throw new IllegalArgumentException( + "Column headers should be supplied when delimiter is present."); + } + return dlpDeidentifyText; + } + } + + public static DLPDeidentifyText.Builder newBuilder() { + return new AutoValue_DLPDeidentifyText.Builder(); + } + + /** + * The transform converts the contents of input PCollection into {@link Table.Row}s and then calls + * Cloud DLP service to perform the deidentification according to provided settings. + * + * @param input input PCollection + * @return PCollection after transformations + */ + @Override + public PCollection> expand( + PCollection> input) { + return input + .apply(ParDo.of(new MapStringToDlpRow(getColumnDelimiter()))) + .apply("Batch Contents", ParDo.of(new BatchRequestForDLP(getBatchSizeBytes()))) + .apply( + "DLPDeidentify", + ParDo.of( + new DeidentifyText( + getProjectId(), + getInspectTemplateName(), + getDeidentifyTemplateName(), + getInspectConfig(), + getDeidentifyConfig(), + getHeaderColumns()))); + } + + /** DoFn performing calls to Cloud DLP service on GCP. */ + static class DeidentifyText + extends DoFn>, KV> { + private final String projectId; + private final String inspectTemplateName; + private final String deidentifyTemplateName; + private final InspectConfig inspectConfig; + private final DeidentifyConfig deidentifyConfig; + private final PCollectionView> headerColumns; + private transient DeidentifyContentRequest.Builder requestBuilder; + private transient DlpServiceClient dlpServiceClient; + + @Setup + public void setup() throws IOException { + requestBuilder = + DeidentifyContentRequest.newBuilder().setParent(ProjectName.of(projectId).toString()); + if (inspectTemplateName != null) { + requestBuilder.setInspectTemplateName(inspectTemplateName); + } + if (inspectConfig != null) { + requestBuilder.setInspectConfig(inspectConfig); + } + if (deidentifyConfig != null) { + requestBuilder.setDeidentifyConfig(deidentifyConfig); + } + if (deidentifyTemplateName != null) { + requestBuilder.setDeidentifyTemplateName(deidentifyTemplateName); + } + dlpServiceClient = DlpServiceClient.create(); + } + + @Teardown + public void teardown() { + dlpServiceClient.close(); + } + + /** + * @param projectId ID of GCP project that should be used for deidentification. + * @param inspectTemplateName Template name for inspection. Optional. + * @param deidentifyTemplateName Template name for deidentification. Either this or + * deidentifyConfig is required. + * @param inspectConfig Configuration object for inspection. Optional. + * @param deidentifyConfig Deidentification config containing data transformations. Either this + * or deidentifyTemplateName is required. + * @param headerColumns Header row of the table if applicable. + */ + public DeidentifyText( + String projectId, + String inspectTemplateName, + String deidentifyTemplateName, + InspectConfig inspectConfig, + DeidentifyConfig deidentifyConfig, + PCollectionView> headerColumns) { + this.projectId = projectId; + this.inspectTemplateName = inspectTemplateName; + this.deidentifyTemplateName = deidentifyTemplateName; + this.inspectConfig = inspectConfig; + this.deidentifyConfig = deidentifyConfig; + this.headerColumns = headerColumns; + } + + @ProcessElement + public void processElement(ProcessContext c) throws IOException { + String fileName = c.element().getKey(); + List dlpTableHeaders; + if (headerColumns != null) { + dlpTableHeaders = + c.sideInput(headerColumns).stream() + .map(header -> FieldId.newBuilder().setName(header).build()) + .collect(Collectors.toList()); + } else { + // handle unstructured input + dlpTableHeaders = new ArrayList<>(); + dlpTableHeaders.add(FieldId.newBuilder().setName("value").build()); + } + Table table = + Table.newBuilder() + .addAllHeaders(dlpTableHeaders) + .addAllRows(c.element().getValue()) + .build(); + ContentItem contentItem = ContentItem.newBuilder().setTable(table).build(); + this.requestBuilder.setItem(contentItem); + DeidentifyContentResponse response = + dlpServiceClient.deidentifyContent(this.requestBuilder.build()); + c.output(KV.of(fileName, response)); + } + } +} diff --git a/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPInspectText.java b/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPInspectText.java new file mode 100644 index 000000000000..ff58674fbfcc --- /dev/null +++ b/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPInspectText.java @@ -0,0 +1,240 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import com.google.auto.value.AutoValue; +import com.google.cloud.dlp.v2.DlpServiceClient; +import com.google.privacy.dlp.v2.ContentItem; +import com.google.privacy.dlp.v2.FieldId; +import com.google.privacy.dlp.v2.InspectConfig; +import com.google.privacy.dlp.v2.InspectContentRequest; +import com.google.privacy.dlp.v2.InspectContentResponse; +import com.google.privacy.dlp.v2.ProjectName; +import com.google.privacy.dlp.v2.Table; +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; +import java.util.stream.Collectors; +import javax.annotation.Nullable; +import org.apache.beam.sdk.annotations.Experimental; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.PCollectionView; + +/** + * A {@link PTransform} connecting to Cloud DLP (https://cloud.google.com/dlp/docs/libraries) and + * inspecting text for identifying data according to provided settings. The transform supports both + * delimited columnar input data (eg. CSV) and unstructured input. + * + *

    If the headerColumns property is set and a sideinput with table headers is added to the + * PTransform, delimiter also should be set, else the results will be incorrect. If headerColumns is + * neither set nor passed as sideinput, input is assumed to be unstructured. + * + *

    Batch size defines how big are batches sent to DLP at once in bytes. + * + *

    The transform consumes {@link KV} of {@link String}s (assumed to be filename as key and + * contents as value) and outputs {@link KV} of {@link String} (eg. filename) and {@link + * InspectContentResponse}, which will contain a list of {@link + * com.google.privacy.dlp.v2.InspectResult} for the user to consume. + * + *

    Either inspectTemplateName (String) or inspectConfig {@link InspectConfig} need to be set. + * + *

    Batch size defines how big are batches sent to DLP at once in bytes. + */ +@Experimental +@AutoValue +public abstract class DLPInspectText + extends PTransform< + PCollection>, PCollection>> { + + public static final Integer DLP_PAYLOAD_LIMIT_BYTES = 524000; + + /** @return Template name for data inspection. */ + @Nullable + public abstract String getInspectTemplateName(); + + /** + * @return Configuration object for data inspection. If present, supersedes the template settings. + */ + @Nullable + public abstract InspectConfig getInspectConfig(); + + /** @return Size of input elements batch to be sent to Cloud DLP service in one request. */ + public abstract Integer getBatchSizeBytes(); + + /** @return ID of Google Cloud project to be used when deidentifying data. */ + public abstract String getProjectId(); + + /** @return Delimiter to be used when splitting values from input strings into columns. */ + @Nullable + public abstract String getColumnDelimiter(); + + /** @return List of column names if the input KV value is a delimited row. */ + @Nullable + public abstract PCollectionView> getHeaderColumns(); + + @AutoValue.Builder + public abstract static class Builder { + /** @param inspectTemplateName Template name for data inspection. */ + public abstract Builder setInspectTemplateName(String inspectTemplateName); + + /** + * @param inspectConfig Configuration object for data inspection. If present, supersedes the + * template settings. + */ + public abstract Builder setInspectConfig(InspectConfig inspectConfig); + + /** + * @param batchSize Size of input elements batch to be sent to Cloud DLP service in one request. + */ + public abstract Builder setBatchSizeBytes(Integer batchSize); + + /** @param projectId ID of Google Cloud project to be used when deidentifying data. */ + public abstract Builder setProjectId(String projectId); + + /** + * @param delimiter Delimiter to be used when splitting values from input strings into columns. + */ + public abstract Builder setColumnDelimiter(String delimiter); + + /** @param headerColumns List of column names if the input KV value is a delimited row. */ + public abstract Builder setHeaderColumns(PCollectionView> headerColumns); + + abstract DLPInspectText autoBuild(); + + public DLPInspectText build() { + DLPInspectText inspectText = autoBuild(); + if (inspectText.getInspectTemplateName() == null && inspectText.getInspectConfig() == null) { + throw new IllegalArgumentException( + "Either inspectTemplateName or inspectConfig must be supplied!"); + } + if (inspectText.getBatchSizeBytes() > DLP_PAYLOAD_LIMIT_BYTES) { + throw new IllegalArgumentException( + String.format( + "Batch size is too large! It should be smaller or equal than %d.", + DLP_PAYLOAD_LIMIT_BYTES)); + } + if (inspectText.getColumnDelimiter() == null && inspectText.getHeaderColumns() != null) { + throw new IllegalArgumentException( + "Column delimiter should be set if headers are present."); + } + if (inspectText.getHeaderColumns() == null && inspectText.getColumnDelimiter() != null) { + throw new IllegalArgumentException( + "Column headers should be supplied when delimiter is present."); + } + return inspectText; + } + } + + public static Builder newBuilder() { + return new AutoValue_DLPInspectText.Builder(); + } + + /** + * The transform converts the contents of input PCollection into {@link Table.Row}s and then calls + * Cloud DLP service to perform the data inspection according to provided settings. + * + * @param input input PCollection + * @return PCollection after transformations + */ + @Override + public PCollection> expand( + PCollection> input) { + return input + .apply(ParDo.of(new MapStringToDlpRow(getColumnDelimiter()))) + .apply("Batch Contents", ParDo.of(new BatchRequestForDLP(getBatchSizeBytes()))) + .apply( + "DLPInspect", + ParDo.of( + new InspectData( + getProjectId(), + getInspectTemplateName(), + getInspectConfig(), + getHeaderColumns()))); + } + + /** Performs calls to Cloud DLP service on GCP to inspect input data. */ + static class InspectData + extends DoFn>, KV> { + private final String projectId; + private final String inspectTemplateName; + private final InspectConfig inspectConfig; + private final PCollectionView> headerColumns; + private transient DlpServiceClient dlpServiceClient; + private transient InspectContentRequest.Builder requestBuilder; + + /** + * @param projectId ID of GCP project that should be used for data inspection. + * @param inspectTemplateName Template name for inspection. + * @param inspectConfig Configuration object for inspection. + * @param headerColumns Header row of the table if applicable. + */ + public InspectData( + String projectId, + String inspectTemplateName, + InspectConfig inspectConfig, + PCollectionView> headerColumns) { + this.projectId = projectId; + this.inspectTemplateName = inspectTemplateName; + this.inspectConfig = inspectConfig; + this.headerColumns = headerColumns; + } + + @Setup + public void setup() throws IOException { + this.requestBuilder = + InspectContentRequest.newBuilder().setParent(ProjectName.of(this.projectId).toString()); + if (inspectTemplateName != null) { + requestBuilder.setInspectTemplateName(this.inspectTemplateName); + } + if (inspectConfig != null) { + requestBuilder.setInspectConfig(inspectConfig); + } + dlpServiceClient = DlpServiceClient.create(); + } + + @Teardown + public void teardown() { + dlpServiceClient.close(); + } + + @ProcessElement + public void processElement(ProcessContext c) throws IOException { + List tableHeaders; + if (headerColumns != null) { + tableHeaders = + c.sideInput(headerColumns).stream() + .map(header -> FieldId.newBuilder().setName(header).build()) + .collect(Collectors.toList()); + } else { + tableHeaders = new ArrayList<>(); + tableHeaders.add(FieldId.newBuilder().setName("value").build()); + } + Table table = + Table.newBuilder().addAllHeaders(tableHeaders).addAllRows(c.element().getValue()).build(); + ContentItem contentItem = ContentItem.newBuilder().setTable(table).build(); + this.requestBuilder.setItem(contentItem); + InspectContentResponse response = + dlpServiceClient.inspectContent(this.requestBuilder.build()); + c.output(KV.of(c.element().getKey(), response)); + } + } +} diff --git a/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPReidentifyText.java b/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPReidentifyText.java new file mode 100644 index 000000000000..5dc20cbc3697 --- /dev/null +++ b/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/DLPReidentifyText.java @@ -0,0 +1,286 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import com.google.auto.value.AutoValue; +import com.google.cloud.dlp.v2.DlpServiceClient; +import com.google.privacy.dlp.v2.ContentItem; +import com.google.privacy.dlp.v2.DeidentifyConfig; +import com.google.privacy.dlp.v2.FieldId; +import com.google.privacy.dlp.v2.InspectConfig; +import com.google.privacy.dlp.v2.ProjectName; +import com.google.privacy.dlp.v2.ReidentifyContentRequest; +import com.google.privacy.dlp.v2.ReidentifyContentResponse; +import com.google.privacy.dlp.v2.Table; +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; +import java.util.stream.Collectors; +import javax.annotation.Nullable; +import org.apache.beam.sdk.annotations.Experimental; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.PCollectionView; + +/** + * A {@link PTransform} connecting to Cloud DLP (https://cloud.google.com/dlp/docs/libraries) and + * inspecting text for identifying data according to provided settings. + * + *

    The transform supports both delimited columnar input data and unstructured input. + * + *

    If the headerColumns property is set and a sideinput with headers is added to the PTransform, + * delimiter also should be set, else the results will be incorrect. If headerColumns is neither set + * nor passed as sideinput, input is assumed to be unstructured. + * + *

    Batch size defines how big are batches sent to DLP at once in bytes. + * + *

    The transform consumes {@link KV} of {@link String}s (assumed to be filename as key and + * contents as value) and outputs {@link KV} of {@link String} (eg. filename) and {@link + * ReidentifyContentResponse}, which will contain {@link Table} of results for the user to consume. + * + *

    Batch size defines how big are batches sent to DLP at once in bytes. + * + *

    Either reidentifyTemplateName {@link String} or reidentifyConfig {@link DeidentifyConfig} need + * to be set. inspectConfig {@link InspectConfig} and inspectTemplateName {@link String} are + * optional. + * + *

    Batch size defines how big are batches sent to DLP at once in bytes. + */ +@Experimental +@AutoValue +public abstract class DLPReidentifyText + extends PTransform< + PCollection>, PCollection>> { + + public static final Integer DLP_PAYLOAD_LIMIT_BYTES = 524000; + + /** @return Template name for data inspection. */ + @Nullable + public abstract String getInspectTemplateName(); + + /** @return Template name for data reidentification. */ + @Nullable + public abstract String getReidentifyTemplateName(); + + /** + * @return Configuration object for data inspection. If present, supersedes the template settings. + */ + @Nullable + public abstract InspectConfig getInspectConfig(); + + /** @return Configuration object for reidentification. If present, supersedes the template. */ + @Nullable + public abstract DeidentifyConfig getReidentifyConfig(); + + /** @return Delimiter to be used when splitting values from input strings into columns. */ + @Nullable + public abstract String getColumnDelimiter(); + + /** @return List of column names if the input KV value is a delimited row. */ + @Nullable + public abstract PCollectionView> getHeaderColumns(); + + /** @return Size of input elements batch to be sent to Cloud DLP service in one request. */ + public abstract Integer getBatchSizeBytes(); + + /** @return ID of Google Cloud project to be used when deidentifying data. */ + public abstract String getProjectId(); + + @AutoValue.Builder + public abstract static class Builder { + /** @param inspectTemplateName Template name for data inspection. */ + public abstract Builder setInspectTemplateName(String inspectTemplateName); + + /** + * @param inspectConfig Configuration object for data inspection. If present, supersedes the + * template settings. + */ + public abstract Builder setInspectConfig(InspectConfig inspectConfig); + + /** + * @param reidentifyConfig Configuration object for data deidentification. If present, + * supersedes the template settings. + */ + public abstract Builder setReidentifyConfig(DeidentifyConfig reidentifyConfig); + + /** @param reidentifyTemplateName Template name for data deidentification. */ + public abstract Builder setReidentifyTemplateName(String reidentifyTemplateName); + + /** + * @param batchSize Size of input elements batch to be sent to Cloud DLP service in one request. + */ + public abstract Builder setBatchSizeBytes(Integer batchSize); + /** @param headerColumns List of column names if the input KV value is a delimited row. */ + public abstract Builder setHeaderColumns(PCollectionView> headerColumns); + + /** + * @param delimiter Delimiter to be used when splitting values from input strings into columns. + */ + public abstract Builder setColumnDelimiter(String delimiter); + + /** @param projectId ID of Google Cloud project to be used when deidentifying data. */ + public abstract Builder setProjectId(String projectId); + + abstract DLPReidentifyText autoBuild(); + + public DLPReidentifyText build() { + DLPReidentifyText dlpReidentifyText = autoBuild(); + if (dlpReidentifyText.getReidentifyConfig() == null + && dlpReidentifyText.getReidentifyTemplateName() == null) { + throw new IllegalArgumentException( + "Either reidentifyConfig or reidentifyTemplateName need to be set!"); + } + if (dlpReidentifyText.getBatchSizeBytes() > DLP_PAYLOAD_LIMIT_BYTES) { + throw new IllegalArgumentException( + String.format( + "Batch size is too large! It should be smaller or equal than %d.", + DLP_PAYLOAD_LIMIT_BYTES)); + } + if (dlpReidentifyText.getColumnDelimiter() == null + && dlpReidentifyText.getHeaderColumns() != null) { + throw new IllegalArgumentException( + "Column delimiter should be set if headers are present."); + } + if (dlpReidentifyText.getHeaderColumns() == null + && dlpReidentifyText.getColumnDelimiter() != null) { + throw new IllegalArgumentException( + "Column headers should be supplied when delimiter is present."); + } + return dlpReidentifyText; + } + } + + public static DLPReidentifyText.Builder newBuilder() { + return new AutoValue_DLPReidentifyText.Builder(); + } + + /** + * The transform converts the contents of input PCollection into {@link Table.Row}s and then calls + * Cloud DLP service to perform the reidentification according to provided settings. + * + * @param input input PCollection + * @return PCollection after transformations + */ + @Override + public PCollection> expand( + PCollection> input) { + return input + .apply(ParDo.of(new MapStringToDlpRow(getColumnDelimiter()))) + .apply("Batch Contents", ParDo.of(new BatchRequestForDLP(getBatchSizeBytes()))) + .apply( + "DLPReidentify", + ParDo.of( + new ReidentifyText( + getProjectId(), + getInspectTemplateName(), + getReidentifyTemplateName(), + getInspectConfig(), + getReidentifyConfig(), + getHeaderColumns()))); + } + + /** Performs the calls to Cloud DLP service on GCP. */ + static class ReidentifyText + extends DoFn>, KV> { + private final String projectId; + private final String inspectTemplateName; + private final String reidentifyTemplateName; + private final InspectConfig inspectConfig; + private final DeidentifyConfig reidentifyConfig; + private final PCollectionView> headerColumns; + private transient ReidentifyContentRequest.Builder requestBuilder; + private transient DlpServiceClient dlpServiceClient; + + @Setup + public void setup() throws IOException { + requestBuilder = + ReidentifyContentRequest.newBuilder().setParent(ProjectName.of(projectId).toString()); + if (inspectTemplateName != null) { + requestBuilder.setInspectTemplateName(inspectTemplateName); + } + if (inspectConfig != null) { + requestBuilder.setInspectConfig(inspectConfig); + } + if (reidentifyConfig != null) { + requestBuilder.setReidentifyConfig(reidentifyConfig); + } + if (reidentifyTemplateName != null) { + requestBuilder.setReidentifyTemplateName(reidentifyTemplateName); + } + dlpServiceClient = DlpServiceClient.create(); + } + + @Teardown + public void teardown() { + dlpServiceClient.close(); + } + + /** + * @param projectId ID of GCP project that should be used for deidentification. + * @param inspectTemplateName Template name for inspection. Optional. + * @param reidentifyTemplateName Template name for reidentification. Either this or + * reidentifyConfig is required. + * @param inspectConfig Configuration object for inspection. Optional. + * @param reidentifyConfig Reidentification config containing data transformations. Either this + * or reidentifyTemplateName is required. + * @param headerColumns Header row of the table if applicable. + */ + public ReidentifyText( + String projectId, + String inspectTemplateName, + String reidentifyTemplateName, + InspectConfig inspectConfig, + DeidentifyConfig reidentifyConfig, + PCollectionView> headerColumns) { + this.projectId = projectId; + this.inspectTemplateName = inspectTemplateName; + this.reidentifyTemplateName = reidentifyTemplateName; + this.inspectConfig = inspectConfig; + this.reidentifyConfig = reidentifyConfig; + this.headerColumns = headerColumns; + } + + @ProcessElement + public void processElement(ProcessContext context) throws IOException { + List tableHeaders; + if (headerColumns != null) { + tableHeaders = + context.sideInput(headerColumns).stream() + .map(header -> FieldId.newBuilder().setName(header).build()) + .collect(Collectors.toList()); + } else { + // handle unstructured input. + tableHeaders = new ArrayList<>(); + tableHeaders.add(FieldId.newBuilder().setName("value").build()); + } + Table table = + Table.newBuilder() + .addAllHeaders(tableHeaders) + .addAllRows(context.element().getValue()) + .build(); + ContentItem contentItem = ContentItem.newBuilder().setTable(table).build(); + this.requestBuilder.setItem(contentItem); + ReidentifyContentResponse response = + dlpServiceClient.reidentifyContent(requestBuilder.build()); + context.output(KV.of(context.element().getKey(), response)); + } + } +} diff --git a/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/MapStringToDlpRow.java b/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/MapStringToDlpRow.java new file mode 100644 index 000000000000..944656c59fb1 --- /dev/null +++ b/sdks/java/extensions/ml/src/main/java/org/apache/beam/sdk/extensions/ml/MapStringToDlpRow.java @@ -0,0 +1,59 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import com.google.privacy.dlp.v2.Table; +import com.google.privacy.dlp.v2.Value; +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.values.KV; + +/** + * Maps {@link KV}s of {@link String}s into KV<{@link String}, {@link Table.Row}> for further + * processing in the DLP transforms. + * + *

    If a delimiter of values isn't provided, input is assumed to be unstructured and the input KV + * value is saved in a single column of output {@link Table.Row}. + */ +class MapStringToDlpRow extends DoFn, KV> { + private final String delimiter; + + /** + * @param delimiter Delimiter of values in the delimited value row that may be in the value of + * input KV. + */ + public MapStringToDlpRow(String delimiter) { + this.delimiter = delimiter; + } + + @ProcessElement + public void processElement(ProcessContext context) { + Table.Row.Builder rowBuilder = Table.Row.newBuilder(); + String line = Objects.requireNonNull(context.element().getValue()); + if (delimiter != null) { + List values = Arrays.asList(line.split(delimiter)); + values.forEach( + value -> rowBuilder.addValues(Value.newBuilder().setStringValue(value).build())); + } else { + rowBuilder.addValues(Value.newBuilder().setStringValue(line).build()); + } + context.output(KV.of(context.element().getKey(), rowBuilder.build())); + } +} diff --git a/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/BatchRequestForDlpTest.java b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/BatchRequestForDlpTest.java new file mode 100644 index 000000000000..3e9a74178929 --- /dev/null +++ b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/BatchRequestForDlpTest.java @@ -0,0 +1,63 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import static org.junit.Assert.assertEquals; + +import com.google.privacy.dlp.v2.Table; +import java.util.ArrayList; +import java.util.List; +import org.apache.beam.sdk.testing.PAssert; +import org.apache.beam.sdk.testing.TestPipeline; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.transforms.SerializableFunction; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.sdk.values.PCollection; +import org.junit.Rule; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +@RunWith(JUnit4.class) +public class BatchRequestForDlpTest { + + @Rule public TestPipeline testPipeline = TestPipeline.create(); + + @Test + public void batchesRequests() { + PCollection>> batchedRows = + testPipeline + .apply(Create.of(KV.of("key", "value1"), KV.of("key", "value2"))) + .apply(ParDo.of(new MapStringToDlpRow(null))) + .apply(ParDo.of(new BatchRequestForDLP(524000))); + PAssert.that(batchedRows).satisfies(new VerifyPCollectionSize()); + testPipeline.run().waitUntilFinish(); + } + + private static class VerifyPCollectionSize + implements SerializableFunction>>, Void> { + @Override + public Void apply(Iterable>> input) { + List>> itemList = new ArrayList<>(); + input.forEach(itemList::add); + assertEquals(1, itemList.size()); + return null; + } + } +} diff --git a/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPDeidentifyTextTest.java b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPDeidentifyTextTest.java new file mode 100644 index 000000000000..c2e5741d81db --- /dev/null +++ b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPDeidentifyTextTest.java @@ -0,0 +1,101 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import static org.junit.Assert.assertThrows; + +import java.util.List; +import org.apache.beam.sdk.testing.TestPipeline; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.View; +import org.apache.beam.sdk.values.PCollectionView; +import org.junit.Rule; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +@RunWith(JUnit4.class) +public class DLPDeidentifyTextTest { + + @Rule public TestPipeline testPipeline = TestPipeline.create(); + + private static final Integer BATCH_SIZE_SMALL = 200; + private static final String DELIMITER = ";"; + private static final String TEMPLATE_NAME = "test_template"; + private static final String PROJECT_ID = "test_id"; + + @Test + public void throwsExceptionWhenDeidentifyConfigAndTemplatesAreEmpty() { + assertThrows( + "Either deidentifyConfig or deidentifyTemplateName need to be set!", + IllegalArgumentException.class, + () -> + DLPDeidentifyText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(BATCH_SIZE_SMALL) + .setColumnDelimiter(DELIMITER) + .build()); + } + + @Test + public void throwsExceptionWhenDelimiterIsNullAndHeadersAreSet() { + PCollectionView> header = + testPipeline.apply(Create.of("header")).apply(View.asList()); + assertThrows( + "Column delimiter should be set if headers are present.", + IllegalArgumentException.class, + () -> + DLPDeidentifyText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(BATCH_SIZE_SMALL) + .setDeidentifyTemplateName(TEMPLATE_NAME) + .setHeaderColumns(header) + .build()); + testPipeline.run().waitUntilFinish(); + } + + @Test + public void throwsExceptionWhenBatchSizeIsTooLarge() { + assertThrows( + String.format( + "Batch size is too large! It should be smaller or equal than %d.", + DLPDeidentifyText.DLP_PAYLOAD_LIMIT_BYTES), + IllegalArgumentException.class, + () -> + DLPDeidentifyText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(Integer.MAX_VALUE) + .setDeidentifyTemplateName(TEMPLATE_NAME) + .setColumnDelimiter(DELIMITER) + .build()); + } + + @Test + public void throwsExceptionWhenDelimiterIsSetAndHeadersAreNot() { + assertThrows( + "Column headers should be supplied when delimiter is present.", + IllegalArgumentException.class, + () -> + DLPDeidentifyText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(BATCH_SIZE_SMALL) + .setDeidentifyTemplateName(TEMPLATE_NAME) + .setColumnDelimiter(DELIMITER) + .build()); + } +} diff --git a/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPInspectTextTest.java b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPInspectTextTest.java new file mode 100644 index 000000000000..46c8fa3a3096 --- /dev/null +++ b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPInspectTextTest.java @@ -0,0 +1,101 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import static org.junit.Assert.assertThrows; + +import java.util.List; +import org.apache.beam.sdk.testing.TestPipeline; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.View; +import org.apache.beam.sdk.values.PCollectionView; +import org.junit.Rule; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +@RunWith(JUnit4.class) +public class DLPInspectTextTest { + + @Rule public TestPipeline testPipeline = TestPipeline.create(); + + private static final Integer BATCH_SIZE_SMALL = 200; + private static final String DELIMITER = ";"; + private static final String TEMPLATE_NAME = "test_template"; + private static final String PROJECT_ID = "test_id"; + + @Test + public void throwsExceptionWhenDeidentifyConfigAndTemplatesAreEmpty() { + assertThrows( + "Either inspectTemplateName or inspectConfig must be supplied!", + IllegalArgumentException.class, + () -> + DLPInspectText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(BATCH_SIZE_SMALL) + .setColumnDelimiter(DELIMITER) + .build()); + } + + @Test + public void throwsExceptionWhenDelimiterIsNullAndHeadersAreSet() { + PCollectionView> header = + testPipeline.apply(Create.of("header")).apply(View.asList()); + assertThrows( + "Column delimiter should be set if headers are present.", + IllegalArgumentException.class, + () -> + DLPInspectText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(BATCH_SIZE_SMALL) + .setInspectTemplateName(TEMPLATE_NAME) + .setHeaderColumns(header) + .build()); + testPipeline.run().waitUntilFinish(); + } + + @Test + public void throwsExceptionWhenBatchSizeIsTooLarge() { + assertThrows( + String.format( + "Batch size is too large! It should be smaller or equal than %d.", + DLPInspectText.DLP_PAYLOAD_LIMIT_BYTES), + IllegalArgumentException.class, + () -> + DLPInspectText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(Integer.MAX_VALUE) + .setInspectTemplateName(TEMPLATE_NAME) + .setColumnDelimiter(DELIMITER) + .build()); + } + + @Test + public void throwsExceptionWhenDelimiterIsSetAndHeadersAreNot() { + assertThrows( + "Column headers should be supplied when delimiter is present.", + IllegalArgumentException.class, + () -> + DLPInspectText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(BATCH_SIZE_SMALL) + .setInspectTemplateName(TEMPLATE_NAME) + .setColumnDelimiter(DELIMITER) + .build()); + } +} diff --git a/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPReidentifyTextTest.java b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPReidentifyTextTest.java new file mode 100644 index 000000000000..9fc0f0a9d7a7 --- /dev/null +++ b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPReidentifyTextTest.java @@ -0,0 +1,101 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import static org.junit.Assert.assertThrows; + +import java.util.List; +import org.apache.beam.sdk.testing.TestPipeline; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.View; +import org.apache.beam.sdk.values.PCollectionView; +import org.junit.Rule; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +@RunWith(JUnit4.class) +public class DLPReidentifyTextTest { + + @Rule public TestPipeline testPipeline = TestPipeline.create(); + + private static final Integer BATCH_SIZE_SMALL = 200; + private static final String DELIMITER = ";"; + private static final String TEMPLATE_NAME = "test_template"; + private static final String PROJECT_ID = "test_id"; + + @Test + public void throwsExceptionWhenDeidentifyConfigAndTemplatesAreEmpty() { + assertThrows( + "Either reidentifyConfig or reidentifyTemplateName need to be set!", + IllegalArgumentException.class, + () -> + DLPReidentifyText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(BATCH_SIZE_SMALL) + .setColumnDelimiter(DELIMITER) + .build()); + } + + @Test + public void throwsExceptionWhenDelimiterIsNullAndHeadersAreSet() { + PCollectionView> header = + testPipeline.apply(Create.of("header")).apply(View.asList()); + assertThrows( + "Column delimiter should be set if headers are present.", + IllegalArgumentException.class, + () -> + DLPReidentifyText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(BATCH_SIZE_SMALL) + .setReidentifyTemplateName(TEMPLATE_NAME) + .setHeaderColumns(header) + .build()); + testPipeline.run().waitUntilFinish(); + } + + @Test + public void throwsExceptionWhenBatchSizeIsTooLarge() { + assertThrows( + String.format( + "Batch size is too large! It should be smaller or equal than %d.", + DLPDeidentifyText.DLP_PAYLOAD_LIMIT_BYTES), + IllegalArgumentException.class, + () -> + DLPReidentifyText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(Integer.MAX_VALUE) + .setReidentifyTemplateName(TEMPLATE_NAME) + .setColumnDelimiter(DELIMITER) + .build()); + } + + @Test + public void throwsExceptionWhenDelimiterIsSetAndHeadersAreNot() { + assertThrows( + "Column headers should be supplied when delimiter is present.", + IllegalArgumentException.class, + () -> + DLPReidentifyText.newBuilder() + .setProjectId(PROJECT_ID) + .setBatchSizeBytes(BATCH_SIZE_SMALL) + .setReidentifyTemplateName(TEMPLATE_NAME) + .setColumnDelimiter(DELIMITER) + .build()); + } +} diff --git a/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPTextOperationsIT.java b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPTextOperationsIT.java new file mode 100644 index 000000000000..0ebbfb7b0008 --- /dev/null +++ b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/DLPTextOperationsIT.java @@ -0,0 +1,159 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import static org.junit.Assert.assertTrue; + +import com.google.privacy.dlp.v2.CharacterMaskConfig; +import com.google.privacy.dlp.v2.DeidentifyConfig; +import com.google.privacy.dlp.v2.DeidentifyContentResponse; +import com.google.privacy.dlp.v2.FieldId; +import com.google.privacy.dlp.v2.Finding; +import com.google.privacy.dlp.v2.InfoType; +import com.google.privacy.dlp.v2.InfoTypeTransformations; +import com.google.privacy.dlp.v2.InspectConfig; +import com.google.privacy.dlp.v2.InspectContentResponse; +import com.google.privacy.dlp.v2.Likelihood; +import com.google.privacy.dlp.v2.PrimitiveTransformation; +import java.util.ArrayList; +import java.util.List; +import org.apache.beam.sdk.extensions.gcp.options.GcpOptions; +import org.apache.beam.sdk.testing.PAssert; +import org.apache.beam.sdk.testing.TestPipeline; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.SerializableFunction; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.sdk.values.PCollection; +import org.junit.Rule; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +@RunWith(JUnit4.class) +public class DLPTextOperationsIT { + @Rule public TestPipeline testPipeline = TestPipeline.create(); + + private static final String IDENTIFYING_TEXT = "mary.sue@example.com"; + private static InfoType emailAddress = InfoType.newBuilder().setName("EMAIL_ADDRESS").build(); + private static final InspectConfig inspectConfig = + InspectConfig.newBuilder() + .addInfoTypes(emailAddress) + .setMinLikelihood(Likelihood.LIKELY) + .build(); + + @Test + public void inspectsText() { + String projectId = testPipeline.getOptions().as(GcpOptions.class).getProject(); + PCollection> inspectionResult = + testPipeline + .apply(Create.of(KV.of("", IDENTIFYING_TEXT))) + .apply( + DLPInspectText.newBuilder() + .setBatchSizeBytes(524000) + .setProjectId(projectId) + .setInspectConfig(inspectConfig) + .build()); + PAssert.that(inspectionResult).satisfies(new VerifyInspectionResult()); + testPipeline.run().waitUntilFinish(); + } + + @Test + public void deidentifiesText() { + String projectId = testPipeline.getOptions().as(GcpOptions.class).getProject(); + + PCollection> deidentificationResult = + testPipeline + .apply(Create.of(KV.of("", IDENTIFYING_TEXT))) + .apply( + DLPDeidentifyText.newBuilder() + .setBatchSizeBytes(524000) + .setProjectId(projectId) + .setDeidentifyConfig(getDeidentifyConfig()) + .build()); + PAssert.that(deidentificationResult) + .satisfies(new VerifyDeidentificationResult("####################")); + testPipeline.run().waitUntilFinish(); + } + + private DeidentifyConfig getDeidentifyConfig() { + CharacterMaskConfig characterMaskConfig = + CharacterMaskConfig.newBuilder().setMaskingCharacter("#").build(); + PrimitiveTransformation primitiveTransformation = + PrimitiveTransformation.newBuilder().setCharacterMaskConfig(characterMaskConfig).build(); + InfoTypeTransformations.InfoTypeTransformation infoTypeTransformation = + InfoTypeTransformations.InfoTypeTransformation.newBuilder() + .addInfoTypes(emailAddress) + .setPrimitiveTransformation(primitiveTransformation) + .build(); + return DeidentifyConfig.newBuilder() + .setInfoTypeTransformations( + InfoTypeTransformations.newBuilder().addTransformations(infoTypeTransformation).build()) + .build(); + } + + private static class VerifyInspectionResult + implements SerializableFunction>, Void> { + @Override + public Void apply(Iterable> input) { + List matches = new ArrayList<>(); + input.forEach( + item -> { + List resultList = item.getValue().getResult().getFindingsList(); + matches.add( + resultList.stream() + .anyMatch(finding -> finding.getInfoType().equals(emailAddress))); + }); + assertTrue(matches.contains(Boolean.TRUE)); + return null; + } + } + + private static class VerifyDeidentificationResult + implements SerializableFunction>, Void> { + private final String expectedValue; + + public VerifyDeidentificationResult(String expectedValue) { + this.expectedValue = expectedValue; + } + + @Override + public Void apply(Iterable> input) { + List matches = new ArrayList<>(); + input.forEach( + item -> { + item.getValue() + .getItem() + .getTable() + .getRowsList() + .forEach( + row -> + matches.add( + row.getValuesList().stream() + .anyMatch(value -> value.getStringValue().equals(expectedValue)))); + assertTrue( + item.getValue() + .getItem() + .getTable() + .getHeadersList() + .contains(FieldId.newBuilder().setName("value").build())); + }); + assertTrue(matches.contains(Boolean.TRUE)); + return null; + } + } +} diff --git a/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/MapStringToDlpRowTest.java b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/MapStringToDlpRowTest.java new file mode 100644 index 000000000000..577a5dc7ed34 --- /dev/null +++ b/sdks/java/extensions/ml/src/test/java/org/apache/beam/sdk/extensions/ml/MapStringToDlpRowTest.java @@ -0,0 +1,69 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.extensions.ml; + +import com.google.privacy.dlp.v2.Table; +import com.google.privacy.dlp.v2.Value; +import org.apache.beam.sdk.testing.PAssert; +import org.apache.beam.sdk.testing.TestPipeline; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.sdk.values.PCollection; +import org.junit.Rule; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.JUnit4; + +@RunWith(JUnit4.class) +public class MapStringToDlpRowTest { + @Rule public TestPipeline testPipeline = TestPipeline.create(); + + @Test + public void mapsStringToRow() { + PCollection> rowCollection = + testPipeline + .apply(Create.of(KV.of("key", "value"))) + .apply(ParDo.of(new MapStringToDlpRow(null))); + PAssert.that(rowCollection) + .containsInAnyOrder( + KV.of( + "key", + Table.Row.newBuilder() + .addValues(Value.newBuilder().setStringValue("value").build()) + .build())); + testPipeline.run().waitUntilFinish(); + } + + @Test + public void mapsDelimitedStringToRow() { + PCollection> rowCollection = + testPipeline + .apply(Create.of(KV.of("key", "value,secondValue"))) + .apply(ParDo.of(new MapStringToDlpRow(","))); + PAssert.that(rowCollection) + .containsInAnyOrder( + KV.of( + "key", + Table.Row.newBuilder() + .addValues(Value.newBuilder().setStringValue("value").build()) + .addValues(Value.newBuilder().setStringValue("secondValue").build()) + .build())); + testPipeline.run().waitUntilFinish(); + } +} From 006b8ceafab48fbbbe84eeceb723b0fd8a4950ae Mon Sep 17 00:00:00 2001 From: Piotr Szuberski Date: Tue, 2 Jun 2020 14:47:20 +0200 Subject: [PATCH 139/151] [BEAM-10171] Add Kinesis, Spanner, Jdbc IOs to the portability roadmap --- website/www/site/content/en/roadmap/connectors-multi-sdk.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/website/www/site/content/en/roadmap/connectors-multi-sdk.md b/website/www/site/content/en/roadmap/connectors-multi-sdk.md index 55d11fd73d32..500c44c58545 100644 --- a/website/www/site/content/en/roadmap/connectors-multi-sdk.md +++ b/website/www/site/content/en/roadmap/connectors-multi-sdk.md @@ -76,8 +76,11 @@ Work related to making cross-language transforms available on Direct runner Ongoing and planned work related to making existing connectors/transforms available to other SDKs through the cross-language transforms framework. +* Java JdbcIO - In progress - [BEAM-10135](https://issues.apache.org/jira/browse/BEAM-10135), [BEAM-10136](https://issues.apache.org/jira/browse/BEAM-10136) * Java KafkaIO - completed - [BEAM-7029](https://issues.apache.org/jira/browse/BEAM-7029) +* Java KinesisIO - In progress - [BEAM-10137](https://issues.apache.org/jira/browse/BEAM-10137), [BEAM-10138](https://issues.apache.org/jira/browse/BEAM-10138) * Java PubSubIO - In progress - [BEAM-7738](https://issues.apache.org/jira/browse/BEAM-7738) +* Java SpannerIO - In progress - [BEAM-10139](https://issues.apache.org/jira/browse/BEAM-10139), [BEAM-10140](https://issues.apache.org/jira/browse/BEAM-10140) * Java SQL - completed - [BEAM-8603](https://issues.apache.org/jira/browse/BEAM-8603) ### Portable Beam schema From 0c451363db15126025d2b558213945c0bc0071b3 Mon Sep 17 00:00:00 2001 From: David Moravek Date: Fri, 29 May 2020 16:43:22 +0200 Subject: [PATCH 140/151] [BEAM-8850,BEAM-8849] FlinkBatchTranslationContext respects input parameters during lookups. Add support for a multiple translation variants for a single urn. --- .../flink/FlinkBatchPipelineTranslator.java | 15 ++- .../flink/FlinkBatchTransformTranslators.java | 52 ++++++---- .../flink/FlinkBatchTranslationContext.java | 61 +++++++----- .../utils/CountingPipelineVisitor.java | 47 +++++++++ .../utils/LookupPipelineVisitor.java | 98 +++++++++++++++++++ 5 files changed, 221 insertions(+), 52 deletions(-) create mode 100644 runners/flink/src/main/java/org/apache/beam/runners/flink/translation/utils/CountingPipelineVisitor.java create mode 100644 runners/flink/src/main/java/org/apache/beam/runners/flink/translation/utils/LookupPipelineVisitor.java diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchPipelineTranslator.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchPipelineTranslator.java index 772c9c9a8dce..7286713019ef 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchPipelineTranslator.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchPipelineTranslator.java @@ -46,6 +46,7 @@ public FlinkBatchPipelineTranslator(ExecutionEnvironment env, PipelineOptions op @Override @SuppressWarnings("rawtypes, unchecked") public void translate(Pipeline pipeline) { + batchContext.init(pipeline); super.translate(pipeline); // terminate dangling DataSets @@ -63,7 +64,7 @@ public CompositeBehavior enterCompositeTransform(TransformHierarchy.Node node) { LOG.info("{} enterCompositeTransform- {}", genSpaces(this.depth), node.getFullName()); this.depth++; - BatchTransformTranslator translator = getTranslator(node); + BatchTransformTranslator translator = getTranslator(node, batchContext); if (translator != null) { applyBatchTransform(node.getTransform(), node, translator); @@ -88,7 +89,7 @@ public void visitPrimitiveTransform(TransformHierarchy.Node node) { // currently visiting and translate it into its Flink alternative. PTransform transform = node.getTransform(); BatchTransformTranslator translator = - FlinkBatchTransformTranslators.getTranslator(transform); + FlinkBatchTransformTranslators.getTranslator(transform, batchContext); if (translator == null) { String transformUrn = PTransformTranslation.urnForTransform(transform); throw new UnsupportedOperationException( @@ -115,11 +116,17 @@ public void visitPrimitiveTransform(TransformHierarchy.Node node) { /** A translator of a {@link PTransform}. */ public interface BatchTransformTranslator { + + default boolean canTranslate(TransformT transform, FlinkBatchTranslationContext context) { + return true; + } + void translateNode(TransformT transform, FlinkBatchTranslationContext context); } /** Returns a translator for the given node, if it is possible, otherwise null. */ - private static BatchTransformTranslator getTranslator(TransformHierarchy.Node node) { + private static BatchTransformTranslator getTranslator( + TransformHierarchy.Node node, FlinkBatchTranslationContext context) { @Nullable PTransform transform = node.getTransform(); // Root of the graph is null @@ -127,6 +134,6 @@ private static BatchTransformTranslator getTranslator(TransformHierarchy.Node return null; } - return FlinkBatchTransformTranslators.getTranslator(transform); + return FlinkBatchTransformTranslators.getTranslator(transform, context); } } diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java index 8e3b623850be..3f5104d1b7c3 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java @@ -105,40 +105,50 @@ class FlinkBatchTransformTranslators { // -------------------------------------------------------------------------------------------- @SuppressWarnings("rawtypes") - private static final Map + private static final Map> TRANSLATORS = new HashMap<>(); - static { - TRANSLATORS.put(PTransformTranslation.IMPULSE_TRANSFORM_URN, new ImpulseTranslatorBatch()); + private static void registerTranslator( + String urn, FlinkBatchPipelineTranslator.BatchTransformTranslator translator) { + if (!TRANSLATORS.containsKey(urn)) { + TRANSLATORS.put(urn, new ArrayList<>()); + } + TRANSLATORS.get(urn).add(translator); + } - TRANSLATORS.put( + static { + registerTranslator(PTransformTranslation.IMPULSE_TRANSFORM_URN, new ImpulseTranslatorBatch()); + registerTranslator( PTransformTranslation.CREATE_VIEW_TRANSFORM_URN, new CreatePCollectionViewTranslatorBatch()); - - TRANSLATORS.put( + registerTranslator( PTransformTranslation.COMBINE_PER_KEY_TRANSFORM_URN, new CombinePerKeyTranslatorBatch()); - TRANSLATORS.put( + registerTranslator( PTransformTranslation.GROUP_BY_KEY_TRANSFORM_URN, new GroupByKeyTranslatorBatch()); - TRANSLATORS.put(PTransformTranslation.RESHUFFLE_URN, new ReshuffleTranslatorBatch()); - - TRANSLATORS.put( + registerTranslator(PTransformTranslation.RESHUFFLE_URN, new ReshuffleTranslatorBatch()); + registerTranslator( PTransformTranslation.FLATTEN_TRANSFORM_URN, new FlattenPCollectionTranslatorBatch()); - - TRANSLATORS.put( + registerTranslator( PTransformTranslation.ASSIGN_WINDOWS_TRANSFORM_URN, new WindowAssignTranslatorBatch()); - - TRANSLATORS.put(PTransformTranslation.PAR_DO_TRANSFORM_URN, new ParDoTranslatorBatch()); - - TRANSLATORS.put(PTransformTranslation.READ_TRANSFORM_URN, new ReadSourceTranslatorBatch()); + registerTranslator(PTransformTranslation.PAR_DO_TRANSFORM_URN, new ParDoTranslatorBatch()); + registerTranslator(PTransformTranslation.READ_TRANSFORM_URN, new ReadSourceTranslatorBatch()); } + @SuppressWarnings("unchecked") static FlinkBatchPipelineTranslator.BatchTransformTranslator getTranslator( - PTransform transform) { - @Nullable String urn = PTransformTranslation.urnForTransformOrNull(transform); - return urn == null ? null : TRANSLATORS.get(urn); + PTransform transform, FlinkBatchTranslationContext context) { + @Nullable final String urn = PTransformTranslation.urnForTransformOrNull(transform); + if (urn != null && TRANSLATORS.containsKey(urn)) { + for (FlinkBatchPipelineTranslator.BatchTransformTranslator translator : + TRANSLATORS.get(urn)) { + if (translator.canTranslate(transform, context)) { + return translator; + } + } + } + return null; } - @SuppressWarnings("unchecked") private static String getCurrentTransformName(FlinkBatchTranslationContext context) { return context.getCurrentTransform().getFullName(); } @@ -604,7 +614,7 @@ public void translateNode( throw new RuntimeException(e); } - Map, Coder> outputCoderMap = context.getOutputCoders(); + final Map, Coder> outputCoderMap = context.getOutputCoders(transform); String fullName = getCurrentTransformName(context); if (usesStateOrTimers) { diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTranslationContext.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTranslationContext.java index 8e366cf85d42..1af8020cdc19 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTranslationContext.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTranslationContext.java @@ -19,9 +19,10 @@ import java.util.HashMap; import java.util.Map; -import java.util.stream.Collectors; -import org.apache.beam.runners.core.construction.TransformInputs; import org.apache.beam.runners.flink.translation.types.CoderTypeInformation; +import org.apache.beam.runners.flink.translation.utils.CountingPipelineVisitor; +import org.apache.beam.runners.flink.translation.utils.LookupPipelineVisitor; +import org.apache.beam.sdk.Pipeline; import org.apache.beam.sdk.coders.Coder; import org.apache.beam.sdk.options.PipelineOptions; import org.apache.beam.sdk.runners.AppliedPTransform; @@ -32,7 +33,6 @@ import org.apache.beam.sdk.values.PValue; import org.apache.beam.sdk.values.TupleTag; import org.apache.beam.sdk.values.WindowingStrategy; -import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Iterables; import org.apache.flink.api.common.typeinfo.TypeInformation; import org.apache.flink.api.java.DataSet; import org.apache.flink.api.java.ExecutionEnvironment; @@ -57,9 +57,12 @@ class FlinkBatchTranslationContext { private AppliedPTransform currentTransform; + private final CountingPipelineVisitor countingPipelineVisitor = new CountingPipelineVisitor(); + private final LookupPipelineVisitor lookupPipelineVisitor = new LookupPipelineVisitor(); + // ------------------------------------------------------------------------ - public FlinkBatchTranslationContext(ExecutionEnvironment env, PipelineOptions options) { + FlinkBatchTranslationContext(ExecutionEnvironment env, PipelineOptions options) { this.env = env; this.options = options; this.dataSets = new HashMap<>(); @@ -68,13 +71,18 @@ public FlinkBatchTranslationContext(ExecutionEnvironment env, PipelineOptions op this.danglingDataSets = new HashMap<>(); } + void init(Pipeline pipeline) { + pipeline.traverseTopologically(countingPipelineVisitor); + pipeline.traverseTopologically(lookupPipelineVisitor); + } + // ------------------------------------------------------------------------ - public Map> getDanglingDataSets() { + Map> getDanglingDataSets() { return danglingDataSets; } - public ExecutionEnvironment getExecutionEnvironment() { + ExecutionEnvironment getExecutionEnvironment() { return env; } @@ -83,13 +91,13 @@ public PipelineOptions getPipelineOptions() { } @SuppressWarnings("unchecked") - public DataSet> getInputDataSet(PValue value) { + DataSet> getInputDataSet(PValue value) { // assume that the DataSet is used as an input if retrieved here danglingDataSets.remove(value); return (DataSet>) dataSets.get(value); } - public void setOutputDataSet(PValue value, DataSet> set) { + void setOutputDataSet(PValue value, DataSet> set) { if (!dataSets.containsKey(value)) { dataSets.put(value, set); danglingDataSets.put(value, set); @@ -99,41 +107,37 @@ public void setOutputDataSet(PValue value, DataSet> set) { /** * Sets the AppliedPTransform which carries input/output. * - * @param currentTransform + * @param currentTransform Current transformation. */ - public void setCurrentTransform(AppliedPTransform currentTransform) { + void setCurrentTransform(AppliedPTransform currentTransform) { this.currentTransform = currentTransform; } - public AppliedPTransform getCurrentTransform() { + AppliedPTransform getCurrentTransform() { return currentTransform; } - public Map, Coder> getOutputCoders() { - return currentTransform.getOutputs().entrySet().stream() - .filter(e -> e.getValue() instanceof PCollection) - .collect(Collectors.toMap(e -> e.getKey(), e -> ((PCollection) e.getValue()).getCoder())); + Map, Coder> getOutputCoders(PTransform transform) { + return lookupPipelineVisitor.getOutputCoders(transform); } @SuppressWarnings("unchecked") - public DataSet getSideInputDataSet(PCollectionView value) { + DataSet getSideInputDataSet(PCollectionView value) { return (DataSet) broadcastDataSets.get(value); } - public void setSideInputDataSet( + void setSideInputDataSet( PCollectionView value, DataSet> set) { if (!broadcastDataSets.containsKey(value)) { broadcastDataSets.put(value, set); } } - @SuppressWarnings("unchecked") - public TypeInformation> getTypeInfo(PCollection collection) { + TypeInformation> getTypeInfo(PCollection collection) { return getTypeInfo(collection.getCoder(), collection.getWindowingStrategy()); } - @SuppressWarnings("unchecked") - public TypeInformation> getTypeInfo( + TypeInformation> getTypeInfo( Coder coder, WindowingStrategy windowingStrategy) { WindowedValue.FullWindowedValueCoder windowedValueCoder = WindowedValue.getFullCoder(coder, windowingStrategy.getWindowFn().windowCoder()); @@ -142,20 +146,23 @@ public TypeInformation> getTypeInfo( } Map, PValue> getInputs(PTransform transform) { - return currentTransform.getInputs(); + return lookupPipelineVisitor.getInputs(transform); } - @SuppressWarnings("unchecked") T getInput(PTransform transform) { - return (T) Iterables.getOnlyElement(TransformInputs.nonAdditionalInputs(currentTransform)); + return lookupPipelineVisitor.getInput(transform); } Map, PValue> getOutputs(PTransform transform) { - return currentTransform.getOutputs(); + return lookupPipelineVisitor.getOutputs(transform); } - @SuppressWarnings("unchecked") T getOutput(PTransform transform) { - return (T) Iterables.getOnlyElement(currentTransform.getOutputs().values()); + return lookupPipelineVisitor.getOutput(transform); + } + + /** {@link CountingPipelineVisitor#getNumConsumers(PValue)}. */ + int getNumConsumers(PValue value) { + return countingPipelineVisitor.getNumConsumers(value); } } diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/utils/CountingPipelineVisitor.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/utils/CountingPipelineVisitor.java new file mode 100644 index 000000000000..5f92d9fd652c --- /dev/null +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/utils/CountingPipelineVisitor.java @@ -0,0 +1,47 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.runners.flink.translation.utils; + +import java.util.HashMap; +import java.util.Map; +import org.apache.beam.sdk.Pipeline; +import org.apache.beam.sdk.runners.TransformHierarchy; +import org.apache.beam.sdk.values.PValue; + +/** Pipeline visitors that fills a lookup table of {@link PValue} to number of consumers. */ +public class CountingPipelineVisitor extends Pipeline.PipelineVisitor.Defaults { + + private final Map numConsumers = new HashMap<>(); + + @Override + public void visitPrimitiveTransform(TransformHierarchy.Node node) { + for (PValue input : node.getInputs().values()) { + numConsumers.merge(input, 1, Integer::sum); + } + } + + /** + * Calculate number of consumers of a given {@link PValue}. + * + * @param value PValue to perform calculation for. + * @return Number of consumers. + */ + public int getNumConsumers(PValue value) { + return numConsumers.get(value); + } +} diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/utils/LookupPipelineVisitor.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/utils/LookupPipelineVisitor.java new file mode 100644 index 000000000000..662e4d666a6b --- /dev/null +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/utils/LookupPipelineVisitor.java @@ -0,0 +1,98 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.runners.flink.translation.utils; + +import java.util.HashMap; +import java.util.Map; +import java.util.stream.Collectors; +import org.apache.beam.runners.core.construction.TransformInputs; +import org.apache.beam.sdk.Pipeline; +import org.apache.beam.sdk.coders.Coder; +import org.apache.beam.sdk.runners.AppliedPTransform; +import org.apache.beam.sdk.runners.TransformHierarchy; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.PInput; +import org.apache.beam.sdk.values.POutput; +import org.apache.beam.sdk.values.PValue; +import org.apache.beam.sdk.values.TupleTag; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Iterables; + +/** + * Pipeline visitor that fills lookup table of {@link PTransform} to {@link AppliedPTransform} for + * usage in {@link + * org.apache.beam.runners.flink.FlinkBatchPortablePipelineTranslator.BatchTranslationContext}. + */ +public class LookupPipelineVisitor extends Pipeline.PipelineVisitor.Defaults { + + private final Map, AppliedPTransform> lookupTable = new HashMap<>(); + + @Override + public CompositeBehavior enterCompositeTransform(TransformHierarchy.Node node) { + if ((node.getTransform()) != null) { + final AppliedPTransform applied = node.toAppliedPTransform(getPipeline()); + lookupTable.put(applied.getTransform(), applied); + } + return CompositeBehavior.ENTER_TRANSFORM; + } + + @Override + public void visitPrimitiveTransform(TransformHierarchy.Node node) { + final AppliedPTransform applied = node.toAppliedPTransform(getPipeline()); + lookupTable.put(applied.getTransform(), applied); + } + + private + AppliedPTransform> applied( + PTransform transform) { + @SuppressWarnings("unchecked") + final AppliedPTransform> applied = + (AppliedPTransform>) + lookupTable.get(transform); + if (applied == null) { + throw new IllegalArgumentException( + String.format("AppliedPTransform for %s does not exist.", transform)); + } + return applied; + } + + public Map, PValue> getInputs(PTransform transform) { + return applied(transform).getInputs(); + } + + @SuppressWarnings("unchecked") + public T getInput(PTransform transform) { + return (T) Iterables.getOnlyElement(TransformInputs.nonAdditionalInputs(applied(transform))); + } + + public Map, PValue> getOutputs(PTransform transform) { + return applied(transform).getOutputs(); + } + + @SuppressWarnings("unchecked") + public T getOutput(PTransform transform) { + return (T) Iterables.getOnlyElement(applied(transform).getOutputs().values()); + } + + @SuppressWarnings("unchecked") + public Map, Coder> getOutputCoders(PTransform transform) { + return getOutputs(transform).entrySet().stream() + .filter(e -> e.getValue() instanceof PCollection) + .collect(Collectors.toMap(Map.Entry::getKey, e -> ((PCollection) e.getValue()).getCoder())); + } +} From 3c4536dc98f4574ab86f873d50796da3de41a804 Mon Sep 17 00:00:00 2001 From: David Moravek Date: Mon, 1 Jun 2020 12:33:24 +0200 Subject: [PATCH 141/151] [BEAM-8848] Flink Batch Runner: optimize GBK translation for non-merging windows. --- .../flink/FlinkBatchTransformTranslators.java | 96 +++++++++++++-- .../runners/flink/FlinkPipelineOptions.java | 7 ++ .../FlinkExplodeWindowsFunction.java | 37 ++++++ .../FlinkNonMergingReduceFunction.java | 112 ++++++++++++++++++ .../types/WindowedKvKeySelector.java | 60 ++++++++++ .../flink/batch/NonMergingGroupByKeyTest.java | 80 +++++++++++++ .../flink_java_pipeline_options.html | 5 + .../flink_python_pipeline_options.html | 5 + 8 files changed, 391 insertions(+), 11 deletions(-) create mode 100644 runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkExplodeWindowsFunction.java create mode 100644 runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkNonMergingReduceFunction.java create mode 100644 runners/flink/src/main/java/org/apache/beam/runners/flink/translation/types/WindowedKvKeySelector.java create mode 100644 runners/flink/src/test/java/org/apache/beam/runners/flink/batch/NonMergingGroupByKeyTest.java diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java index 3f5104d1b7c3..d17b4405dfa2 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java @@ -34,19 +34,23 @@ import org.apache.beam.runners.core.construction.ReadTranslation; import org.apache.beam.runners.flink.translation.functions.FlinkAssignWindows; import org.apache.beam.runners.flink.translation.functions.FlinkDoFnFunction; +import org.apache.beam.runners.flink.translation.functions.FlinkExplodeWindowsFunction; import org.apache.beam.runners.flink.translation.functions.FlinkIdentityFunction; import org.apache.beam.runners.flink.translation.functions.FlinkMergingNonShuffleReduceFunction; import org.apache.beam.runners.flink.translation.functions.FlinkMultiOutputPruningFunction; +import org.apache.beam.runners.flink.translation.functions.FlinkNonMergingReduceFunction; import org.apache.beam.runners.flink.translation.functions.FlinkPartialReduceFunction; import org.apache.beam.runners.flink.translation.functions.FlinkReduceFunction; import org.apache.beam.runners.flink.translation.functions.FlinkStatefulDoFnFunction; import org.apache.beam.runners.flink.translation.types.CoderTypeInformation; import org.apache.beam.runners.flink.translation.types.KvKeySelector; +import org.apache.beam.runners.flink.translation.types.WindowedKvKeySelector; import org.apache.beam.runners.flink.translation.wrappers.ImpulseInputFormat; import org.apache.beam.runners.flink.translation.wrappers.SourceInputFormat; import org.apache.beam.sdk.coders.CannotProvideCoderException; import org.apache.beam.sdk.coders.Coder; import org.apache.beam.sdk.coders.CoderRegistry; +import org.apache.beam.sdk.coders.IterableCoder; import org.apache.beam.sdk.coders.KvCoder; import org.apache.beam.sdk.coders.ListCoder; import org.apache.beam.sdk.coders.VoidCoder; @@ -65,6 +69,7 @@ import org.apache.beam.sdk.transforms.reflect.DoFnSignatures; import org.apache.beam.sdk.transforms.windowing.BoundedWindow; import org.apache.beam.sdk.transforms.windowing.GlobalWindow; +import org.apache.beam.sdk.transforms.windowing.TimestampCombiner; import org.apache.beam.sdk.transforms.windowing.WindowFn; import org.apache.beam.sdk.util.WindowedValue; import org.apache.beam.sdk.values.KV; @@ -91,6 +96,7 @@ import org.apache.flink.api.java.operators.MapOperator; import org.apache.flink.api.java.operators.MapPartitionOperator; import org.apache.flink.api.java.operators.SingleInputUdfOperator; +import org.apache.flink.api.java.operators.UnsortedGrouping; import org.apache.flink.configuration.Configuration; import org.apache.flink.optimizer.Optimizer; import org.joda.time.Instant; @@ -120,18 +126,21 @@ private static void registerTranslator( registerTranslator(PTransformTranslation.IMPULSE_TRANSFORM_URN, new ImpulseTranslatorBatch()); registerTranslator( PTransformTranslation.CREATE_VIEW_TRANSFORM_URN, - new CreatePCollectionViewTranslatorBatch()); + new CreatePCollectionViewTranslatorBatch<>()); registerTranslator( - PTransformTranslation.COMBINE_PER_KEY_TRANSFORM_URN, new CombinePerKeyTranslatorBatch()); + PTransformTranslation.COMBINE_PER_KEY_TRANSFORM_URN, new CombinePerKeyTranslatorBatch<>()); registerTranslator( - PTransformTranslation.GROUP_BY_KEY_TRANSFORM_URN, new GroupByKeyTranslatorBatch()); - registerTranslator(PTransformTranslation.RESHUFFLE_URN, new ReshuffleTranslatorBatch()); + PTransformTranslation.GROUP_BY_KEY_TRANSFORM_URN, + new NonMergingGroupByKeyTranslatorBatch<>()); registerTranslator( - PTransformTranslation.FLATTEN_TRANSFORM_URN, new FlattenPCollectionTranslatorBatch()); + PTransformTranslation.GROUP_BY_KEY_TRANSFORM_URN, new GroupByKeyTranslatorBatch<>()); + registerTranslator(PTransformTranslation.RESHUFFLE_URN, new ReshuffleTranslatorBatch<>()); registerTranslator( - PTransformTranslation.ASSIGN_WINDOWS_TRANSFORM_URN, new WindowAssignTranslatorBatch()); - registerTranslator(PTransformTranslation.PAR_DO_TRANSFORM_URN, new ParDoTranslatorBatch()); - registerTranslator(PTransformTranslation.READ_TRANSFORM_URN, new ReadSourceTranslatorBatch()); + PTransformTranslation.FLATTEN_TRANSFORM_URN, new FlattenPCollectionTranslatorBatch<>()); + registerTranslator( + PTransformTranslation.ASSIGN_WINDOWS_TRANSFORM_URN, new WindowAssignTranslatorBatch<>()); + registerTranslator(PTransformTranslation.PAR_DO_TRANSFORM_URN, new ParDoTranslatorBatch<>()); + registerTranslator(PTransformTranslation.READ_TRANSFORM_URN, new ReadSourceTranslatorBatch<>()); } @SuppressWarnings("unchecked") @@ -139,7 +148,7 @@ static FlinkBatchPipelineTranslator.BatchTransformTranslator getTranslator( PTransform transform, FlinkBatchTranslationContext context) { @Nullable final String urn = PTransformTranslation.urnForTransformOrNull(transform); if (urn != null && TRANSLATORS.containsKey(urn)) { - for (FlinkBatchPipelineTranslator.BatchTransformTranslator translator : + for (FlinkBatchPipelineTranslator.BatchTransformTranslator> translator : TRANSLATORS.get(urn)) { if (translator.canTranslate(transform, context)) { return translator; @@ -241,6 +250,73 @@ public void translateNode( } } + /** + * Optimized group by key translation for non-merging windows. + * + * @param Key type. + * @param Input type. + */ + private static class NonMergingGroupByKeyTranslatorBatch + implements FlinkBatchPipelineTranslator.BatchTransformTranslator< + PTransform>, PCollection>>>> { + + @Override + public boolean canTranslate( + PTransform>, PCollection>>> transform, + FlinkBatchTranslationContext context) { + final WindowingStrategy windowingStrategy = + context.getInput(transform).getWindowingStrategy(); + return windowingStrategy.getWindowFn().isNonMerging() + && windowingStrategy.getTimestampCombiner() == TimestampCombiner.END_OF_WINDOW + && windowingStrategy.getWindowFn().windowCoder().consistentWithEquals(); + } + + @Override + public void translateNode( + PTransform>, PCollection>>> transform, + FlinkBatchTranslationContext context) { + final int numConsumers = + context.getOutputs(transform).values().stream().mapToInt(context::getNumConsumers).sum(); + final boolean multipleConsumers = numConsumers > 1; + final boolean reIterableResult = + multipleConsumers + || context + .getPipelineOptions() + .as(FlinkPipelineOptions.class) + .getReIterableGroupByKeyResult(); + final DataSet>> inputDataSet = + context.getInputDataSet(context.getInput(transform)); + final KvCoder inputCoder = + (KvCoder) context.getInput(transform).getCoder(); + final WindowingStrategy windowingStrategy = + context.getInput(transform).getWindowingStrategy(); + final String fullName = getCurrentTransformName(context); + final UnsortedGrouping>> inputGrouping = + new FlatMapOperator<>( + inputDataSet, + inputDataSet.getType(), + new FlinkExplodeWindowsFunction<>(), + "ExplodeWindows: " + fullName) + .groupBy( + new WindowedKvKeySelector<>( + inputCoder.getKeyCoder(), windowingStrategy.getWindowFn().windowCoder())); + final TypeInformation>>> outputTypeInfo = + new CoderTypeInformation<>( + WindowedValue.getFullCoder( + KvCoder.of( + inputCoder.getKeyCoder(), IterableCoder.of(inputCoder.getValueCoder())), + windowingStrategy.getWindowFn().windowCoder())); + final DataSet>>> outputDataSet = + new GroupReduceOperator<>( + inputGrouping, + outputTypeInfo, + new FlinkNonMergingReduceFunction<>(windowingStrategy, reIterableResult), + fullName) + .returns(outputTypeInfo); + context.setOutputDataSet(context.getOutput(transform), outputDataSet); + } + } + private static class GroupByKeyTranslatorBatch implements FlinkBatchPipelineTranslator.BatchTransformTranslator< PTransform>, PCollection>>>> { @@ -806,6 +882,4 @@ private static void transformSideInputs( outputDataSet.withBroadcastSet(broadcastSet, input.getTagInternal().getId()); } } - - private FlinkBatchTransformTranslators() {} } diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkPipelineOptions.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkPipelineOptions.java index 22bff18dbdc2..6c42e2f5efb4 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkPipelineOptions.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkPipelineOptions.java @@ -267,4 +267,11 @@ public interface FlinkPipelineOptions String getReportCheckpointDuration(); void setReportCheckpointDuration(String metricNamespace); + + @Description( + "Flag indicating whether result of GBK needs to be re-iterable. Re-iterable result implies that all values for a single key must fit in memory as we currently do not support spilling to disk.") + @Default.Boolean(false) + Boolean getReIterableGroupByKeyResult(); + + void setReIterableGroupByKeyResult(Boolean reIterableGroupByKeyResult); } diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkExplodeWindowsFunction.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkExplodeWindowsFunction.java new file mode 100644 index 000000000000..b307878fb025 --- /dev/null +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkExplodeWindowsFunction.java @@ -0,0 +1,37 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.runners.flink.translation.functions; + +import org.apache.beam.sdk.util.WindowedValue; +import org.apache.flink.api.common.functions.FlatMapFunction; +import org.apache.flink.util.Collector; + +/** + * Explode {@link WindowedValue} that belongs to multiple windows into multiple "single window" + * {@link WindowedValue values}, so we can safely group elements by (K, W) tuples. + * + * @param Value type. + */ +public class FlinkExplodeWindowsFunction + implements FlatMapFunction, WindowedValue> { + + @Override + public void flatMap(WindowedValue value, Collector> coll) { + value.explodeWindows().forEach(coll::collect); + } +} diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkNonMergingReduceFunction.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkNonMergingReduceFunction.java new file mode 100644 index 000000000000..8855411472f6 --- /dev/null +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkNonMergingReduceFunction.java @@ -0,0 +1,112 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.runners.flink.translation.functions; + +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.Objects; +import java.util.concurrent.atomic.AtomicBoolean; +import org.apache.beam.sdk.transforms.windowing.BoundedWindow; +import org.apache.beam.sdk.transforms.windowing.PaneInfo; +import org.apache.beam.sdk.util.WindowedValue; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.sdk.values.WindowingStrategy; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Iterables; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Iterators; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.PeekingIterator; +import org.apache.flink.api.common.functions.GroupReduceFunction; +import org.apache.flink.util.Collector; +import org.joda.time.Instant; + +/** + * Reduce function for non-merging GBK implementation. Implementation tries to return non-iterable + * results when possible, so we do not have to materialize all values for a single key in memory. + * + * @param Key type. + * @param Input type. + */ +public class FlinkNonMergingReduceFunction + implements GroupReduceFunction< + WindowedValue>, WindowedValue>>> { + + private static class OnceIterable implements Iterable { + + private final Iterator iterator; + + private final AtomicBoolean used = new AtomicBoolean(false); + + OnceIterable(Iterator iterator) { + this.iterator = iterator; + } + + @Override + public Iterator iterator() { + if (used.compareAndSet(false, true)) { + return iterator; + } + throw new IllegalStateException( + "GBK result is not re-iterable. You can enable re-iterations by setting '--reIterableGroupByKeyResult=true'."); + } + } + + private final WindowingStrategy windowingStrategy; + private final boolean reIterableResult; + + public FlinkNonMergingReduceFunction( + WindowingStrategy windowingStrategy, boolean reIterableResult) { + this.windowingStrategy = windowingStrategy; + this.reIterableResult = reIterableResult; + } + + @Override + public void reduce( + Iterable>> input, + Collector>>> coll) { + final PeekingIterator>> iterator = + Iterators.peekingIterator(input.iterator()); + final WindowedValue> first = iterator.peek(); + final BoundedWindow window = Iterables.getOnlyElement(first.getWindows()); + @SuppressWarnings("unchecked") + final Instant outputTimestamp = + ((WindowingStrategy) windowingStrategy) + .getWindowFn() + .getOutputTime(first.getTimestamp(), window); + final Instant combinedTimestamp = + windowingStrategy.getTimestampCombiner().assign(window, outputTimestamp); + final Iterable values; + if (reIterableResult) { + final List lst = new ArrayList<>(); + iterator.forEachRemaining(wv -> lst.add(wv.getValue().getValue())); + values = lst; + } else { + values = + new OnceIterable<>( + Iterators.transform( + iterator, + (WindowedValue> wv) -> + Objects.requireNonNull(wv).getValue().getValue())); + } + coll.collect( + WindowedValue.of( + KV.of(first.getValue().getKey(), values), + combinedTimestamp, + first.getWindows(), + PaneInfo.ON_TIME_AND_ONLY_FIRING)); + } +} diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/types/WindowedKvKeySelector.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/types/WindowedKvKeySelector.java new file mode 100644 index 000000000000..4158c026e203 --- /dev/null +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/types/WindowedKvKeySelector.java @@ -0,0 +1,60 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.runners.flink.translation.types; + +import org.apache.beam.sdk.coders.Coder; +import org.apache.beam.sdk.transforms.windowing.BoundedWindow; +import org.apache.beam.sdk.util.CoderUtils; +import org.apache.beam.sdk.util.WindowedValue; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Iterables; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.primitives.Bytes; +import org.apache.flink.api.common.typeinfo.TypeInformation; +import org.apache.flink.api.java.functions.KeySelector; +import org.apache.flink.api.java.typeutils.ResultTypeQueryable; + +/** + * {@link KeySelector} that extracts the key from a {@link KV} and returns it in encoded form as a + * {@code byte} array. + */ +public class WindowedKvKeySelector + implements KeySelector>, byte[]>, ResultTypeQueryable { + + private final Coder keyCoder; + private final Coder windowCoder; + + public WindowedKvKeySelector(Coder keyCoder, Coder windowCoder) { + this.keyCoder = keyCoder; + this.windowCoder = windowCoder; + } + + @Override + public byte[] getKey(WindowedValue> value) throws Exception { + final byte[] encodedKey = CoderUtils.encodeToByteArray(keyCoder, value.getValue().getKey()); + @SuppressWarnings("unchecked") + final byte[] encodedWindow = + CoderUtils.encodeToByteArray( + (Coder) windowCoder, Iterables.getOnlyElement(value.getWindows())); + return Bytes.concat(encodedKey, encodedWindow); + } + + @Override + public TypeInformation getProducedType() { + return new EncodedValueTypeInformation(); + } +} diff --git a/runners/flink/src/test/java/org/apache/beam/runners/flink/batch/NonMergingGroupByKeyTest.java b/runners/flink/src/test/java/org/apache/beam/runners/flink/batch/NonMergingGroupByKeyTest.java new file mode 100644 index 000000000000..935ca21e6bf0 --- /dev/null +++ b/runners/flink/src/test/java/org/apache/beam/runners/flink/batch/NonMergingGroupByKeyTest.java @@ -0,0 +1,80 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.runners.flink.batch; + +import java.util.Arrays; +import java.util.Objects; +import org.apache.beam.runners.flink.FlinkCapabilities; +import org.apache.beam.runners.flink.FlinkPipelineOptions; +import org.apache.beam.runners.flink.FlinkTestPipeline; +import org.apache.beam.sdk.Pipeline; +import org.apache.beam.sdk.PipelineResult; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.GroupByKey; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.values.KV; +import org.apache.flink.test.util.AbstractTestBase; +import org.junit.Assert; +import org.junit.Assume; +import org.junit.Test; + +public class NonMergingGroupByKeyTest extends AbstractTestBase { + + private static class ReiterateDoFn extends DoFn>, Void> { + + @ProcessElement + public void processElement(@Element KV> el) { + el.getValue().iterator(); + // this should throw an exception + el.getValue().iterator(); + } + } + + @Test + public void testDisabledReIterationThrowsAnException() { + // If output during closing is not supported, we can not chain DoFns and results + // are therefore materialized during output serialization. + Assume.assumeTrue(FlinkCapabilities.supportsOutputDuringClosing()); + final Pipeline p = FlinkTestPipeline.createForBatch(); + p.apply(Create.of(Arrays.asList(KV.of("a", 1), KV.of("b", 2), KV.of("c", 3)))) + .apply(GroupByKey.create()) + .apply(ParDo.of(new ReiterateDoFn<>())); + Pipeline.PipelineExecutionException resultException = null; + try { + p.run().waitUntilFinish(); + } catch (Pipeline.PipelineExecutionException exception) { + resultException = exception; + } + Assert.assertEquals( + IllegalStateException.class, Objects.requireNonNull(resultException).getCause().getClass()); + Assert.assertTrue( + resultException.getCause().getMessage().contains("GBK result is not re-iterable.")); + } + + @Test + public void testEnabledReIterationDoesNotThrowAnException() { + final Pipeline p = FlinkTestPipeline.createForBatch(); + p.getOptions().as(FlinkPipelineOptions.class).setReIterableGroupByKeyResult(true); + p.apply(Create.of(Arrays.asList(KV.of("a", 1), KV.of("b", 2), KV.of("c", 3)))) + .apply(GroupByKey.create()) + .apply(ParDo.of(new ReiterateDoFn<>())); + final PipelineResult.State state = p.run().waitUntilFinish(); + Assert.assertEquals(PipelineResult.State.DONE, state); + } +} diff --git a/website/www/site/layouts/shortcodes/flink_java_pipeline_options.html b/website/www/site/layouts/shortcodes/flink_java_pipeline_options.html index 317b06141c37..956446920c71 100644 --- a/website/www/site/layouts/shortcodes/flink_java_pipeline_options.html +++ b/website/www/site/layouts/shortcodes/flink_java_pipeline_options.html @@ -132,6 +132,11 @@ The degree of parallelism to be used when distributing operations onto workers. If the parallelism is not set, the configured Flink default is used, or 1 if none can be found. Default: -1 + + reIterableGroupByKeyResult + Flag indicating whether result of GBK needs to be re-iterable. Re-iterable result implies that all values for a single key must fit in memory as we currently do not support spilling to disk. + Default: false + reportCheckpointDuration If not null, reports the checkpoint duration of each ParDo stage in the provided metric namespace. diff --git a/website/www/site/layouts/shortcodes/flink_python_pipeline_options.html b/website/www/site/layouts/shortcodes/flink_python_pipeline_options.html index 4170e25c543c..9abe5086df74 100644 --- a/website/www/site/layouts/shortcodes/flink_python_pipeline_options.html +++ b/website/www/site/layouts/shortcodes/flink_python_pipeline_options.html @@ -132,6 +132,11 @@ The degree of parallelism to be used when distributing operations onto workers. If the parallelism is not set, the configured Flink default is used, or 1 if none can be found. Default: -1 + + re_iterable_group_by_key_result + Flag indicating whether result of GBK needs to be re-iterable. Re-iterable result implies that all values for a single key must fit in memory as we currently do not support spilling to disk. + Default: false + report_checkpoint_duration If not null, reports the checkpoint duration of each ParDo stage in the provided metric namespace. From 23a1fb711bce2af3a42b06f522139babcc72b285 Mon Sep 17 00:00:00 2001 From: David Moravek Date: Thu, 26 Mar 2020 10:03:19 +0100 Subject: [PATCH 142/151] [BEAM-8848] Code review. --- .../flink/FlinkBatchTransformTranslators.java | 34 ++++++++----------- .../FlinkNonMergingReduceFunction.java | 2 +- 2 files changed, 15 insertions(+), 21 deletions(-) diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java index d17b4405dfa2..264fa4c43302 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkBatchTransformTranslators.java @@ -83,6 +83,8 @@ import org.apache.beam.sdk.values.WindowingStrategy; import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Lists; import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Maps; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.Multimap; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.MultimapBuilder; import org.apache.flink.api.common.functions.RichGroupReduceFunction; import org.apache.flink.api.common.operators.Order; import org.apache.flink.api.common.typeinfo.TypeInformation; @@ -111,36 +113,28 @@ class FlinkBatchTransformTranslators { // -------------------------------------------------------------------------------------------- @SuppressWarnings("rawtypes") - private static final Map> - TRANSLATORS = new HashMap<>(); - - private static void registerTranslator( - String urn, FlinkBatchPipelineTranslator.BatchTransformTranslator translator) { - if (!TRANSLATORS.containsKey(urn)) { - TRANSLATORS.put(urn, new ArrayList<>()); - } - TRANSLATORS.get(urn).add(translator); - } + private static final Multimap + TRANSLATORS = MultimapBuilder.hashKeys().arrayListValues().build(); static { - registerTranslator(PTransformTranslation.IMPULSE_TRANSFORM_URN, new ImpulseTranslatorBatch()); - registerTranslator( + TRANSLATORS.put(PTransformTranslation.IMPULSE_TRANSFORM_URN, new ImpulseTranslatorBatch()); + TRANSLATORS.put( PTransformTranslation.CREATE_VIEW_TRANSFORM_URN, new CreatePCollectionViewTranslatorBatch<>()); - registerTranslator( + TRANSLATORS.put( PTransformTranslation.COMBINE_PER_KEY_TRANSFORM_URN, new CombinePerKeyTranslatorBatch<>()); - registerTranslator( + TRANSLATORS.put( PTransformTranslation.GROUP_BY_KEY_TRANSFORM_URN, new NonMergingGroupByKeyTranslatorBatch<>()); - registerTranslator( + TRANSLATORS.put( PTransformTranslation.GROUP_BY_KEY_TRANSFORM_URN, new GroupByKeyTranslatorBatch<>()); - registerTranslator(PTransformTranslation.RESHUFFLE_URN, new ReshuffleTranslatorBatch<>()); - registerTranslator( + TRANSLATORS.put(PTransformTranslation.RESHUFFLE_URN, new ReshuffleTranslatorBatch<>()); + TRANSLATORS.put( PTransformTranslation.FLATTEN_TRANSFORM_URN, new FlattenPCollectionTranslatorBatch<>()); - registerTranslator( + TRANSLATORS.put( PTransformTranslation.ASSIGN_WINDOWS_TRANSFORM_URN, new WindowAssignTranslatorBatch<>()); - registerTranslator(PTransformTranslation.PAR_DO_TRANSFORM_URN, new ParDoTranslatorBatch<>()); - registerTranslator(PTransformTranslation.READ_TRANSFORM_URN, new ReadSourceTranslatorBatch<>()); + TRANSLATORS.put(PTransformTranslation.PAR_DO_TRANSFORM_URN, new ParDoTranslatorBatch<>()); + TRANSLATORS.put(PTransformTranslation.READ_TRANSFORM_URN, new ReadSourceTranslatorBatch<>()); } @SuppressWarnings("unchecked") diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkNonMergingReduceFunction.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkNonMergingReduceFunction.java index 8855411472f6..21a9cac71283 100644 --- a/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkNonMergingReduceFunction.java +++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkNonMergingReduceFunction.java @@ -61,7 +61,7 @@ public Iterator iterator() { return iterator; } throw new IllegalStateException( - "GBK result is not re-iterable. You can enable re-iterations by setting '--reIterableGroupByKeyResult=true'."); + "GBK result is not re-iterable. You can enable re-iterations by setting '--reIterableGroupByKeyResult'."); } } From 423b79ce28de9f0876859b1fae03a74d101d8ccf Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 2 Jun 2020 10:59:33 -0700 Subject: [PATCH 143/151] wip --- .../sdk/transforms/SerializableFunction.java | 1 - .../beam/sdk/io/gcp/healthcare/FhirIO.java | 61 +++---- .../healthcare/HttpHealthcareApiClient.java | 15 +- .../sdk/io/gcp/healthcare/FhirIOTestUtil.java | 44 ++--- .../sdk/io/gcp/healthcare/FhirIOUpdateIT.java | 158 ++++++++++++++++++ .../sdk/io/gcp/healthcare/FhirIOWriteIT.java | 52 ------ 6 files changed, 221 insertions(+), 110 deletions(-) create mode 100644 sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java index cbd7d01d80fe..f1e870513f10 100644 --- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java +++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java @@ -17,7 +17,6 @@ */ package org.apache.beam.sdk.transforms; -import com.fasterxml.jackson.core.JsonProcessingException; import java.io.IOException; import java.io.Serializable; diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java index 19ece0754b9d..911db6c8bc3c 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java @@ -1284,7 +1284,7 @@ public void executeBundles(ProcessContext context) { * @param fhirStore the fhir store * @return the fhir io . create resources */ - public static FhirIO.CreateResources createResources(ValueProvider fhirStore){ + public static FhirIO.CreateResources createResources(ValueProvider fhirStore) { return new CreateResources(fhirStore); } @@ -1295,7 +1295,7 @@ public static FhirIO.CreateResources createResources(ValueProvider FhirIO.CreateResources createResources(String fhirStore){ + public static FhirIO.CreateResources createResources(String fhirStore) { return new CreateResources(fhirStore); } /** @@ -1353,8 +1353,7 @@ public CreateResources withIfNotExistFunction( * @param typeFunction for extracting type from a resource. * @return the create resources */ - public CreateResources withTypeFunction( - SerializableFunction typeFunction) { + public CreateResources withTypeFunction(SerializableFunction typeFunction) { this.typeFunction = typeFunction; return this; } @@ -1388,7 +1387,8 @@ public FhirIO.Write.Result expand(PCollection input) { input .apply( ParDo.of( - new CreateFn(fhirStore, typeFunction, formatBodyFunction, ifNoneExistFunction))) + new CreateFn( + fhirStore, typeFunction, formatBodyFunction, ifNoneExistFunction))) .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } @@ -1419,8 +1419,7 @@ public void initClient() throws IOException { } @ProcessElement - public void create(ProcessContext context) - throws IOException { + public void create(ProcessContext context) throws IOException { T input = context.element(); String body = formatBodyFunction.apply(input); String type = typeFunction.apply(input); @@ -1448,7 +1447,7 @@ public void create(ProcessContext context) * @param fhirStore the fhir store * @return the update resources */ - public static UpdateResources update(ValueProvider fhirStore){ + public static UpdateResources update(ValueProvider fhirStore) { return new UpdateResources(fhirStore); } @@ -1459,24 +1458,24 @@ public static UpdateResources update(ValueProvider fhi * @param fhirStore the fhir store * @return the update resources */ - public static UpdateResources update(String fhirStore){ + public static UpdateResources update(String fhirStore) { return new UpdateResources(fhirStore); } /** * {@link PTransform} for Updating FHIR resources resources. * - * This transform assumes the input {@link PCollection} contains - * {@link KV} of resource name, value pairs and by default will call {@code .toString} to extract - * string values. - * However, the user can override this behavior by specifying a {@link SerializableFunction} with - * custom logic to extract the resource name and body from the {@link KV} in - * {@link UpdateResources#withResourceNameFunction(SerializableFunction)} and - * {@link UpdateResources#withFormatBodyFunction(SerializableFunction)} + *

    This transform assumes the input {@link PCollection} contains {@link KV} of resource name, + * value pairs and by default will call {@code .toString} to extract string values. However, the + * user can override this behavior by specifying a {@link SerializableFunction} with custom logic + * to extract the resource name and body from the {@link KV} in {@link + * UpdateResources#withResourceNameFunction(SerializableFunction)} and {@link + * UpdateResources#withFormatBodyFunction(SerializableFunction)} * *

    https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/update */ - public static class UpdateResources extends PTransform, Write.Result> { + public static class UpdateResources + extends PTransform, Write.Result> { private final ValueProvider fhirStore; private SerializableFunction formatBodyFunction; private SerializableFunction resourceNameFunction; @@ -1530,13 +1529,11 @@ public UpdateResources withFormatBodyFunction( * @param etagFunction ETag function * @return the update resources */ - public UpdateResources withETagFunction( - SerializableFunction etagFunction) { + public UpdateResources withETagFunction(SerializableFunction etagFunction) { this.etagFunction = etagFunction; return this; } - @Override public FhirIO.Write.Result expand(PCollection input) { checkArgument( @@ -1548,7 +1545,10 @@ public FhirIO.Write.Result expand(PCollection input) { return Write.Result.in( input.getPipeline(), input - .apply(ParDo.of(new UpdateFn(fhirStore, formatBodyFunction, resourceNameFunction, etagFunction))) + .apply( + ParDo.of( + new UpdateFn( + fhirStore, formatBodyFunction, resourceNameFunction, etagFunction))) .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } @@ -1579,8 +1579,7 @@ public void initClient() throws IOException { } @ProcessElement - public void update(ProcessContext context) - throws IOException { + public void update(ProcessContext context) throws IOException { T input = context.element(); String body = formatBodyFunction.apply(input); try { @@ -1588,7 +1587,7 @@ public void update(ProcessContext context) mapper.readTree(body); String resourceName = resourceNameFunction.apply(input); String etag = null; - if (etagFunction != null){ + if (etagFunction != null) { etag = etagFunction.apply(input); } HttpBody result = client.fhirUpdate(fhirStore.get(), resourceName, body, etag); @@ -1608,8 +1607,8 @@ public void update(ProcessContext context) * @param fhirStore the fhir store * @return the conditional update */ - public static ConditionalUpdate conditionalUpdate(ValueProvider fhirStore){ - return new ConditionalUpdate(fhirStore); + public static ConditionalUpdate conditionalUpdate(ValueProvider fhirStore) { + return new ConditionalUpdate(fhirStore); } /** @@ -1619,7 +1618,7 @@ public static ConditionalUpdate conditionalUpdate(ValueProvider f * @param fhirStore the fhir store * @return the conditional update */ - public static ConditionalUpdate conditionalUpdate(String fhirStore){ + public static ConditionalUpdate conditionalUpdate(String fhirStore) { return new ConditionalUpdate(fhirStore); } @@ -1653,7 +1652,6 @@ public static class ConditionalUpdate extends PTransform, Writ this.fhirStore = StaticValueProvider.of(fhirStore); } - /** * With search parameters function conditional update. * @@ -1714,7 +1712,10 @@ public FhirIO.Write.Result expand(PCollection input) { .apply( ParDo.of( new ConditionalUpdateFn( - fhirStore, typeFunction, searchParametersFunction, formatBodyFunction, + fhirStore, + typeFunction, + searchParametersFunction, + formatBodyFunction, etagFunction))) .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); } @@ -1759,7 +1760,7 @@ public void conditionalUpdate(ProcessContext context) throws IOException { mapper.readTree(body); Map searchParameters = searchParametersFunction.apply(input); String etag = null; - if (etagFunction != null){ + if (etagFunction != null) { etag = etagFunction.apply(input); } client.fhirConditionalUpdate(fhirStore.get(), type, body, searchParameters, etag); diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java index dbad6125dbc1..f0c02f4a08fb 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java @@ -460,10 +460,7 @@ public HttpBody executeFhirHttpRequest(FhirHttpRequest fhirHttpRequest) if (!Strings.isNullOrEmpty(fhirHttpRequest.pathSuffix)) { uriString += fhirHttpRequest.pathSuffix; } - uri = - new URIBuilder(uriString) - .setParameter("access_token", credentials.getAccessToken().getTokenValue()) - .build(); + uri = new URIBuilder(uriString).build(); } catch (URISyntaxException e) { LOG.error("URL error when making executeBundle request to FHIR API. " + e.getMessage()); throw new IllegalArgumentException(e); @@ -483,6 +480,7 @@ public HttpBody executeFhirHttpRequest(FhirHttpRequest fhirHttpRequest) requestBuilder .setUri(uri) .setEntity(requestEntity) + .addHeader("Authorization", "Bearer " + credentials.getAccessToken().getTokenValue()) .addHeader("User-Agent", USER_AGENT) .addHeader("Content-Type", FHIRSTORE_HEADER_CONTENT_TYPE) .addHeader("Accept-Charset", FHIRSTORE_HEADER_ACCEPT_CHARSET) @@ -532,7 +530,10 @@ public HttpBody fhirCreate( @Override public HttpBody fhirConditionalUpdate( - String fhirStore, String type, String resource, Map searchParameters, + String fhirStore, + String type, + String resource, + Map searchParameters, @Nullable String etag) throws IOException, HealthcareHttpException { Map headers = new HashMap<>(); @@ -548,8 +549,8 @@ public HttpBody fhirConditionalUpdate( } @Override - public HttpBody fhirUpdate(String fhirStore, String relativeResourceName, String resource, - @Nullable String etag) + public HttpBody fhirUpdate( + String fhirStore, String relativeResourceName, String resource, @Nullable String etag) throws IOException, HealthcareHttpException { Map headers = new HashMap<>(); if (etag != null) { diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java index 61af5fa8f50b..385d6403297a 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java @@ -45,37 +45,42 @@ class FhirIOTestUtil { public static final String DEFAULT_TEMP_BUCKET = "temp-storage-for-healthcare-io-tests"; - - public static class ExtractIDSearchQuery implements - SerializableFunction { + public static class ExtractIDSearchQuery implements SerializableFunction { private ObjectMapper mapper; - ExtractIDSearchQuery(){ + ExtractIDSearchQuery() { mapper = new ObjectMapper(); } @Override - public String apply(String resource) throws IOException { - Map map = mapper.readValue(resource.toString().getBytes(), Map.class); - String id = map.get("id"); - return String.format("_id=%s", id); - } + public String apply(String resource) { + try { + Map map = mapper.readValue(resource.getBytes(), Map.class); + String id = map.get("id"); + return String.format("_id=%s", id); + } catch (IOException e) { + throw new RuntimeException(e); + } + } } - public static class GetByKey implements - SerializableFunction { + public static class GetByKey implements SerializableFunction { private final String key; private ObjectMapper mapper; - public GetByKey(String key){ + public GetByKey(String key) { this.key = key; mapper = new ObjectMapper(); } @Override - public String apply(String resource) throws IOException { - Map map = mapper.readValue(resource.getBytes(), Map.class); - return map.get(key); + public String apply(String resource) { + try { + Map map = mapper.readValue(resource.getBytes(), Map.class); + return map.get(key); + } catch (IOException e) { + throw new RuntimeException(e); + } } } @@ -83,9 +88,8 @@ public String apply(String resource) throws IOException { // TODO read update resources function. // TODO spot check resource update utility. - private static Stream readAllTestResources(String subDir, String version ) { - Path resourceDir = Paths.get("build", "resources", "test", - subDir, version); + private static Stream readAllTestResources(String subDir, String version) { + Path resourceDir = Paths.get("build", "resources", "test", subDir, version); String absolutePath = resourceDir.toFile().getAbsolutePath(); File dir = new File(absolutePath); File[] fhirJsons = dir.listFiles(); @@ -100,8 +104,8 @@ private static Stream readAllTestResources(String subDir, String version } }) .map(String::new); - } + private static Stream readPrettyBundles(String version) { return readAllTestResources("transactional_bundles", version); } @@ -134,7 +138,7 @@ private static Stream readPrettyResources(String version) { readPrettyResources("DSTU2").collect(Collectors.toList()); static final List STU3_PRETTY_RESOURCES = readPrettyResources("STU3").collect(Collectors.toList()); - static final List R4_PRETTY_RESOURCES= + static final List R4_PRETTY_RESOURCES = readPrettyResources("R4").collect(Collectors.toList()); static final Map> RESOURCES; diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java new file mode 100644 index 000000000000..2a03a3448445 --- /dev/null +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java @@ -0,0 +1,158 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.io.gcp.healthcare; + +import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.BUNDLES; +import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.DEFAULT_TEMP_BUCKET; +import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.RESOURCES; +import static org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.HEALTHCARE_DATASET_TEMPLATE; + +import java.io.IOException; +import java.security.SecureRandom; +import java.util.Arrays; +import java.util.Collection; +import java.util.HashMap; +import org.apache.beam.sdk.Pipeline; +import org.apache.beam.sdk.extensions.gcp.options.GcpOptions; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Write.Result; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.GetByKey; +import org.apache.beam.sdk.options.PipelineOptionsFactory; +import org.apache.beam.sdk.testing.PAssert; +import org.apache.beam.sdk.testing.TestPipeline; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.WithKeys; +import org.apache.beam.sdk.values.KV; +import org.junit.After; +import org.junit.AfterClass; +import org.junit.Before; +import org.junit.Rule; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.Parameterized; +import org.junit.runners.Parameterized.Parameters; + +@RunWith(Parameterized.class) +public class FhirIOUpdateIT { + + @Parameters(name = "{0}") + public static Collection versions() { + return Arrays.asList("DSTU2", "STU3", "R4"); + } + + private final String fhirStoreName; + private FhirIOTestOptions options; + private transient HealthcareApiClient client; + private String healthcareDataset; + private long testTime = System.currentTimeMillis(); + + public String version; + + @Rule public transient TestPipeline pipeline = TestPipeline.create(); + + public FhirIOUpdateIT(String version) { + this.version = version; + this.fhirStoreName = + "FHIR_store_" + version + "_write_it_" + testTime + "_" + (new SecureRandom().nextInt(32)); + } + + @Before + public void setup() throws Exception { + if (client == null) { + client = new HttpHealthcareApiClient(); + } + PipelineOptionsFactory.register(FhirIOTestOptions.class); + String project = TestPipeline.testingPipelineOptions().as(GcpOptions.class).getProject(); + healthcareDataset = String.format(HEALTHCARE_DATASET_TEMPLATE, project); + options = TestPipeline.testingPipelineOptions().as(FhirIOTestOptions.class); + options.setGcsTempPath( + String.format("gs://%s/FhirIOWrite%sIT/%s/temp/", DEFAULT_TEMP_BUCKET, version, testTime)); + options.setGcsDeadLetterPath( + String.format( + "gs://%s/FhirIOWrite%sIT/%s/deadletter/", DEFAULT_TEMP_BUCKET, version, testTime)); + options.setFhirStore(healthcareDataset + "/fhirStores/" + fhirStoreName); + HealthcareApiClient client = new HttpHealthcareApiClient(); + client.createFhirStore(healthcareDataset, fhirStoreName, version); + } + + @After + public void teardownFhirStore() throws IOException { + HealthcareApiClient client = new HttpHealthcareApiClient(); + client.deleteFhirStore(healthcareDataset + "/fhirStores/" + fhirStoreName); + // clean up GCS objects if any. + } + + @AfterClass + public static void teardownBucket() throws IOException { + FhirIOTestUtil.tearDownTempBucket(); + } + + // TODO(jaketf) add IT for conditional create, update, conditional update transforms. + @Test + public void testFhirIO_CreateResources() { + Result writeResult = + (Result) + pipeline + .apply("Create Test Resources", Create.of(RESOURCES.get(version))) + .apply( + FhirIO.createResources(options.getFhirStore()) + .withTypeFunction(new GetByKey("resourceType")) + .withIfNotExistFunction(new FhirIOTestUtil.ExtractIDSearchQuery()) + .withFormatBodyFunction(x -> x)); + + PAssert.that(writeResult.getFailedBodies()).empty(); + + pipeline.run().waitUntilFinish(); + } + + @Test + public void testFhirIO_Update() { + // TODO write initial resources to FHIR + Result writeResult = + (Result) + pipeline + .apply("Create Test Resources", Create.of(RESOURCES.get(version))) + .apply("Extract ID keys", WithKeys.of(new GetByKey("id"))) + .apply( + "Update Resources", + FhirIO.>update(options.getFhirStore()) + .withResourceNameFunction(x -> x.getKey()) + .withFormatBodyFunction(x -> ((KV) x).getValue())); + + PAssert.that(writeResult.getFailedBodies()).empty(); + + pipeline.run().waitUntilFinish(); + // TODO spot check update results + } + + @Test + public void testFhirIO_ConditionalUpdate() { + // TODO write initial resources to FHIR + Result writeResult = + (Result) + pipeline + .apply("Create Test Resources", Create.of(RESOURCES.get(version))) + .apply( + "Conditional Update Resources", + FhirIO.conditionalUpdate(options.getFhirStore()) + .withTypeFunction(x -> "patient") + .withFormatBodyFunction(x -> "{}") + .withSearchParametersFunction(x -> new HashMap<>())); + // TODO spot check update results + } +} diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java index 4f127c050add..cef78fdb70bb 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOWriteIT.java @@ -26,9 +26,7 @@ import java.security.SecureRandom; import java.util.Arrays; import java.util.Collection; -import com.fasterxml.jackson.databind.ObjectMapper; import java.util.HashMap; -import java.util.Map; import org.apache.beam.sdk.Pipeline; import org.apache.beam.sdk.extensions.gcp.options.GcpOptions; import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure; @@ -134,54 +132,4 @@ public void testFhirIO_Import() { pipeline.run().waitUntilFinish(); } - - // TODO(jaketf) add IT for conditional create, update, conditional update transforms. - @Test - public void testFhirIO_CreateResources() { - FhirIO.Write.Result writeResult = - (Result) pipeline - .apply(Create.of(BUNDLES.get(version))) - .apply(FhirIO.createResources(options.getFhirStore()) - .withTypeFunction(new GetByKey("resourceType")) - .withIfNotExistFunction(new FhirIOTestUtil.ExtractIDSearchQuery()) - .withFormatBodyFunction(x -> x) - ); - - - PAssert.that(writeResult.getFailedBodies()).empty(); - - pipeline.run().waitUntilFinish(); - } - - @Test - public void testFhirIO_Update() { - // TODO write initial resources to FHIR - FhirIO.Write.Result writeResult = - (Result) pipeline - .apply("Create Test Resources", Create.of(RESOURCES.get(version))) - .apply("Extract ID keys", WithKeys.of(new GetByKey("id"))) - .apply("Update Resources", - FhirIO.>update(options.getFhirStore()) - .withResourceNameFunction(x -> x.getKey()) - .withFormatBodyFunction(x -> ((KV) x).getValue())); - - PAssert.that(writeResult.getFailedBodies()).empty(); - - pipeline.run().waitUntilFinish(); - // TODO spot check update results - } - - @Test - public void testFhirIO_ConditionalUpdate() { - // TODO write initial resources to FHIR - FhirIO.Write.Result writeResult = - (Result) pipeline - .apply("Create Test Resources", Create.of(RESOURCES.get(version))) - .apply("Conditional Update Resources", - FhirIO.conditionalUpdate(options.getFhirStore()) - .withTypeFunction(x -> "patient") - .withFormatBodyFunction(x -> "{}") - .withSearchParametersFunction(x -> new HashMap<>())); - // TODO spot check update results - } } From 6b61b59859a52df6602523e1dd76ab1e6178c0b2 Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 2 Jun 2020 16:32:27 -0700 Subject: [PATCH 144/151] create IT --- .../sdk/transforms/SerializableFunction.java | 3 +- .../beam/sdk/io/gcp/healthcare/FhirIO.java | 1 - .../healthcare/HttpHealthcareApiClient.java | 3 +- .../sdk/io/gcp/healthcare/FhirIOTestUtil.java | 44 +- .../sdk/io/gcp/healthcare/FhirIOUpdateIT.java | 19 +- ..._ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json | 14018 --- ..._1fd2683f-2a56-47c7-b674-98f2cc8319e7.json | 10877 --- ..._4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json | 17399 ---- ..._8ed31d3e-7352-4055-89c4-f017db3f594e.json | 9279 -- ..._f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json | 10047 -- .../hospitalInformation1586309771387.json | 825 - .../practitionerInformation1586309771387.json | 617 - ..._d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json | 16391 ---- ..._af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json | 31841 ------ ..._a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json | 16971 ---- ..._fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json | 80348 ---------------- ..._55a5307d-5f23-49c1-9100-7d5c513abca3.json | 16018 --- .../R4/hospitalInformation1586368892823.json | 1182 - .../practitionerInformation1586368892823.json | 978 - ..._02a63c07-9fcc-42ba-aec0-9d5399ac4796.json | 16003 --- ..._88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json | 15372 --- ..._df27a976-5c5e-4b84-ad00-fe32972dce9c.json | 22688 ----- ..._136f997d-0a94-4573-97da-a53b5060a612.json | 28126 ------ ..._74779846-85a4-4b26-9da4-414a5fec1aed.json | 18231 ---- ..._3024090f-fe14-40a9-8fae-79952d3c95ce.json | 32061 ------ .../hospitalInformation1586298239556.json | 880 - .../practitionerInformation1586298239556.json | 523 - .../hospitalInformation1589831190233.json | 183 - .../practitionerInformation1589831190233.json | 135 - .../R4/hospitalInformation1589831190233.json | 318 - .../practitionerInformation1589831190233.json | 354 - .../hospitalInformation1589831190233.json | 234 - .../practitionerInformation1589831190233.json | 135 - 33 files changed, 33 insertions(+), 362071 deletions(-) delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Elma843_Hoppe518_1fd2683f-2a56-47c7-b674-98f2cc8319e7.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Ernesto186_Dietrich576_4ecb4cbb-6df7-41e0-8e89-6e7a142721a5.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Kortney212_Bosco882_8ed31d3e-7352-4055-89c4-f017db3f594e.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Terry864_Hintz995_f04ef974-6d6f-4e1c-804f-cd4d62aabb4f.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/hospitalInformation1586309771387.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/practitionerInformation1586309771387.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/Emerson869_Prohaska837_d89e3bd8-4d0f-4735-8d16-d0f646a9dcd6.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/Lorette239_Marvin195_af0e4a42-a1ef-4c2f-ad31-9338a8b8fb7b.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/Norberto865_Cole117_a5e08ef9-fd71-4273-a53a-d5f5df7926f4.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/Robbyn526_DuBuque211_fcf2f472-77ac-47d7-9c9a-a6702bd2bb80.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/Seymour882_Shanahan202_55a5307d-5f23-49c1-9100-7d5c513abca3.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/hospitalInformation1586368892823.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/R4/practitionerInformation1586368892823.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Alexander630_Romaguera67_02a63c07-9fcc-42ba-aec0-9d5399ac4796.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Basil991_Pfannerstill264_88fb71f7-d445-4e5b-8af2-962e8f8e5fb6.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Cris921_Lang846_df27a976-5c5e-4b84-ad00-fe32972dce9c.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Damon455_Will178_136f997d-0a94-4573-97da-a53b5060a612.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Dannette613_Maggio310_74779846-85a4-4b26-9da4-414a5fec1aed.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/Shavonne800_Hilll811_3024090f-fe14-40a9-8fae-79952d3c95ce.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/hospitalInformation1586298239556.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/STU3/practitionerInformation1586298239556.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/hospitalInformation1589831190233.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/DSTU2/practitionerInformation1589831190233.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/hospitalInformation1589831190233.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/R4/practitionerInformation1589831190233.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/hospitalInformation1589831190233.json delete mode 100644 sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/practitionerInformation1589831190233.json diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java index f1e870513f10..a1dba9e688fe 100644 --- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java +++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/SerializableFunction.java @@ -17,7 +17,6 @@ */ package org.apache.beam.sdk.transforms; -import java.io.IOException; import java.io.Serializable; /** @@ -36,5 +35,5 @@ public interface SerializableFunction extends ProcessFunction, Serializable { /** Returns the result of invoking this function on the given input. */ @Override - OutputT apply(InputT input) throws IOException; + OutputT apply(InputT input); } diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java index 160c60af2cf3..c74ec8e3e072 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java @@ -132,7 +132,6 @@ * FhirIO.Write.Result#getFailedBodies()} to retrieve a {@link PCollection} of {@link * HealthcareIOError} containing the {@link String} that failed to be ingested and the * exception. - * *

    Conditional Creating / Updating Resources

    * {@link FhirIO} supports interfaces for conditional update. These can be useful to handle * scenarios where an executeBundle failed. For example if you tried to create a resource that diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java index a6d2bc0566c7..40b368d2a920 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java @@ -417,6 +417,7 @@ enum Method { this.payload = payload; this.method = Method.POST; this.headers = new HashMap<>(); + this.parameters = new HashMap<>(); } public static FhirHttpRequest of(String fhirStore, String payload) { @@ -486,7 +487,7 @@ public HttpBody executeFhirHttpRequest(FhirHttpRequest fhirHttpRequest) .addHeader("Accept-Charset", FHIRSTORE_HEADER_ACCEPT_CHARSET) .addHeader("Accept", FHIRSTORE_HEADER_ACCEPT); - // add additional headers + // add additional parameters for (Map.Entry param : fhirHttpRequest.parameters.entrySet()) { requestBuilder.addParameter(param.getKey(), param.getValue()); } diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java index 385d6403297a..0de5d9062d70 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java @@ -28,6 +28,7 @@ import java.io.File; import java.io.IOException; import java.net.URI; +import java.nio.charset.StandardCharsets; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; @@ -55,13 +56,14 @@ public static class ExtractIDSearchQuery implements SerializableFunction map = mapper.readValue(resource.getBytes(), Map.class); + Map map = + mapper.readValue(resource.getBytes(StandardCharsets.UTF_8), Map.class); String id = map.get("id"); return String.format("_id=%s", id); } catch (IOException e) { throw new RuntimeException(e); } - } + } } public static class GetByKey implements SerializableFunction { @@ -76,7 +78,8 @@ public GetByKey(String key) { @Override public String apply(String resource) { try { - Map map = mapper.readValue(resource.getBytes(), Map.class); + Map map = + mapper.readValue(resource.getBytes(StandardCharsets.UTF_8), Map.class); return map.get(key); } catch (IOException e) { throw new RuntimeException(e); @@ -106,21 +109,21 @@ private static Stream readAllTestResources(String subDir, String version .map(String::new); } - private static Stream readPrettyBundles(String version) { - return readAllTestResources("transactional_bundles", version); + private static List readPrettyBundles(String version) { + return readAllTestResources("transactional_bundles", version).collect(Collectors.toList()); } - private static Stream readPrettyResources(String version) { - return readAllTestResources("resources", version); + private static List readResources(String version) { + return readAllTestResources("resources", version) // stream of file contents + .map((String x) -> x.split("\\r?\\n")) // split lines + .flatMap(Arrays::stream) // flatten lines for all files + .collect(Collectors.toList()); } // Could generate more messages at scale using a tool like // https://synthetichealth.github.io/synthea/ if necessary chose not to avoid the dependency. - static final List DSTU2_PRETTY_BUNDLES = - readPrettyBundles("DSTU2").collect(Collectors.toList()); - static final List STU3_PRETTY_BUNDLES = - readPrettyBundles("STU3").collect(Collectors.toList()); - static final List R4_PRETTY_BUNDLES = - readPrettyBundles("R4").collect(Collectors.toList()); + static final List DSTU2_PRETTY_BUNDLES = readPrettyBundles("DSTU2"); + static final List STU3_PRETTY_BUNDLES = readPrettyBundles("STU3"); + static final List R4_PRETTY_BUNDLES = readPrettyBundles("R4"); static final Map> BUNDLES; @@ -134,20 +137,17 @@ private static Stream readPrettyResources(String version) { // Could generate more messages at scale using a tool like // https://synthetichealth.github.io/synthea/ if necessary chose not to avoid the dependency. - static final List DSTU2_PRETTY_RESOURCES = - readPrettyResources("DSTU2").collect(Collectors.toList()); - static final List STU3_PRETTY_RESOURCES = - readPrettyResources("STU3").collect(Collectors.toList()); - static final List R4_PRETTY_RESOURCES = - readPrettyResources("R4").collect(Collectors.toList()); + static final List DSTU2_RESOURCES = readResources("DSTU2"); + static final List STU3_RESOURCES = readResources("STU3"); + static final List R4_RESOURCES = readResources("R4"); static final Map> RESOURCES; static { Map> m = new HashMap<>(); - m.put("DSTU2", DSTU2_PRETTY_RESOURCES); - m.put("STU3", STU3_PRETTY_RESOURCES); - m.put("R4", R4_PRETTY_RESOURCES); + m.put("DSTU2", DSTU2_RESOURCES); + m.put("STU3", STU3_RESOURCES); + m.put("R4", R4_RESOURCES); RESOURCES = Collections.unmodifiableMap(m); } diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java index 2a03a3448445..fe5bad28caf4 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java @@ -17,7 +17,6 @@ */ package org.apache.beam.sdk.io.gcp.healthcare; -import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.BUNDLES; import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.DEFAULT_TEMP_BUCKET; import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.RESOURCES; import static org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.HEALTHCARE_DATASET_TEMPLATE; @@ -27,9 +26,7 @@ import java.util.Arrays; import java.util.Collection; import java.util.HashMap; -import org.apache.beam.sdk.Pipeline; import org.apache.beam.sdk.extensions.gcp.options.GcpOptions; -import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure; import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Write.Result; import org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.GetByKey; import org.apache.beam.sdk.options.PipelineOptionsFactory; @@ -102,20 +99,20 @@ public static void teardownBucket() throws IOException { FhirIOTestUtil.tearDownTempBucket(); } - // TODO(jaketf) add IT for conditional create, update, conditional update transforms. @Test public void testFhirIO_CreateResources() { - Result writeResult = + Result createResult = (Result) pipeline - .apply("Create Test Resources", Create.of(RESOURCES.get(version))) + .apply("Seed Test Resources", Create.of(RESOURCES.get(version))) .apply( + "Create FHIR Resources", FhirIO.createResources(options.getFhirStore()) .withTypeFunction(new GetByKey("resourceType")) .withIfNotExistFunction(new FhirIOTestUtil.ExtractIDSearchQuery()) .withFormatBodyFunction(x -> x)); - PAssert.that(writeResult.getFailedBodies()).empty(); + PAssert.that(createResult.getFailedBodies()).empty(); pipeline.run().waitUntilFinish(); } @@ -123,10 +120,10 @@ public void testFhirIO_CreateResources() { @Test public void testFhirIO_Update() { // TODO write initial resources to FHIR - Result writeResult = + Result updateResult = (Result) pipeline - .apply("Create Test Resources", Create.of(RESOURCES.get(version))) + .apply("Seed Test Resources", Create.of(RESOURCES.get(version))) .apply("Extract ID keys", WithKeys.of(new GetByKey("id"))) .apply( "Update Resources", @@ -134,7 +131,7 @@ public void testFhirIO_Update() { .withResourceNameFunction(x -> x.getKey()) .withFormatBodyFunction(x -> ((KV) x).getValue())); - PAssert.that(writeResult.getFailedBodies()).empty(); + PAssert.that(updateResult.getFailedBodies()).empty(); pipeline.run().waitUntilFinish(); // TODO spot check update results @@ -143,7 +140,7 @@ public void testFhirIO_Update() { @Test public void testFhirIO_ConditionalUpdate() { // TODO write initial resources to FHIR - Result writeResult = + Result conditionalUpdateResult = (Result) pipeline .apply("Create Test Resources", Create.of(RESOURCES.get(version))) diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json b/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json deleted file mode 100644 index 677f4a31ef9e..000000000000 --- a/sdks/java/io/google-cloud-platform/src/test/resources/DSTU2/Amelia635_Krajcik437_ed7a9f5c-37ea-4767-95ba-a6783e9500b3.json +++ /dev/null @@ -1,14018 +0,0 @@ -{ - "resourceType": "Bundle", - "type": "transaction", - "entry": [ - { - "fullUrl": "urn:uuid:ed7a9f5c-37ea-4767-95ba-a6783e9500b3", - "resource": { - "resourceType": "Patient", - "id": "ed7a9f5c-37ea-4767-95ba-a6783e9500b3", - "text": { - "status": "generated", - "div": "
    Generated by Synthea.Version identifier: v2.5.0-340-gabc9fc4a\n . Person seed: 3529060201889641636 Population seed: 1586309754086
    " - }, - "extension": [ - { - "url": "http://hl7.org/fhir/StructureDefinition/us-core-race", - "valueCodeableConcept": { - "coding": [ - { - "system": "http://hl7.org/fhir/v3/Race", - "code": "2106-3", - "display": "White" - } - ], - "text": "White" - } - }, - { - "url": "http://hl7.org/fhir/StructureDefinition/us-core-ethnicity", - "valueCodeableConcept": { - "coding": [ - { - "system": "http://hl7.org/fhir/v3/Ethnicity", - "code": "2186-5", - "display": "Not Hispanic or Latino" - } - ], - "text": "Not Hispanic or Latino" - } - }, - { - "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName", - "valueString": "Shantay950 Collier206" - }, - { - "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", - "valueCode": "F" - }, - { - "url": "http://hl7.org/fhir/StructureDefinition/birthPlace", - "valueAddress": { - "city": "Quincy", - "state": "Massachusetts", - "country": "US" - } - }, - { - "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years", - 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"display": "Dr. Gillian484 Brakus656" - } - }, - "request": { - "method": "POST", - "url": "MedicationRequest" - } - }, - { - "fullUrl": "urn:uuid:457d2594-ad89-4c5a-a863-eb983d000719", - "resource": { - "resourceType": "Claim", - "id": "457d2594-ad89-4c5a-a863-eb983d000719", - "status": "active", - "type": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/claim-type", - "code": "pharmacy" - } - ] - }, - "use": "claim", - "patient": { - "reference": "urn:uuid:a5e08ef9-fd71-4273-a53a-d5f5df7926f4" - }, - "billablePeriod": { - "start": "2012-05-15T09:41:37-07:00", - "end": "2012-05-15T10:41:37-07:00" - }, - "created": "2012-05-15T10:41:37-07:00", - "provider": { - "reference": "urn:uuid:23834663-ed53-3da9-b330-d6e1ecb8428e", - "display": "SOUTHCOAST HOSPITAL GROUP, INC" - }, - "priority": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/processpriority", - "code": "normal" - } - ] - }, - "prescription": { - "reference": "urn:uuid:1123b665-2688-4488-bd77-96f11c96ba58" - 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}, - "participant": [ - { - "role": [ - { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "116153009", - "display": "Patient" - } - ], - "text": "Patient" - } - ], - "member": { - "reference": "urn:uuid:a5e08ef9-fd71-4273-a53a-d5f5df7926f4", - "display": "Norberto865 Cole117" - } - }, - { - "role": [ - { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "223366009", - "display": "Healthcare professional (occupation)" - } - ], - "text": "Healthcare professional (occupation)" - } - ], - "member": { - "reference": "urn:uuid:f411d1de-1d0c-365f-8a71-8d225cb962af", - "display": "Dr. Gillian484 Brakus656" - } - }, - { - "role": [ - { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "224891009", - "display": "Healthcare services (qualifier value)" - } - ], - "text": "Healthcare services (qualifier value)" - } - ], - "member": { - "reference": "urn:uuid:23834663-ed53-3da9-b330-d6e1ecb8428e", - "display": "SOUTHCOAST HOSPITAL GROUP, INC" - } - } - ], - "reasonCode": [ - { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "44465007", - "display": "Sprain of ankle" - } - ], - "text": "Sprain of ankle" - } - ], - "managingOrganization": [ - { - "reference": "urn:uuid:23834663-ed53-3da9-b330-d6e1ecb8428e", - "display": "SOUTHCOAST HOSPITAL GROUP, INC" - } - ] - }, - "request": { - "method": "POST", - "url": "CareTeam" - } - }, - { - "fullUrl": "urn:uuid:50175367-bf28-4bc0-87d6-88f8dc0f984e", - "resource": { - "resourceType": "CarePlan", - "id": "50175367-bf28-4bc0-87d6-88f8dc0f984e", - "text": { - "status": "generated", - "div": "
    Care Plan for Physical therapy procedure.
    Activities:
    • Physical therapy procedure
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    Activities:
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    • Musculoskeletal care

    Care plan is meant to treat Whiplash injury to neck.
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"resource": { - "resourceType": "PractitionerRole", - "id": "d163bdcf-8294-4320-85b8-86e0680dc34a", - "meta": { - "profile": [ - "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole" - ] - }, - "practitioner": { - "reference": "urn:uuid:a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8", - "display": "Dr. Cathryn51 Hilpert278" - }, - "organization": { - "reference": "urn:uuid:58fe1815-1e8a-38ed-a91a-17d4ef18c8d8", - "display": "PCP68975" - }, - "code": [ - { - "coding": [ - { - "system": "http://nucc.org/provider-taxonomy", - "code": "208D00000X", - "display": "General Practice" - } - ], - "text": "General Practice" - } - ], - "specialty": [ - { - "coding": [ - { - "system": "http://nucc.org/provider-taxonomy", - "code": "208D00000X", - "display": "General Practice" - } - ], - "text": "General Practice" - } - ], - "location": [ - { - "display": "PCP68975" - } - ], - "telecom": [ - { - "system": "phone", - "value": "508-881-4368" - } - ] - } - }, - { - "fullUrl": "urn:uuid:861aa935-d89f-3b41-861b-b791fa112253", - "resource": { - "resourceType": "Practitioner", - "id": "861aa935-d89f-3b41-861b-b791fa112253", - "meta": { - "profile": [ - "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner" - ] - }, - "extension": [ - { - "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension", - "valueInteger": 2 - } - ], - "identifier": [ - { - "system": "http://hl7.org/fhir/sid/us-npi", - "value": "93440" - } - ], - "active": true, - "name": [ - { - "family": "Reynolds644", - "given": [ - "Salena230" - ], - "prefix": [ - "Dr." - ] - } - ], - "telecom": [ - { - "extension": [ - { - "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-direct", - "valueBoolean": true - } - ], - "system": "email", - "value": "Salena230.Reynolds644@example.com", - "use": "work" - } - ], - "address": [ - { - "line": [ - "9 HOPE AVENUE" - ], - "city": "WALTHAM", - "state": "MA", - "postalCode": "2453", - "country": "US" - } - ], - "gender": "female" - } - }, - { - "fullUrl": "urn:uuid:689adf0e-16fd-4546-9764-69d26ef64777", - "resource": { - "resourceType": "PractitionerRole", - "id": "689adf0e-16fd-4546-9764-69d26ef64777", - "meta": { - "profile": [ - "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole" - ] - }, - "practitioner": { - "reference": "urn:uuid:861aa935-d89f-3b41-861b-b791fa112253", - "display": "Dr. Salena230 Reynolds644" - }, - "organization": { - "reference": "urn:uuid:d672f853-e2a5-324e-98fa-c6d5f8dfc255", - "display": "WALTHAM URGENT CARE" - }, - "code": [ - { - "coding": [ - { - "system": "http://nucc.org/provider-taxonomy", - "code": "208D00000X", - "display": "General Practice" - } - ], - "text": "General Practice" - } - ], - "specialty": [ - { - "coding": [ - { - "system": "http://nucc.org/provider-taxonomy", - "code": "208D00000X", - "display": "General Practice" - } - ], - "text": "General Practice" - } - ], - "location": [ - { - "display": "WALTHAM URGENT CARE" - } - ], - "telecom": [ - { - "system": "phone", - "value": "617-243-5591" - } - ] - } - } - ] -} diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/hospitalInformation1589831190233.json b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/hospitalInformation1589831190233.json deleted file mode 100644 index dfe338def8e6..000000000000 --- a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/hospitalInformation1589831190233.json +++ /dev/null @@ -1,234 +0,0 @@ -{ - "resourceType": "Bundle", - "type": "collection", - "entry": [ - { - "fullUrl": "urn:uuid:465de31f-3098-365c-af70-48a071e1f5aa", - "resource": { - "resourceType": "Organization", - "id": "465de31f-3098-365c-af70-48a071e1f5aa", - "extension": [ - { - "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension", - "valueInteger": 27 - }, - { - "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension", - "valueInteger": 0 - }, - { - "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension", - "valueInteger": 0 - }, - { - "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension", - "valueInteger": 0 - } - ], - "identifier": [ - { - "system": "https://github.com/synthetichealth/synthea", - "value": "465de31f-3098-365c-af70-48a071e1f5aa" - } - ], - "type": [ - { - "coding": [ - { - "system": "http://hl7.org/fhir/organization-type", - "code": "prov", - "display": "Healthcare Provider" - } - ], - "text": "Healthcare Provider" - } - ], - "name": "METROWEST MEDICAL CENTER", - "telecom": [ - { - "system": "phone", - "value": "5083831000" - } - ], - "address": [ - { - "extension": [ - { - "url": "http://hl7.org/fhir/StructureDefinition/geolocation", - "extension": [ - { - "url": "latitude", - "valueDecimal": 42.307905 - }, - { - "url": "longitude", - "valueDecimal": -71.436196 - } - ] - } - ], - "line": [ - "115 LINCOLN STREET" - ], - "city": "FRAMINGHAM", - "state": "MA", - "postalCode": "01701", - "country": "US" - } - ] - } - }, - { - "fullUrl": "urn:uuid:58fe1815-1e8a-38ed-a91a-17d4ef18c8d8", - "resource": { - "resourceType": "Organization", - "id": "58fe1815-1e8a-38ed-a91a-17d4ef18c8d8", - "extension": [ - { - "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension", - "valueInteger": 30 - }, - { - "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension", - "valueInteger": 23 - }, - { - "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension", - "valueInteger": 5 - }, - { - "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension", - "valueInteger": 17 - } - ], - "identifier": [ - { - "system": "https://github.com/synthetichealth/synthea", - "value": "58fe1815-1e8a-38ed-a91a-17d4ef18c8d8" - } - ], - "type": [ - { - "coding": [ - { - "system": "http://hl7.org/fhir/organization-type", - "code": "prov", - "display": "Healthcare Provider" - } - ], - "text": "Healthcare Provider" - } - ], - "name": "PCP68975", - "telecom": [ - { - "system": "phone", - "value": "508-881-4368" - } - ], - "address": [ - { - "extension": [ - { - "url": "http://hl7.org/fhir/StructureDefinition/geolocation", - "extension": [ - { - "url": "latitude", - "valueDecimal": 42.257754999999996 - }, - { - "url": "longitude", - "valueDecimal": -71.473526 - } - ] - } - ], - "line": [ - "259 MAIN ST" - ], - "city": "ASHLAND", - "state": "MA", - "postalCode": "01721-2115", - "country": "US" - } - ] - } - }, - { - "fullUrl": "urn:uuid:d672f853-e2a5-324e-98fa-c6d5f8dfc255", - "resource": { - "resourceType": "Organization", - "id": "d672f853-e2a5-324e-98fa-c6d5f8dfc255", - "extension": [ - { - "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension", - "valueInteger": 2 - }, - { - "url": "http://synthetichealth.github.io/synthea/utilization-procedures-extension", - "valueInteger": 0 - }, - { - "url": "http://synthetichealth.github.io/synthea/utilization-labs-extension", - "valueInteger": 0 - }, - { - "url": "http://synthetichealth.github.io/synthea/utilization-prescriptions-extension", - "valueInteger": 0 - } - ], - "identifier": [ - { - "system": "https://github.com/synthetichealth/synthea", - "value": "d672f853-e2a5-324e-98fa-c6d5f8dfc255" - } - ], - "type": [ - { - "coding": [ - { - "system": "http://hl7.org/fhir/organization-type", - "code": "prov", - "display": "Healthcare Provider" - } - ], - "text": "Healthcare Provider" - } - ], - "name": "WALTHAM URGENT CARE", - "telecom": [ - { - "system": "phone", - "value": "617-243-5591" - } - ], - "address": [ - { - "extension": [ - { - "url": "http://hl7.org/fhir/StructureDefinition/geolocation", - "extension": [ - { - "url": "latitude", - "valueDecimal": 42.3700513 - }, - { - "url": "longitude", - "valueDecimal": -71.2490152 - } - ] - } - ], - "line": [ - "9 HOPE AVENUE" - ], - "city": "WALTHAM", - "state": "MA", - "postalCode": "2453", - "country": "US" - } - ] - } - } - ] -} diff --git a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/practitionerInformation1589831190233.json b/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/practitionerInformation1589831190233.json deleted file mode 100644 index 9e963d958d03..000000000000 --- a/sdks/java/io/google-cloud-platform/src/test/resources/resources/STU3/practitionerInformation1589831190233.json +++ /dev/null @@ -1,135 +0,0 @@ -{ - "resourceType": "Bundle", - "type": "collection", - "entry": [ - { - "fullUrl": "urn:uuid:c16820ae-2954-32d4-863c-e9ceb741154c", - "resource": { - "resourceType": "Practitioner", - "id": "c16820ae-2954-32d4-863c-e9ceb741154c", - "extension": [ - { - "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension", - "valueInteger": 27 - } - ], - "identifier": [ - { - "system": "http://hl7.org/fhir/sid/us-npi", - "value": "530" - } - ], - "active": true, - "name": [ - { - "family": "Murphy561", - "given": [ - "Mari763" - ], - "prefix": [ - "Dr." - ] - } - ], - "address": [ - { - "line": [ - "115 LINCOLN STREET" - ], - "city": "FRAMINGHAM", - "state": "MA", - "postalCode": "01701", - "country": "US" - } - ], - "gender": "female" - } - }, - { - "fullUrl": "urn:uuid:a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8", - "resource": { - "resourceType": "Practitioner", - "id": "a0f721c3-b8d1-3227-a8bf-27e5bf1ef5e8", - "extension": [ - { - "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension", - "valueInteger": 30 - } - ], - "identifier": [ - { - "system": "http://hl7.org/fhir/sid/us-npi", - "value": "35750" - } - ], - "active": true, - "name": [ - { - "family": "Hilpert278", - "given": [ - "Cathryn51" - ], - "prefix": [ - "Dr." - ] - } - ], - "address": [ - { - "line": [ - "259 MAIN ST" - ], - "city": "ASHLAND", - "state": "MA", - "postalCode": "01721-2115", - "country": "US" - } - ], - "gender": "female" - } - }, - { - "fullUrl": "urn:uuid:861aa935-d89f-3b41-861b-b791fa112253", - "resource": { - "resourceType": "Practitioner", - "id": "861aa935-d89f-3b41-861b-b791fa112253", - "extension": [ - { - "url": "http://synthetichealth.github.io/synthea/utilization-encounters-extension", - "valueInteger": 2 - } - ], - "identifier": [ - { - "system": "http://hl7.org/fhir/sid/us-npi", - "value": "93440" - } - ], - "active": true, - "name": [ - { - "family": "Reynolds644", - "given": [ - "Salena230" - ], - "prefix": [ - "Dr." - ] - } - ], - "address": [ - { - "line": [ - "9 HOPE AVENUE" - ], - "city": "WALTHAM", - "state": "MA", - "postalCode": "2453", - "country": "US" - } - ], - "gender": "female" - } - } - ] -} From 39c2d9df0ac1eb592c0fbcc6777a78e75c37e478 Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 2 Jun 2020 16:35:02 -0700 Subject: [PATCH 145/151] split create / update ITs --- .../sdk/io/gcp/healthcare/FhirIOCreateIT.java | 119 ++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOCreateIT.java diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOCreateIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOCreateIT.java new file mode 100644 index 000000000000..05741bc26d0f --- /dev/null +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOCreateIT.java @@ -0,0 +1,119 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.beam.sdk.io.gcp.healthcare; + +import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.DEFAULT_TEMP_BUCKET; +import static org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.RESOURCES; +import static org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.HEALTHCARE_DATASET_TEMPLATE; + +import java.io.IOException; +import java.security.SecureRandom; +import java.util.Arrays; +import java.util.Collection; +import java.util.HashMap; +import org.apache.beam.sdk.extensions.gcp.options.GcpOptions; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Write.Result; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.GetByKey; +import org.apache.beam.sdk.options.PipelineOptionsFactory; +import org.apache.beam.sdk.testing.PAssert; +import org.apache.beam.sdk.testing.TestPipeline; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.WithKeys; +import org.apache.beam.sdk.values.KV; +import org.junit.After; +import org.junit.AfterClass; +import org.junit.Before; +import org.junit.Rule; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.junit.runners.Parameterized; +import org.junit.runners.Parameterized.Parameters; + +@RunWith(Parameterized.class) +public class FhirIOCreateIT { + + @Parameters(name = "{0}") + public static Collection versions() { + return Arrays.asList("DSTU2", "STU3", "R4"); + } + + private final String fhirStoreName; + private FhirIOTestOptions options; + private transient HealthcareApiClient client; + private String healthcareDataset; + private long testTime = System.currentTimeMillis(); + + public String version; + + @Rule public transient TestPipeline pipeline = TestPipeline.create(); + + public FhirIOCreateIT(String version) { + this.version = version; + this.fhirStoreName = + "FHIR_store_" + version + "_write_it_" + testTime + "_" + (new SecureRandom().nextInt(32)); + } + + @Before + public void setup() throws Exception { + if (client == null) { + client = new HttpHealthcareApiClient(); + } + PipelineOptionsFactory.register(FhirIOTestOptions.class); + String project = TestPipeline.testingPipelineOptions().as(GcpOptions.class).getProject(); + healthcareDataset = String.format(HEALTHCARE_DATASET_TEMPLATE, project); + options = TestPipeline.testingPipelineOptions().as(FhirIOTestOptions.class); + options.setGcsTempPath( + String.format("gs://%s/FhirIOWrite%sIT/%s/temp/", DEFAULT_TEMP_BUCKET, version, testTime)); + options.setGcsDeadLetterPath( + String.format( + "gs://%s/FhirIOWrite%sIT/%s/deadletter/", DEFAULT_TEMP_BUCKET, version, testTime)); + options.setFhirStore(healthcareDataset + "/fhirStores/" + fhirStoreName); + HealthcareApiClient client = new HttpHealthcareApiClient(); + client.createFhirStore(healthcareDataset, fhirStoreName, version); + } + + @After + public void teardownFhirStore() throws IOException { + HealthcareApiClient client = new HttpHealthcareApiClient(); + client.deleteFhirStore(healthcareDataset + "/fhirStores/" + fhirStoreName); + // clean up GCS objects if any. + } + + @AfterClass + public static void teardownBucket() throws IOException { + FhirIOTestUtil.tearDownTempBucket(); + } + + @Test + public void testFhirIO_CreateResources() { + Result createResult = + (Result) + pipeline + .apply("Seed Test Resources", Create.of(RESOURCES.get(version))) + .apply( + "Create FHIR Resources", + FhirIO.createResources(options.getFhirStore()) + .withTypeFunction(new GetByKey("resourceType")) + .withIfNotExistFunction(new FhirIOTestUtil.ExtractIDSearchQuery()) + .withFormatBodyFunction(x -> x)); + + PAssert.that(createResult.getFailedBodies()).empty(); + + pipeline.run().waitUntilFinish(); + } +} From 3abc1a533378e153a26c7380e511b73989bb9735 Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 2 Jun 2020 17:42:29 -0700 Subject: [PATCH 146/151] conditional update IT --- .../beam/sdk/io/gcp/healthcare/FhirIO.java | 8 ++-- .../sdk/io/gcp/healthcare/FhirIOCreateIT.java | 6 +-- .../sdk/io/gcp/healthcare/FhirIOTestUtil.java | 35 ++++++++++++++++ .../sdk/io/gcp/healthcare/FhirIOUpdateIT.java | 40 +++++++------------ 4 files changed, 55 insertions(+), 34 deletions(-) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java index c74ec8e3e072..0f07a8a8cc76 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java @@ -1538,10 +1538,10 @@ public UpdateResources withETagFunction(SerializableFunction etagFunc public FhirIO.Write.Result expand(PCollection input) { checkArgument( formatBodyFunction != null, - "FhirIO.UpdateResources should always be called with a " + "withFormatBodyFunction."); + "FhirIO.UpdateResources should always be called with a withFormatBodyFunction."); checkArgument( - resourceNameFunction == null, - "resourceNameFunction must be set when using FhirIO.UpdateResources"); + resourceNameFunction != null, + "FhirIO.UpdateResources should always be called with a withResourceNameFunction."); return Write.Result.in( input.getPipeline(), input @@ -1579,7 +1579,7 @@ public void initClient() throws IOException { } @ProcessElement - public void update(ProcessContext context) throws IOException { + public void update(ProcessContext context) { T input = context.element(); String body = formatBodyFunction.apply(input); try { diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOCreateIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOCreateIT.java index 05741bc26d0f..68cb6fae2d9f 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOCreateIT.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOCreateIT.java @@ -25,16 +25,14 @@ import java.security.SecureRandom; import java.util.Arrays; import java.util.Collection; -import java.util.HashMap; import org.apache.beam.sdk.extensions.gcp.options.GcpOptions; import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Write.Result; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.ExtractIDSearchParams; import org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.GetByKey; import org.apache.beam.sdk.options.PipelineOptionsFactory; import org.apache.beam.sdk.testing.PAssert; import org.apache.beam.sdk.testing.TestPipeline; import org.apache.beam.sdk.transforms.Create; -import org.apache.beam.sdk.transforms.WithKeys; -import org.apache.beam.sdk.values.KV; import org.junit.After; import org.junit.AfterClass; import org.junit.Before; @@ -109,7 +107,7 @@ public void testFhirIO_CreateResources() { "Create FHIR Resources", FhirIO.createResources(options.getFhirStore()) .withTypeFunction(new GetByKey("resourceType")) - .withIfNotExistFunction(new FhirIOTestUtil.ExtractIDSearchQuery()) + .withIfNotExistFunction(new ExtractIDSearchParams()) .withFormatBodyFunction(x -> x)); PAssert.that(createResult.getFailedBodies()).empty(); diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java index 0de5d9062d70..b96d22bef1d0 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java @@ -66,6 +66,29 @@ public String apply(String resource) { } } + public static class ExtractIDSearchParams + implements SerializableFunction> { + private ObjectMapper mapper; + + ExtractIDSearchParams() { + mapper = new ObjectMapper(); + } + + @Override + public Map apply(String resource) { + Map searchParams = new HashMap<>(); + try { + Map map = + mapper.readValue(resource.getBytes(StandardCharsets.UTF_8), Map.class); + String id = map.get("id"); + searchParams.put("_id", id); + return searchParams; + } catch (IOException e) { + throw new RuntimeException(e); + } + } + } + public static class GetByKey implements SerializableFunction { private final String key; private ObjectMapper mapper; @@ -159,6 +182,18 @@ static void executeFhirBundles(HealthcareApiClient client, String fhirStore, Lis } } + /** Populate the test resources into the FHIR store and returns a list of resource IDs. */ + static void createFhirResources( + HealthcareApiClient client, String fhirStore, List resources) + throws IOException, HealthcareHttpException { + GetByKey getByKey = new GetByKey("resourceType"); + ExtractIDSearchQuery extractIDSearchQuery = new ExtractIDSearchQuery(); + for (String resource : resources) { + client.fhirCreate( + fhirStore, getByKey.apply(resource), resource, extractIDSearchQuery.apply(resource)); + } + } + public static void tearDownTempBucket() throws IOException { GoogleCredentials credentials = GoogleCredentials.getApplicationDefault(); diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java index fe5bad28caf4..629c75b390b4 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java @@ -25,10 +25,12 @@ import java.security.SecureRandom; import java.util.Arrays; import java.util.Collection; -import java.util.HashMap; +import java.util.List; import org.apache.beam.sdk.extensions.gcp.options.GcpOptions; import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Write.Result; +import org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.ExtractIDSearchParams; import org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.GetByKey; +import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException; import org.apache.beam.sdk.options.PipelineOptionsFactory; import org.apache.beam.sdk.testing.PAssert; import org.apache.beam.sdk.testing.TestPipeline; @@ -49,7 +51,8 @@ public class FhirIOUpdateIT { @Parameters(name = "{0}") public static Collection versions() { - return Arrays.asList("DSTU2", "STU3", "R4"); + // TODO(jaketf) uncomment other versions. + return Arrays.asList(/*"DSTU2", "STU3", */ "R4"); } private final String fhirStoreName; @@ -100,30 +103,15 @@ public static void teardownBucket() throws IOException { } @Test - public void testFhirIO_CreateResources() { - Result createResult = - (Result) - pipeline - .apply("Seed Test Resources", Create.of(RESOURCES.get(version))) - .apply( - "Create FHIR Resources", - FhirIO.createResources(options.getFhirStore()) - .withTypeFunction(new GetByKey("resourceType")) - .withIfNotExistFunction(new FhirIOTestUtil.ExtractIDSearchQuery()) - .withFormatBodyFunction(x -> x)); - - PAssert.that(createResult.getFailedBodies()).empty(); - - pipeline.run().waitUntilFinish(); - } - - @Test - public void testFhirIO_Update() { + public void testFhirIO_Update() throws IOException, HealthcareHttpException { + List initialResources = RESOURCES.get(version); + FhirIOTestUtil.createFhirResources( + client, healthcareDataset + "/fhirStores/" + fhirStoreName, initialResources); // TODO write initial resources to FHIR Result updateResult = (Result) pipeline - .apply("Seed Test Resources", Create.of(RESOURCES.get(version))) + .apply("Seed Test Resources", Create.of(initialResources)) .apply("Extract ID keys", WithKeys.of(new GetByKey("id"))) .apply( "Update Resources", @@ -147,9 +135,9 @@ public void testFhirIO_ConditionalUpdate() { .apply( "Conditional Update Resources", FhirIO.conditionalUpdate(options.getFhirStore()) - .withTypeFunction(x -> "patient") - .withFormatBodyFunction(x -> "{}") - .withSearchParametersFunction(x -> new HashMap<>())); - // TODO spot check update results + .withTypeFunction(new GetByKey("resourceType")) + .withFormatBodyFunction(x -> x) + .withSearchParametersFunction(new ExtractIDSearchParams())); + pipeline.run().waitUntilFinish(); } } From 6e1372cb7ee03933ac8c94d8219941d9518caa58 Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 2 Jun 2020 18:29:27 -0700 Subject: [PATCH 147/151] remove UpdateResources as the interface was too hard to use --- .../beam/sdk/io/gcp/healthcare/FhirIO.java | 162 +----------------- .../gcp/healthcare/HealthcareApiClient.java | 5 + .../healthcare/HttpHealthcareApiClient.java | 15 ++ .../sdk/io/gcp/healthcare/FhirIOTestUtil.java | 29 ++++ .../sdk/io/gcp/healthcare/FhirIOUpdateIT.java | 26 +-- 5 files changed, 53 insertions(+), 184 deletions(-) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java index 0f07a8a8cc76..b4a79a36ca0e 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java @@ -132,7 +132,8 @@ * FhirIO.Write.Result#getFailedBodies()} to retrieve a {@link PCollection} of {@link * HealthcareIOError} containing the {@link String} that failed to be ingested and the * exception. - *

    Conditional Creating / Updating Resources

    + * + *

    Conditional Creating / Updating Resources

    * {@link FhirIO} supports interfaces for conditional update. These can be useful to handle * scenarios where an executeBundle failed. For example if you tried to create a resource that * already exists you can grab the faield bodies of your {@link FhirIO.ExecuteBundles} transform @@ -1440,165 +1441,6 @@ public void create(ProcessContext context) throws IOException { } } - /** - * Update resources update resources. - * - * @param the type parameter - * @param fhirStore the fhir store - * @return the update resources - */ - public static UpdateResources update(ValueProvider fhirStore) { - return new UpdateResources(fhirStore); - } - - /** - * Update resources update resources. - * - * @param the type parameter - * @param fhirStore the fhir store - * @return the update resources - */ - public static UpdateResources update(String fhirStore) { - return new UpdateResources(fhirStore); - } - - /** - * {@link PTransform} for Updating FHIR resources resources. - * - *

    This transform assumes the input {@link PCollection} contains {@link KV} of resource name, - * value pairs and by default will call {@code .toString} to extract string values. However, the - * user can override this behavior by specifying a {@link SerializableFunction} with custom logic - * to extract the resource name and body from the {@link KV} in {@link - * UpdateResources#withResourceNameFunction(SerializableFunction)} and {@link - * UpdateResources#withFormatBodyFunction(SerializableFunction)} - * - *

    https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/update - */ - public static class UpdateResources - extends PTransform, Write.Result> { - private final ValueProvider fhirStore; - private SerializableFunction formatBodyFunction; - private SerializableFunction resourceNameFunction; - private SerializableFunction etagFunction; - public static final TupleTag UPDATE_RESULTS = new TupleTag() {}; - private static final Logger LOG = LoggerFactory.getLogger(UpdateResources.class); - - /** - * Instantiates a new Update resources. - * - * @param fhirStore the fhir store - */ - UpdateResources(ValueProvider fhirStore) { - this.fhirStore = fhirStore; - } - - /** - * Instantiates a new Update resources. - * - * @param fhirStore the fhir store - */ - UpdateResources(String fhirStore) { - this.fhirStore = StaticValueProvider.of(fhirStore); - } - /** - * Add a {@link SerializableFunction} to extract a resource name from the input element. - * - * @param resourceNameFunction the resource name function - * @return the update resources - */ - public UpdateResources withResourceNameFunction( - SerializableFunction resourceNameFunction) { - this.resourceNameFunction = resourceNameFunction; - return this; - } - - /** - * With format body function update resources. - * - * @param formatBodyFunction the format body function - * @return the update resources - */ - public UpdateResources withFormatBodyFunction( - SerializableFunction formatBodyFunction) { - this.formatBodyFunction = formatBodyFunction; - return this; - } - /** - * With ETag function update resources. - * - * @param etagFunction ETag function - * @return the update resources - */ - public UpdateResources withETagFunction(SerializableFunction etagFunction) { - this.etagFunction = etagFunction; - return this; - } - - @Override - public FhirIO.Write.Result expand(PCollection input) { - checkArgument( - formatBodyFunction != null, - "FhirIO.UpdateResources should always be called with a withFormatBodyFunction."); - checkArgument( - resourceNameFunction != null, - "FhirIO.UpdateResources should always be called with a withResourceNameFunction."); - return Write.Result.in( - input.getPipeline(), - input - .apply( - ParDo.of( - new UpdateFn( - fhirStore, formatBodyFunction, resourceNameFunction, etagFunction))) - .setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()))); - } - - static class UpdateFn extends DoFn> { - - private Counter failedUpdates = Metrics.counter(UpdateFn.class, "failed-updates"); - private transient HealthcareApiClient client; - private final ObjectMapper mapper = new ObjectMapper(); - private final ValueProvider fhirStore; - private SerializableFunction formatBodyFunction; - private SerializableFunction resourceNameFunction; - private SerializableFunction etagFunction; - - UpdateFn( - ValueProvider fhirStore, - SerializableFunction formatBodyFunction, - SerializableFunction resourceNameFunction, - @Nullable SerializableFunction etagFunction) { - this.fhirStore = fhirStore; - this.formatBodyFunction = formatBodyFunction; - this.resourceNameFunction = resourceNameFunction; - this.etagFunction = etagFunction; - } - - @Setup - public void initClient() throws IOException { - this.client = new HttpHealthcareApiClient(); - } - - @ProcessElement - public void update(ProcessContext context) { - T input = context.element(); - String body = formatBodyFunction.apply(input); - try { - // Validate that data was set to valid JSON. - mapper.readTree(body); - String resourceName = resourceNameFunction.apply(input); - String etag = null; - if (etagFunction != null) { - etag = etagFunction.apply(input); - } - HttpBody result = client.fhirUpdate(fhirStore.get(), resourceName, body, etag); - context.output(UPDATE_RESULTS, result.getData()); - } catch (IOException | HealthcareHttpException e) { - failedUpdates.inc(); - context.output(HealthcareIOError.of(body, e)); - } - } - } - } /** * Conditional update conditional update. diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java index 3f553f1c7ec7..37fdac994aff 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java @@ -164,6 +164,10 @@ HttpBody fhirConditionalUpdate( HttpBody fhirUpdate(String fhirStore, String type, String resource, @Nullable String etag) throws IOException, HealthcareHttpException; + HttpBody fhirSearch( + String fhirStore, @Nullable String type, Map searchParameters + ) throws IOException, HealthcareHttpException; + /** * Read fhir resource http body. * @@ -198,4 +202,5 @@ FhirStore createFhirStore(String dataset, String name, String version, String pu Empty deleteHL7v2Store(String store) throws IOException; Empty deleteFhirStore(String store) throws IOException; + } diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java index 40b368d2a920..699d480ebee1 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java @@ -408,6 +408,7 @@ static class FhirHttpRequest { private Map parameters; enum Method { + GET, POST, PUT } @@ -469,6 +470,9 @@ public HttpBody executeFhirHttpRequest(FhirHttpRequest fhirHttpRequest) RequestBuilder requestBuilder; switch (fhirHttpRequest.method) { + case GET: + requestBuilder = RequestBuilder.get(); + break; case PUT: requestBuilder = RequestBuilder.put(); break; @@ -564,6 +568,17 @@ public HttpBody fhirUpdate( .setMethod(Method.PUT)); } + @Override + public HttpBody fhirSearch( + String fhirStore, @Nullable String type, Map searchParameters + ) throws IOException, HealthcareHttpException { + return executeFhirHttpRequest( + new FhirHttpRequest(fhirStore, null) + .setPathSuffix(type) + .setMethod(Method.GET) + .setParameters(searchParameters)); + } + /** * Wraps {@link HttpResponse} in an exception with a statusCode field for use with {@link * HealthcareIOError}. diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java index b96d22bef1d0..b8754f7da651 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java @@ -22,6 +22,7 @@ import com.google.api.client.http.HttpRequestInitializer; import com.google.api.client.http.javanet.NetHttpTransport; import com.google.api.client.json.jackson2.JacksonFactory; +import com.google.api.services.healthcare.v1beta1.model.HttpBody; import com.google.api.services.storage.Storage; import com.google.api.services.storage.model.StorageObject; import com.google.auth.oauth2.GoogleCredentials; @@ -41,7 +42,9 @@ import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException; +import org.apache.beam.sdk.transforms.DoFn; import org.apache.beam.sdk.transforms.SerializableFunction; +import org.apache.beam.sdk.values.KV; class FhirIOTestUtil { public static final String DEFAULT_TEMP_BUCKET = "temp-storage-for-healthcare-io-tests"; @@ -229,4 +232,30 @@ public static void tearDownTempBucket() throws IOException { } } } + + public static class ResourceIdToNameFn extends DoFn, KV> { + private transient HealthcareApiClient client; + private ExtractIDSearchParams extractIDSearchParams = new ExtractIDSearchParams(); + private final String fhirStore; + private ObjectMapper mapper; + + public ResourceIdToNameFn(String fhirStore) { + this.fhirStore = fhirStore; + } + + @Setup + void setup() throws IOException { + client = new HttpHealthcareApiClient(); + mapper = new ObjectMapper(); + } + + @ProcessElement + void mapKeys(@Element KV idResourcePair, OutputReceiver> out) + throws IOException, HealthcareHttpException { + Map searchParams = extractIDSearchParams.apply(idResourcePair.getValue()); + String searchResults = client.fhirSearch(fhirStore, null, searchParams).getData(); + + } + } + } diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java index 629c75b390b4..3d8c64c30e40 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java @@ -88,6 +88,8 @@ public void setup() throws Exception { options.setFhirStore(healthcareDataset + "/fhirStores/" + fhirStoreName); HealthcareApiClient client = new HttpHealthcareApiClient(); client.createFhirStore(healthcareDataset, fhirStoreName, version); + FhirIOTestUtil.createFhirResources( + client, healthcareDataset + "/fhirStores/" + fhirStoreName, RESOURCES.get(version)); } @After @@ -102,32 +104,8 @@ public static void teardownBucket() throws IOException { FhirIOTestUtil.tearDownTempBucket(); } - @Test - public void testFhirIO_Update() throws IOException, HealthcareHttpException { - List initialResources = RESOURCES.get(version); - FhirIOTestUtil.createFhirResources( - client, healthcareDataset + "/fhirStores/" + fhirStoreName, initialResources); - // TODO write initial resources to FHIR - Result updateResult = - (Result) - pipeline - .apply("Seed Test Resources", Create.of(initialResources)) - .apply("Extract ID keys", WithKeys.of(new GetByKey("id"))) - .apply( - "Update Resources", - FhirIO.>update(options.getFhirStore()) - .withResourceNameFunction(x -> x.getKey()) - .withFormatBodyFunction(x -> ((KV) x).getValue())); - - PAssert.that(updateResult.getFailedBodies()).empty(); - - pipeline.run().waitUntilFinish(); - // TODO spot check update results - } - @Test public void testFhirIO_ConditionalUpdate() { - // TODO write initial resources to FHIR Result conditionalUpdateResult = (Result) pipeline From ee3c99dcfd33f24ae3e8ea05f275879b3cb2c832 Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 2 Jun 2020 18:32:46 -0700 Subject: [PATCH 148/151] spotless --- .../java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java | 4 +--- .../beam/sdk/io/gcp/healthcare/HealthcareApiClient.java | 6 ++---- .../beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java | 4 ++-- .../apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java | 3 --- .../apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java | 5 ----- 5 files changed, 5 insertions(+), 17 deletions(-) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java index b4a79a36ca0e..070155ed2162 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java @@ -132,8 +132,7 @@ * FhirIO.Write.Result#getFailedBodies()} to retrieve a {@link PCollection} of {@link * HealthcareIOError} containing the {@link String} that failed to be ingested and the * exception. - * - *

    Conditional Creating / Updating Resources

    + *

    Conditional Creating / Updating Resources

    * {@link FhirIO} supports interfaces for conditional update. These can be useful to handle * scenarios where an executeBundle failed. For example if you tried to create a resource that * already exists you can grab the faield bodies of your {@link FhirIO.ExecuteBundles} transform @@ -1441,7 +1440,6 @@ public void create(ProcessContext context) throws IOException { } } - /** * Conditional update conditional update. * diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java index 37fdac994aff..990e4aa839e7 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HealthcareApiClient.java @@ -164,9 +164,8 @@ HttpBody fhirConditionalUpdate( HttpBody fhirUpdate(String fhirStore, String type, String resource, @Nullable String etag) throws IOException, HealthcareHttpException; - HttpBody fhirSearch( - String fhirStore, @Nullable String type, Map searchParameters - ) throws IOException, HealthcareHttpException; + HttpBody fhirSearch(String fhirStore, @Nullable String type, Map searchParameters) + throws IOException, HealthcareHttpException; /** * Read fhir resource http body. @@ -202,5 +201,4 @@ FhirStore createFhirStore(String dataset, String name, String version, String pu Empty deleteHL7v2Store(String store) throws IOException; Empty deleteFhirStore(String store) throws IOException; - } diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java index 699d480ebee1..801d5d60ae9d 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java @@ -570,8 +570,8 @@ public HttpBody fhirUpdate( @Override public HttpBody fhirSearch( - String fhirStore, @Nullable String type, Map searchParameters - ) throws IOException, HealthcareHttpException { + String fhirStore, @Nullable String type, Map searchParameters) + throws IOException, HealthcareHttpException { return executeFhirHttpRequest( new FhirHttpRequest(fhirStore, null) .setPathSuffix(type) diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java index b8754f7da651..831433765666 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java @@ -22,7 +22,6 @@ import com.google.api.client.http.HttpRequestInitializer; import com.google.api.client.http.javanet.NetHttpTransport; import com.google.api.client.json.jackson2.JacksonFactory; -import com.google.api.services.healthcare.v1beta1.model.HttpBody; import com.google.api.services.storage.Storage; import com.google.api.services.storage.model.StorageObject; import com.google.auth.oauth2.GoogleCredentials; @@ -254,8 +253,6 @@ void mapKeys(@Element KV idResourcePair, OutputReceiver searchParams = extractIDSearchParams.apply(idResourcePair.getValue()); String searchResults = client.fhirSearch(fhirStore, null, searchParams).getData(); - } } - } diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java index 3d8c64c30e40..8e095cc0802e 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOUpdateIT.java @@ -25,18 +25,13 @@ import java.security.SecureRandom; import java.util.Arrays; import java.util.Collection; -import java.util.List; import org.apache.beam.sdk.extensions.gcp.options.GcpOptions; import org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Write.Result; import org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.ExtractIDSearchParams; import org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil.GetByKey; -import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException; import org.apache.beam.sdk.options.PipelineOptionsFactory; -import org.apache.beam.sdk.testing.PAssert; import org.apache.beam.sdk.testing.TestPipeline; import org.apache.beam.sdk.transforms.Create; -import org.apache.beam.sdk.transforms.WithKeys; -import org.apache.beam.sdk.values.KV; import org.junit.After; import org.junit.AfterClass; import org.junit.Before; From 29df6d3b0548209318bca0bbc38e6e09c6a25176 Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 2 Jun 2020 18:38:39 -0700 Subject: [PATCH 149/151] remove unused test util DoFn --- .../sdk/io/gcp/healthcare/FhirIOTestUtil.java | 24 ------------------- 1 file changed, 24 deletions(-) diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java index 831433765666..8b493eb21032 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java @@ -231,28 +231,4 @@ public static void tearDownTempBucket() throws IOException { } } } - - public static class ResourceIdToNameFn extends DoFn, KV> { - private transient HealthcareApiClient client; - private ExtractIDSearchParams extractIDSearchParams = new ExtractIDSearchParams(); - private final String fhirStore; - private ObjectMapper mapper; - - public ResourceIdToNameFn(String fhirStore) { - this.fhirStore = fhirStore; - } - - @Setup - void setup() throws IOException { - client = new HttpHealthcareApiClient(); - mapper = new ObjectMapper(); - } - - @ProcessElement - void mapKeys(@Element KV idResourcePair, OutputReceiver> out) - throws IOException, HealthcareHttpException { - Map searchParams = extractIDSearchParams.apply(idResourcePair.getValue()); - String searchResults = client.fhirSearch(fhirStore, null, searchParams).getData(); - } - } } From 74c3c23d609c6af30428c59d39a030bb8d0824dd Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 2 Jun 2020 18:39:51 -0700 Subject: [PATCH 150/151] fix find replace typo --- .../beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java index 801d5d60ae9d..efd2df5c812f 100644 --- a/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java +++ b/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java @@ -598,7 +598,7 @@ public static class HealthcareHttpException extends Exception { } /** - * ConditionalUpdate Exception of {@link HttpResponse}. + * Create Exception of {@link HttpResponse}. * * @param response the HTTP response * @return the healthcare http exception From 709ed00fa06744d18ab9597de10548763e32bc4a Mon Sep 17 00:00:00 2001 From: Jacob Ferriero Date: Tue, 2 Jun 2020 19:02:16 -0700 Subject: [PATCH 151/151] remove unused imports --- .../org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java | 2 -- 1 file changed, 2 deletions(-) diff --git a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java index 8b493eb21032..b96d22bef1d0 100644 --- a/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java +++ b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOTestUtil.java @@ -41,9 +41,7 @@ import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException; -import org.apache.beam.sdk.transforms.DoFn; import org.apache.beam.sdk.transforms.SerializableFunction; -import org.apache.beam.sdk.values.KV; class FhirIOTestUtil { public static final String DEFAULT_TEMP_BUCKET = "temp-storage-for-healthcare-io-tests";