From 71487428536b2cefec8e652ebf590c5c76d4c1d3 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 10:49:13 -0400
Subject: [PATCH 01/17] Adding AWS Omics support

---
 src/cwl_platform/__init__.py       |   4 +-
 src/cwl_platform/omics_platform.py | 178 +++++++++++++++++++++++++++++
 2 files changed, 180 insertions(+), 2 deletions(-)
 create mode 100644 src/cwl_platform/omics_platform.py

diff --git a/src/cwl_platform/__init__.py b/src/cwl_platform/__init__.py
index 25fc722f..86cbe43d 100644
--- a/src/cwl_platform/__init__.py
+++ b/src/cwl_platform/__init__.py
@@ -6,12 +6,12 @@
 
 from .arvados_platform import ArvadosPlatform
 from .sevenbridges_platform import SevenBridgesPlatform
-#from .omics_platform import OmicsPlatform
+from .omics_platform import OmicsPlatform
 
 # Move this for a config file
 SUPPORTED_PLATFORMS = {
     'Arvados': ArvadosPlatform,
-#    'Omics': OmicsPlatform,
+    'Omics': OmicsPlatform,
     'SevenBridges': SevenBridgesPlatform
 }
 
diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
new file mode 100644
index 00000000..d3a373a9
--- /dev/null
+++ b/src/cwl_platform/omics_platform.py
@@ -0,0 +1,178 @@
+'''
+AWS HealthOmics class
+'''
+
+import logging
+import boto3
+import botocore
+
+from .base_platform import Platform
+
+logger = logging.getLogger(__name__)
+
+class OmicsPlatform(Platform):
+    ''' AWS HealthOmics Platform class '''
+    def __init__(self, name):
+        super().__init__(name)
+        self.api = None
+
+    def connect(self):
+        ''' Connect to AWS Omics platform'''
+        self.api = boto3.client('omics')
+
+    def copy_folder(self, reference_project, reference_folder, destination_project):
+        '''
+        Do nothing and return reference folder, which should be an S3 path.
+        '''
+        return reference_folder
+
+    def copy_workflow(self, src_workflow, destination_project):
+        '''Do nothing and return workflow id'''
+        return src_workflow
+
+    def copy_workflows(self, reference_project, destination_project):
+        '''Do nothing. This function seems not used in launcher?'''
+        pass
+
+    def delete_task(self, task):
+        ''' Delete a task/workflow/process '''
+        self.logger.info('TBD: Deleting task %s', task)
+
+    @classmethod
+    def detect(cls):
+        return False
+
+    def get_current_task(self):
+        ''' Get the current task '''
+        return None
+
+    def get_file_id(self, project, file_path):
+        '''Return file s3 path for Omics job input'''
+        return file_path
+
+    def get_folder_id(self, project, folder_path):
+        '''
+        There is not unique ID for a folder in s3, so just return the folder_path
+        The one caveat is that Omics wants trailing slashes on folder paths, so add one.
+        '''
+        return folder_path + "/"
+
+    def get_task_input(self, task, input_name):
+        ''' Retrieve the input field of the task '''
+        self.logger.info("TBD: Getting input for task %s", task)
+        return None
+
+    def get_task_state(self, task, refresh=False):
+        ''' 
+        Get status of run by task_id.
+        task: A dictionary of omics response from start_run. Includes Run ID, Name, Tags, etc.
+        return status of the run (Complete, Failed, Running, Cancelled, Queued).
+        '''
+
+        try:
+            run_info = self.api.get_run(id=task['id'])
+            job_status = run_info['status']
+        except:
+            raise ValueError('No Status information found for job %s. Check job status.', task['id'])
+
+        if job_status == 'COMPLETED':
+            return 'Complete'
+        if job_status == 'FAILED':
+            return 'Failed'
+        if job_status in ['STARTING','RUNNING','STOPPING']:
+            return 'Running'
+        if job_status in ['CANCELLED','DELETED']:
+            return 'Cancelled'
+        if job_status == 'PENDING':
+            return 'Queued'
+
+        raise ValueError('Unknown task state: %s : %s', task['id'], job_status)
+
+    def get_task_output(self, task, output_name):
+        ''' Retrieve the output field of the task '''
+        taskinfo = self.api.get_run(id=task)
+        # TODO: get_run only returns OutputUri. Get file path based on output_name (filename)?
+        filename = None
+        # TODO: We shouldn't be hard-coding stuff like this.  these functions should be very generic.
+        if output_name == 'RecalibratedBAM':
+            filename = taskinfo.name + '.bam'
+        if filename == None:
+            raise ValueError(f"Cannot find output file for: {output_name}")
+        return taskinfo['outputUri'] + filename
+
+    def get_task_output_filename(self, task, output_name):
+        ''' Retrieve the output field of the task and return filename'''
+        self.logger.info("TBD: Getting output filename for task %s", task)
+        return None
+
+    def get_tasks_by_name(self, project, task_name):
+        ''' Get a tasks by its name '''
+        tasks = []
+        runs = self.api.list_runs(name=task_name)
+        for item in runs['items']:
+            run = self.api.get_run(id=item['id'])
+            if 'ProjectId' in project:
+                if run['tags']['ProjectId'] == project['ProjectId']:
+                    tasks.append(run)
+            elif 'ProjectName' in project:
+                if run['tags']['ProjectName'] == project['ProjectName']:
+                    tasks.append(run)
+        return tasks
+
+    def get_project(self):
+        '''
+        Since there is no concept of project in Omics, raise an error.
+        '''
+        raise ValueError("Omics does not support project. Use get_project_by_id or get_project_by_name instead.")
+
+    def get_project_by_name(self, project_name):
+        ''' Return a dictionary of project to provide project_name tag info for omics jobs '''
+        project = {
+            'ProjectName': project_name
+        }
+        return project
+
+    def get_project_by_id(self, project_id):
+        ''' Return a dictionary of project to provide project_id tag info for omics jobs'''
+        project = {
+            'ProjectId': project_id
+        }
+        return project
+
+    def stage_task_output(self, task, project, output_to_export, output_directory_name, download=False):
+        ''' TODO '''
+        return
+
+    def submit_task(self, name, project, workflow, parameters):
+        '''
+        Submit workflow for one sample.
+        name: sample ID.
+        project: dictionary of {'ProjectName':'string'} or {'ProjectId':'string'}, used for add run tag.
+        workflow: workflow ID in omics.
+        parameters: dictionary of input parameters.
+
+        return omics response for start_run.
+        '''
+        # A subfolder is created with the Run ID assigned by Omics such that task output is seperate.
+        base_output_path = 's3://bmsrd-ngs-omics/runs'
+
+        try:
+            logger.debug("Starting run for %s", name)
+            # TODO: The roleArn should be a parameter to this function, and not hard-coded.
+            # Put this in the pipeline_config.py.
+            job = self.api.start_run(workflowId=workflow,
+                                     workflowType='PRIVATE',
+                                     roleArn='arn:aws:iam::483421617021:role/ngs360-servicerole',
+                                     parameters=parameters,
+                                     name=name,
+                                     tags=project,
+                                     outputUri=base_output_path)
+            logger.info('Started run for %s, RunID: %s',name,job['id'])
+            return job
+        except botocore.exceptions.ClientError as err:
+            logger.error('Could not start run for %s: %s', name, err)
+            return None
+
+    def upload_file_to_project(self, filename, project, dest_folder, destination_filename=None, overwrite=False): # pylint: disable=too-many-arguments
+        self.logger.info("TBD: Uploading file %s to project %s", filename, project)
+        return None

From 2aab38583dc9d3653d47c70cf5beedb641568c13 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 10:50:24 -0400
Subject: [PATCH 02/17] Remove hard-coded role arn

---
 src/cwl_platform/omics_platform.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index d3a373a9..c23c9ac8 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -162,7 +162,7 @@ def submit_task(self, name, project, workflow, parameters):
             # Put this in the pipeline_config.py.
             job = self.api.start_run(workflowId=workflow,
                                      workflowType='PRIVATE',
-                                     roleArn='arn:aws:iam::483421617021:role/ngs360-servicerole',
+                                     roleArn=self.role_arn,
                                      parameters=parameters,
                                      name=name,
                                      tags=project,

From b47fad37552d295941c8d2e73c93e63690a04629 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 10:52:35 -0400
Subject: [PATCH 03/17] Remove hard-coded output path

---
 src/cwl_platform/omics_platform.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index c23c9ac8..eff4872b 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -15,6 +15,7 @@ class OmicsPlatform(Platform):
     def __init__(self, name):
         super().__init__(name)
         self.api = None
+        self.role_arn = None
 
     def connect(self):
         ''' Connect to AWS Omics platform'''
@@ -153,8 +154,7 @@ def submit_task(self, name, project, workflow, parameters):
 
         return omics response for start_run.
         '''
-        # A subfolder is created with the Run ID assigned by Omics such that task output is seperate.
-        base_output_path = 's3://bmsrd-ngs-omics/runs'
+        base_output_path = parameters.pop('OutputUri')
 
         try:
             logger.debug("Starting run for %s", name)

From f4b1d196daa7301067f39cd739561d0bdce47889 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 10:54:06 -0400
Subject: [PATCH 04/17] Add boto3 to requirements.txt

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 5099bf4e..d1edd6b2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,4 @@
+boto3
 chardet
 arvados-python-client
 sevenbridges-python

From aeda697361986b5639acacaeeef28f68c47ea020 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 11:05:22 -0400
Subject: [PATCH 05/17] Get role arn from connect() parameters

---
 src/cwl_platform/omics_platform.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index eff4872b..4b67daa4 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -17,10 +17,11 @@ def __init__(self, name):
         self.api = None
         self.role_arn = None
 
-    def connect(self):
+    def connect(self, **kwargs):
         ''' Connect to AWS Omics platform'''
         self.api = boto3.client('omics')
-
+        self.role_arn = kwargs.get('role_arn')
+        
     def copy_folder(self, reference_project, reference_folder, destination_project):
         '''
         Do nothing and return reference folder, which should be an S3 path.

From 4107460216d83757b376964bc8d45104afde0c0b Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 11:08:25 -0400
Subject: [PATCH 06/17] Add stage_output_files

---
 src/cwl_platform/omics_platform.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index 4b67daa4..109dff4f 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -141,6 +141,10 @@ def get_project_by_id(self, project_id):
         }
         return project
 
+    def stage_output_files(self, project, output_files):
+        ''' TODO '''
+        return
+
     def stage_task_output(self, task, project, output_to_export, output_directory_name, download=False):
         ''' TODO '''
         return

From 7f190ab5554b30eb19baeee1a934af3810612848 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 11:09:53 -0400
Subject: [PATCH 07/17] Update get_project

---
 src/cwl_platform/omics_platform.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index 109dff4f..b187794a 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -123,9 +123,9 @@ def get_tasks_by_name(self, project, task_name):
 
     def get_project(self):
         '''
-        Since there is no concept of project in Omics, raise an error.
+        Since there is no concept of project in Omics, return None
         '''
-        raise ValueError("Omics does not support project. Use get_project_by_id or get_project_by_name instead.")
+        return None
 
     def get_project_by_name(self, project_name):
         ''' Return a dictionary of project to provide project_name tag info for omics jobs '''

From 3e45a6ffe0b8269c4652523b0d6e5551a3bf3391 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 11:11:24 -0400
Subject: [PATCH 08/17] Revert get_project

---
 src/cwl_platform/omics_platform.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index b187794a..da83370b 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -123,9 +123,9 @@ def get_tasks_by_name(self, project, task_name):
 
     def get_project(self):
         '''
-        Since there is no concept of project in Omics, return None
+        Since there is no concept of project in Omics, raise an error.
         '''
-        return None
+        raise ValueError("Omics does not support get_project. Use get_project_by_id or get_project_by_name instead.")
 
     def get_project_by_name(self, project_name):
         ''' Return a dictionary of project to provide project_name tag info for omics jobs '''

From 4e5cdfae2441d5cfd3a76b55baafc1951d58efda Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 11:24:28 -0400
Subject: [PATCH 09/17] Add notes for copy_folder

---
 src/cwl_platform/omics_platform.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index da83370b..77c64569 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -25,6 +25,9 @@ def connect(self, **kwargs):
     def copy_folder(self, reference_project, reference_folder, destination_project):
         '''
         Do nothing and return reference folder, which should be an S3 path.
+        NOTE: Launchers copy the reference folder to the destination project so that everything is co-located.
+              However this can cause lots of data duplication in S3.  For now we will just use the reference folder
+              until another use-case is identified that we need to copy the data.
         '''
         return reference_folder
 

From f6f1dd8ce7601a818655c2219237987359c355e4 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 11:26:00 -0400
Subject: [PATCH 10/17] Add trailing slash only if its missing

---
 src/cwl_platform/omics_platform.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index 77c64569..8e93c130 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -60,6 +60,8 @@ def get_folder_id(self, project, folder_path):
         There is not unique ID for a folder in s3, so just return the folder_path
         The one caveat is that Omics wants trailing slashes on folder paths, so add one.
         '''
+        if folder_path.endswith("/"):
+            return folder_path
         return folder_path + "/"
 
     def get_task_input(self, task, input_name):

From e551a391ba9dcd10099a410c46241955f6d3992b Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 11:44:41 -0400
Subject: [PATCH 11/17] Add output_bucket

---
 src/cwl_platform/omics_platform.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index 8e93c130..f098d5f9 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -15,13 +15,15 @@ class OmicsPlatform(Platform):
     def __init__(self, name):
         super().__init__(name)
         self.api = None
+        self.output_bucket = None
         self.role_arn = None
 
     def connect(self, **kwargs):
         ''' Connect to AWS Omics platform'''
         self.api = boto3.client('omics')
+        self.outout_bucket = kwargs.get('output_bucket')
         self.role_arn = kwargs.get('role_arn')
-        
+
     def copy_folder(self, reference_project, reference_folder, destination_project):
         '''
         Do nothing and return reference folder, which should be an S3 path.
@@ -158,13 +160,17 @@ def submit_task(self, name, project, workflow, parameters):
         '''
         Submit workflow for one sample.
         name: sample ID.
-        project: dictionary of {'ProjectName':'string'} or {'ProjectId':'string'}, used for add run tag.
+        project: dictionary of {'ProjectName': 'string'} or {'ProjectId': 'string'}
         workflow: workflow ID in omics.
         parameters: dictionary of input parameters.
 
         return omics response for start_run.
         '''
-        base_output_path = parameters.pop('OutputUri')
+        base_output_path = f"s3://{self.output_bucket}/"
+        if 'ProjectName' in project:
+            base_output_path += f"{project['ProjectName']}/{workflow}/{name}/"
+        else:
+            base_output_path += f"{project['ProjectId']}/{workflow}/{name}/"
 
         try:
             logger.debug("Starting run for %s", name)

From 83803c438418912fa39a8a2c8725b40ae617597e Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 11:47:50 -0400
Subject: [PATCH 12/17] Add output_bucket

---
 src/cwl_platform/omics_platform.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index f098d5f9..90877ff4 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -21,7 +21,7 @@ def __init__(self, name):
     def connect(self, **kwargs):
         ''' Connect to AWS Omics platform'''
         self.api = boto3.client('omics')
-        self.outout_bucket = kwargs.get('output_bucket')
+        self.output_bucket = kwargs.get('output_bucket')
         self.role_arn = kwargs.get('role_arn')
 
     def copy_folder(self, reference_project, reference_folder, destination_project):

From 008806804076fcec4e41f54731f8af0dc0599731 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 14:59:46 -0400
Subject: [PATCH 13/17] Implement throttling to 1 TPS on Omics

---
 requirements.txt                   | 1 +
 src/cwl_platform/omics_platform.py | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/requirements.txt b/requirements.txt
index d1edd6b2..dd8bb0e8 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,3 +2,4 @@ boto3
 chardet
 arvados-python-client
 sevenbridges-python
+tenacity
diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index 90877ff4..0dace8cd 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -6,6 +6,8 @@
 import boto3
 import botocore
 
+from tenacity import retry
+
 from .base_platform import Platform
 
 logger = logging.getLogger(__name__)
@@ -156,6 +158,7 @@ def stage_task_output(self, task, project, output_to_export, output_directory_na
         ''' TODO '''
         return
 
+    @retry(wait=wait_fixed(2))
     def submit_task(self, name, project, workflow, parameters):
         '''
         Submit workflow for one sample.

From 01e5f6fdf2a2bccec41aa5c2a9d38bbeeb41be89 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Mon, 13 May 2024 14:59:55 -0400
Subject: [PATCH 14/17] Implement throttling to 1 TPS on Omics

---
 src/cwl_platform/omics_platform.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index 0dace8cd..1d494fcc 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -6,7 +6,7 @@
 import boto3
 import botocore
 
-from tenacity import retry
+from tenacity import retry, wait_fixed
 
 from .base_platform import Platform
 
@@ -158,7 +158,7 @@ def stage_task_output(self, task, project, output_to_export, output_directory_na
         ''' TODO '''
         return
 
-    @retry(wait=wait_fixed(2))
+    @retry(wait=wait_fixed(1))
     def submit_task(self, name, project, workflow, parameters):
         '''
         Submit workflow for one sample.

From 16670134dc2f3cc454591fec6b6355c7842c61ff Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Sun, 25 Aug 2024 00:27:36 +0000
Subject: [PATCH 15/17] Adding unit tests for AWS Omics

---
 tests/test_omics_platform.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 tests/test_omics_platform.py

diff --git a/tests/test_omics_platform.py b/tests/test_omics_platform.py
new file mode 100644
index 00000000..60530290
--- /dev/null
+++ b/tests/test_omics_platform.py
@@ -0,0 +1,23 @@
+'''
+Test Module for AWS Omics Platform
+'''
+import unittest
+import os
+import mock
+from mock import MagicMock, patch
+
+from cwl_platform.omics_platform import OmicsPlatform
+
+class TestOmicsPlaform(unittest.TestCase):
+    '''
+    Test Class for Omics Platform
+    '''
+    def setUp(self) -> None:
+        self.platform = OmicsPlatform('Omics')
+        return super().setUp()
+
+    def runTest(self):
+        pass
+
+if __name__ == '__main__':
+    unittest.main()

From 406bc2b35183310eaf7787bdb6d2a47d34f4e7a4 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Sun, 25 Aug 2024 00:32:51 +0000
Subject: [PATCH 16/17] Add missing implementations for functions

---
 .coverage                          | Bin 53248 -> 0 bytes
 src/cwl_platform/omics_platform.py |   9 +++++++++
 2 files changed, 9 insertions(+)
 delete mode 100644 .coverage

diff --git a/.coverage b/.coverage
deleted file mode 100644
index dd294d0d04811627f6eb5fc516b248039f21ffd2..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 53248
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diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index 1d494fcc..65732294 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -73,6 +73,9 @@ def get_task_input(self, task, input_name):
         self.logger.info("TBD: Getting input for task %s", task)
         return None
 
+    def get_task_outputs(self, task):
+        raise ValueError("Not yet implemented")
+
     def get_task_state(self, task, refresh=False):
         ''' 
         Get status of run by task_id.
@@ -150,6 +153,12 @@ def get_project_by_id(self, project_id):
         }
         return project
 
+    def rename_file(self, fileid, new_filename):
+        raise ValueError("Not yet implemented")
+
+    def roll_file(self, project, file_name):
+        raise ValueError("Not yet implemented")
+
     def stage_output_files(self, project, output_files):
         ''' TODO '''
         return

From 6a2099dff1cbe2c49c0b2f20747545f175199da3 Mon Sep 17 00:00:00 2001
From: Ryan Golhar <ryan.golhar@bms.com>
Date: Sun, 25 Aug 2024 01:02:49 +0000
Subject: [PATCH 17/17] Add comment

---
 src/cwl_platform/omics_platform.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/cwl_platform/omics_platform.py b/src/cwl_platform/omics_platform.py
index 65732294..1541c0cb 100644
--- a/src/cwl_platform/omics_platform.py
+++ b/src/cwl_platform/omics_platform.py
@@ -21,7 +21,11 @@ def __init__(self, name):
         self.role_arn = None
 
     def connect(self, **kwargs):
-        ''' Connect to AWS Omics platform'''
+        ''' 
+        Connect to AWS Omics platform
+
+        If ~/.aws/credentials or ~/.aws/config does not provide a region, region should be specified in the AWS_DEFAULT_REGION environment variable.
+        '''
         self.api = boto3.client('omics')
         self.output_bucket = kwargs.get('output_bucket')
         self.role_arn = kwargs.get('role_arn')