From 9ea1509174517592eab4f983eea372cf18b9d313 Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Tue, 10 Mar 2026 17:16:01 -0400 Subject: [PATCH 1/7] feat: wip - convert nbs sr 5 --- .../src/libraries/nbs_sr_05.py | 36 ++++++++++++++ .../tests/integration/libraries/nbs_sr_05.py | 49 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 apps/report-execution/src/libraries/nbs_sr_05.py create mode 100644 apps/report-execution/tests/integration/libraries/nbs_sr_05.py diff --git a/apps/report-execution/src/libraries/nbs_sr_05.py b/apps/report-execution/src/libraries/nbs_sr_05.py new file mode 100644 index 0000000000..aa60b865f0 --- /dev/null +++ b/apps/report-execution/src/libraries/nbs_sr_05.py @@ -0,0 +1,36 @@ +from src.db_transaction import Transaction +from src.models import ReportResult, TimeRange + + +def execute( + trx: Transaction, + subset_query: str, + data_source_name: str, + time_range: TimeRange | None = None, + **kwargs, +): + """Basic tabular report. Executes the query described by the data + source and filters (executing subset_sql) and returns the table. + + Conversion notes: + * Lifted the size check to a global check and refined the env var names + * Date formatting still needs to be figured out + """ + content = trx.execute( + f'WITH subset as ({subset_query})\n' + + 'SELECT state_cd, state, phc_code_short_desc, MONTH(event_date) as month, ' + + 'YEAR(event_date) as year, sum(group_case_cnt) as cases\n' + + 'FROM subset\n' + + 'GROUP BY state_cd, state, phc_code_short_desc, ' + + 'MONTH(event_date), YEAR(event_date)\n' + + 'ORDER BY phc_code_short_desc, YEAR(event_date), MONTH(event_date)' + ) + + description = 'SR5: Cases of Reportable Diseases by State' + if time_range is not None: + description += f'\n{time_range.start} - {time_range.end}' + + # TODO: datetimes are formatted '%0m/%0d/%Y %0H:%0M:%0S' in sas. # noqa: FIX002 + # Should this be a util/post processing/sql step in python land? + + return ReportResult(content_type='table', content=content, description=description) diff --git a/apps/report-execution/tests/integration/libraries/nbs_sr_05.py b/apps/report-execution/tests/integration/libraries/nbs_sr_05.py new file mode 100644 index 0000000000..329915c2bc --- /dev/null +++ b/apps/report-execution/tests/integration/libraries/nbs_sr_05.py @@ -0,0 +1,49 @@ +import pytest + +from src.execute_report import execute_report +from src.models import ReportSpec + + +@pytest.mark.usefixtures('setup_containers') +@pytest.mark.integration +class TestIntegrationNbsSr05Library: + """Integration tests for the nbs_custom library.""" + + def test_execute_report_with_time_range(self): + report_spec = ReportSpec.model_validate( + { + 'version': 1, + 'is_export': True, + 'is_builtin': True, + 'report_title': 'NBS Custom', + 'library_name': 'nbs_sr_05', + # Filter operator is used here as it is a stable, small table + 'data_source_name': '[NBS_ODSE].[dbo].[PHCDemographic]', + 'subset_query': 'SELECT * FROM [NBS_ODSE].[dbo].[PHCDemographic]', + 'time_range': {'start': '2024-01-01', 'end': '2024-12-31'}, + } + ) + + result = execute_report(report_spec) + assert result.description == ( + 'SR5: Cases of Reportable Diseases by State\n' + + '2024-01-01 - 2024-12-31' + ) + assert result.content_type == 'table' + + assert len(result.content.data) >= 1 + assert len(result.content.data[0]) == 4 + assert len(result.content.data[0]) == len(result.content.columns) + + record = None + for row in result.content.data: + if ( + row[0] == 'Georgia' + and row[1] == 'Gwinnett County' + and row[2] == 'Pertussis' + ): + record = row + break + + assert record is not None + assert record[3] >= 1 From 03467f81293207425db3322d926c04ac70dd9335 Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Wed, 11 Mar 2026 18:28:55 -0400 Subject: [PATCH 2/7] fix: add test harness, be smarter about containers, harden Transaction --- apps/report-execution/pyproject.toml | 1 + apps/report-execution/pytest.toml | 4 +- apps/report-execution/src/db_transaction.py | 25 ++- .../src/libraries/nbs_custom.py | 2 +- .../src/libraries/nbs_sr_05.py | 20 +- apps/report-execution/tests/conftest.py | 91 +++++++- .../tablefaker_schema/phc_demographic.yaml | 201 ++++++++++++++++++ .../tests/integration/libraries/nbs_sr_05.py | 12 +- apps/report-execution/uv.lock | 152 +++++++++++++ 9 files changed, 486 insertions(+), 22 deletions(-) create mode 100644 apps/report-execution/tests/integration/assets/tablefaker_schema/phc_demographic.yaml diff --git a/apps/report-execution/pyproject.toml b/apps/report-execution/pyproject.toml index 393964825c..991df0a252 100644 --- a/apps/report-execution/pyproject.toml +++ b/apps/report-execution/pyproject.toml @@ -17,6 +17,7 @@ dev = [ "pytest>=9.0.2,<10.0.0", "pytest-mock>=3.15.1", "ruff>=0.15.0,<1.0.0", + "tablefaker>=1.8.0", "testcontainers>=4.14.1", ] diff --git a/apps/report-execution/pytest.toml b/apps/report-execution/pytest.toml index 031d3e55ac..d43640fe9c 100644 --- a/apps/report-execution/pytest.toml +++ b/apps/report-execution/pytest.toml @@ -10,4 +10,6 @@ addopts = [ "--strict-config", "--showlocals", "--import-mode=importlib" -] \ No newline at end of file +] +log_cli = true +log_cli_level = "INFO" diff --git a/apps/report-execution/src/db_transaction.py b/apps/report-execution/src/db_transaction.py index e61d6773bd..2ed736389a 100644 --- a/apps/report-execution/src/db_transaction.py +++ b/apps/report-execution/src/db_transaction.py @@ -9,25 +9,33 @@ class Transaction: """A database transaction abstraction for use in libraries.""" def __init__(self, cursor): - self.cursor = cursor + self._cursor = cursor - def execute(self, query: str, parameters: tuple = ()) -> Table: + def query(self, query: str, parameters: tuple = ()) -> Table: """Execute a query and have the data returned as a Table. DO NOT EXECUTE ANY PERMANENT CREATE, UPDATE, OR DELETE STATEMENTS Positional `?` placeholders can be used in the query and values passed as parameters in a tuple. - - If the query inserts or updates a temporary table, then the returned table - will be empty. """ - data = self.cursor.execute(query, parameters).fetchall() + data = self._cursor.execute(query, parameters).fetchall() columns = self._column_names() return Table(columns=columns, data=data) + def execute(self, query: str, parameters: tuple = ()) -> None: + """Execute a SQL statement and do not return any result. + + DO NOT EXECUTE ANY PERMANENT CREATE, UPDATE, OR DELETE STATEMENTS + + Positional `?` placeholders can be used in the query and values passed as + parameters in a tuple. + """ + self._cursor.execute(query, parameters) + return None + def _column_names(self) -> list[str]: - return [c[0] for c in self.cursor.description] + return [c[0] for c in self._cursor.description] @contextmanager @@ -40,3 +48,6 @@ def db_transaction(connection_string): with connection.cursor() as cursor: trx = Transaction(cursor) yield trx + + # not sure why this is needed - it shouldn't be per docs + connection.commit() diff --git a/apps/report-execution/src/libraries/nbs_custom.py b/apps/report-execution/src/libraries/nbs_custom.py index 2be444f89e..5ef1ef0858 100644 --- a/apps/report-execution/src/libraries/nbs_custom.py +++ b/apps/report-execution/src/libraries/nbs_custom.py @@ -16,7 +16,7 @@ def execute( * Lifted the size check to a global check and refined the env var names * Date formatting still needs to be figured out """ - content = trx.execute(subset_query) + content = trx.query(subset_query) description = f'Custom Report For Table: {data_source_name}' if time_range is not None: diff --git a/apps/report-execution/src/libraries/nbs_sr_05.py b/apps/report-execution/src/libraries/nbs_sr_05.py index aa60b865f0..03c8fe474a 100644 --- a/apps/report-execution/src/libraries/nbs_sr_05.py +++ b/apps/report-execution/src/libraries/nbs_sr_05.py @@ -9,18 +9,29 @@ def execute( time_range: TimeRange | None = None, **kwargs, ): - """Basic tabular report. Executes the query described by the data - source and filters (executing subset_sql) and returns the table. + """Standard Report 05: Cases of Reportable Diseases for a specific state. + + Each row is a disease with columns for the: + * Current month total + * YTD total + * Prior YTD total + * 5 Year Median YTD total + * % change Current YTD vs 5 Year Median YTD Conversion notes: * Lifted the size check to a global check and refined the env var names * Date formatting still needs to be figured out """ - content = trx.execute( + content = trx.query( f'WITH subset as ({subset_query})\n' + 'SELECT state_cd, state, phc_code_short_desc, MONTH(event_date) as month, ' + 'YEAR(event_date) as year, sum(group_case_cnt) as cases\n' + 'FROM subset\n' + + 'WHERE state is not NULL\n' + + 'AND event_date is not NULL\n' + + 'AND DATEPART(dayofyear, event_date) <= ' + + ' DATEPART(dayofyear, CURRENT_TIMESTAMP)\n' + + 'AND YEAR(event_date) >= (YEAR(CURRENT_TIMESTAMP) - 5)\n' + 'GROUP BY state_cd, state, phc_code_short_desc, ' + 'MONTH(event_date), YEAR(event_date)\n' + 'ORDER BY phc_code_short_desc, YEAR(event_date), MONTH(event_date)' @@ -30,7 +41,4 @@ def execute( if time_range is not None: description += f'\n{time_range.start} - {time_range.end}' - # TODO: datetimes are formatted '%0m/%0d/%Y %0H:%0M:%0S' in sas. # noqa: FIX002 - # Should this be a util/post processing/sql step in python land? - return ReportResult(content_type='table', content=content, description=description) diff --git a/apps/report-execution/tests/conftest.py b/apps/report-execution/tests/conftest.py index 12b74042b3..d41079aa8b 100644 --- a/apps/report-execution/tests/conftest.py +++ b/apps/report-execution/tests/conftest.py @@ -3,8 +3,11 @@ from contextlib import contextmanager import pytest -from testcontainers.compose import DockerCompose +import tablefaker +from testcontainers.compose import ContainerIsNotRunning, DockerCompose +from src import utils +from src.db_transaction import db_transaction from src.models import Table @@ -82,21 +85,101 @@ def setup_containers(request): logging.info('Setting up containers tests...') compose_path = os.path.join(os.path.dirname(__file__), '../../../cdc-sandbox') compose_file_name = 'docker-compose.yml' + services = ['report-execution', 'nbs-mssql'] containers = DockerCompose( compose_path, compose_file_name=compose_file_name, - services=['report-execution', 'nbs-mssql'], + services=services, ) report_exec_url = 'http://0.0.0.0:8001/status' + def maybe_get_container(name): + try: + containers.get_container(name) + except ContainerIsNotRunning: + return None + + containers_to_stop = [ + maybe_get_container(service) + for service in services + if maybe_get_container(service) is not None + ] + containers.start() containers.wait_for(report_exec_url) logging.info('Ingestion ready to test!') def teardown(): logging.info('Service logs...\n') - logging.info(containers.get_logs()) logging.info('Tests finished! Tearing down.') - containers.stop() + for container in containers_to_stop: + container.stop() request.addfinalizer(teardown) + + +def get_faker_sql(schema_name: str) -> str: + """Process a fakertable schema and return the sql as a string.""" + faker_path = os.path.join( + os.path.dirname(__file__), + 'integration', + 'assets', + 'tablefaker_schema', + schema_name, + ) + target_file_path = os.path.join(os.path.dirname(__file__), 'fake.sql') + tablefaker.to_sql(faker_path, target_file_path=target_file_path) + with open(target_file_path) as f: + result = f.read() + + os.remove(target_file_path) + return result + + +def temp_name(table_name: str) -> str: + """Assumes `[schema].[dbo].[table name]` format.""" + return table_name[0:-1] + '_temp]' + + +@pytest.fixture(scope='class') +def fake_db_table(request): + """Replace a DB table with fake table per the tablefaker schema.""" + db_table = request.module.db_table + fk_tables = getattr(request.module, 'db_fk_tables', []) + faker_schema = request.module.faker_schema + faker_sql = get_faker_sql(faker_schema) + + conn_string = utils.get_env_or_error('DATABASE_CONN_STRING') + with db_transaction(conn_string) as trx: + for fk_table in fk_tables: + temp_fk_table = temp_name(fk_table) + trx.execute( + f"IF OBJECT_ID('{temp_fk_table}') IS NOT NULL " + f'DROP TABLE {temp_fk_table}' + ) + trx.execute(f'SELECT * INTO {temp_fk_table} FROM {fk_table}') + trx.execute(f'DELETE {fk_table}') + logging.info(f'cleared FK table: {fk_table}') + + temp_db_table = temp_name(db_table) + trx.execute( + f"IF OBJECT_ID('{temp_db_table}') IS NOT NULL DROP TABLE {temp_db_table}" + ) + trx.execute(f'SELECT * INTO {temp_db_table} FROM {db_table}') + trx.execute(f'DELETE {db_table}') + logging.info(f'cleared table: {db_table}') + trx.execute(faker_sql) + logging.info('Inserted fake data') + + # avoid connection inside connection + yield + + with db_transaction(conn_string) as trx: + logging.info('back') + trx.execute(f'DELETE {db_table}') + trx.execute(f'INSERT INTO {db_table} SELECT * FROM {temp_db_table}') + logging.info(f'Restored table: {db_table}') + + for fk_table in fk_tables: + trx.execute(f'INSERT INTO {fk_table} SELECT * FROM {temp_name(fk_table)}') + logging.info(f'Restored FK table: {fk_table}') diff --git a/apps/report-execution/tests/integration/assets/tablefaker_schema/phc_demographic.yaml b/apps/report-execution/tests/integration/assets/tablefaker_schema/phc_demographic.yaml new file mode 100644 index 0000000000..b85fff1a27 --- /dev/null +++ b/apps/report-execution/tests/integration/assets/tablefaker_schema/phc_demographic.yaml @@ -0,0 +1,201 @@ +config: + seed: 4 + +tables: + # Table backing PHCDemographic view + - table_name: "[NBS_ODSE].[dbo].[PublicHealthCaseFact]" + row_count: 1000 + columns: + # required columns: + - column_name: public_health_case_uid + data: row_id + is_primary_key: true + - column_name: case_class_cd + data: random.choice(["N", "C", ""]) + - column_name: PHC_code + data: random.choice(["10190", "10140", "502651"]) + - column_name: PHC_code_desc + data: | + if PHC_code == "10190": + return "Pertussis" + elif PHC_code == "10140": + return "Measles" + elif PHC_code == "502651": + return "Salmonellosis" + - column_name: prog_area_cd + data: | + if PHC_code in ("10190", "10140"): + return "GCD" + elif PHC_code == "502651": + return "FOOD" + + # Case basics + - column_name: PHC_code_short_desc + type: string + data: PHC_code_desc + - column_name: event_date + data: fake.date_between(start_date="-6y", end_date="+1w") + null_percentage: 0.05 + - column_name: group_case_cnt + data: fake.random_int(1, 90) + + # Location + - column_name: state + type: string + data: random.choice(["Georgia", "Tennessee"]) + - column_name: state_cd + type: string + data: | + if state == "Georgia": + return "13" + elif state == "Tennessee": + return "47" + else: + return None + +# === Columns not needed for reports yet === +# adults_in_house_nbr smallint NULL, +# ageInMonths smallint NULL, +# ageInYears smallint NULL, +# age_category_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# age_reported_time datetime NULL, +# age_reported_unit_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# age_reported numeric(8,0) NULL, +# awareness_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# awareness_desc_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# birth_gender_cd char(1) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# birth_order_nbr smallint NULL, +# birth_time datetime NULL, +# birth_time_calc datetime NULL, +# birth_time_std datetime NULL, +# case_type_cd char(1) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# cd_system_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# cd_system_desc_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# census_block_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# census_minor_civil_division_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# census_track_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# cnty_code_desc_txt varchar(200) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# children_in_house_nbr smallint NULL, +# city_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# city_desc_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# confidentiality_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# confidentiality_desc_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# confirmation_method_cd varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# confirmation_method_time datetime NULL, +# county varchar(255) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# cntry_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# cnty_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# curr_sex_cd char(1) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# deceased_ind_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# deceased_time datetime NULL, +# detection_method_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# detection_method_desc_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# diagnosis_date datetime NULL, +# disease_imported_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# disease_imported_desc_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# education_level_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# ELP_class_cd varchar(10) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# ELP_from_time datetime NULL, +# ELP_to_time datetime NULL, +# ethnic_group_ind varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# ethnic_group_ind_desc varchar(50) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# event_type varchar(10) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# education_level_desc_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# firstNotificationSenddate datetime NULL, +# firstNotificationdate datetime NULL, +# firstNotificationStatus varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# firstNotificationSubmittedBy bigint NULL, +# geoLatitude real NULL, +# geoLongitude real NULL, +# investigation_status_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# investigatorAssigneddate datetime NULL, +# investigatorName varchar(102) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# investigatorPhone varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# jurisdiction_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# lastNotificationdate datetime NULL, +# lastNotificationSenddate datetime NULL, +# lastNotificationSubmittedBy bigint NULL, +# marital_status_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# marital_status_desc_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# mart_record_creation_date datetime NULL, +# mart_record_creation_time datetime NULL, +# mmwr_week numeric(8,0) NULL, +# mmwr_year numeric(8,0) NULL, +# MSA_congress_district_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# multiple_birth_ind varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# notifCreatedCount int NULL, +# notificationdate datetime NULL, +# notifSentCount int NULL, +# occupation_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# onSetDate datetime NULL, +# organizationName varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# outcome_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# outbreak_from_time datetime NULL, +# outbreak_ind varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# outbreak_name varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# outbreak_to_time datetime NULL, +# PAR_type_cd varchar(50) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# pat_age_at_onset numeric(8,0) NULL, +# pat_age_at_onset_unit_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# postal_locator_uid bigint NULL, +# person_cd varchar(50) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# person_code_desc varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# person_uid bigint NULL, +# PHC_add_time datetime NULL, +# PHC_code_short_desc varchar(50) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# prim_lang_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# prim_lang_desc_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# providerPhone varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# providerName varchar(102) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# PST_record_status_time datetime NULL, +# PST_record_status_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# race_concatenated_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# race_concatenated_desc_txt varchar(500) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# region_district_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# record_status_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# reporterName varchar(102) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# reporterPhone varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# rpt_cnty_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# rpt_form_cmplt_time datetime NULL, +# rpt_source_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# rpt_source_desc_txt varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# rpt_to_county_time datetime NULL, +# rpt_to_state_time datetime NULL, +# shared_ind varchar(1) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# state_code_short_desc_txt varchar(200) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# status_cd char(1) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# street_addr1 varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# street_addr2 varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# ELP_use_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# zip_cd varchar(20) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# patientName varchar(102) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# jurisdiction varchar(50) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# investigationstartdate datetime NULL, +# program_jurisdiction_oid bigint NULL, +# report_date datetime NULL, +# person_parent_uid bigint NULL, +# person_local_id varchar(50) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# sub_addr_as_of_date datetime NULL, +# state_case_id varchar(199) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# LOCAL_ID varchar(50) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# NOTIFCURRENTSTATE varchar(50) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# age_reported_unit_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# birth_gender_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# case_class_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# cntry_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# curr_sex_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# investigation_status_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# occupation_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# outcome_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# pat_age_at_onset_unit_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# prog_area_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# rpt_cnty_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# outbreak_name_desc varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# confirmation_method_desc_txt varchar(300) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# LASTUPDATE datetime NULL, +# PHCTXT varchar(2000) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# NOTITXT varchar(2000) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# NOTIFICATION_LOCAL_ID varchar(50) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, +# HSPTL_ADMISSION_DT datetime NULL, +# HSPTL_DISCHARGE_DT datetime NULL, +# hospitalized_ind varchar(100) COLLATE SQL_Latin1_General_CP1_CI_AS NULL, diff --git a/apps/report-execution/tests/integration/libraries/nbs_sr_05.py b/apps/report-execution/tests/integration/libraries/nbs_sr_05.py index 329915c2bc..93791f2043 100644 --- a/apps/report-execution/tests/integration/libraries/nbs_sr_05.py +++ b/apps/report-execution/tests/integration/libraries/nbs_sr_05.py @@ -1,10 +1,16 @@ +import logging + import pytest from src.execute_report import execute_report from src.models import ReportSpec +db_table = '[NBS_ODSE].[dbo].[PublicHealthCaseFact]' +db_fk_tables = ['[NBS_ODSE].[dbo].[SubjectRaceInfo]'] +faker_schema = 'phc_demographic.yaml' + -@pytest.mark.usefixtures('setup_containers') +@pytest.mark.usefixtures('setup_containers', 'fake_db_table') @pytest.mark.integration class TestIntegrationNbsSr05Library: """Integration tests for the nbs_custom library.""" @@ -26,10 +32,10 @@ def test_execute_report_with_time_range(self): result = execute_report(report_spec) assert result.description == ( - 'SR5: Cases of Reportable Diseases by State\n' - + 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+] + [[package]] name = "testcontainers" version = "4.14.1" From 81a3c3934afaaa50bfda3645476ee0ce8e8ea846 Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Thu, 12 Mar 2026 12:10:34 -0400 Subject: [PATCH 3/7] fix: cleanup --- apps/report-execution/demo.jl | 58 + apps/report-execution/tests/conftest.py | 19 +- apps/report-execution/tests/fake.sql | 1003 +++++++++++++++++ .../tablefaker_schema/phc_demographic.yaml | 3 +- 4 files changed, 1079 insertions(+), 4 deletions(-) create mode 100644 apps/report-execution/demo.jl create mode 100644 apps/report-execution/tests/fake.sql diff --git a/apps/report-execution/demo.jl b/apps/report-execution/demo.jl new file mode 100644 index 0000000000..1b4a951dbc --- /dev/null +++ b/apps/report-execution/demo.jl @@ -0,0 +1,58 @@ +using HTTP +using JSON + +nbs_custom_basic = """ +{ + "version": 1, + "is_export": true, + "is_builtin": true, + "report_title": "NBS Custom", + "library_name": "nbs_custom", + "data_source_name": "[NBS_ODSE].[dbo].[Filter_operator]", + "subset_query": "SELECT * FROM [NBS_ODSE].[dbo].[Filter_operator]", + "time_range": {"start": "2024-01-01", "end": "2024-12-31"} +} +""" + +nbs_custom_with_where = """ +{ + "version": 1, + "is_export": true, + "is_builtin": true, + "report_title": "NBS Custom", + "library_name": "nbs_custom", + "data_source_name": "[NBS_ODSE].[dbo].[Filter_operator]", + "subset_query": "SELECT config_key, config_value, short_name FROM [NBS_ODSE].[dbo].[NBS_Configuratino] WHERE config_value != default_value" +} +""" + +nbs_sr_05 = """ +{ + "version": 1, + "is_export": true, + "is_builtin": true, + "report_title": "SR2: Disease statistics by state", + "library_name": "nbs_sr_05", + "data_source_name": "[NBS_ODSE].[dbo].[PHCDemographic]", + "subset_query": "'SELECT * FROM [NBS_ODSE].[dbo].[PHCDemographic]'" +} +""" + +function execute_report(spec) + resp = HTTP.post( + "http://localhost:8001/report/execute", + body = spec, + headers = ["Content-Type" => "application/json", "Accept" => "application/json"], + ) + resp_json = String(take!(resp.body)) + parsed = JSON.parse(resp_json) + csv = parsed["content"] + fname = tempname() + open(fname, "w") do f + write(f, csv) + end + + parsed["content"] = "Data writtenn to $fname" + + JSON.json(stdout, j; pretty=true) +end diff --git a/apps/report-execution/tests/conftest.py b/apps/report-execution/tests/conftest.py index d41079aa8b..f1a6f704a7 100644 --- a/apps/report-execution/tests/conftest.py +++ b/apps/report-execution/tests/conftest.py @@ -133,11 +133,20 @@ def get_faker_sql(schema_name: str) -> str: result = f.read() os.remove(target_file_path) + + # KLUDGE: NULL writing is not always correct + result = result.replace(' nan,', ' NULL,') + result = result.replace(' nan)', ' NULL)') + result = result.replace(' ,', ' NULL,') + result = result.replace(' )', ' NULL)') return result def temp_name(table_name: str) -> str: - """Assumes `[schema].[dbo].[table name]` format.""" + """Assumes `[schema].[dbo].[table name]` format. + + Not using temp tables as the usage spans connections. + """ return table_name[0:-1] + '_temp]' @@ -150,7 +159,11 @@ def fake_db_table(request): faker_sql = get_faker_sql(faker_schema) conn_string = utils.get_env_or_error('DATABASE_CONN_STRING') + + # swap out original data for fake data with db_transaction(conn_string) as trx: + # Tables with foreign keys pointing to the table we want to replace need to + # be backed up and cleared out to avoid FK constraint violations for fk_table in fk_tables: temp_fk_table = temp_name(fk_table) trx.execute( @@ -169,13 +182,13 @@ def fake_db_table(request): trx.execute(f'DELETE {db_table}') logging.info(f'cleared table: {db_table}') trx.execute(faker_sql) - logging.info('Inserted fake data') + logging.info(f'Inserted fake data: {db_table}') # avoid connection inside connection yield + # restore the original data with db_transaction(conn_string) as trx: - logging.info('back') trx.execute(f'DELETE {db_table}') trx.execute(f'INSERT INTO {db_table} SELECT * FROM {temp_db_table}') logging.info(f'Restored table: {db_table}') diff --git a/apps/report-execution/tests/fake.sql b/apps/report-execution/tests/fake.sql new file mode 100644 index 0000000000..68d3e8f3dc --- /dev/null +++ b/apps/report-execution/tests/fake.sql @@ -0,0 +1,1003 @@ +INSERT INTO [NBS_ODSE].[dbo].[PublicHealthCaseFact] +(public_health_case_uid,case_class_cd,PHC_code,event_date,group_case_cnt,state,PHC_code_desc,prog_area_cd,PHC_code_short_desc,state_cd) +VALUES +(1, 'N', '502651', '2021-08-12', nan, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(2, 'N', '10190', '2024-07-13', 62.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(3, 'N', '502651', '2021-02-14', 9.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(4, '', '10190', '2020-04-23', 71.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(5, 'C', '10190', '2025-09-19', 8.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', 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'GCD', 'Measles', '13'), +(908, '', '10140', NULL, 24.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(909, 'N', '10140', NULL, 70.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(910, '', '502651', '2023-10-02', 18.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(911, 'C', '502651', '2023-02-21', nan, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(912, '', '10190', '2024-12-13', 25.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(913, '', '10140', '2025-10-28', 85.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(914, 'C', '502651', '2024-02-09', 42.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(915, '', '10190', '2021-09-22', nan, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(916, 'C', '10190', '2024-04-02', 52.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(917, 'N', '10140', '2025-05-28', 2.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(918, 'N', '10140', '2023-05-23', 41.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(919, 'N', '10190', '2025-04-19', 27.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(920, 'N', '502651', '2021-04-30', 25.0, , 'Salmonellosis', 'FOOD', 'Salmonellosis', ), +(921, 'N', '10190', '2025-12-29', 6.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(922, 'N', '10190', '2023-01-28', nan, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(923, '', '502651', '2020-04-13', 52.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(924, 'N', '10190', '2021-11-17', 64.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(925, 'C', '10140', '2024-01-15', 56.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(926, 'N', '10140', '2022-06-13', 65.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(927, 'N', '502651', '2020-07-09', 38.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(928, '', '502651', '2021-05-05', 17.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(929, 'C', '502651', '2020-12-17', 83.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(930, '', '502651', '2025-09-26', 64.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(931, 'C', '10140', '2020-08-23', 56.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(932, 'N', '502651', '2025-06-29', 60.0, , 'Salmonellosis', 'FOOD', 'Salmonellosis', ), +(933, '', '10190', '2024-05-02', 19.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(934, 'C', '502651', '2022-10-18', 32.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(935, 'N', '502651', '2021-05-30', 11.0, , 'Salmonellosis', 'FOOD', 'Salmonellosis', ), +(936, 'N', '502651', '2022-05-26', 9.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(937, '', '10190', '2025-04-09', 24.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(938, 'C', '502651', '2024-11-19', 67.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(939, 'C', '502651', '2020-12-12', 47.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(940, 'C', '10140', '2025-12-31', 48.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(941, 'C', '10140', '2025-12-12', 41.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(942, 'C', '10190', '2023-04-27', 85.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(943, 'C', '10140', '2025-04-01', 38.0, , 'Measles', 'GCD', 'Measles', ), +(944, '', '10140', '2023-12-30', 34.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(945, 'N', '502651', '2025-10-05', 33.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(946, 'N', '502651', '2023-09-14', 3.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(947, '', '10140', '2023-08-15', 11.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(948, 'C', '10190', '2024-04-08', 28.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(949, 'N', '502651', '2023-08-30', 56.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(950, '', '10140', '2021-09-06', 86.0, , 'Measles', 'GCD', 'Measles', ), +(951, '', '10140', NULL, 34.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(952, 'N', '502651', '2025-02-07', 19.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(953, 'N', '10140', '2022-09-21', 9.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(954, '', '10140', '2021-11-24', 23.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(955, 'N', '10190', '2023-10-01', 20.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(956, '', '10190', '2025-04-24', 51.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(957, 'N', '10190', '2020-07-13', 76.0, , 'Pertussis', 'GCD', 'Pertussis', ), +(958, 'C', '502651', '2025-10-25', 11.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(959, '', '502651', NULL, 2.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(960, 'C', '502651', '2022-06-14', 20.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(961, '', '10140', '2021-09-29', 68.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(962, 'C', '10140', '2022-05-27', 16.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(963, 'N', '502651', '2025-09-18', 34.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(964, 'N', '10140', '2025-02-01', 7.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(965, 'N', '502651', '2021-02-08', 41.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(966, 'N', '502651', '2020-08-14', 80.0, , 'Salmonellosis', 'FOOD', 'Salmonellosis', ), +(967, 'C', '502651', '2023-01-18', 90.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(968, '', '10140', '2023-09-04', 85.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(969, '', '502651', '2023-06-03', 12.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(970, 'C', '10190', '2024-07-18', 62.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(971, 'C', '10140', '2021-10-04', 23.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(972, 'N', '502651', '2021-04-14', 74.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(973, 'N', '10190', '2022-05-14', 50.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(974, 'N', '502651', '2023-02-07', 75.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(975, 'N', '10140', '2021-07-06', 79.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(976, 'C', '502651', '2022-08-05', 5.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(977, 'C', '10140', '2021-04-17', 61.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(978, 'C', '10190', '2023-06-26', 45.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(979, '', '10190', '2026-03-18', 24.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(980, 'C', '502651', '2023-06-05', 20.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(981, 'C', '10190', '2021-03-26', 20.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(982, 'N', '10190', '2021-10-14', 1.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(983, 'N', '10140', '2024-11-18', 10.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(984, '', '502651', '2025-04-13', 87.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(985, 'C', '10190', '2020-12-25', 40.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(986, '', '10140', '2024-12-07', 40.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(987, 'N', '502651', '2021-01-10', nan, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(988, 'C', '10140', '2022-02-18', 21.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(989, 'C', '10190', '2025-10-26', 79.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(990, 'C', '10140', NULL, 5.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(991, 'C', '10140', '2022-11-03', 24.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(992, 'N', '502651', '2023-07-31', 86.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), +(993, 'N', '10140', '2022-02-25', 21.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(994, '', '502651', '2025-11-13', 17.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), +(995, '', '10140', '2023-08-10', 68.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), +(996, 'C', '10190', '2021-08-02', 41.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(997, '', '10140', NULL, 9.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), +(998, 'N', '10190', '2023-10-23', 47.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), +(999, '', '10190', '2024-09-13', 83.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), +(1000, 'C', '10190', '2025-11-20', 70.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'); \ No newline at end of file diff --git a/apps/report-execution/tests/integration/assets/tablefaker_schema/phc_demographic.yaml b/apps/report-execution/tests/integration/assets/tablefaker_schema/phc_demographic.yaml index b85fff1a27..3a0d0da82e 100644 --- a/apps/report-execution/tests/integration/assets/tablefaker_schema/phc_demographic.yaml +++ b/apps/report-execution/tests/integration/assets/tablefaker_schema/phc_demographic.yaml @@ -38,11 +38,12 @@ tables: null_percentage: 0.05 - column_name: group_case_cnt data: fake.random_int(1, 90) + null_percentage: 0.05 # Location - column_name: state type: string - data: random.choice(["Georgia", "Tennessee"]) + data: random.choice(["Georgia", "Tennessee"]) if random.random() < .95 else None - column_name: state_cd type: string data: | From f814d5cbb1cdd9cc074f19cb3c5f8c32e57610cc Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Thu, 12 Mar 2026 16:22:20 -0400 Subject: [PATCH 4/7] fix: report description --- apps/report-execution/demo.jl | 58 ------------------- .../src/libraries/nbs_sr_05.py | 42 +++++++++++++- 2 files changed, 39 insertions(+), 61 deletions(-) delete mode 100644 apps/report-execution/demo.jl diff --git a/apps/report-execution/demo.jl b/apps/report-execution/demo.jl deleted file mode 100644 index 1b4a951dbc..0000000000 --- a/apps/report-execution/demo.jl +++ /dev/null @@ -1,58 +0,0 @@ -using HTTP -using JSON - -nbs_custom_basic = """ -{ - "version": 1, - "is_export": true, - "is_builtin": true, - "report_title": "NBS Custom", - "library_name": "nbs_custom", - "data_source_name": "[NBS_ODSE].[dbo].[Filter_operator]", - "subset_query": "SELECT * FROM [NBS_ODSE].[dbo].[Filter_operator]", - "time_range": {"start": "2024-01-01", "end": "2024-12-31"} -} -""" - -nbs_custom_with_where = """ -{ - "version": 1, - "is_export": true, - "is_builtin": true, - "report_title": "NBS Custom", - "library_name": "nbs_custom", - "data_source_name": "[NBS_ODSE].[dbo].[Filter_operator]", - "subset_query": "SELECT config_key, config_value, short_name FROM [NBS_ODSE].[dbo].[NBS_Configuratino] WHERE config_value != default_value" -} -""" - -nbs_sr_05 = """ -{ - "version": 1, - "is_export": true, - "is_builtin": true, - "report_title": "SR2: Disease statistics by state", - "library_name": "nbs_sr_05", - "data_source_name": "[NBS_ODSE].[dbo].[PHCDemographic]", - "subset_query": "'SELECT * FROM [NBS_ODSE].[dbo].[PHCDemographic]'" -} -""" - -function execute_report(spec) - resp = HTTP.post( - "http://localhost:8001/report/execute", - body = spec, - headers = ["Content-Type" => "application/json", "Accept" => "application/json"], - ) - resp_json = String(take!(resp.body)) - parsed = JSON.parse(resp_json) - csv = parsed["content"] - fname = tempname() - open(fname, "w") do f - write(f, csv) - end - - parsed["content"] = "Data writtenn to $fname" - - JSON.json(stdout, j; pretty=true) -end diff --git a/apps/report-execution/src/libraries/nbs_sr_05.py b/apps/report-execution/src/libraries/nbs_sr_05.py index 03c8fe474a..fd9652ad72 100644 --- a/apps/report-execution/src/libraries/nbs_sr_05.py +++ b/apps/report-execution/src/libraries/nbs_sr_05.py @@ -37,8 +37,44 @@ def execute( + 'ORDER BY phc_code_short_desc, YEAR(event_date), MONTH(event_date)' ) - description = 'SR5: Cases of Reportable Diseases by State' + header = 'SR5: Cases of Reportable Diseases by State' + subheader = None if time_range is not None: - description += f'\n{time_range.start} - {time_range.end}' + subheader = f'\n{time_range.start} - {time_range.end}' - return ReportResult(content_type='table', content=content, description=description) + description = ( + '*Data Source:* nbs_ods.PHCDemographic (publichealthcasefact)\n' + '*Output:* Report demonstrates, in table form, the total number of ' + 'Investigation(s) [both Individual and Summary] by County irrespective of ' + 'Case Status.\n' + 'Output:\n' + '* Does not include Investigation(s) that have been logically deleted\n' + '* Is filtered based on the state, disease(s) and advanced criteria selected ' + 'by user\n' + '* Will not include Investigation(s) that do not have a value for the State ' + 'selected by the user\n' + '* Is based on month and year of the calculated Event Date\n' + '*Calculations:*' + '* *Current Month Totals by disease:* Total Investigation(s) [both Individual ' + 'and Summary] where the Year and Month of the Event Date equal the current ' + 'Year and Month\n' + '* *Current Year Totals by disease:* Total Investigation(s) [both Individual ' + 'and Summary] where the Year of the Event Date equal the current Year\n' + '* *Previous Year Totals by disease:* Total Investigation(s) [both ' + 'Individual and Summary] where the Year of the Event Date equal last Year\n' + '* *5-Year median:* Median number of Investigation(s) [both Individual and ' + 'Summary] for the past five years\n' + '* *Percentage change (current year vs. 5 year median):* Percentage change ' + 'between the Current Year Totals by disease and the 5-Year median\n' + ' * *Event Date:* Derived using the hierarchy of Onset Date, Diagnosis Date, ' + 'Report to County, Report to State and Date the Investigation was created in ' + 'the NBS.\n' + ) + + return ReportResult( + content_type='table', + content=content, + header=header, + subheader=subheader, + description=description, + ) From f446a2eabeb94cd2951943740b15335c12b02435 Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Thu, 12 Mar 2026 17:29:03 -0400 Subject: [PATCH 5/7] fix: build out the analytic columns --- .../src/libraries/nbs_sr_05.py | 79 +- apps/report-execution/tests/fake.sql | 1003 ----------------- .../tests/integration/libraries/nbs_sr_05.py | 5 +- .../tests/integration/main.py | 2 +- 4 files changed, 71 insertions(+), 1018 deletions(-) delete mode 100644 apps/report-execution/tests/fake.sql diff --git a/apps/report-execution/src/libraries/nbs_sr_05.py b/apps/report-execution/src/libraries/nbs_sr_05.py index fd9652ad72..ea65786d6f 100644 --- a/apps/report-execution/src/libraries/nbs_sr_05.py +++ b/apps/report-execution/src/libraries/nbs_sr_05.py @@ -24,23 +24,78 @@ def execute( """ content = trx.query( f'WITH subset as ({subset_query})\n' - + 'SELECT state_cd, state, phc_code_short_desc, MONTH(event_date) as month, ' - + 'YEAR(event_date) as year, sum(group_case_cnt) as cases\n' - + 'FROM subset\n' - + 'WHERE state is not NULL\n' - + 'AND event_date is not NULL\n' - + 'AND DATEPART(dayofyear, event_date) <= ' - + ' DATEPART(dayofyear, CURRENT_TIMESTAMP)\n' - + 'AND YEAR(event_date) >= (YEAR(CURRENT_TIMESTAMP) - 5)\n' - + 'GROUP BY state_cd, state, phc_code_short_desc, ' - + 'MONTH(event_date), YEAR(event_date)\n' - + 'ORDER BY phc_code_short_desc, YEAR(event_date), MONTH(event_date)' + + ', base_data as (' + 'SELECT state_cd, state, phc_code_short_desc, MONTH(event_date) as month, ' + 'YEAR(event_date) as year, sum(group_case_cnt) as cases\n' + 'FROM subset\n' + 'WHERE state is not NULL\n' + 'AND event_date is not NULL\n' + 'AND DATEPART(dayofyear, event_date) <= ' + ' DATEPART(dayofyear, CURRENT_TIMESTAMP)\n' + 'AND YEAR(event_date) >= (YEAR(CURRENT_TIMESTAMP) - 5)\n' + 'GROUP BY state_cd, state, phc_code_short_desc, ' + 'MONTH(event_date), YEAR(event_date)\n' + ')\n' + + ', diseases as (\n' + 'SELECT DISTINCT phc_code_short_desc\n' + 'FROM base_data\n' + ')\n' + + ', year_data as (\n' + 'SELECT phc_code_short_desc, year, SUM(cases) as cases\n' + 'FROM base_data\n' + 'GROUP BY phc_code_short_desc, year' + ')\n' + + ', this_month as (\n' + 'SELECT phc_code_short_desc, SUM(cases) as curr_month\n' + 'FROM base_data\n' + 'WHERE month = MONTH(CURRENT_TIMESTAMP)\n' + 'AND year = YEAR(CURRENT_TIMESTAMP)\n' + 'GROUP BY phc_code_short_desc' + ')\n' + + ', this_year as (\n' + 'SELECT phc_code_short_desc, SUM(cases) as curr_ytd\n' + 'FROM year_data\n' + 'WHERE year = YEAR(CURRENT_TIMESTAMP)\n' + 'GROUP BY phc_code_short_desc' + ')\n' + + ', last_year as (\n' + 'SELECT phc_code_short_desc, SUM(cases) as last_ytd\n' + 'FROM year_data\n' + 'WHERE year = (YEAR(CURRENT_TIMESTAMP) - 1)\n' + 'GROUP BY phc_code_short_desc' + ')\n' + + ', median_year as (\n' + 'SELECT DISTINCT phc_code_short_desc, PERCENTILE_CONT(0.5) WITHIN GROUP ' + '(ORDER BY cases) OVER (PARTITION BY phc_code_short_desc) as median_ytd\n' + 'FROM year_data\n' + ')\n' + + 'SELECT d.phc_code_short_desc, COALESCE(curr_month, 0) as curr_month, \n' + 'COALESCE(curr_ytd, 0) as curr_ytd, COALESCE(last_ytd, 0) as last_ytd, \n' + 'COALESCE(median_ytd, 0) as median_ytd, \n' + 'IIF(' + ' COALESCE(median_ytd, 0) = 0, ' + ' 0, ' + ' COALESCE((curr_ytd - median_ytd) / median_ytd, 0)) as pct_chg\n' + 'FROM diseases d\n' + 'LEFT JOIN this_month tm on tm.phc_code_short_desc = d.phc_code_short_desc\n' + 'LEFT JOIN this_year ty on ty.phc_code_short_desc = d.phc_code_short_desc\n' + 'LEFT JOIN last_year ly on ly.phc_code_short_desc = d.phc_code_short_desc\n' + 'LEFT JOIN median_year my on my.phc_code_short_desc = d.phc_code_short_desc\n' + 'ORDER BY d.phc_code_short_desc asc' ) header = 'SR5: Cases of Reportable Diseases by State' subheader = None if time_range is not None: - subheader = f'\n{time_range.start} - {time_range.end}' + subheader = f'{time_range.start} - {time_range.end}' description = ( '*Data Source:* nbs_ods.PHCDemographic (publichealthcasefact)\n' diff --git a/apps/report-execution/tests/fake.sql b/apps/report-execution/tests/fake.sql deleted file mode 100644 index 68d3e8f3dc..0000000000 --- a/apps/report-execution/tests/fake.sql +++ /dev/null @@ -1,1003 +0,0 @@ -INSERT INTO [NBS_ODSE].[dbo].[PublicHealthCaseFact] -(public_health_case_uid,case_class_cd,PHC_code,event_date,group_case_cnt,state,PHC_code_desc,prog_area_cd,PHC_code_short_desc,state_cd) -VALUES -(1, 'N', '502651', '2021-08-12', nan, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(2, 'N', '10190', '2024-07-13', 62.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(3, 'N', '502651', '2021-02-14', 9.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(4, '', '10190', '2020-04-23', 71.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(5, 'C', '10190', '2025-09-19', 8.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(6, 'N', '10140', '2021-07-12', 69.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(7, '', '10190', '2022-05-12', 23.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(8, 'C', '10140', '2025-03-03', 34.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(9, 'C', '10190', '2021-06-25', 4.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(10, '', '10140', '2025-03-07', 34.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(11, '', '10140', '2025-01-04', 25.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(12, 'N', '10140', '2021-03-08', nan, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(13, 'C', '10190', '2023-12-19', 48.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(14, '', '502651', '2020-09-17', 78.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(15, 'N', '10190', '2022-03-22', 50.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(16, '', '502651', '2023-03-28', 23.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(17, 'C', '10190', '2021-09-05', 36.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(18, 'N', '10140', '2020-09-23', 71.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(19, '', '502651', '2025-04-02', 1.0, , 'Salmonellosis', 'FOOD', 'Salmonellosis', ), -(20, 'N', '10140', '2025-08-30', 74.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(21, '', '10140', '2024-06-08', 40.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(22, 'C', '502651', '2025-04-18', 66.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(23, 'C', '10190', '2021-05-14', 55.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(24, 'C', '502651', '2023-10-19', 56.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(25, 'C', '10190', '2022-11-28', nan, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(26, 'C', '502651', '2022-01-10', 6.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(27, 'C', '10190', '2020-09-05', 60.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(28, 'N', '502651', '2023-12-18', 36.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(29, '', '10190', '2023-04-25', 83.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(30, 'C', '10190', '2023-01-11', 44.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(31, 'C', '502651', '2021-01-23', 87.0, , 'Salmonellosis', 'FOOD', 'Salmonellosis', ), -(32, 'C', '10190', '2021-05-15', nan, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(33, 'C', '10190', '2025-09-09', 82.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(34, 'N', '502651', '2024-01-01', 36.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(35, 'C', '10190', '2021-04-18', 56.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(36, 'C', '10190', '2024-09-08', 42.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(37, 'C', '10140', '2024-01-05', 26.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(38, 'C', '502651', '2025-08-20', 13.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(39, '', '502651', '2025-03-30', 30.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(40, 'C', '10140', '2021-11-11', 75.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(41, '', '10190', NULL, 31.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(42, '', '10140', '2020-12-04', 23.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(43, '', '502651', '2021-12-10', 4.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(44, 'C', '10140', '2020-06-13', 90.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(45, '', '502651', '2020-09-08', 37.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(46, '', '10190', '2024-08-12', 42.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(47, '', '10190', '2020-04-19', 37.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(48, '', '10140', NULL, 20.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(49, 'N', '10190', '2024-11-09', 53.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(50, 'N', '502651', '2025-05-18', 80.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(51, 'C', '10140', '2024-04-14', 10.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(52, 'N', '10190', '2021-12-16', 25.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(53, '', '10140', '2025-07-29', 38.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(54, 'N', '10190', '2021-01-05', 49.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(55, 'C', '502651', '2023-10-18', 21.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(56, 'N', '10140', '2022-03-09', 2.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(57, 'C', '10140', '2022-05-18', 59.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(58, '', '10140', '2021-03-18', nan, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(59, 'C', '10190', '2026-03-12', 74.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(60, 'N', '10190', '2020-10-10', 27.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(61, '', '10140', '2022-09-29', 27.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(62, 'N', '502651', '2020-11-15', 8.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(63, '', '10140', '2020-07-10', 22.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(64, 'C', '10190', '2023-10-11', 20.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(65, 'C', '10190', '2023-11-04', 70.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(66, 'C', '10140', '2023-02-22', 32.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(67, '', '10190', '2022-02-15', 5.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(68, '', '10140', '2020-12-04', 68.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(69, 'C', '502651', '2021-12-15', 53.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(70, '', '10190', '2024-02-11', 26.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(71, 'C', '10190', '2023-01-25', 31.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(72, '', '10190', '2022-10-31', 63.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(73, '', '10140', NULL, 54.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(74, '', '10140', '2022-11-11', 83.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(75, 'C', '10190', '2025-07-18', 28.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(76, '', '10140', '2023-03-12', 5.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(77, '', '10190', '2020-05-30', 33.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(78, 'C', '10140', '2021-08-26', 27.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(79, '', '502651', '2024-11-03', 54.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(80, 'C', '502651', '2025-06-05', 19.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(81, 'C', '502651', '2022-02-23', 41.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(82, 'C', '10190', '2023-08-06', 73.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(83, 'C', '10190', '2022-08-14', 84.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(84, '', '502651', '2024-02-17', 6.0, , 'Salmonellosis', 'FOOD', 'Salmonellosis', ), -(85, 'N', '10190', '2023-03-02', 12.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(86, '', '502651', '2022-10-12', 74.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(87, '', '10140', '2025-08-10', 22.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(88, 'C', '502651', '2022-03-21', 85.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(89, 'N', '502651', NULL, 83.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(90, 'C', '502651', '2022-02-01', 54.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(91, 'C', '10140', '2023-05-16', 84.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(92, 'C', '10190', '2025-01-06', 35.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(93, '', '502651', NULL, 51.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(94, 'C', '10140', '2025-12-12', 10.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(95, '', '10190', '2025-05-12', 36.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(96, '', '10140', '2025-12-24', 86.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(97, 'C', '10190', '2021-05-05', 51.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(98, '', '10190', '2025-08-08', 17.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(99, 'N', '10140', '2024-10-22', 35.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(100, 'N', '10140', '2024-03-17', 8.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(101, 'N', '502651', '2025-06-06', 89.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(102, 'N', '10190', '2024-01-06', 73.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(103, 'N', '10140', '2023-01-13', 52.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(104, '', '502651', '2025-10-10', 28.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(105, '', '10140', '2024-12-29', 28.0, , 'Measles', 'GCD', 'Measles', ), -(106, '', '502651', '2025-09-29', 2.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(107, '', '10190', '2023-11-12', 33.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(108, '', '10140', '2020-11-20', 49.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(109, 'C', '502651', '2025-06-23', 71.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(110, 'N', '10140', '2020-07-06', 26.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(111, 'C', '10140', '2021-03-02', 78.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(112, 'C', '10190', '2022-03-08', 72.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(113, 'C', '10190', '2024-11-06', 61.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(114, '', '10190', '2025-09-13', 57.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(115, 'C', '502651', '2020-05-08', 5.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(116, '', '502651', '2024-05-18', 15.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(117, 'C', '10190', '2023-02-18', 33.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(118, 'N', '10140', '2023-11-08', 18.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(119, 'C', '502651', '2020-06-09', 11.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(120, '', '502651', '2024-10-23', 67.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(121, 'C', '502651', '2025-08-22', 39.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(122, 'C', '502651', '2025-03-27', 10.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(123, 'N', '10140', '2020-09-14', 70.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(124, '', '10140', '2022-12-03', 27.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(125, 'N', '10190', '2024-12-06', 40.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(126, '', '502651', '2022-07-13', nan, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(127, 'N', '10190', '2025-05-05', nan, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(128, '', '10190', '2020-10-06', 15.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(129, '', '502651', '2025-09-14', 47.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(130, 'N', '502651', '2023-04-11', 56.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(131, '', '10190', '2022-09-11', 57.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(132, 'N', '10140', '2020-08-05', 26.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(133, 'C', '10140', '2024-01-10', 62.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(134, 'N', '10190', '2022-09-25', 72.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), 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'10140', '2021-09-06', 86.0, , 'Measles', 'GCD', 'Measles', ), -(951, '', '10140', NULL, 34.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(952, 'N', '502651', '2025-02-07', 19.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(953, 'N', '10140', '2022-09-21', 9.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(954, '', '10140', '2021-11-24', 23.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(955, 'N', '10190', '2023-10-01', 20.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(956, '', '10190', '2025-04-24', 51.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(957, 'N', '10190', '2020-07-13', 76.0, , 'Pertussis', 'GCD', 'Pertussis', ), -(958, 'C', '502651', '2025-10-25', 11.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(959, '', '502651', NULL, 2.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(960, 'C', '502651', '2022-06-14', 20.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(961, '', '10140', '2021-09-29', 68.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(962, 'C', '10140', '2022-05-27', 16.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(963, 'N', '502651', '2025-09-18', 34.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(964, 'N', '10140', '2025-02-01', 7.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(965, 'N', '502651', '2021-02-08', 41.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(966, 'N', '502651', '2020-08-14', 80.0, , 'Salmonellosis', 'FOOD', 'Salmonellosis', ), -(967, 'C', '502651', '2023-01-18', 90.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(968, '', '10140', '2023-09-04', 85.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(969, '', '502651', '2023-06-03', 12.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(970, 'C', '10190', '2024-07-18', 62.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(971, 'C', '10140', '2021-10-04', 23.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(972, 'N', '502651', '2021-04-14', 74.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(973, 'N', '10190', '2022-05-14', 50.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(974, 'N', '502651', '2023-02-07', 75.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(975, 'N', '10140', '2021-07-06', 79.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(976, 'C', '502651', '2022-08-05', 5.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(977, 'C', '10140', '2021-04-17', 61.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(978, 'C', '10190', '2023-06-26', 45.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(979, '', '10190', '2026-03-18', 24.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(980, 'C', '502651', '2023-06-05', 20.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(981, 'C', '10190', '2021-03-26', 20.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(982, 'N', '10190', '2021-10-14', 1.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(983, 'N', '10140', '2024-11-18', 10.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(984, '', '502651', '2025-04-13', 87.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(985, 'C', '10190', '2020-12-25', 40.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(986, '', '10140', '2024-12-07', 40.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(987, 'N', '502651', '2021-01-10', nan, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(988, 'C', '10140', '2022-02-18', 21.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(989, 'C', '10190', '2025-10-26', 79.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(990, 'C', '10140', NULL, 5.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(991, 'C', '10140', '2022-11-03', 24.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(992, 'N', '502651', '2023-07-31', 86.0, 'Tennessee', 'Salmonellosis', 'FOOD', 'Salmonellosis', '47'), -(993, 'N', '10140', '2022-02-25', 21.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(994, '', '502651', '2025-11-13', 17.0, 'Georgia', 'Salmonellosis', 'FOOD', 'Salmonellosis', '13'), -(995, '', '10140', '2023-08-10', 68.0, 'Georgia', 'Measles', 'GCD', 'Measles', '13'), -(996, 'C', '10190', '2021-08-02', 41.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(997, '', '10140', NULL, 9.0, 'Tennessee', 'Measles', 'GCD', 'Measles', '47'), -(998, 'N', '10190', '2023-10-23', 47.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'), -(999, '', '10190', '2024-09-13', 83.0, 'Georgia', 'Pertussis', 'GCD', 'Pertussis', '13'), -(1000, 'C', '10190', '2025-11-20', 70.0, 'Tennessee', 'Pertussis', 'GCD', 'Pertussis', '47'); \ No newline at end of file diff --git a/apps/report-execution/tests/integration/libraries/nbs_sr_05.py b/apps/report-execution/tests/integration/libraries/nbs_sr_05.py index 93791f2043..58d9f79ddd 100644 --- a/apps/report-execution/tests/integration/libraries/nbs_sr_05.py +++ b/apps/report-execution/tests/integration/libraries/nbs_sr_05.py @@ -31,9 +31,10 @@ def test_execute_report_with_time_range(self): ) result = execute_report(report_spec) - assert result.description == ( - 'SR5: Cases of Reportable Diseases by State\n' + '2024-01-01 - 2024-12-31' + assert result.header == ( + 'SR5: Cases of Reportable Diseases by State' ) + assert result.subheader == '2024-01-01 - 2024-12-31' assert result.content_type == 'table' logging.info(result.content.data) diff --git a/apps/report-execution/tests/integration/main.py b/apps/report-execution/tests/integration/main.py index f5bb6beadd..22338e181f 100644 --- a/apps/report-execution/tests/integration/main.py +++ b/apps/report-execution/tests/integration/main.py @@ -36,6 +36,6 @@ def test_report_runs(self): result = json.loads(response.read()) assert ( - result['description'] + result['header'] == 'Custom Report For Table: [NBS_ODSE].[dbo].[Filter_code]' ) From 709063dc32f9d26059e06ef724686c0012c81b2d Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Thu, 12 Mar 2026 17:39:39 -0400 Subject: [PATCH 6/7] fix: state not used, clean up desc, leave breadcrumbs for later --- .../src/libraries/nbs_sr_05.py | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/apps/report-execution/src/libraries/nbs_sr_05.py b/apps/report-execution/src/libraries/nbs_sr_05.py index ea65786d6f..41fa3d6f5d 100644 --- a/apps/report-execution/src/libraries/nbs_sr_05.py +++ b/apps/report-execution/src/libraries/nbs_sr_05.py @@ -19,23 +19,22 @@ def execute( * % change Current YTD vs 5 Year Median YTD Conversion notes: - * Lifted the size check to a global check and refined the env var names - * Date formatting still needs to be figured out + * Export included the year as a column + * Export has columns in different order """ content = trx.query( + # State filtering is assumed to happen in the filters f'WITH subset as ({subset_query})\n' ', base_data as (' - 'SELECT state_cd, state, phc_code_short_desc, MONTH(event_date) as month, ' + 'SELECT phc_code_short_desc, MONTH(event_date) as month, ' 'YEAR(event_date) as year, sum(group_case_cnt) as cases\n' 'FROM subset\n' - 'WHERE state is not NULL\n' 'AND event_date is not NULL\n' 'AND DATEPART(dayofyear, event_date) <= ' ' DATEPART(dayofyear, CURRENT_TIMESTAMP)\n' 'AND YEAR(event_date) >= (YEAR(CURRENT_TIMESTAMP) - 5)\n' - 'GROUP BY state_cd, state, phc_code_short_desc, ' - 'MONTH(event_date), YEAR(event_date)\n' + 'GROUP BY phc_code_short_desc, MONTH(event_date), YEAR(event_date)\n' ')\n' ', diseases as (\n' @@ -91,6 +90,10 @@ def execute( 'LEFT JOIN median_year my on my.phc_code_short_desc = d.phc_code_short_desc\n' 'ORDER BY d.phc_code_short_desc asc' ) + + # TODO: + # column header names + # sub header header = 'SR5: Cases of Reportable Diseases by State' subheader = None @@ -100,8 +103,7 @@ def execute( description = ( '*Data Source:* nbs_ods.PHCDemographic (publichealthcasefact)\n' '*Output:* Report demonstrates, in table form, the total number of ' - 'Investigation(s) [both Individual and Summary] by County irrespective of ' - 'Case Status.\n' + 'Investigation(s) [both Individual and Summary] irrespective of Case Status.\n' 'Output:\n' '* Does not include Investigation(s) that have been logically deleted\n' '* Is filtered based on the state, disease(s) and advanced criteria selected ' From 5d61d7aab59e49ebf3e3e88e34782252f82ae19b Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Thu, 12 Mar 2026 17:41:43 -0400 Subject: [PATCH 7/7] fix: linting --- .../src/libraries/nbs_sr_05.py | 20 +++++++++---------- .../tests/integration/libraries/nbs_sr_05.py | 4 +--- 2 files changed, 11 insertions(+), 13 deletions(-) diff --git a/apps/report-execution/src/libraries/nbs_sr_05.py b/apps/report-execution/src/libraries/nbs_sr_05.py index 41fa3d6f5d..9552c9b9ac 100644 --- a/apps/report-execution/src/libraries/nbs_sr_05.py +++ b/apps/report-execution/src/libraries/nbs_sr_05.py @@ -25,7 +25,7 @@ def execute( content = trx.query( # State filtering is assumed to happen in the filters f'WITH subset as ({subset_query})\n' - + # base_data CTE ', base_data as (' 'SELECT phc_code_short_desc, MONTH(event_date) as month, ' 'YEAR(event_date) as year, sum(group_case_cnt) as cases\n' @@ -36,18 +36,18 @@ def execute( 'AND YEAR(event_date) >= (YEAR(CURRENT_TIMESTAMP) - 5)\n' 'GROUP BY phc_code_short_desc, MONTH(event_date), YEAR(event_date)\n' ')\n' - + # diseases CTE ', diseases as (\n' 'SELECT DISTINCT phc_code_short_desc\n' 'FROM base_data\n' ')\n' - + # year_data CTE ', year_data as (\n' 'SELECT phc_code_short_desc, year, SUM(cases) as cases\n' 'FROM base_data\n' 'GROUP BY phc_code_short_desc, year' ')\n' - + # this_month CTE ', this_month as (\n' 'SELECT phc_code_short_desc, SUM(cases) as curr_month\n' 'FROM base_data\n' @@ -55,27 +55,27 @@ def execute( 'AND year = YEAR(CURRENT_TIMESTAMP)\n' 'GROUP BY phc_code_short_desc' ')\n' - + # this_year CTE ', this_year as (\n' 'SELECT phc_code_short_desc, SUM(cases) as curr_ytd\n' 'FROM year_data\n' 'WHERE year = YEAR(CURRENT_TIMESTAMP)\n' 'GROUP BY phc_code_short_desc' ')\n' - + # last_year CTE ', last_year as (\n' 'SELECT phc_code_short_desc, SUM(cases) as last_ytd\n' 'FROM year_data\n' 'WHERE year = (YEAR(CURRENT_TIMESTAMP) - 1)\n' 'GROUP BY phc_code_short_desc' ')\n' - + # median_year CTE ', median_year as (\n' 'SELECT DISTINCT phc_code_short_desc, PERCENTILE_CONT(0.5) WITHIN GROUP ' '(ORDER BY cases) OVER (PARTITION BY phc_code_short_desc) as median_ytd\n' 'FROM year_data\n' ')\n' - + # Result select 'SELECT d.phc_code_short_desc, COALESCE(curr_month, 0) as curr_month, \n' 'COALESCE(curr_ytd, 0) as curr_ytd, COALESCE(last_ytd, 0) as last_ytd, \n' 'COALESCE(median_ytd, 0) as median_ytd, \n' @@ -90,8 +90,8 @@ def execute( 'LEFT JOIN median_year my on my.phc_code_short_desc = d.phc_code_short_desc\n' 'ORDER BY d.phc_code_short_desc asc' ) - - # TODO: + + # TODO: # noqa: FIX002 # column header names # sub header diff --git a/apps/report-execution/tests/integration/libraries/nbs_sr_05.py b/apps/report-execution/tests/integration/libraries/nbs_sr_05.py index 58d9f79ddd..9682b2211e 100644 --- a/apps/report-execution/tests/integration/libraries/nbs_sr_05.py +++ b/apps/report-execution/tests/integration/libraries/nbs_sr_05.py @@ -31,9 +31,7 @@ def test_execute_report_with_time_range(self): ) result = execute_report(report_spec) - assert result.header == ( - 'SR5: Cases of Reportable Diseases by State' - ) + assert result.header == ('SR5: Cases of Reportable Diseases by State') assert result.subheader == '2024-01-01 - 2024-12-31' assert result.content_type == 'table' logging.info(result.content.data)