[APP-445] feat: Convert NBSSR00007

apps/modernization-api/src/main/resources/db/changelog/report-execution-changelog.yml

@@ -24,3 +24,6 @@ databaseChangeLog:
         - sqlFile:
             path: db/report/execution/libraries/nbs_sr_02.sql
             splitStatements: false
+        - sqlFile:
+            path: db/report/execution/libraries/nbs_sr_07.sql
+            splitStatements: false

apps/modernization-api/src/main/resources/db/report/execution/libraries/nbs_sr_05.sql

@@ -1,4 +1,4 @@
--- Migrate the NBSCUSTOM.SAS library to the nbs_sr_05 python library
+-- Migrate the NBSSR00005.SAS library to the nbs_sr_05 python library
 
 USE [NBS_ODSE]
 

apps/modernization-api/src/main/resources/db/report/execution/libraries/nbs_sr_07.sql

@@ -0,0 +1,43 @@
+-- Migrate the NBSSR00007.SAS library to the nbs_sr_07 python library
+
+USE [NBS_ODSE]
+
+DECLARE @pyLib VARCHAR(50) = 'nbs_sr_07'
+DECLARE @sasLib VARCHAR(50) = 'NBSSR00007.SAS'
+DECLARE @desc VARCHAR(300) = 'SR7: Cases of Selected Diseases vs. 5-Year Median for Selected Time Period. Report demonstrates, in table form, Investigation(s) [both Individual and Summary] by year-to-date, and 5-year median irrespective of Case Status'
+
+IF EXISTS (SELECT * FROM [dbo].[Report_Library] WHERE UPPER(library_name) = @sasLib)
+BEGIN
+    UPDATE [dbo].[Report_Library]
+    SET
+        library_name = @pyLib,
+        runner = 'python',
+        desc_txt = @desc,
+        last_chg_time = CURRENT_TIMESTAMP,
+        last_chg_user_id = 99999999
+    WHERE
+        UPPER(library_name) = @sasLib;
+END
+ELSE
+BEGIN
+    -- Create a row for this library
+    INSERT INTO [dbo].[Report_Library] (
+        library_name,
+        desc_txt,
+        runner,
+        is_builtin_ind,
+        add_time,
+        add_user_id,
+        last_chg_time,
+        last_chg_user_id
+    ) VALUES (
+        @pyLib,
+        @desc,
+        'python',
+        'Y',
+        CURRENT_TIMESTAMP,
+        99999999,
+        CURRENT_TIMESTAMP,
+        99999999
+    );
+END

apps/report-execution/src/libraries/nbs_sr_07.py

@@ -0,0 +1,73 @@
+from src.db_transaction import Transaction
+from src.libraries.nbs_sr_05 import execute as execute_nbs_sr_05
+from src.models import ReportResult, Table
+
+
+def execute(
+    trx: Transaction,
+    subset_query: str,
+    data_source_name: str,
+    **kwargs,
+):
+    """Standard Report 07: Cases of Selected Diseases vs. 5-Year Median for a
+    specific state.
+
+    Each row has columns for the:
+    * Disease
+    * type (e.g. Five Year Median YTD or Current YTD)
+    * Number of Cases
+
+    Conversion notes:
+    * Matched "export format"
+    * Remove references to "Bar Graph" since export is a table
+    * Use results of nbs_sr_05.py for the following:
+    * - subheader
+    * - content (data is modified to fit expected table format of nbs_sr_07.py)
+    """
+    nbs_sr_05_report_result = execute_nbs_sr_05(
+        trx, subset_query, data_source_name, **kwargs
+    )
+    nbs_sr_05_report_result_rows = nbs_sr_05_report_result.content.data
+
+    modified_table = Table(columns=['Disease', 'type', 'Number of Cases'], data=[])
+
+    for row in nbs_sr_05_report_result_rows:
+        rows_to_add = [
+            (row[3], 'Five Year Median YTD', row[6]),
+            (row[3], 'Current YTD', row[2]),
+        ]
+        modified_table.data.extend(rows_to_add)
+
+    header = (
+        'SR7: Cases of Selected Diseases vs. 5-Year Median for Selected Time Period'
+    )
+    description = (
+        '<u>Report content</u>\n'
+        'Data Source: nbs_ods.PHCDemographic (publichealthcasefact)\n'
+        'Output: Report demonstrates, in table form, '
+        'Investigation(s) [both Individual and Summary] '
+        'by year-to-date, and 5-year median irrespective of Case Status.\n'
+        'Output:\n'
+        '1) Does not include Investigation(s) that have been logically deleted\n'
+        '2) Is filtered based on the state, disease(s) and advanced criteria selected '
+        'by user\n'
+        '3) Will not include Investigation(s) that do not have a value for the State '
+        'selected by the user\n'
+        '4) Is based on month and year of the calculated Event Date\n'
+        'Calculations:'
+        '1) Current Year Totals by disease: Total Investigation(s) [both Individual '
+        'and Summary] where the Year of the Event Date equal the current Year\n'
+        '2) 5-Year median: Median number of Investigation(s) [both Individual and '
+        'Summary] for the past five years\n'
+        '3) 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=modified_table,
+        header=header,
+        subheader=nbs_sr_05_report_result.subheader,
+        description=description,
+    )

apps/report-execution/tests/integration/libraries/nbs_sr_07.py

@@ -0,0 +1,85 @@
+import datetime
+
+import pytest
+import yaml
+
+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', 'fake_db_table')
+@pytest.mark.integration
+class TestIntegrationNbsSr07Library:
+    """Integration tests for the nbs_sr_07 library."""
+
+    @pytest.fixture(autouse=True)
+    def set_time(self, time_machine):
+        time_machine.move_to(datetime.datetime(2024, 6, 24))
+
+    def test_execute_report_check_data(self, snapshot):
+        report_spec = ReportSpec.model_validate(
+            {
+                'version': 1,
+                'is_export': True,
+                'is_builtin': True,
+                'report_title': 'SR7',
+                'library_name': 'nbs_sr_07',
+                '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.content_type == 'table'
+
+        data = result.content.data
+        assert len(data) == 6
+        assert len(data[0]) == len(result.content.columns)
+
+        snapshot.assert_match(yaml.dump(data), 'snapshot.yml')
+
+        for disease in ['Pertussis', 'Measles', 'Salmonellosis']:
+            disease_rows = list()
+            for row in result.content.data:
+                if row[0] == disease:
+                    disease_rows.append(row)
+            # ensure there are 2 rows per disease
+            assert len(disease_rows) == 2
+            assert disease_rows[0][1] == 'Five Year Median YTD'
+            assert disease_rows[0][2] >= 100
+            assert disease_rows[1][1] == 'Current YTD'
+            assert disease_rows[1][2] >= 100
+
+    def test_execute_report_check_metadata(self):
+        """Check the metadata and column names are correct with a frozen date."""
+        report_spec = ReportSpec.model_validate(
+            {
+                'version': 1,
+                'is_export': True,
+                'is_builtin': True,
+                'report_title': 'NBS Custom',
+                'library_name': 'nbs_sr_07',
+                '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.header
+            == 'SR7: Cases of Selected Diseases vs. 5-Year Median for Selected '
+            'Time Period'
+        )
+        assert result.subheader == 'N/A, Georgia, Tennessee | 06/24/2024'
+        assert len(result.description) > 100
+        assert result.content_type == 'table'
+
+        assert result.content.columns[0] == 'Disease'
+        assert result.content.columns[1] == 'type'
+        assert result.content.columns[2] == 'Number of Cases'

apps/report-execution/tests/integration/libraries/snapshots/nbs_sr_07/test_execute_report_check_data/snapshot.yml

@@ -0,0 +1,27 @@
+- !!python/tuple
+  - Measles
+  - Five Year Median YTD
+  - 1016.0
+- !!python/tuple
+  - Measles
+  - Current YTD
+  - !!python/object/apply:decimal.Decimal
+    - '928.00000'
+- !!python/tuple
+  - Pertussis
+  - Five Year Median YTD
+  - 834.0
+- !!python/tuple
+  - Pertussis
+  - Current YTD
+  - !!python/object/apply:decimal.Decimal
+    - '1464.00000'
+- !!python/tuple
+  - Salmonellosis
+  - Five Year Median YTD
+  - 785.0
+- !!python/tuple
+  - Salmonellosis
+  - Current YTD
+  - !!python/object/apply:decimal.Decimal
+    - '1424.00000'