Merge pull request #900 from populationgenomics/dev

Release: AnalysisUpdateModel.active bug fix and formatting

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 7.3.2
+current_version = 7.3.3
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[A-z0-9-]+)

.pre-commit-config.yaml

@@ -31,36 +31,16 @@ repos:
               metamist/audit/README\.md
           )$
 
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
-        name: isort (python)
-
-  - repo: https://github.com/ambv/black
-    rev: 23.12.1
-    hooks:
-      - id: black
-        args: [.]
-        pass_filenames: false
-        always_run: true
-        exclude: ^metamist/
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: "6.1.0"
-    hooks:
-      - id: flake8
-        additional_dependencies: [flake8-bugbear, flake8-quotes]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: v0.5.2
     hooks:
       # Run the linter.
-      - id: ruff
-        args: [ --fix ]
+      # - id: ruff
+      #   args: [ --fix ]
       # Run the formatter.
-      # - id: ruff-format
+      - id: ruff-format
 
   # Using system installation of pylint to support checking python module imports
   - repo: local

api/graphql/schema.py

@@ -5,6 +5,7 @@
 Note, we silence a lot of linting here because GraphQL looks at type annotations
 and defaults to decide the GraphQL schema, so it might not necessarily look correct.
 """
+
 import datetime
 from inspect import isclass
 

api/routes/analysis.py

@@ -124,7 +124,11 @@ async def update_analysis(
     """Update status of analysis"""
     atable = AnalysisLayer(connection)
     await atable.update_analysis(
-        analysis_id, status=analysis.status, output=analysis.output, meta=analysis.meta
+        analysis_id,
+        status=analysis.status,
+        output=analysis.output,
+        meta=analysis.meta,
+        active=analysis.active,
     )
     return True
 

api/routes/project_insights.py

@@ -7,7 +7,12 @@
     ProjectInsightsSummary,
 )
 
-router = APIRouter(prefix='/project-insights', tags=['project-insights',])
+router = APIRouter(
+    prefix='/project-insights',
+    tags=[
+        'project-insights',
+    ],
+)
 
 
 @router.post(

api/server.py

@@ -25,7 +25,7 @@
 from db.python.utils import get_logger
 
 # This tag is automatically updated by bump2version
-_VERSION = '7.3.2'
+_VERSION = '7.3.3'
 
 
 logger = get_logger()

codecov.yml

@@ -5,7 +5,11 @@ coverage:
         # basic
         target: auto
         threshold: 0%
+        informational: true
         paths:
           - "db"
           - "scripts"
           - "metamist/parser"
+    patch:
+      default:
+        informational: true

db/backup/backup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3
 # pylint: disable=broad-exception-caught,broad-exception-raised
-""" Daily back up function for databases within a local
-MariaDB instance """
+"""Daily back up function for databases within a local
+MariaDB instance"""
 
 import json
 import os

db/backup/recovery_test.py

@@ -1,4 +1,4 @@
-""" A script to test that tests the validity of a database backup
+"""A script to test that tests the validity of a database backup
 in the event of recovery.
 NOTE: DO NOT RUN THIS SCRIPT ON A PRODUCTION SERVER.
 It will drop the local mysql database after each run.

db/backup/restore.py

@@ -1,5 +1,5 @@
-""" A script to restore the database instance to the latest
-backup """
+"""A script to restore the database instance to the latest
+backup"""
 
 import os
 import subprocess

db/deploy/main.py

@@ -22,10 +22,14 @@
 changelog_file = 'project.xml'
 
 
-def read_db_credentials(env: Literal['prod', 'dev']) -> Dict[Literal['dbname', 'username', 'password', 'host'], str]:
+def read_db_credentials(
+    env: Literal['prod', 'dev'],
+) -> Dict[Literal['dbname', 'username', 'password', 'host'], str]:
     """Get database credentials from Secret Manager."""
     try:
-        secret_path = SECRET_CLIENT.secret_version_path(SECRET_PROJECT, SECRET_NAME, 'latest')
+        secret_path = SECRET_CLIENT.secret_version_path(
+            SECRET_PROJECT, SECRET_NAME, 'latest'
+        )
         response = SECRET_CLIENT.access_secret_version(request={'name': secret_path})
         return json.loads(response.payload.data.decode('UTF-8'))[env]
     except Exception as e:  # Broad exception for example; refine as needed
@@ -35,7 +39,10 @@ def read_db_credentials(env: Literal['prod', 'dev']) -> Dict[Literal['dbname', '
 
 
 @app.post('/execute-liquibase')
-async def execute_liquibase(request: Request, environment: Literal['prod', 'dev'] = Query(default='dev', regex='^(prod|dev)$')):
+async def execute_liquibase(
+    request: Request,
+    environment: Literal['prod', 'dev'] = Query(default='dev', regex='^(prod|dev)$'),
+):
     """Endpoint to remotely trigger Liquibase commands on a GCP VM using XML content."""
     xml_content = await request.body()
 
@@ -67,10 +74,25 @@ async def execute_liquibase(request: Request, environment: Literal['prod', 'dev'
 
             try:
                 # Execute the gcloud command
-                result = subprocess.run(liquibase_command, check=True, capture_output=True, text=True, env={'LIQUIBASE_COMMAND_PASSWORD': db_password, 'LIQUIBASE_COMMAND_USERNAME': db_username, **os.environ},)
-                logger.log_text(f'Liquibase update successful: {result.stdout}', severity='INFO')
+                result = subprocess.run(
+                    liquibase_command,
+                    check=True,
+                    capture_output=True,
+                    text=True,
+                    env={
+                        'LIQUIBASE_COMMAND_PASSWORD': db_password,
+                        'LIQUIBASE_COMMAND_USERNAME': db_username,
+                        **os.environ,
+                    },
+                )
+                logger.log_text(
+                    f'Liquibase update successful: {result.stdout}', severity='INFO'
+                )
                 os.remove(temp_file_path)
-                return {'message': 'Liquibase update executed successfully', 'output': result.stdout}
+                return {
+                    'message': 'Liquibase update executed successfully',
+                    'output': result.stdout,
+                }
             except subprocess.CalledProcessError as e:
                 text = f'Failed to execute Liquibase update: {e.stderr}'
                 logger.log_text(text, severity='ERROR')
@@ -79,4 +101,5 @@ async def execute_liquibase(request: Request, environment: Literal['prod', 'dev'
 
 if __name__ == '__main__':
     import uvicorn
+
     uvicorn.run(app, host='0.0.0.0', port=int(os.environ.get('PORT', 8080)))

db/python/connect.py

@@ -3,6 +3,7 @@
 """
 Code for connecting to Postgres database
 """
+
 import abc
 import asyncio
 import json
@@ -229,7 +230,6 @@ async def audit_log_id(self):
 
         async with self._audit_log_lock:
             if not self._audit_log_id:
-
                 # make this import here, otherwise we'd have a circular import
                 from db.python.tables.audit_log import (  # pylint: disable=import-outside-toplevel,R0401
                     AuditLogTable,
@@ -328,9 +328,9 @@ def get_connection_string(self):
         if self.port:
             _host += f':{self.port}'
 
-        options: dict[str, str | int] = (
-            {}
-        )  # {'min_size': self.min_pool_size, 'max_size': self.max_pool_size}
+        options: dict[
+            str, str | int
+        ] = {}  # {'min_size': self.min_pool_size, 'max_size': self.max_pool_size}
         _options = '&'.join(f'{k}={v}' for k, v in options.items())
 
         url = f'mysql://{u_p}@{_host}/{self.dbname}?{_options}'

db/python/layers/analysis.py

@@ -572,6 +572,7 @@ async def update_analysis(
         status: AnalysisStatus,
         meta: dict[str, Any] = None,
         output: str | None = None,
+        active: bool | None = None,
     ):
         """
         Update the status of an analysis, set timestamp_completed if relevant
@@ -586,4 +587,5 @@ async def update_analysis(
             status=status,
             meta=meta,
             output=output,
+            active=active,
         )

db/python/layers/family.py

@@ -275,11 +275,13 @@ async def import_pedigree(
         missing_external_family_ids = [
             f for f in external_family_ids if f not in external_family_id_map
         ]
-        external_participant_ids_map = await participant_table.get_id_map_by_external_ids(
-            list(external_participant_ids),
-            project=self.connection.project_id,
-            # Allow missing participants if we're creating them
-            allow_missing=create_missing_participants,
+        external_participant_ids_map = (
+            await participant_table.get_id_map_by_external_ids(
+                list(external_participant_ids),
+                project=self.connection.project_id,
+                # Allow missing participants if we're creating them
+                allow_missing=create_missing_participants,
+            )
         )
 
         async with self.connection.connection.transaction():