lint: misc ruff 0.16 fixes

chord_metadata_service/patients/api_views.py

@@ -1,11 +1,11 @@
 import asyncio
+from datetime import datetime
 
 from adrf.views import APIView
 from asgiref.sync import async_to_sync
-from bento_lib.auth.permissions import Permission, P_QUERY_DATA
+from bento_lib.auth.permissions import P_QUERY_DATA, Permission
 from bento_lib.responses import errors
 from bento_lib.search import build_search_response
-from datetime import datetime
 from django.contrib.postgres.aggregates import ArrayAgg
 from django.core.exceptions import ValidationError
 from django.db.models import Count, F, Q
@@ -19,11 +19,11 @@
 from rest_framework.settings import api_settings
 
 from chord_metadata_service.authz.middleware import authz_middleware
-from chord_metadata_service.authz.viewset import BentoAuthzScopedModelViewSet, BentoAuthzScopedModelGenericListViewSet
+from chord_metadata_service.authz.viewset import BentoAuthzScopedModelGenericListViewSet, BentoAuthzScopedModelViewSet
 from chord_metadata_service.chord import data_types as dts
 from chord_metadata_service.discovery import responses as dres
 from chord_metadata_service.discovery.censorship import get_threshold, thresholded_count
-from chord_metadata_service.discovery.exceptions import DiscoveryScopeException, DiscoveryEmptyException
+from chord_metadata_service.discovery.exceptions import DiscoveryEmptyException, DiscoveryScopeException
 from chord_metadata_service.discovery.filtering import discovery_filter_queryset
 from chord_metadata_service.discovery.pydantic_models import DiscoveryQuery
 from chord_metadata_service.discovery.scope import get_request_discovery_scope
@@ -39,15 +39,15 @@
 from chord_metadata_service.phenopackets.models import Phenopacket
 from chord_metadata_service.phenopackets.serializers import PhenopacketSerializer
 from chord_metadata_service.restapi.api_renderers import (
-    PhenopacketsRenderer,
+    IndividualBentoSearchRenderer,
     IndividualCSVRenderer,
     IndividualXLSXRenderer,
-    IndividualBentoSearchRenderer,
+    PhenopacketsRenderer,
     csv_fields_error_response,
 )
 from chord_metadata_service.restapi.constants import MODEL_ID_PATTERN
-from chord_metadata_service.restapi.pagination import LargeResultsSetPagination, BatchResultsSetPagination
 from chord_metadata_service.restapi.negociation import FormatInPostContentNegotiation
+from chord_metadata_service.restapi.pagination import BatchResultsSetPagination, LargeResultsSetPagination
 from chord_metadata_service.restapi.utils import (
     build_experiments_by_subject,
     get_biosamples_with_experiment_details,

chord_metadata_service/patients/cleanup.py

@@ -1,9 +1,9 @@
-import chord_metadata_service.phenopackets.models as pm
-
 from structlog.stdlib import BoundLogger
 
+import chord_metadata_service.phenopackets.models as pm
 from chord_metadata_service.cleanup.remove import remove_not_referenced
 from chord_metadata_service.utils import build_id_set_from_model
+
 from .models import Individual
 
 __all__ = [

chord_metadata_service/patients/descriptions.py

@@ -1,6 +1,5 @@
 from chord_metadata_service.restapi.description_utils import EXTRA_PROPERTIES, ontology_class
 
-
 # TODO: This is part of another app
 INDIVIDUAL = {
     "description": "A subject of a phenopacket, representing either a human (typically) or another organism.",

chord_metadata_service/patients/filters.py

@@ -2,6 +2,7 @@
 from django.db.models import Q
 
 from chord_metadata_service.discovery.full_text_search import full_text_search_vector
+
 from .models import Individual
 
 GENOMIC_INTERPRETATION_QUERY = "phenopackets__interpretations__diagnosis__genomic_interpretations"

chord_metadata_service/patients/models.py

@@ -1,15 +1,17 @@
 from django.apps import apps
+from django.contrib.postgres.fields import ArrayField
 from django.contrib.postgres.indexes import GinIndex
 from django.db import models
 from django.db.models import JSONField
-from django.contrib.postgres.fields import ArrayField
-from chord_metadata_service.discovery.scopeable_model import BaseScopeableModel
+
 from chord_metadata_service.discovery.full_text_search import BaseFTSModel, ToFTSReprMixin
+from chord_metadata_service.discovery.scopeable_model import BaseScopeableModel
 from chord_metadata_service.discovery.types import ModelScopeFilters
-from chord_metadata_service.restapi.models import BaseTimeStamp, IndexableMixin, SchemaType, BaseExtraProperties
+from chord_metadata_service.restapi.models import BaseExtraProperties, BaseTimeStamp, IndexableMixin, SchemaType
 from chord_metadata_service.restapi.schema_ref import SchemaRefs
 from chord_metadata_service.restapi.validators import JsonSchemaValidator, ontology_validator
-from .values import PatientStatus, Sex, KaryotypicSex
+
+from .values import KaryotypicSex, PatientStatus, Sex
 
 
 class VitalStatus(BaseTimeStamp, IndexableMixin, ToFTSReprMixin):

chord_metadata_service/patients/schemas.py

@@ -1,20 +1,21 @@
 from django.conf import settings
+
 from chord_metadata_service.restapi.constants import MODEL_ID_PATTERN
 from chord_metadata_service.restapi.schema_utils import (
     DATE_TIME,
     DRAFT_07,
     SchemaTypes,
     array_of,
     base_type,
-    string_with_pattern,
     enum_of,
-    tag_ids_and_describe,
+    string_with_pattern,
     sub_schema_uri,
+    tag_ids_and_describe,
 )
-from chord_metadata_service.restapi.schemas import ONTOLOGY_CLASS, EXTRA_PROPERTIES_SCHEMA, TIME_ELEMENT_SCHEMA
-from .descriptions import INDIVIDUAL, VITAL_STATUS
-from .values import Sex, KaryotypicSex
+from chord_metadata_service.restapi.schemas import EXTRA_PROPERTIES_SCHEMA, ONTOLOGY_CLASS, TIME_ELEMENT_SCHEMA
 
+from .descriptions import INDIVIDUAL, VITAL_STATUS
+from .values import KaryotypicSex, Sex
 
 phenopacket_base_uri = f"{settings.SCHEMAS_BASE_URL}/phenopacket"
 

chord_metadata_service/patients/serializers.py

@@ -1,5 +1,6 @@
 from chord_metadata_service.phenopackets.serializers import BiosampleSerializer, SimplePhenopacketSerializer
 from chord_metadata_service.restapi.serializers import GenericSerializer
+
 from .models import Individual, VitalStatus
 
 __all__ = [

chord_metadata_service/patients/summaries.py

@@ -7,6 +7,7 @@
 from chord_metadata_service.discovery.censorship import thresholded_count
 from chord_metadata_service.discovery.fields import get_age_numeric_binned
 from chord_metadata_service.discovery.stats import queryset_stats_for_field
+
 from . import models
 
 __all__ = ["individual_summary"]

chord_metadata_service/patients/tests/constants.py

@@ -1,6 +1,7 @@
-import uuid
 import random
+import uuid
 from datetime import date, timedelta
+
 import isodate
 
 

chord_metadata_service/patients/tests/test_api.py

@@ -1,16 +1,16 @@
 import csv
 import io
-import openpyxl
 import random
 import uuid
-
-from bento_lib.discovery import DiscoveryConfig
 from copy import deepcopy
 
-from django.db.models import Q, F, Value
-from django.urls import reverse
+import openpyxl
+from bento_lib.discovery import DiscoveryConfig
+from django.db.models import F, Q, Value
 from django.test import TestCase, override_settings
+from django.urls import reverse
 from rest_framework import status
+
 from chord_metadata_service.authz.tests.helpers import AuthzAPITestCase
 from chord_metadata_service.chord import models as cm
 from chord_metadata_service.chord.dataset_schema import KatsuDatasetModel
@@ -19,9 +19,9 @@
 from chord_metadata_service.discovery import responses as dres
 from chord_metadata_service.discovery.fields_utils import JSONBPathFilter
 from chord_metadata_service.discovery.tests.constants import (
+    CONFIG_PUBLIC_TEST_SEARCH_SEX_ONLY,
     DISCOVERY_CONFIG_EXTRA_PROPERTIES,
     DISCOVERY_CONFIG_TEST,
-    CONFIG_PUBLIC_TEST_SEARCH_SEX_ONLY,
     DISCOVERY_ZERO_COUNTS,
 )
 from chord_metadata_service.experiments import models as ex_m
@@ -612,7 +612,7 @@ class DiscoveryFilteringIndividualsTest(AuthzAPITestCase, ProjectTestCase):
 
     @staticmethod
     def response_threshold_check(response):
-        return response["count"] if "count" in response else dres.INSUFFICIENT_DATA_AVAILABLE
+        return response.get("count", dres.INSUFFICIENT_DATA_AVAILABLE)
 
     def setUp(self):
         random.seed(self.random_seed)
@@ -1269,20 +1269,19 @@ class DiscoveryAgeRangeFilteringIndividualsTest(AuthzAPITestCase):
 
     @staticmethod
     def response_threshold_check(response):
-        return response["count"] if "count" in response else dres.INSUFFICIENT_DATA_AVAILABLE
+        return response.get("count", dres.INSUFFICIENT_DATA_AVAILABLE)
 
     def setUp(self):
         individuals = [c.generate_valid_individual(gen_random_age=(1, 100)) for _ in range(self.random_range)]
         for individual in individuals:
             Individual.objects.create(**individual)
 
         for individual in Individual.objects.all():
-            if individual.time_at_last_encounter:
-                if "age" in individual.time_at_last_encounter:
-                    age_numeric, age_unit = iso_duration_to_years(individual.time_at_last_encounter["age"])
-                    individual.age_numeric = age_numeric
-                    individual.age_unit = age_unit if age_unit else ""
-                    individual.save()
+            if individual.time_at_last_encounter and "age" in individual.time_at_last_encounter:
+                age_numeric, age_unit = iso_duration_to_years(individual.time_at_last_encounter["age"])
+                individual.age_numeric = age_numeric
+                individual.age_unit = age_unit if age_unit else ""
+                individual.save()
 
     @override_settings(CONFIG_PUBLIC=DISCOVERY_CONFIG_TEST)
     def test_discovery_filtering_age_range(self):

chord_metadata_service/patients/tests/test_models.py

@@ -1,10 +1,10 @@
 from chord_metadata_service.chord.tests.helpers import ProjectTestCase
-from chord_metadata_service.phenopackets.tests import constants as c
 from chord_metadata_service.phenopackets import models as m
+from chord_metadata_service.phenopackets.tests import constants as c
 from chord_metadata_service.restapi.models import SchemaType
 
-from ..models import Individual, VitalStatus
 from ..filters import IndividualFilter
+from ..models import Individual, VitalStatus
 
 
 class IndividualTest(ProjectTestCase):

chord_metadata_service/patients/values.py

@@ -1,6 +1,5 @@
 from abc import ABC
 
-
 __all__ = [
     "Sex",
     "KaryotypicSex",

chord_metadata_service/utils.py

@@ -1,18 +1,19 @@
+from typing import Any
+
 from django.db.models import Model, QuerySet
-from typing import Any, Set, Type
 
 __all__ = [
     "build_id_set",
     "build_id_set_from_model",
 ]
 
 
-async def build_id_set(qs: QuerySet, field: str) -> Set[Any]:
+async def build_id_set(qs: QuerySet, field: str) -> set[Any]:
     s = set()
     async for v in qs.values_list(field, flat=True):
         s.add(v)
     return s
 
 
-async def build_id_set_from_model(m: Type[Model], field: str) -> Set[Any]:
+async def build_id_set_from_model(m: type[Model], field: str) -> set[Any]:
     return await build_id_set(m.objects.all(), field)

docs/conf.py

@@ -14,11 +14,11 @@
 import datetime
 import os
 import sys
+from pathlib import Path
+
 import django
 import toml
 
-from pathlib import Path
-
 sys.path.insert(0, os.path.abspath(".."))
 os.environ["DJANGO_SETTINGS_MODULE"] = "chord_metadata_service.metadata.settings"
 django.setup()

scripts/ingest.py

@@ -1,5 +1,6 @@
-import sys
 import json
+import sys
+
 import requests
 
 """
@@ -47,19 +48,15 @@ def create_project(katsu_server_url, project_title):
     try:
         r = requests.post(katsu_server_url + "/api/projects", json=project_request)
     except requests.exceptions.ConnectionError:
-        print("Connection to the API server {} cannot be established.".format(katsu_server_url))
+        print(f"Connection to the API server {katsu_server_url} cannot be established.")
         sys.exit()
 
     if r.status_code == 201:
         project_uuid = r.json()["identifier"]
-        print("Project {} with uuid {} has been created!".format(project_title, project_uuid))
+        print(f"Project {project_title} with uuid {project_uuid} has been created!")
         return project_uuid
     elif r.status_code == 400:
-        print(
-            "A project of title '{}' exists, please choose a different title, or delete this project.".format(
-                project_title
-            )
-        )
+        print(f"A project of title '{project_title}' exists, please choose a different title, or delete this project.")
         sys.exit()
     else:
         print(r.json())
@@ -88,14 +85,10 @@ def create_dataset(katsu_server_url, project_uuid, dataset_title):
 
     if r2.status_code == 201:
         dataset_uuid = r2.json()["identifier"]
-        print("Dataset {} with uuid {} has been created!".format(dataset_title, dataset_uuid))
+        print(f"Dataset {dataset_title} with uuid {dataset_uuid} has been created!")
         return dataset_uuid
     elif r2.status_code == 400:
-        print(
-            "A dataset of title '{}' exists, please choose a different title, or delete this dataset.".format(
-                dataset_title
-            )
-        )
+        print(f"A dataset of title '{dataset_title}' exists, please choose a different title, or delete this dataset.")
         sys.exit()
     else:
         print(r2.json())
@@ -115,7 +108,7 @@ def create_table(katsu_server_url, dataset_uuid, table_name):
 
     if r3.status_code == 200 or r3.status_code == 201:
         table_id = r3.json()["id"]
-        print("Table {} with uuid {} has been created!".format(table_name, table_id))
+        print(f"Table {table_name} with uuid {table_id} has been created!")
         return table_id
     else:
         print("Something went wrong...")
@@ -139,7 +132,7 @@ def ingest_phenopackets(katsu_server_url, table_id, phenopackets_json_location):
     r4 = requests.post(katsu_server_url + "/private/ingest", json=private_ingest_request)
 
     if r4.status_code == 200 or r4.status_code == 201 or r4.status_code == 204:
-        print("Phenopackets have been ingested from source at {}".format(phenopackets_json_location))
+        print(f"Phenopackets have been ingested from source at {phenopackets_json_location}")
     elif r4.status_code == 400:
         print(r4.text)
         sys.exit()
@@ -165,7 +158,7 @@ def main():
         katsu_server_url = config["katsu_server_url"]
         phenopackets_json_location = config["phenopackets_json_location"]
     except KeyError as e:
-        print("Config file corrupted: missing key {}".format(str(e)))
+        print(f"Config file corrupted: missing key {e!s}")
         sys.exit()
 
     project_uuid = create_project(katsu_server_url, project_title)

scripts/remove_from_db.py

@@ -1,5 +1,5 @@
-import sys
 import subprocess
+import sys
 
 """
 A script that automates the process of deleting the data
@@ -26,15 +26,16 @@ def main():
 
     for table in sys.argv[1:]:
         response = subprocess.run(
-            'python ../manage.py shell --command="{}"'.format(script + "{}.objects.all().delete();".format(table)),
+            'python ../manage.py shell --command="{}"'.format(script + f"{table}.objects.all().delete();"),
             shell=True,
             stderr=subprocess.PIPE,
+            check=False,
         )
         if response.returncode:
             print(response.stderr)
-            print('"{}" does not seem to be a valid table'.format(table))
+            print(f'"{table}" does not seem to be a valid table')
         else:
-            print("Deleted data on table {}".format(table))
+            print(f"Deleted data on table {table}")
 
 
 if __name__ == "__main__":