Ran pre commit hooks

analyses/models.py

@@ -27,7 +27,6 @@
 from analyses.base_models.with_downloads_models import WithDownloadsModel
 from emgapiv2.async_utils import anysync_property
 
-
 # Some models associated with MGnify Analyses (MGYS, MGYA etc).
 
 
@@ -106,7 +105,8 @@ async def get_or_create_for_ena_study(self, ena_study_accession):
         )
         return study
 
-class PublicStudyManager(BasePublicStudyManager,  StudyManager):
+
+class PublicStudyManager(BasePublicStudyManager, StudyManager):
     """
     A custom manager that filters out private studies by default.
     """

analyses/tests.py

@@ -9,20 +9,19 @@
 from rest_framework import status
 
 from ena.models import Study as ENAStudy
+
 from .management.commands.import_v5_analysis import logger
-from .models import (
-    Analysis,
-    Assembler,
-    Biome,
-    ComputeResourceHeuristic,
-    Run,
-    Study, )
+from .models import Analysis, Assembler, Biome, ComputeResourceHeuristic, Run, Study
+
 
 def create_analysis(is_private=False):
     run = Run.objects.first()
     return Analysis.objects.create(
-        study=run.study, run=run, ena_study=run.ena_study, sample=run.sample,
-        is_private=is_private
+        study=run.study,
+        run=run,
+        ena_study=run.ena_study,
+        sample=run.sample,
+        is_private=is_private,
     )
 
 
@@ -38,12 +37,12 @@ def test_biome_lineage_path_generator():
     assert Biome.lineage_to_path("root") == "root"
     assert Biome.lineage_to_path("Root") == "root"
     assert (
-            Biome.lineage_to_path("root:Host-associated:Human:Digestive system")
-            == "root.host_associated.human.digestive_system"
+        Biome.lineage_to_path("root:Host-associated:Human:Digestive system")
+        == "root.host_associated.human.digestive_system"
     )
     assert (
-            Biome.lineage_to_path("root:Host-associated:Human:Digestive system (bowel)")
-            == "root.host_associated.human.digestive_system_bowel"
+        Biome.lineage_to_path("root:Host-associated:Human:Digestive system (bowel)")
+        == "root.host_associated.human.digestive_system_bowel"
     )
 
 
@@ -194,7 +193,7 @@ def test_biome_importer(httpx_mock):
 
 @pytest.mark.django_db(transaction=True)
 def test_analysis_inheritance(
-        raw_read_run,
+    raw_read_run,
 ):
     for run in Run.objects.all():
         analysis = Analysis.objects.create(

emgapiv2/test_data_privacy.py

@@ -5,17 +5,21 @@
 from rest_framework import status
 
 from analyses.management.commands.import_v5_analysis import logger
-from analyses.models import Run, Analysis, Study
+from analyses.models import Analysis, Run, Study
 from ena.models import Study as ENAStudy
 
 
 def create_analysis(is_private=False):
     run = Run.objects.first()
     return Analysis.objects.create(
-        study=run.study, run=run, ena_study=run.ena_study, sample=run.sample,
-        is_private=is_private
+        study=run.study,
+        run=run,
+        ena_study=run.ena_study,
+        sample=run.sample,
+        is_private=is_private,
     )
 
+
 @pytest.mark.django_db(transaction=True)
 def test_public_api_studies_endpoint(api_client):
     """Test that public API only returns public studies"""
@@ -28,7 +32,7 @@ def test_public_api_studies_endpoint(api_client):
     response = api_client.get(url)
 
     assert response.status_code == status.HTTP_200_OK
-    assert len(response.json()['items']) == 1  # Only public study
+    assert len(response.json()["items"]) == 1  # Only public study
 
     assert response.json()["items"][0]["accession"] == public_study.accession
 
@@ -44,8 +48,8 @@ def test_public_api_analyses_endpoint(raw_read_run, api_client):
 
     assert response.status_code == status.HTTP_200_OK
     # Only public analysis should be returned
-    assert len(response.json()['items']) == 1
-    assert response.json()['items'][0]["accession"] == public_analysis.accession
+    assert len(response.json()["items"]) == 1
+    assert response.json()["items"][0]["accession"] == public_analysis.accession
 
 
 @pytest.mark.django_db(transaction=True)
@@ -80,10 +84,12 @@ def test_admin_view_analyses(raw_read_run, admin_client):
 
 @pytest.mark.django_db(transaction=True)
 def test_study_manager_methods():
-# def test_manager_methods(raw_read_run):
+    # def test_manager_methods(raw_read_run):
     """Test various manager methods for privacy handling"""
     ena_study = ENAStudy.objects.create(accession="PRJ1", title="Project 1")
-    public_study = Study.objects.create(ena_study=ena_study, title="Public Study", is_private=False)
+    public_study = Study.objects.create(
+        ena_study=ena_study, title="Public Study", is_private=False
+    )
     private_study = Study.objects.create(title="Private Study", is_private=True)
 
     assert Study.objects.count() == 1
@@ -93,6 +99,7 @@ def test_study_manager_methods():
     assert private_studies.count() == 1
     assert private_studies.first() == private_study
 
+
 @pytest.mark.django_db(transaction=True)
 def test_manager_analysis_methods(raw_read_run):
     public_analysis = create_analysis(is_private=False)