feat: upgrade to sodar core v1 (#1973)

backend/beaconsite/tests/test_views.py

@@ -4,10 +4,10 @@
 from django.urls import reverse
 
 from beaconsite.models import Consortium, Site
-from variants.tests.helpers import ViewTestBase
+from variants.tests.helpers import TestViewsBase
 
 
-class TestIndexView(ViewTestBase):
+class TestIndexView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(reverse("beaconsite:index"))
@@ -18,7 +18,7 @@ def test_render(self):
         self.assertEqual(response.context["site_list"][0].pk, self.site.pk)
 
 
-class TestConsortiumListView(ViewTestBase):
+class TestConsortiumListView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(reverse("beaconsite:consortium-list"))
@@ -27,7 +27,7 @@ def test_render(self):
         self.assertEqual(response.context["object_list"][0].pk, self.consortium.pk)
 
 
-class TestConsortiumCreateView(ViewTestBase):
+class TestConsortiumCreateView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(reverse("beaconsite:consortium-create"))
@@ -60,7 +60,7 @@ def test_create(self):
         self.assertEqual(Consortium.objects.count(), 2)
 
 
-class TestConsortiumUpdateView(ViewTestBase):
+class TestConsortiumUpdateView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(
@@ -110,7 +110,7 @@ def test_update(self):
         self.assertEqual([self.project.pk], [p.pk for p in self.consortium.projects.all()])
 
 
-class TestConsortiumDeleteView(ViewTestBase):
+class TestConsortiumDeleteView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(
@@ -139,7 +139,7 @@ def test_delete(self):
         self.assertEqual(Consortium.objects.all().count(), 0)
 
 
-class TestSiteListView(ViewTestBase):
+class TestSiteListView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(reverse("beaconsite:site-list"))
@@ -148,7 +148,7 @@ def test_render(self):
         self.assertEqual(response.context["object_list"][0].pk, self.site.pk)
 
 
-class TestSiteCreateView(ViewTestBase):
+class TestSiteCreateView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(reverse("beaconsite:site-create"))
@@ -184,7 +184,7 @@ def test_create(self):
         self.assertEqual(Site.objects.count(), 2)
 
 
-class TestSiteUpdateView(ViewTestBase):
+class TestSiteUpdateView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(
@@ -246,7 +246,7 @@ def test_update(self):
         self.assertEqual([self.consortium.pk], [s.pk for s in self.site.consortia.all()])
 
 
-class TestSiteDeleteView(ViewTestBase):
+class TestSiteDeleteView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(

backend/cases_import/models/executors.py

@@ -136,7 +136,7 @@ def __init__(self, project: Project):
     def _build_fs_options(self, project: Project) -> FileSystemOptions:
         """Build `FileSystemOptions` from project settings."""
         app_settings = AppSettingAPI()
-        kwargs = {"app_name": "cases_import", "project": project}
+        kwargs = {"plugin_name": "cases_import", "project": project}
 
         path = app_settings.get(setting_name="import_data_path", **kwargs) or None
         if not path:

backend/cases_import/tests/test_models_executor.py

@@ -51,7 +51,7 @@ def _setUpExecutor(self, action, fac_kwargs=None):
 
         app_settings = AppSettingAPI()
         app_settings.set(
-            app_name="cases_import",
+            plugin_name="cases_import",
             setting_name="import_data_protocol",
             value="file",
             project=self.project,

backend/cases_qc/tests/test_views_api.py

@@ -91,7 +91,7 @@ def _setUpExecutor(self, fac_kwargs: typing.Dict[str, str]):
 
         app_settings = AppSettingAPI()
         app_settings.set(
-            app_name="cases_import",
+            plugin_name="cases_import",
             setting_name="import_data_protocol",
             value="file",
             project=self.project,

backend/genepanels/forms.py

@@ -24,8 +24,11 @@ def __init__(self, *args, **kwargs):
         self.fields["genes"] = self._build_genes_field()
 
     def _build_genes_field(self):
-        rows = [entry.symbol for entry in self.instance.genepanelentry_set.all()]
-        initial_value = "\n".join(rows)
+        if self.instance.pk:
+            rows = [entry.symbol for entry in self.instance.genepanelentry_set.all()]
+            initial_value = "\n".join(rows)
+        else:
+            initial_value = ""
         return forms.CharField(
             label="Genes",
             widget=forms.Textarea,

backend/genepanels/tests/test_models.py

@@ -24,7 +24,9 @@ def test_create(self):
 
     def test_get_absolute_url(self):
         category = GenePanelCategoryFactory()
-        self.assertEqual(category.get_absolute_url(), f"/genepanels/category/{category.sodar_uuid}")
+        self.assertEqual(
+            category.get_absolute_url(), f"/genepanels/category/{category.sodar_uuid}/"
+        )
 
     def test_str(self):
         category = GenePanelCategoryFactory()
@@ -46,7 +48,7 @@ def test_create(self):
 
     def test_get_absolute_url(self):
         panel = GenePanelFactory()
-        self.assertEqual(panel.get_absolute_url(), f"/genepanels/panel/{panel.sodar_uuid}")
+        self.assertEqual(panel.get_absolute_url(), f"/genepanels/panel/{panel.sodar_uuid}/")
 
     def test_get_hgnc_list(self):
         panel = GenePanelFactory()

backend/genepanels/tests/test_views.py

@@ -10,7 +10,7 @@
     GenePanelEntryFactory,
     GenePanelFactory,
 )
-from variants.tests.helpers import ViewTestBase
+from variants.tests.helpers import TestViewsBase
 
 ANNONARS_GENE_RESPONSE = {
     "TTN": {
@@ -54,7 +54,7 @@ def _set_annonars_mocker(self, mock_):
         )
 
 
-class IndexViewTest(ViewTestBase):
+class IndexViewTest(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.panel = GenePanelFactory()
@@ -67,7 +67,7 @@ def test_render(self):
         self.assertEquals(response.context["show_retired"], False)
 
 
-class GenePanelCategoryListView(ViewTestBase):
+class GenePanelCategoryListView(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.panel = GenePanelFactory()
@@ -88,7 +88,7 @@ def test_render_show_retired(self):
         self.assertEquals(response.context["show_retired"], True)
 
 
-class GenePanelCategoryCreateView(ViewTestBase):
+class GenePanelCategoryCreateView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(reverse("genepanels:category-create"))
@@ -117,7 +117,7 @@ def test_create(self):
         self.assertEqual(GenePanelCategory.objects.count(), 1)
 
 
-class GenePanelCategoryUpdateView(ViewTestBase):
+class GenePanelCategoryUpdateView(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.panel = GenePanelFactory()
@@ -164,7 +164,7 @@ def test_update(self):
             self.assertEqual(getattr(self.category, key), post_data[key])
 
 
-class GenePanelCategoryDeleteView(ViewTestBase):
+class GenePanelCategoryDeleteView(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.category = GenePanelCategoryFactory()
@@ -197,7 +197,7 @@ def test_delete(self):
         self.assertEqual(GenePanelCategory.objects.all().count(), 0)
 
 
-class GenePanelCreateView(AnnonarsMockerMixin, ViewTestBase):
+class GenePanelCreateView(AnnonarsMockerMixin, TestViewsBase):
     def setUp(self):
         super().setUp()
         self.category = GenePanelCategoryFactory()
@@ -300,7 +300,7 @@ def test_create_with_gene_list_including_nonexistent_gene(self, mock):
         )
 
 
-class GenePanelUpdateView(AnnonarsMockerMixin, ViewTestBase):
+class GenePanelUpdateView(AnnonarsMockerMixin, TestViewsBase):
     def setUp(self):
         super().setUp()
         self.panel = GenePanelFactory(state=GenePanelState.DRAFT.value)
@@ -356,7 +356,7 @@ def test_update(self, mock):
         self.assertEqual(self.panel.category, self.category)
 
 
-class GenePanelDeleteView(ViewTestBase):
+class GenePanelDeleteView(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.panel = GenePanelFactory(state=GenePanelState.DRAFT.value)
@@ -437,7 +437,7 @@ def test_post_non_draft_state(self, state):
         self.assertEqual(GenePanel.objects.count(), 1)
 
 
-class GenePanelReleaseView(ViewTestBase):
+class GenePanelReleaseView(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.panel = GenePanelFactory(state=GenePanelState.DRAFT.value, version_minor=2)
@@ -527,7 +527,7 @@ def test_post_non_draft_state(self, state):
         self.assertEqual(self.old_panel.state, GenePanelState.ACTIVE.value)
 
 
-class GenePanelRetireView(ViewTestBase):
+class GenePanelRetireView(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.panel = GenePanelFactory(state=GenePanelState.ACTIVE.value, version_minor=2)
@@ -608,7 +608,7 @@ def test_post_non_active_state(self, state):
         self.assertEqual(self.panel.state, state)
 
 
-class GenePanelCopyAsDraftView(ViewTestBase):
+class GenePanelCopyAsDraftView(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.panel = GenePanelFactory(state=GenePanelState.ACTIVE.value, version_minor=2)

backend/seqmeta/tests/test_models.py

@@ -12,7 +12,7 @@ def test_create(self):
 
     def test_get_absolute_url(self):
         kit = EnrichmentKitFactory()
-        self.assertEqual(kit.get_absolute_url(), f"/seqmeta/enrichmentkit/{kit.sodar_uuid}")
+        self.assertEqual(kit.get_absolute_url(), f"/seqmeta/enrichmentkit/{kit.sodar_uuid}/")
 
     def test_str(self):
         kit = EnrichmentKitFactory()

backend/seqmeta/tests/test_views.py

@@ -1,10 +1,10 @@
 from django.urls import reverse
 
 from seqmeta.tests.factories import TargetBedFileFactory
-from variants.tests.helpers import ViewTestBase
+from variants.tests.helpers import TestViewsBase
 
 
-class IndexViewTest(ViewTestBase):
+class IndexViewTest(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.targetbedfile = TargetBedFileFactory()
@@ -17,7 +17,7 @@ def test_render(self):
         self.assertEqual(response.context["object_list"].count(), 1)
 
 
-class EnrichmentKitListViewTest(ViewTestBase):
+class EnrichmentKitListViewTest(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.targetbedfile = TargetBedFileFactory()
@@ -30,7 +30,7 @@ def test_render(self):
         self.assertEqual(response.context["object_list"].count(), 1)
 
 
-class EnrichmentKitDetailView(ViewTestBase):
+class EnrichmentKitDetailView(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.targetbedfile = TargetBedFileFactory()

backend/varannos/tests/test_models.py

@@ -17,7 +17,7 @@ def test_create(self):
 
     def test_get_absolute_url(self):
         obj = VarAnnoSetFactory()
-        self.assertEqual(obj.get_absolute_url(), f"/varannos/varannoset/details/{obj.sodar_uuid}")
+        self.assertEqual(obj.get_absolute_url(), f"/varannos/varannoset/details/{obj.sodar_uuid}/")
 
     def test_days_since_modification(self):
         with freeze_time((datetime.now() - timedelta(days=10)).strftime("%Y-%m-%d")):

backend/varannos/tests/test_views.py

@@ -1,10 +1,10 @@
 from django.urls import reverse
 
 from varannos.tests.factories import VarAnnoSetFactory
-from variants.tests.helpers import ViewTestBase
+from variants.tests.helpers import TestViewsBase
 
 
-class TestVarAnnoSetListView(ViewTestBase):
+class TestVarAnnoSetListView(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.varannoset = VarAnnoSetFactory(project=self.project)
@@ -18,7 +18,7 @@ def test_render(self):
         self.assertIsNotNone(response.context["object_list"])
 
 
-class TestVarAnnoSetDetailView(ViewTestBase):
+class TestVarAnnoSetDetailView(TestViewsBase):
     def setUp(self):
         super().setUp()
         self.varannoset = VarAnnoSetFactory(project=self.project)

backend/varfish/users/management/commands/initdev.py

@@ -282,7 +282,7 @@ def _create_project(
             for setting_name, value in setting_value.items():
                 if project_settings.get(setting_name) != value:
                     app_settings.set(
-                        app_name="cases_import",
+                        plugin_name="cases_import",
                         setting_name=setting_name,
                         value=value,
                         project=project,