refactor: migrate seqvars to TanStack Query (#2090) (#2094)

varfish-org · Nov 7, 2024 · 24475ba · 24475ba
1 parent cb16a6e
commit 24475ba
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Showing 32 changed files with 5,204 additions and 1,681 deletions.
diff --git a/backend/seqvars/models/base.py b/backend/seqvars/models/base.py
@@ -613,6 +613,7 @@ def clone_with_presetsset(
         # First, handle the "normal" presets categories.  A side-effect of the
         # code below is that the UUIDs of the presets are changed and we rely
         # on this when createing the predefined queries.
+        uuid_old_to_new = {}
         for key in (
             "seqvarsquerypresetsfrequency_set",
             "seqvarsquerypresetsvariantprio_set",
@@ -628,6 +629,7 @@ def clone_with_presetsset(
                 obj.id = None
                 obj._state.adding = True
                 new_uuid = uuid_object.uuid4()
+                uuid_old_to_new[obj.sodar_uuid] = new_uuid
                 obj.sodar_uuid = new_uuid
                 obj.presetssetversion = result
                 obj.save()
@@ -640,28 +642,28 @@ def clone_with_presetsset(
             obj.sodar_uuid = uuid_object.uuid4()
             obj.presetssetversion = result
             obj.quality = SeqvarsQueryPresetsQuality.objects.get(
-                sodar_uuid=obj.quality.sodar_uuid,
+                sodar_uuid=uuid_old_to_new[obj.quality.sodar_uuid],
             )
             obj.frequency = SeqvarsQueryPresetsFrequency.objects.get(
-                sodar_uuid=obj.frequency.sodar_uuid,
+                sodar_uuid=uuid_old_to_new[obj.frequency.sodar_uuid],
             )
             obj.consequence = SeqvarsQueryPresetsConsequence.objects.get(
-                sodar_uuid=obj.consequence.sodar_uuid,
+                sodar_uuid=uuid_old_to_new[obj.consequence.sodar_uuid],
             )
             obj.locus = SeqvarsQueryPresetsLocus.objects.get(
-                sodar_uuid=obj.locus.sodar_uuid,
+                sodar_uuid=uuid_old_to_new[obj.locus.sodar_uuid],
             )
             obj.phenotypeprio = SeqvarsQueryPresetsPhenotypePrio.objects.get(
-                sodar_uuid=obj.phenotypeprio.sodar_uuid,
+                sodar_uuid=uuid_old_to_new[obj.phenotypeprio.sodar_uuid],
             )
             obj.variantprio = SeqvarsQueryPresetsVariantPrio.objects.get(
-                sodar_uuid=obj.variantprio.sodar_uuid,
+                sodar_uuid=uuid_old_to_new[obj.variantprio.sodar_uuid],
             )
             obj.clinvar = SeqvarsQueryPresetsClinvar.objects.get(
-                sodar_uuid=obj.clinvar.sodar_uuid,
+                sodar_uuid=uuid_old_to_new[obj.clinvar.sodar_uuid],
             )
             obj.columns = SeqvarsQueryPresetsColumns.objects.get(
-                sodar_uuid=obj.columns.sodar_uuid,
+                sodar_uuid=uuid_old_to_new[obj.columns.sodar_uuid],
             )
             obj.save()
 

diff --git a/backend/seqvars/tests/test_models.py b/backend/seqvars/tests/test_models.py
@@ -126,6 +126,7 @@ def test_clone_factory_default(self):
         # Note: only smoke test implemented so far.
         project = ProjectFactory()
         querypresetset = create_seqvarspresetsset_short_read_genome()
+        querypresetset.save()
         querypresetset.clone_with_latest_version(project=project)
 
 

diff --git a/backend/seqvars/tests/test_permissions_api.py b/backend/seqvars/tests/test_permissions_api.py
@@ -2134,6 +2134,7 @@ def cleanup():
     def test_create_from(self):
         # TODO: change after https://github.com/varfish-org/varfish-server/issues/1920
         presetsset_factory = create_seqvarspresetsset_short_read_exome_legacy()
+        presetsset_factory.save()
         presetsset = presetsset_factory.clone_with_latest_version(project=self.project)
         version = presetsset.versions.all()[0]
         predefinedquery = version.seqvarspredefinedquery_set.all()[0]

diff --git a/backend/seqvars/tests/test_views_api.py b/backend/seqvars/tests/test_views_api.py
@@ -2033,6 +2033,7 @@ def test_create_from(self):
         with self.login(self.superuser):
             # TODO: change after https://github.com/varfish-org/varfish-server/issues/1920
             presetsset_factory = create_seqvarspresetsset_short_read_exome_legacy()
+            presetsset_factory.save()
             presetsset = presetsset_factory.clone_with_latest_version(project=self.project)
             version = presetsset.versions.all()[0]
             predefinedquery = version.seqvarspredefinedquery_set.all()[0]

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
diff --git a/frontend/package.json b/frontend/package.json
@@ -40,6 +40,7 @@
     "jquery": "^3.7.1",
     "lodash.debounce": "^4.0.8",
     "luxon": "^3.5.0",
+    "object-deep-merge": "^1.0.4",
     "pinia": "^2.2.2",
     "plotly.js-dist": "^2.34.0",
     "remeda": "^2.6.0",