Update tests

Author: dglemos

gene2phenotype_project/gene2phenotype_app/tests/delete_data/test_delete_lgd.py

@@ -45,6 +45,7 @@ class LGDDeleteLGDEndpoint(TestCase):
         "gene2phenotype_app/fixtures/lgd_phenotype.json",
         "gene2phenotype_app/fixtures/lgd_phenotype_summary.json",
         "gene2phenotype_app/fixtures/lgd_variant_type.json",
+        "gene2phenotype_app/fixtures/lgd_variant_type_publication.json",
         "gene2phenotype_app/fixtures/lgd_variant_type_comment.json",
         "gene2phenotype_app/fixtures/lgd_variant_type_description.json",
         "gene2phenotype_app/fixtures/lgd_variant_consequence.json",

gene2phenotype_project/gene2phenotype_app/tests/delete_data/test_delete_lgd_publication.py

@@ -8,6 +8,7 @@
     LGDPhenotype,
     LGDPhenotypeSummary,
     LGDVariantType,
+    LGDVariantTypePublication,
     LGDVariantTypeComment,
     LGDVariantTypeDescription,
     LGDMolecularMechanismEvidence,
@@ -44,6 +45,7 @@ class LGDDeletePublication(TestCase):
         "gene2phenotype_app/fixtures/lgd_phenotype.json",
         "gene2phenotype_app/fixtures/lgd_phenotype_summary.json",
         "gene2phenotype_app/fixtures/lgd_variant_type.json",
+        "gene2phenotype_app/fixtures/lgd_variant_type_publication.json",
         "gene2phenotype_app/fixtures/lgd_variant_type_comment.json",
         "gene2phenotype_app/fixtures/lgd_variant_type_description.json",
         "gene2phenotype_app/fixtures/lgd_variant_consequence.json",
@@ -232,12 +234,12 @@ def test_lgd_publication_delete(self):
         )
         self.assertEqual(len(lgd_phenotype_summary), 1)
 
-        lgd_variant_type = LGDVariantType.objects.filter(
-            lgd__stable_id__stable_id="G2P00002",
+        lgd_variant_type_publications = LGDVariantTypePublication.objects.filter(
+            lgd_variant_type__lgd__stable_id__stable_id="G2P00002",
             publication__pmid=15214012,
             is_deleted=1,
         )
-        self.assertEqual(len(lgd_variant_type), 3)
+        self.assertEqual(len(lgd_variant_type_publications), 3)
 
         lgd_variant_description = LGDVariantTypeDescription.objects.filter(
             lgd__stable_id__stable_id="G2P00002",

gene2phenotype_project/gene2phenotype_app/tests/delete_data/test_delete_lgd_variant_type.py

@@ -29,6 +29,7 @@ class LGDEditVariantTypesEndpoint(TestCase):
         "gene2phenotype_app/fixtures/source.json",
         "gene2phenotype_app/fixtures/lgd_publication.json",
         "gene2phenotype_app/fixtures/lgd_variant_type.json",
+        "gene2phenotype_app/fixtures/lgd_variant_type_publication.json",
     ]
 
     def setUp(self):

gene2phenotype_project/gene2phenotype_app/tests/delete_data/test_delete_lgd_variant_type_description.py

@@ -29,6 +29,7 @@ class LGDEditVariantTypeDescriptionEndpoint(TestCase):
         "gene2phenotype_app/fixtures/source.json",
         "gene2phenotype_app/fixtures/lgd_publication.json",
         "gene2phenotype_app/fixtures/lgd_variant_type.json",
+        "gene2phenotype_app/fixtures/lgd_variant_type_publication.json",
         "gene2phenotype_app/fixtures/lgd_variant_type_description.json",
     ]
 

gene2phenotype_project/gene2phenotype_app/tests/insert_data/test_add_variant_types.py

@@ -6,6 +6,8 @@
 from gene2phenotype_app.models import (
     User,
     LGDVariantType,
+    LGDVariantTypePublication,
+    LGDVariantTypeComment,
     LocusGenotypeDisease,
     OntologyTerm,
 )
@@ -33,6 +35,7 @@ class LGDEditVariantTypesTests(TestCase):
         "gene2phenotype_app/fixtures/source.json",
         "gene2phenotype_app/fixtures/lgd_publication.json",
         "gene2phenotype_app/fixtures/lgd_variant_type.json",
+        "gene2phenotype_app/fixtures/lgd_variant_type_publication.json",
     ]
 
     def setUp(self):
@@ -233,6 +236,10 @@ def test_readd_soft_deleted_variant_updates_inheritance_flags(self):
             inherited=True,
             de_novo=True,
             unknown_inheritance=True,
+            is_deleted=1,
+        )
+        LGDVariantTypePublication.objects.create(
+            lgd_variant_type=lgd_variant,
             publication_id=3,
             is_deleted=1,
         )
@@ -263,11 +270,16 @@ def test_readd_soft_deleted_variant_updates_inheritance_flags(self):
         self.assertFalse(lgd_variant.inherited)
         self.assertFalse(lgd_variant.de_novo)
         self.assertFalse(lgd_variant.unknown_inheritance)
+        self.assertTrue(
+            LGDVariantTypePublication.objects.filter(
+                lgd_variant_type=lgd_variant, publication_id=3, is_deleted=0
+            ).exists()
+        )
 
     def test_reuse_existing_row_with_new_publication_updates_inheritance_flags(self):
         """
-        Test that converting an existing publication-less row into a
-        publication-linked row replaces inheritance flags with the latest payload.
+        Test that adding a publication link to an existing publication-less
+        variant type replaces inheritance flags with the latest payload.
         """
         user = User.objects.get(email="john@test.ac.uk")
         refresh = RefreshToken.for_user(user)
@@ -281,7 +293,6 @@ def test_reuse_existing_row_with_new_publication_updates_inheritance_flags(self)
             inherited=True,
             de_novo=True,
             unknown_inheritance=True,
-            publication=None,
             is_deleted=0,
         )
 
@@ -307,7 +318,69 @@ def test_reuse_existing_row_with_new_publication_updates_inheritance_flags(self)
         self.assertEqual(response.status_code, 201)
 
         lgd_variant.refresh_from_db()
-        self.assertEqual(lgd_variant.publication_id, 3)
+        self.assertTrue(
+            LGDVariantTypePublication.objects.filter(
+                lgd_variant_type=lgd_variant, publication_id=3, is_deleted=0
+            ).exists()
+        )
         self.assertFalse(lgd_variant.inherited)
         self.assertFalse(lgd_variant.de_novo)
         self.assertFalse(lgd_variant.unknown_inheritance)
+
+    def test_add_variant_type_with_multiple_publications_no_duplication(self):
+        """
+        Test that adding a variant type supported by more than one publication
+        creates exactly one LGDVariantType row, one LGDVariantTypePublication
+        row per publication, and does not duplicate the comment.
+        """
+        user = User.objects.get(email="john@test.ac.uk")
+        refresh = RefreshToken.for_user(user)
+        access_token = str(refresh.access_token)
+        self.client.cookies[settings.SIMPLE_JWT["AUTH_COOKIE"]] = access_token
+
+        payload = {
+            "variant_types": [
+                {
+                    "comment": "supported by two papers",
+                    "de_novo": False,
+                    "inherited": True,
+                    "primary_type": "protein_changing",
+                    "secondary_type": "stop_gained",
+                    "supporting_papers": ["12451214", "20512146"],
+                    "unknown_inheritance": False,
+                }
+            ]
+        }
+
+        response = self.client.post(
+            self.url_add_variant,
+            payload,
+            content_type="application/json",
+        )
+        self.assertEqual(response.status_code, 201)
+
+        stop_gained = OntologyTerm.objects.get(term="stop_gained")
+        lgd_variant_qs = LGDVariantType.objects.filter(
+            lgd__stable_id__stable_id="G2P00002",
+            variant_type_ot=stop_gained,
+            is_deleted=0,
+        )
+        self.assertEqual(len(lgd_variant_qs), 1)
+
+        lgd_variant = lgd_variant_qs.first()
+        lgd_variant_publications = LGDVariantTypePublication.objects.filter(
+            lgd_variant_type=lgd_variant, is_deleted=0
+        )
+        self.assertEqual(len(lgd_variant_publications), 2)
+        self.assertEqual(
+            set(lgd_variant_publications.values_list("publication__pmid", flat=True)),
+            {12451214, 20512146},
+        )
+
+        lgd_variant_comments = LGDVariantTypeComment.objects.filter(
+            lgd_variant_type=lgd_variant, is_deleted=0
+        )
+        self.assertEqual(len(lgd_variant_comments), 1)
+        self.assertEqual(
+            lgd_variant_comments.first().comment, "supported by two papers"
+        )

gene2phenotype_project/gene2phenotype_app/tests/update_data/test_merge_records.py

@@ -41,6 +41,7 @@ class LGDEditPublicationsEndpoint(TestCase):
         "gene2phenotype_app/fixtures/lgd_phenotype.json",
         "gene2phenotype_app/fixtures/lgd_variant_consequence.json",
         "gene2phenotype_app/fixtures/lgd_variant_type.json",
+        "gene2phenotype_app/fixtures/lgd_variant_type_publication.json",
         "gene2phenotype_app/fixtures/lgd_variant_type_comment.json",
     ]
 
@@ -190,11 +191,16 @@ def test_merge_records(self):
             stable_id=stable_id_obj.id, is_deleted=0
         )
         # Check if all variant types were merged correctly
+        # Note: a variant type is unique per (lgd, variant_type_ot), so the source
+        # record's "intron_variant" row is skipped during the merge since the
+        # target record already has one (with a different supporting publication)
         lgd_variant_type_list = LGDVariantType.objects.filter(lgd=lgd_obj.id)
-        self.assertEqual(len(lgd_variant_type_list), 3)
+        self.assertEqual(len(lgd_variant_type_list), 2)
         for variant_type in lgd_variant_type_list:
             if (
-                variant_type.publication.id == 1
+                variant_type.publications.filter(
+                    publication_id=1, is_deleted=0
+                ).exists()
                 and variant_type.variant_type_ot.term == "intron_variant"
             ):
                 variant_type_comment_list = LGDVariantTypeComment.objects.filter(