SCKAN-275 feat: Update models

MetaCell · Mar 20, 2024 · 40f20b9 · 40f20b9
1 parent 776237e
commit 40f20b9
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Showing 9 changed files with 179 additions and 178 deletions.
diff --git a/backend/composer/admin.py b/backend/composer/admin.py
@@ -19,7 +19,8 @@
     Tag,
     Via,
     FunctionalCircuitRole,
-    ProjectionPhenotype, Destination, Synonym, AnatomicalEntityMeta, Layer, Region, AnatomicalEntityIntersection
+    ProjectionPhenotype, Destination, Synonym, AnatomicalEntityMeta, Layer, Region, AnatomicalEntityIntersection,
+    AnatomicalEntity
 )
 
 
@@ -117,10 +118,9 @@ class AnatomicalEntityIntersectionAdmin(admin.ModelAdmin):
     raw_id_fields = ('layer', 'region',)
 
 
-class AnatomicalEntityAdmin(admin.ModelAdmin):
-    list_display = ('name', 'ontology_uri', 'region_layer',)
-    search_fields = ('name',)
-    raw_id_fields = ('region_layer',)
+class AnatomicalEntityNewAdmin(admin.ModelAdmin):
+    raw_id_fields = ('simple_entity', 'region_layer')
+    search_fields = ('simple_entity', 'region_layer')
     inlines = [SynonymInline]
 
 
@@ -232,7 +232,7 @@ def get_form(self, request, obj=None, change=False, **kwargs):
 admin.site.register(Layer, LayerAdmin)
 admin.site.register(Region, RegionAdmin)
 admin.site.register(AnatomicalEntityIntersection, AnatomicalEntityIntersectionAdmin)
-admin.site.register(AnatomicalEntity, AnatomicalEntityAdmin)
+admin.site.register(AnatomicalEntity, AnatomicalEntityNewAdmin)
 admin.site.register(Phenotype)
 admin.site.register(Sex)
 admin.site.register(ConnectivityStatement, ConnectivityStatementAdmin)

diff --git a/backend/composer/management/commands/ingest_statements.py b/backend/composer/management/commands/ingest_statements.py
@@ -13,13 +13,19 @@ def add_arguments(self, parser):
             action='store_true',
             help='Set this flag to update upstream statements.',
         )
+        parser.add_argument(
+            '--update_anatomic_entities',
+            action='store_true',
+            help='Set this flag to try move anatomical entities to specific layer, region.',
+        )
 
     def handle(self, *args, **options):
         update_upstream = options['update_upstream']
+        update_anatomic_entities = options['update_anatomic_entities']
 
         start_time = time.time()
 
-        ingest_statements(update_upstream)
+        ingest_statements(update_upstream, update_anatomic_entities)
 
         end_time = time.time()
 

diff --git a/...nd/composer/migrations/0046_anatomicalentityintersection_anatomicalentitymeta_and_more.py b/...nd/composer/migrations/0046_anatomicalentityintersection_anatomicalentitymeta_and_more.py
@@ -1,4 +1,4 @@
-# Generated by Django 4.1.4 on 2024-03-19 14:14
+# Generated by Django 4.1.4 on 2024-03-20 13:39
 
 from django.db import migrations, models
 import django.db.models.deletion
@@ -40,14 +40,19 @@ class Migration(migrations.Migration):
                 ("ontology_uri", models.URLField(unique=True)),
             ],
             options={
-                "verbose_name_plural": "Anatomical Entities",
+                "verbose_name_plural": "Anatomical Entities Meta",
                 "ordering": ["name"],
             },
         ),
         migrations.AlterField(
-            model_name="anatomicalentity",
-            name="ontology_uri",
-            field=models.URLField(),
+            model_name="synonym",
+            name="anatomical_entity",
+            field=models.ForeignKey(
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="synonyms",
+                to="composer.anatomicalentity",
+            ),
         ),
         migrations.CreateModel(
             name="Layer",
@@ -66,42 +71,16 @@ class Migration(migrations.Migration):
             ],
             bases=("composer.anatomicalentitymeta",),
         ),
-        migrations.CreateModel(
-            name="Region",
-            fields=[
-                (
-                    "anatomicalentitymeta_ptr",
-                    models.OneToOneField(
-                        auto_created=True,
-                        on_delete=django.db.models.deletion.CASCADE,
-                        parent_link=True,
-                        primary_key=True,
-                        serialize=False,
-                        to="composer.anatomicalentitymeta",
-                    ),
-                ),
-                (
-                    "layers",
-                    models.ManyToManyField(
-                        through="composer.AnatomicalEntityIntersection",
-                        to="composer.layer",
-                    ),
-                ),
-            ],
-            bases=("composer.anatomicalentitymeta",),
-        ),
         migrations.CreateModel(
             name="AnatomicalEntityNew",
             fields=[
                 (
-                    "anatomicalentitymeta_ptr",
-                    models.OneToOneField(
+                    "id",
+                    models.BigAutoField(
                         auto_created=True,
-                        on_delete=django.db.models.deletion.CASCADE,
-                        parent_link=True,
                         primary_key=True,
                         serialize=False,
-                        to="composer.anatomicalentitymeta",
+                        verbose_name="ID",
                     ),
                 ),
                 (
@@ -112,22 +91,16 @@ class Migration(migrations.Migration):
                         to="composer.anatomicalentityintersection",
                     ),
                 ),
+                (
+                    "simple_entity",
+                    models.OneToOneField(
+                        blank=True,
+                        null=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        to="composer.anatomicalentitymeta",
+                    ),
+                ),
             ],
-            bases=("composer.anatomicalentitymeta",),
-        ),
-        migrations.AddField(
-            model_name="anatomicalentityintersection",
-            name="layer",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE, to="composer.layer"
-            ),
-        ),
-        migrations.AddField(
-            model_name="anatomicalentityintersection",
-            name="region",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE, to="composer.region"
-            ),
         ),
         migrations.AddField(
             model_name="connectivitystatement",
@@ -165,7 +138,7 @@ class Migration(migrations.Migration):
             name="anatomical_entities_new",
             field=models.ManyToManyField(
                 blank=True,
-                related_name="via_connection_layers_new",
+                related_name="via_connection_layers",
                 to="composer.anatomicalentitynew",
             ),
         ),
@@ -174,4 +147,42 @@ class Migration(migrations.Migration):
             name="from_entities_new",
             field=models.ManyToManyField(blank=True, to="composer.anatomicalentitynew"),
         ),
+        migrations.CreateModel(
+            name="Region",
+            fields=[
+                (
+                    "anatomicalentitymeta_ptr",
+                    models.OneToOneField(
+                        auto_created=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        parent_link=True,
+                        primary_key=True,
+                        serialize=False,
+                        to="composer.anatomicalentitymeta",
+                    ),
+                ),
+                (
+                    "layers",
+                    models.ManyToManyField(
+                        through="composer.AnatomicalEntityIntersection",
+                        to="composer.layer",
+                    ),
+                ),
+            ],
+            bases=("composer.anatomicalentitymeta",),
+        ),
+        migrations.AddField(
+            model_name="anatomicalentityintersection",
+            name="layer",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE, to="composer.layer"
+            ),
+        ),
+        migrations.AddField(
+            model_name="anatomicalentityintersection",
+            name="region",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE, to="composer.region"
+            ),
+        ),
     ]
diff --git a/...ser/migrations/0047_auto_20240319_1414.py → ...ser/migrations/0047_auto_20240320_1340.py b/...ser/migrations/0047_auto_20240319_1414.py → ...ser/migrations/0047_auto_20240320_1340.py
@@ -1,23 +1,26 @@
-# Generated by Django 4.1.4 on 2024-03-19 14:07
+# Generated by Django 4.1.4 on 2024-03-20 13:40
 
 from django.db import migrations
 
 
 def copy_anatomical_entities_to_new(apps, schema_editor):
     AnatomicalEntity = apps.get_model('composer', 'AnatomicalEntity')
     AnatomicalEntityNew = apps.get_model('composer', 'AnatomicalEntityNew')
+    AnatomicalEntityMeta = apps.get_model('composer', 'AnatomicalEntityMeta')
     Destination = apps.get_model('composer', 'Destination')
     Via = apps.get_model('composer', 'Via')
     ConnectivityStatement = apps.get_model('composer', 'ConnectivityStatement')
     Synonym = apps.get_model('composer', 'Synonym')
 
     # Copy AnatomicalEntity instances to AnatomicalEntityNew
     for entity in AnatomicalEntity.objects.all():
-        new_entity = AnatomicalEntityNew.objects.create(
+        new_entity_meta = AnatomicalEntityMeta.objects.create(
             name=entity.name,
             ontology_uri=entity.ontology_uri,
         )
 
+        new_entity = AnatomicalEntityNew.objects.create(simple_entity=new_entity_meta)
+
         # Update ManyToMany relationships for Destination
         for destination in Destination.objects.filter(anatomical_entities=entity):
             destination.anatomical_entities_new.add(new_entity)
@@ -46,6 +49,4 @@ class Migration(migrations.Migration):
         ("composer", "0046_anatomicalentityintersection_anatomicalentitymeta_and_more"),
     ]
 
-    operations = [
-        migrations.RunPython(copy_anatomical_entities_to_new),
-    ]
+    operations = [migrations.RunPython(copy_anatomical_entities_to_new), ]
diff --git a/backend/composer/migrations/0048_remove_connectivitystatement_origins_and_more.py b/backend/composer/migrations/0048_remove_connectivitystatement_origins_and_more.py
@@ -1,11 +1,11 @@
-# Generated by Django 4.1.4 on 2024-03-19 16:03
+# Generated by Django 4.1.4 on 2024-03-20 14:13
 
 from django.db import migrations
 
 
 class Migration(migrations.Migration):
     dependencies = [
-        ("composer", "0047_auto_20240319_1414"),
+        ("composer", "0047_auto_20240320_1340"),
     ]
 
     operations = [

diff --git a/backend/composer/migrations/0049_rename_anatomicalentitynew_anatomicalentity_and_more.py b/backend/composer/migrations/0049_rename_anatomicalentitynew_anatomicalentity_and_more.py
@@ -1,4 +1,4 @@
-# Generated by Django 4.1.4 on 2024-03-19 16:08
+# Generated by Django 4.1.4 on 2024-03-20 14:14
 
 from django.db import migrations, models
 import django.db.models.deletion
@@ -19,16 +19,16 @@ class Migration(migrations.Migration):
             old_name="from_entities_new",
             new_name="from_entities",
         ),
+        migrations.RenameField(
+            model_name="via",
+            old_name="anatomical_entities_new",
+            new_name="anatomical_entities",
+        ),
         migrations.RenameField(
             model_name="via",
             old_name="from_entities_new",
             new_name="from_entities",
         ),
-        # Assuming the intention was to rename 'origins_new' to 'origins',
-        # 'anatomical_entities_new' to 'anatomical_entities', and similar for other fields
-        # Note: For ManyToManyFields, if Django's migration system doesn't support direct renaming,
-        # you may need a more complex approach to adjust the intermediary table instead of simple field renaming.
-        # For now, let's assume renaming is what you intended:
         migrations.RenameField(
             model_name="connectivitystatement",
             old_name="origins_new",
@@ -39,19 +39,17 @@ class Migration(migrations.Migration):
             old_name="anatomical_entities_new",
             new_name="anatomical_entities",
         ),
-        migrations.RenameField(
-            model_name="via",
-            old_name="anatomical_entities_new",
-            new_name="anatomical_entities",
-        ),
         migrations.RenameField(
             model_name="synonym",
             old_name="anatomical_entity_new",
             new_name="anatomical_entity",
         ),
+        migrations.AlterUniqueTogether(
+            name="synonym",
+            unique_together=set(),
+        ),
         migrations.AlterUniqueTogether(
             name="synonym",
             unique_together={("anatomical_entity", "name")},
         ),
     ]
-
diff --git a/backend/composer/migrations/0050_alter_anatomicalentity_options_and_more.py b/backend/composer/migrations/0050_alter_anatomicalentity_options_and_more.py