Merge pull request #288 from MetaCell/feature/CSCKAN-290

Feature/csckan-290 - change region/layer model to be independent models from AEMeta - and related changes

backend/composer/admin.py

@@ -98,11 +98,15 @@ class SentenceAdmin(
     )
 
 class AnatomicalEntityAdmin(admin.ModelAdmin):
-    search_fields = ('simple_entity__name', 'region_layer__layer__name', 'region_layer__region__name')
-    autocomplete_fields = ('simple_entity', 'region_layer')
-    list_display = ('simple_entity', 'region_layer', "synonyms", "ontology_uri")
+    list_display = ('simple_entity', 'region_layer', 'synonyms', 'ontology_uri' )
     list_display_links = ('simple_entity', 'region_layer')
+    search_fields = (
+        'simple_entity__name',  'simple_entity__ontology_uri', 
+        'region_layer__layer__name', 'region_layer__region__name',
+        'region_layer__layer__ontology_uri', 'region_layer__region__ontology_uri',
+    )
     inlines = (SynonymInline,)
+    autocomplete_fields = ('simple_entity', 'region_layer')
 
     # we need to make efficient queries to the database to get the list of anatomical entities
     def get_queryset(self, request: HttpRequest) -> QuerySet[Any]:
@@ -130,22 +134,66 @@ def get_model_perms(self, request):
         return {}
 
 
+class LayerAdminForm(forms.ModelForm):
+    class Meta:
+        model = Layer
+        fields = '__all__'
+        labels = {
+            'ae_meta': 'layer',
+        }
+
+
+class RegionAdminForm(forms.ModelForm):
+    class Meta:
+        model = Region
+        fields = '__all__'
+        labels = {
+            'ae_meta': 'region',
+        }
+
+
 class LayerAdmin(admin.ModelAdmin):
-    list_display = ('name', 'ontology_uri',)
-    search_fields = ('name',)
+    form = LayerAdminForm
+    list_display = ('layer_name', 'ontology_uri')
+    list_display_links = ('layer_name', 'ontology_uri')
+    search_fields = ('ae_meta__name', 'ae_meta__ontology_uri')
+    autocomplete_fields = ('ae_meta',)
+
+    @admin.display(description="Layer Name")
+    def layer_name(self, obj):
+        return obj.ae_meta.name
+
+    @admin.display(description="Ontology URI")
+    def ontology_uri(self, obj):
+        return obj.ae_meta.ontology_uri
+
 
 
 class RegionAdmin(admin.ModelAdmin):
-    list_display = ('name', 'ontology_uri',)
-    search_fields = ('name',)
-    filter_horizontal = ('layers',)
+    form = RegionAdminForm
+    list_display = ('region_name', 'ontology_uri')
+    list_display_links = ('region_name', 'ontology_uri')
+    search_fields = ('ae_meta__name', 'ae_meta__ontology_uri')
+    autocomplete_fields = ('ae_meta',)
+
+    @admin.display(description="Region Name")
+    def region_name(self, obj):
+        return obj.ae_meta.name
+
+    @admin.display(description="Ontology URI")
+    def ontology_uri(self, obj):
+        return obj.ae_meta.ontology_uri
+
 
 
 class AnatomicalEntityIntersectionAdmin(nested_admin.NestedModelAdmin, admin.ModelAdmin):
     list_display = ('layer', 'region')
-    search_fields = ("region__name", "layer__name")
-    list_filter = ('layer', 'region',)
-    raw_id_fields = ('layer', 'region',)
+    raw_id_fields = ('layer', 'region')
+    list_filter = ('layer', 'region')
+    search_fields = (
+        'layer__ae_meta__name', 'region__ae_meta__name',
+        'layer__ae_meta__ontology_uri', 'region__ae_meta__ontology_uri'
+    )
 
     def get_model_perms(self, request):
         return {}

backend/composer/api/serializers.py

@@ -81,29 +81,6 @@ class Meta:
         dept = 2
 
 
-class LayerSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = Layer
-        fields = (
-            "id",
-            "name",
-            "ontology_uri",
-        )
-
-
-class RegionSerializer(serializers.ModelSerializer):
-    layers = LayerSerializer(many=True, read_only=True)
-
-    class Meta:
-        model = Region
-        fields = (
-            "id",
-            "name",
-            "ontology_uri",
-            "layers",
-        )
-
-
 class AnatomicalEntityMetaSerializer(serializers.ModelSerializer):
     class Meta:
         model = AnatomicalEntityMeta
@@ -115,8 +92,8 @@ class Meta:
 
 
 class AnatomicalEntityIntersectionSerializer(serializers.ModelSerializer):
-    layer = LayerSerializer(read_only=True)
-    region = RegionSerializer(read_only=True)
+    layer = AnatomicalEntityMetaSerializer(read_only=True)
+    region = AnatomicalEntityMetaSerializer(read_only=True)
 
     class Meta:
         model = AnatomicalEntityIntersection

backend/composer/migrations/0053_alter_anatomicalentity_options_and_more.py

@@ -0,0 +1,116 @@
+# Generated by Django 4.1.4 on 2024-07-08 13:18
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+def populate_intersection_anatomical_entity_meta_id_from_layer_region(apps, schema_editor):
+    """
+    populating the new fields from AnatomicalEntityIntersection
+    layer_id -> layer_meta_id
+    region_id -> region_meta_id
+    """
+    AnatomicalEntityIntersection = apps.get_model("composer", "AnatomicalEntityIntersection")
+    for intersection in AnatomicalEntityIntersection.objects.all():
+        intersection.layer_meta_id = intersection.layer_id
+        intersection.region_meta_id = intersection.region_id
+        intersection.save()
+
+
+def populate_layer_region_ae_meta_ids_from_anatomicalentitymeta_ptr_id(apps, schema_editor):
+    """
+    populating the new fields from Layer and Region
+    anatomicalentitymeta_ptr_id -> layer_ae_meta_id
+    anatomicalentitymeta_ptr_id -> region_ae_meta_id
+    """
+    Layer = apps.get_model("composer", "Layer")
+    Region = apps.get_model("composer", "Region")
+
+    for layer in Layer.objects.all():
+        layer.layer_ae_meta_id = layer.anatomicalentitymeta_ptr_id
+        layer.save()
+
+    for region in Region.objects.all():
+        region.region_ae_meta_id = region.anatomicalentitymeta_ptr_id
+        region.save()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("composer", "0052_alter_anatomicalentity_options_and_more"),
+    ]
+
+    # Steps taken in migration:
+    # 1. create new fields for layer and region - layer_ae_meta, region_ae_meta
+    # 2. create new fields for AnatomicalEntityIntersection - layer_meta, region_meta
+    # 3. populate the new fields in AnatomicalEntityIntersection from the old fields - layer, region
+    # 4. populate the new fields in Layer and Region from the old fields - anatomicalentitymeta_ptr_id
+    operations = [
+        migrations.AlterModelOptions(
+            name="anatomicalentity",
+            options={
+                "verbose_name": "Anatomical Entity",
+                "verbose_name_plural": "Anatomical Entities",
+            },
+        ),
+
+        migrations.AddField(
+            model_name="layer",
+            name="layer_ae_meta",
+            field=models.ForeignKey(
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="layer_meta",
+                to="composer.anatomicalentitymeta",
+            ),
+        ),
+        migrations.AddField(
+            model_name="region",
+            name="region_ae_meta",
+            field=models.ForeignKey(
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="region_meta",
+                to="composer.anatomicalentitymeta",
+            ),
+        ),
+
+        # ------------------------
+        migrations.AddField(
+            model_name="anatomicalentityintersection",
+            name="layer_meta",
+            field=models.ForeignKey(
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="layer_intersection",
+                to="composer.anatomicalentitymeta",
+            ),
+        ),
+        migrations.AddField(
+            model_name="anatomicalentityintersection",
+            name="region_meta",
+            field=models.ForeignKey(
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="region_intersection",
+                to="composer.anatomicalentitymeta",
+            ),
+        ),
+
+        # ------------------------
+
+        migrations.RunPython(
+            code=populate_intersection_anatomical_entity_meta_id_from_layer_region,
+            reverse_code=migrations.RunPython.noop,
+        ),
+
+        # ------------------------
+
+        migrations.RunPython(
+            code=populate_layer_region_ae_meta_ids_from_anatomicalentitymeta_ptr_id,
+            reverse_code=migrations.RunPython.noop,
+        ),
+
+    ]
+
+

backend/composer/migrations/0054_auto_20240709_0909.py

@@ -0,0 +1,104 @@
+# Generated by Django 4.1.4 on 2024-07-09 07:09
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("composer", "0053_alter_anatomicalentity_options_and_more"),
+    ]
+
+    # Steps taken in migration:
+    # 1. create new models for layer and region - NewLayer, NewRegion
+    # 2. copy the necessary columns from the old models to the new models - layer_ae_meta, region_ae_meta
+    # 3. remove the old models - Layer, Region and it's fk from AnatomicalEntityIntersection
+    # 4. rename the new models to the old models - Layer, Region
+
+    operations = [
+        migrations.CreateModel(
+            name="NewLayer",
+            fields=[
+                (
+                    "layer_id",
+                    models.BigAutoField(
+                        auto_created=True, 
+                        primary_key=True, 
+                        serialize=False,
+                    ),
+                ),
+                (
+                    "layer_ae_meta",
+                    models.ForeignKey(
+                        null=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="layer_meta",
+                        to="composer.anatomicalentitymeta",
+                    ),
+                )
+            ]
+        ),
+        migrations.RunSQL(
+            sql="INSERT INTO composer_newlayer (layer_ae_meta_id) SELECT anatomicalentitymeta_ptr_id FROM composer_layer",
+            reverse_sql="",
+        ),
+        migrations.RemoveField(
+            model_name="anatomicalentityintersection",
+            name="layer",
+        ),
+        migrations.DeleteModel(
+            name="Layer",
+        ),
+        migrations.RenameModel(
+            old_name="NewLayer",
+            new_name="Layer",
+        ),
+
+
+        # ----------------------------
+        migrations.CreateModel(
+            name="NewRegion",
+            fields=[
+                (
+                    "region_id",
+                    models.BigAutoField(
+                        auto_created=True, 
+                        primary_key=True, 
+                        serialize=False,
+                    ),
+                ),
+                (
+                    "region_ae_meta",
+                    models.ForeignKey(
+                        null=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="region_meta",
+                        to="composer.anatomicalentitymeta",
+                    ),
+                )
+            ]
+        ),
+        migrations.RunSQL(
+            sql="INSERT INTO composer_newregion (region_ae_meta_id) SELECT anatomicalentitymeta_ptr_id FROM composer_region",
+            reverse_sql="",
+        ),
+        migrations.RemoveField(
+            model_name="anatomicalentityintersection",
+            name="region",
+        ), 
+        migrations.DeleteModel(
+            name="Region",  
+        ),
+        migrations.RenameModel(
+            old_name="NewRegion",
+            new_name="Region",
+        ),
+
+
+
+
+    ]

backend/composer/migrations/0055_auto_20240708_1540.py

@@ -0,0 +1,31 @@
+# Generated by Django 4.1.4 on 2024-07-08 13:40
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("composer", "0054_auto_20240709_0909"),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name="layer",
+            options={"verbose_name": "Layer", "verbose_name_plural": "Layers"},
+        ),
+        migrations.AlterModelOptions(
+            name="region",
+            options={"verbose_name": "Region", "verbose_name_plural": "Regions"},
+        ),
+        migrations.RenameField(
+            model_name="anatomicalentityintersection",
+            old_name="layer_meta",
+            new_name="layer",
+        ),
+        migrations.RenameField(
+            model_name="anatomicalentityintersection",
+            old_name="region_meta",
+            new_name="region",
+        ),
+    ]