Feature/sckan-279 - Admin interface changes for region + layer

backend/composer/admin.py

@@ -1,9 +1,13 @@
+from typing import Any
+from django.db.models.query import QuerySet
+from django.http import HttpRequest
 import nested_admin
 from adminsortable2.admin import SortableAdminBase, SortableStackedInline
 from django.contrib import admin
 from django.contrib.auth.admin import UserAdmin as BaseUserAdmin
 from django.contrib.auth.models import User
 from fsm_admin.mixins import FSMTransitionMixin
+from django import forms
 
 from composer.models import (
     Phenotype,
@@ -38,6 +42,10 @@ class ProvenanceInline(admin.StackedInline):
     model = Provenance
     extra = 1
 
+class SynonymeInline(admin.StackedInline):
+    model = Synonym
+    extra = 1
+
 
 class ProvenanceNestedInline(nested_admin.NestedStackedInline):
     model = Provenance
@@ -89,26 +97,32 @@ class SentenceAdmin(
         NoteSentenceInline,
     )
 
-
-class SynonymInline(admin.TabularInline):
-    model = Synonym
-    extra = 1
-
-
 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")
+    list_display_links = ('simple_entity', 'region_layer')
+    inlines = (SynonymeInline,)
 
-    def get_model_perms(self, request):
-        """
-        Return empty dict to hide the model from admin index.
-        """
-        return {}
+    # we need to make efficient queries to the database to get the list of anatomical entities
+    def get_queryset(self, request: HttpRequest) -> QuerySet[Any]:
+        return super().get_queryset(request) \
+            .select_related('simple_entity', 'region_layer__layer', 'region_layer__region') \
+            .prefetch_related('synonyms')
+
+    @admin.display(description="Synonyms")
+    def synonyms(self, obj):
+        synonyms = obj.synonyms.all()
+        return ', '.join([synonym.name for synonym in synonyms])
 
 
 class AnatomicalEntityMetaAdmin(admin.ModelAdmin):
     list_display = ("name", "ontology_uri")
     list_display_links = ("name", "ontology_uri")
-    search_fields = ("name",)
+    search_fields = ("name", "ontology_uri")
+
+    def get_model_perms(self, request):
+        return {}
 
 
 class LayerAdmin(admin.ModelAdmin):
@@ -122,11 +136,15 @@ class RegionAdmin(admin.ModelAdmin):
     filter_horizontal = ('layers',)
 
 
-class AnatomicalEntityIntersectionAdmin(admin.ModelAdmin):
-    list_display = ('layer', 'region',)
+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',)
 
+    def get_model_perms(self, request):
+        return {}
+
 
 class ViaInline(SortableStackedInline):
     model = Via

backend/composer/migrations/0051_alter_anatomicalentity_region_layer.py

@@ -0,0 +1,24 @@
+# Generated by Django 4.1.4 on 2024-04-03 13:57
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("composer", "0050_alter_anatomicalentityintersection_options_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="anatomicalentity",
+            name="region_layer",
+            field=models.OneToOneField(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                to="composer.anatomicalentityintersection",
+            ),
+        ),
+    ]

backend/composer/models.py

@@ -254,26 +254,36 @@ class Meta:
         verbose_name = "Region/Layer Combination"
         verbose_name_plural = "Region/Layer Combinations"
 
+    def __str__(self):
+        return f'{self.region.name} - {self.layer.name}'
+
 
 class AnatomicalEntity(models.Model):
     simple_entity = models.OneToOneField(AnatomicalEntityMeta, on_delete=models.CASCADE, null=True, blank=True)
-    region_layer = models.ForeignKey(AnatomicalEntityIntersection, on_delete=models.CASCADE, null=True, blank=True)
+    region_layer = models.OneToOneField(AnatomicalEntityIntersection, on_delete=models.CASCADE, null=True, blank=True)
 
     @property
     def name(self):
-        return self.simple_entity.name if self.simple_entity \
-            else f'{self.region_layer.region.name},{self.region_layer.layer.name}'
+        if self.simple_entity:
+            return self.simple_entity.name
+        elif self.region_layer:
+            return f'{self.region_layer.region.name},{self.region_layer.layer.name}'
+        return 'Unknown Anatomical Entity'
 
     @property
     def ontology_uri(self):
-        return self.simple_entity.ontology_uri if self.simple_entity \
-            else f'{self.region_layer.region.ontology_uri},{self.region_layer.layer.ontology_uri}'
-
+        if self.simple_entity:
+            return self.simple_entity.ontology_uri
+        elif self.region_layer:
+            return f'{self.region_layer.region.ontology_uri},{self.region_layer.layer.ontology_uri}'
+        return 'Unknown URI'
 
     def __str__(self):
         return self.name
 
     class Meta:
+        verbose_name = "Anatomical Entity"
+        verbose_name_plural = "Anatomical Entities"
         constraints = [
             CheckConstraint(
                 check=(

backend/composer/signals.py

@@ -5,8 +5,8 @@
 from django_fsm.signals import post_transition
 
 from .enums import CSState, NoteType
-from .models import ConnectivityStatement, ExportBatch, Note, Sentence, AnatomicalEntity, AnatomicalEntityIntersection, \
-    AnatomicalEntityMeta
+from .models import ConnectivityStatement, ExportBatch, Note, Sentence, Synonym, \
+    AnatomicalEntity, Layer, Region
 from .services.export_services import compute_metrics, ConnectivityStatementStateService
 
 
@@ -48,14 +48,12 @@ def post_transition_cs(sender, instance, name, source, target, **kwargs):
             # add important tag to CS when transition to COMPOSE_NOW from NPO Approved or Exported
             instance = ConnectivityStatementStateService.add_important_tag(instance)
 
-
-@receiver(post_save, sender=AnatomicalEntityIntersection)
-def create_region_layer_anatomical_entity(sender, instance=None, created=False, **kwargs):
+@receiver(post_save, sender=Layer)
+def create_layer_anatomical_entity(sender, instance=None, created=False, **kwargs):
     if created and instance:
-        AnatomicalEntity.objects.create(region_layer=instance)
-
+        AnatomicalEntity.objects.create(simple_entity=instance) 
 
-@receiver(post_save, sender=AnatomicalEntityMeta)
-def create_simple_anatomical_entity(sender, instance=None, created=False, **kwargs):
+@receiver(post_save, sender=Region)
+def create_region_anatomical_entity(sender, instance=None, created=False, **kwargs):
     if created and instance:
         AnatomicalEntity.objects.create(simple_entity=instance)