#51 refactor: NoteTag to Tag

backend/composer/admin.py

@@ -15,7 +15,7 @@
     ConnectivityStatement,
     Doi,
     Note,
-    NoteTag,
+    Tag,
     Profile,
     Provenance,
     Specie,
@@ -43,7 +43,7 @@ class DoiInline(admin.StackedInline):
     extra = 1
 
 
-class DoiiNestedInline(nested_admin.NestedStackedInline):
+class DoiNestedInline(nested_admin.NestedStackedInline):
     model = Doi
     extra = 1
 
@@ -65,7 +65,7 @@ class ConnectivityStatementInline(nested_admin.NestedStackedInline):
     model = ConnectivityStatement
     extra = 1
     fields = ("provenance", "knowledge_statement")
-    inlines = (DoiiNestedInline,)
+    inlines = (DoiNestedInline,)
 
 
 # Define a new User admin
@@ -164,6 +164,6 @@ def pmcid(self, obj):
 admin.site.register(AnatomicalEntity, AnatomicalEntityAdmin)
 admin.site.register(AnsDivision)
 admin.site.register(ConnectivityStatement, ConnectivityStatementAdmin)
-admin.site.register(NoteTag)
+admin.site.register(Tag)
 admin.site.register(Provenance, ProvenanceAdmin)
 admin.site.register(Specie)

backend/composer/management/commands/ingest_nlp_sentence.py

@@ -34,9 +34,7 @@ def handle(self, *args, **options):
                     out_of_scope = row[OUT_OF_SCOPE].lower()
                     if out_of_scope and out_of_scope.lower() == "yes":
                         # skip out of scope records
-                        self.stdout.write(
-                            f"{rowid}: out of scope."
-                        )
+                        self.stdout.write(f"{rowid}: out of scope.")
                         continue
                     rowid = row[ID]
                     pmid = row[PMID] if row[PMID] != "0" else None

backend/composer/migrations/0033_rename_notetag_tag_remove_note_tags_and_more.py

@@ -0,0 +1,55 @@
+# Generated by Django 4.1.4 on 2023-01-09 14:36
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("composer", "0032_remove_provenance_provenance_pmid_pmcd_unique"),
+    ]
+
+    operations = [
+        migrations.RenameModel(
+            old_name="NoteTag",
+            new_name="Tag",
+        ),
+        migrations.RemoveField(
+            model_name="note",
+            name="tags",
+        ),
+        migrations.AddField(
+            model_name="connectivitystatement",
+            name="tags",
+            field=models.ManyToManyField(to="composer.tag", verbose_name="Tags"),
+        ),
+        migrations.AddField(
+            model_name="provenance",
+            name="tags",
+            field=models.ManyToManyField(to="composer.tag", verbose_name="Tags"),
+        ),
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="path",
+            field=models.ManyToManyField(
+                blank=True, through="composer.Via", to="composer.anatomicalentity"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="via",
+            name="anatomical_entity",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                to="composer.anatomicalentity",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="via",
+            name="connectivity_statement",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                to="composer.connectivitystatement",
+            ),
+        ),
+    ]

backend/composer/migrations/0034_alter_tag_options.py

@@ -0,0 +1,17 @@
+# Generated by Django 4.1.4 on 2023-01-09 14:45
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("composer", "0033_rename_notetag_tag_remove_note_tags_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name="tag",
+            options={"ordering": ["tag"], "verbose_name_plural": "Tags"},
+        ),
+    ]

backend/composer/models.py

@@ -56,8 +56,8 @@ class Meta:
         verbose_name_plural = "Anatomical Entities"
 
 
-class NoteTag(models.Model):
-    """Note Tag"""
+class Tag(models.Model):
+    """Tag"""
 
     tag = models.CharField(max_length=200, db_index=True, unique=True)
 
@@ -66,7 +66,7 @@ def __str__(self):
 
     class Meta:
         ordering = ["tag"]
-        verbose_name_plural = "Note Tags"
+        verbose_name_plural = "Tags"
 
 
 class Provenance(models.Model):
@@ -77,6 +77,7 @@ class Provenance(models.Model):
     state = FSMField(default=ProvenanceState.OPEN, protected=True)
     pmid = models.BigIntegerField(db_index=True, null=True, blank=True)
     pmcid = models.CharField(max_length=10, db_index=True, null=True, blank=True)
+    tags = models.ManyToManyField(Tag, verbose_name="Tags")
     owner = models.ForeignKey(
         User,
         verbose_name="Triage Operator",
@@ -161,18 +162,14 @@ class Meta:
         ]
 
 
-
-
 class Via(models.Model):
     """Via"""
 
     connectivity_statement = models.ForeignKey(
         "ConnectivityStatement",
         on_delete=models.CASCADE,
     )
-    anatomical_entity = models.ForeignKey(
-        AnatomicalEntity, on_delete=models.DO_NOTHING
-    )
+    anatomical_entity = models.ForeignKey(AnatomicalEntity, on_delete=models.DO_NOTHING)
     ordering = models.PositiveIntegerField(
         default=0,
         blank=False,
@@ -217,9 +214,7 @@ class ConnectivityStatement(models.Model):
     owner = models.ForeignKey(
         User, verbose_name="Curator", on_delete=models.DO_NOTHING, null=True, blank=True
     )
-    path = models.ManyToManyField(
-        AnatomicalEntity, through=Via, blank=True
-    )
+    path = models.ManyToManyField(AnatomicalEntity, through=Via, blank=True)
     laterality = models.CharField(
         max_length=20, default=Laterality.UNKNOWN, choices=Laterality.choices
     )
@@ -234,6 +229,7 @@ class ConnectivityStatement(models.Model):
         blank=True,
     )
     species = models.ManyToManyField(Specie, verbose_name="Species", blank=True)
+    tags = models.ManyToManyField(Tag, verbose_name="Tags")
     biological_sex = models.CharField(max_length=200, null=True, blank=True)
     apinatomy_model = models.CharField(max_length=200, null=True, blank=True)
 
@@ -309,7 +305,6 @@ class Meta:
         ]
 
 
-
 class Doi(models.Model):
     """DOI see https://doi.org/"""
 
@@ -334,7 +329,6 @@ class Note(models.Model):
     """Note"""
 
     note = models.TextField()
-    tags = models.ManyToManyField(NoteTag, verbose_name="Tags")
     user = models.ForeignKey(User, verbose_name="User", on_delete=models.DO_NOTHING)
     provenance = models.ForeignKey(
         Provenance,

backend/composer/serializers.py

@@ -9,7 +9,7 @@
     ConnectivityStatement,
     Doi,
     Note,
-    NoteTag,
+    Tag,
     Provenance,
     Specie,
     Profile,
@@ -61,11 +61,11 @@ class Meta:
         fields = "__all__"
 
 
-class NoteTagSerializer(serializers.ModelSerializer):
+class TagSerializer(serializers.ModelSerializer):
     """Note Tag"""
 
     class Meta:
-        model = NoteTag
+        model = Tag
         fields = "__all__"
 
 
@@ -133,6 +133,7 @@ class Meta:
 
 class ViaViewSerializer(serializers.ModelSerializer):
     """Via"""
+
     # anatomical_entity = AnatomicalEntitySerializer(read_only=False)
 
     class Meta:
@@ -143,6 +144,7 @@ class Meta:
 
 class ConnectivityStatementSerializer(serializers.ModelSerializer):
     """Connectivity Statement"""
+
     available_transitions = serializers.SerializerMethodField()
     path = ViaViewSerializer(source="via_set", many=True, read_only=True)
 
@@ -158,6 +160,7 @@ class Meta:
 
 class ConnectivityStatementViewSerializer(ConnectivityStatementSerializer):
     """Connectivity Statement"""
+
     provenance = ProvenanceSerializer(read_only=True)
 
     class Meta(ConnectivityStatementSerializer.Meta):

backend/composer/urls.py

@@ -5,11 +5,12 @@
     AnsDivisionViewSet,
     ConnectivityStatementViewSet,
     NoteViewSet,
-    NoteTagViewSet,
+    TagViewSet,
     ProvenanceViewSet,
     SpecieViewSet,
     ProfileViewSet,
-    ViaViewSet
+    TagViewSet,
+    ViaViewSet,
 )
 
 # Create a router and register our viewsets with it.
@@ -24,11 +25,12 @@
     basename="connectivity-statement",
 )
 router.register(r"note", NoteViewSet, basename="note")
-router.register(r"note-tag", NoteTagViewSet, basename="note-tag")
+router.register(r"note-tag", TagViewSet, basename="note-tag")
 router.register(r"provenance", ProvenanceViewSet, basename="provenance")
 router.register(r"specie", SpecieViewSet, basename="specie")
 router.register(r"profile", ProfileViewSet, basename="profile")
-router.register(r'via', ViaViewSet, basename="via")
+router.register(r"tag", TagViewSet, basename="tag")
+router.register(r"via", ViaViewSet, basename="via")
 
 # The API URLs are now determined automatically by the router.
 urlpatterns = [

backend/composer/views.py

@@ -8,23 +8,23 @@
     AnsDivision,
     ConnectivityStatement,
     Note,
-    NoteTag,
+    Tag,
     Provenance,
     Specie,
     Profile,
-    Via
+    Via,
 )
 from .serializers import (
     AnatomicalEntitySerializer,
     AnsDivisionSerializer,
     ConnectivityStatementSerializer,
     ConnectivityStatementViewSerializer,
     NoteSerializer,
-    NoteTagSerializer,
+    TagSerializer,
     ProvenanceSerializer,
     SpecieSerializer,
     ProfileSerializer,
-    ViaSerializer
+    ViaSerializer,
 )
 from .services import ConnectivityStatementService
 
@@ -117,13 +117,13 @@ def transition(self, request, pk=None, transition=None):
         return Response(self.get_serializer(cs).data)
 
 
-class NoteTagViewSet(ModelCreateRetrieveViewSet):
+class TagViewSet(viewsets.ReadOnlyModelViewSet):
     """
-    NoteTag
+    Tag
     """
 
-    queryset = NoteTag.objects.all()
-    serializer_class = NoteTagSerializer
+    queryset = Tag.objects.all()
+    serializer_class = TagSerializer
     permission_classes = [
         permissions.IsAuthenticatedOrReadOnly,
     ]
@@ -172,9 +172,11 @@ def get_queryset(self):
         return super().get_queryset().filter(user=self.request.user)
 
 
-class ViaViewSet(mixins.CreateModelMixin,
+class ViaViewSet(
+    mixins.CreateModelMixin,
     mixins.DestroyModelMixin,
-    viewsets.GenericViewSet,):
+    viewsets.GenericViewSet,
+):
     """
     Via
     """