Merge pull request #41 from MetaCell/feature/38

#38 feat: provenance add pmcid and remove uri and add pm(c)id uri pro…

backend/composer/admin.py

@@ -1,6 +1,7 @@
 from django.contrib import admin
 from django.contrib.auth.admin import UserAdmin as BaseUserAdmin
 from django.contrib.auth.models import User
+from django.utils.html import format_html
 
 from adminsortable2.admin import SortableAdminBase, SortableStackedInline
 from fsm_admin.mixins import FSMTransitionMixin
@@ -48,11 +49,19 @@ class UserAdmin(BaseUserAdmin):
 class ProvenanceAdmin(FSMTransitionMixin, admin.ModelAdmin):
     # The name of one or more FSMFields on the model to transition
     fsm_field = ("state",)
-    readonly_fields = ("state",)
-    list_display = ("title", "pmid", "uri")
-    list_display_links = ("title", "pmid", "uri")
-    search_fields = ("title", "description", "pmid",)
-
+    readonly_fields = ("pmid_uri", "pmcid_uri", "state")
+    list_display = ("title", "pmid", "pmcid")
+    list_display_links = ("title", "pmid", "pmcid")
+    search_fields = ("title", "description", "pmid", "pmcid")
+
+    @admin.display(description='PMID')
+    def pmid_uri(self, obj):
+        return format_html("<a href='{url}' target='blank'>{url}</a>", url=obj.pmid_uri) if obj.pmid_uri else ""
+
+    @admin.display(description='PMCID')
+    def pmcid_uri(self, obj):
+        return format_html("<a href='{url}' target='blank'>{url}</a>", url=obj.pmcid_uri) if obj.pmcid_uri else ""
+
     inlines = (ConnectivityStatementInline, NoteProvenanceInline,)
 
 
@@ -67,10 +76,10 @@ class ConnectivityStatementAdmin(SortableAdminBase, FSMTransitionMixin, admin.Mo
     fsm_field = ("state",)
     readonly_fields = ("state",)
     autocomplete_fields = ("provenance", "origin", "destination")
-    list_display = ("provenance", "pmid", "short_ks", "origin", "destination", "state", "curator")
-    list_display_links = ("provenance", "short_ks", "state")
+    list_display = ("provenance", "pmid", "pmcid", "short_ks", "origin", "destination", "state", "curator")
+    list_display_links = ("provenance", "pmid", "pmcid", "short_ks", "state")
     list_select_related = ("provenance", "origin", "destination")
-    search_fields = ("provenance__title", "provenance__description", "provenance__pmid", "knowledge_statement", "origin__name", "destination__name")
+    search_fields = ("provenance__title", "provenance__description", "provenance__pmid", "provenance__pmcid", "knowledge_statement", "origin__name", "destination__name")
 
     fieldsets = ()
 
@@ -84,6 +93,10 @@ def short_ks(self, obj):
     def pmid(self, obj):
         return obj.provenance.pmid
 
+    @admin.display(description='PMCID')
+    def pmcid(self, obj):
+        return obj.provenance.pmcid
+
     def formfield_for_foreignkey(self, db_field, request, **kwargs):
         if db_field.name == "curator":
             kwargs["queryset"] = User.objects.filter(profile__is_curator=True)

backend/composer/migrations/0026_remove_provenance_uri_provenance_pmcid_and_more.py

@@ -0,0 +1,31 @@
+# Generated by Django 4.1.4 on 2023-01-05 14:15
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('composer', '0025_remove_connectivitystatement_state_valid_and_more'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='provenance',
+            name='uri',
+        ),
+        migrations.AddField(
+            model_name='provenance',
+            name='pmcid',
+            field=models.CharField(blank=True, db_index=True, max_length=10, null=True, unique=True),
+        ),
+        migrations.AlterField(
+            model_name='provenance',
+            name='pmid',
+            field=models.BigIntegerField(blank=True, db_index=True, null=True, unique=True),
+        ),
+        migrations.AddConstraint(
+            model_name='provenance',
+            constraint=models.CheckConstraint(check=models.Q(('pmid__isnull', False), ('pmcid__isnull', False), _connector='OR'), name='provenance_pmid_pmcd_valid'),
+        ),
+    ]

backend/composer/models.py

@@ -113,9 +113,9 @@ class Provenance(models.Model):
     """Provenance"""
     title = models.CharField(max_length=200, db_index=True)
     description = models.TextField(db_index=True)
-    pmid = models.BigIntegerField(db_index=True)
-    uri = models.URLField()
     state = FSMField(default=ProvenanceState.OPEN, protected=True)
+    pmid = models.BigIntegerField(db_index=True, unique=True, null=True, blank=True)
+    pmcid = models.CharField(max_length=10, db_index=True, unique=True, null=True, blank=True)
 
     def __str__(self):
         return self.title
@@ -139,12 +139,21 @@ def excluded(self):
     @transition(field=state, source=ProvenanceState.OPEN, target=ProvenanceState.DUPLICATE)
     def duplicate(self):
         ...
+
+    @property
+    def pmid_uri(self):
+        return f"https://pubmed.ncbi.nlm.nih.gov/{self.pmid}/" if self.pmid else None
+
+    @property
+    def pmcid_uri(self):
+        return f"https://www.ncbi.nlm.nih.gov/pmc/articles/{self.pmcid}/" if self.pmcid else None
 
     class Meta:
         ordering = ["title"]
         verbose_name_plural = "Provenances"
         constraints = [
             models.CheckConstraint(check=models.Q(state__in=[l[0] for l in ProvenanceState.choices]), name="provenance_state_valid"),
+            models.CheckConstraint(check=models.Q(pmid__isnull=False) | models.Q(pmcid__isnull=False), name="provenance_pmid_pmcd_valid"),
         ]
 
 

backend/composer/serializers.py

@@ -61,14 +61,22 @@ class ProvenanceSerializer(serializers.ModelSerializer):
     """Provenance"""
     notes = NoteSerializer(many=True, read_only=True)
     available_transitions = serializers.SerializerMethodField()
+    pmid_uri = serializers.SerializerMethodField()
+    pmcid_uri = serializers.SerializerMethodField()
 
     def get_available_transitions(self, instance):
         return [t.name for t in instance.get_available_state_transitions()]
+
+    def get_pmid_uri(self, instance):
+        return instance.pmid_uri
+
+    def get_pmcid_uri(self, instance):
+        return instance.pmcid_uri
 
     class Meta:
         model = Provenance
         fields = '__all__'
-        read_only_fields = ('state', 'available_transitions')
+        read_only_fields = ('state', 'available_transitions', 'pmid_uri', 'pmcid_uri',)
 
 
 class ViaFromConnectivityStatementSerializer(serializers.ModelSerializer):