Merge pull request #537 from MetaCell/main

update dev from main

Author: ddelpiano

applications/composer/backend/backend/settings.py

@@ -396,6 +396,7 @@
 
 SOCIAL_AUTH_ORCID_KEY = "APP-GRRGRZ5EZQLQ6WZT"
 SOCIAL_AUTH_ORCID_SECRET = "a1363a17-22b0-4a99-81fc-a1a86a371251"
+SOCIAL_AUTH_ORCID_SCOPE = ["openid"]
 
 SOCIAL_AUTH_AUTHENTICATION_BACKENDS = ("social_core.backends.orcid.ORCIDOAuth2",)
 AUTHENTICATION_BACKENDS = (

applications/composer/backend/composer/migrations/0098_migrate_reference_uri_to_http.py

@@ -0,0 +1,51 @@
+# Generated by Django on 2025-03-04
+
+from django.db import migrations
+
+
+def convert_reference_uri_https_to_http(apps, schema_editor):
+    """
+    Converts all reference_uri values from https to http.
+    """
+    ConnectivityStatement = apps.get_model("composer", "ConnectivityStatement")
+    
+    # Get all statements with reference_uri starting with https://
+    statements_with_https = ConnectivityStatement.objects.filter(
+        reference_uri__startswith="https://uri.interlex.org/composer/uris/set/"
+    )
+    
+    # Update each statement to use http instead of https
+    for statement in statements_with_https:
+        statement.reference_uri = statement.reference_uri.replace("https://", "http://", 1)
+        statement.save(update_fields=["reference_uri"])
+
+
+def reverse_convert_reference_uri_http_to_https(apps, schema_editor):
+    """
+    Reverse migration: Converts reference_uri values back from http to https.
+    """
+    ConnectivityStatement = apps.get_model("composer", "ConnectivityStatement")
+    
+    # Get all statements with reference_uri starting with http://
+    statements_with_http = ConnectivityStatement.objects.filter(
+        reference_uri__startswith="http://uri.interlex.org/composer/uris/set/"
+    )
+    
+    # Update each statement to use https instead of http
+    for statement in statements_with_http:
+        statement.reference_uri = statement.reference_uri.replace("http://", "https://", 1)
+        statement.save(update_fields=["reference_uri"])
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("composer", "0097_relationship_custom_ingestion_code"),
+    ]
+
+    operations = [
+        migrations.RunPython(
+            convert_reference_uri_https_to_http,
+            reverse_code=reverse_convert_reference_uri_http_to_https
+        ),
+    ]

applications/composer/backend/composer/utils.py

@@ -15,7 +15,7 @@ def doi_uri(doi):
 
 
 def create_reference_uri(population_name, population_index):
-    return f"https://uri.interlex.org/composer/uris/set/{population_name}/{population_index}"
+    return f"http://uri.interlex.org/composer/uris/set/{population_name}/{population_index}"
 
 def join_entities(entities):
     # Joins entity names with commas, and 'and' before the last name
@@ -45,5 +45,3 @@ def generate_connectivity_statement_curie_id_for_composer_statements(statement):
     if statement.population:
         return f"neuron type {statement.population.name} {statement.population_index}"
     return None
-
-

applications/composer/backend/requirements.txt

@@ -1,10 +1,10 @@
-packaging==21.3
-Django==4.2.26
+packaging>=22.0
+Django==4.2.29
 uvicorn==0.20.0
 starlette>=0.41.3
 pillow>=11.0.0
 psycopg2-binary==2.9.5
-djangorestframework==3.14.0
+djangorestframework==3.15.2
 django-filter==23.5
 django-fsm==2.8.1
 django-fsm-admin@git+https://github.com/gadventures/django-fsm-admin@master
@@ -14,15 +14,17 @@ django-jazzmin==2.6.0
 drf-spectacular==0.25.1
 drf-spectacular-sidecar==2022.12.1
 drf-writable-nested==0.7.0
-social-auth-app-django==5.0.0
+social-auth-app-django==5.4.3
 pyontutils==0.1.38
 drf-react-template-framework==0.0.17
-aiohttp==3.11.18
+aiohttp==3.13.3
 crossref-commons==0.0.7
-neurondm==0.1.8
+neurondm==0.1.10
 django-cors-headers==4.3.1
 django-debug-toolbar==4.3.0
 django-sslserver-v2==1.0
-black==22.12.0
+black==26.3.1
 pytest==8.3.3
 python-dotenv==1.1.0
+awscli==1.44.38
+pyasn1==0.6.3

applications/composer/backend/version.py

@@ -1 +1 @@
-VERSION = "6.0.0"
+VERSION = "6.0.1"

applications/composer/frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "frontend",
-  "version": "6.0.0",
+  "version": "6.0.1",
   "private": true,
   "main": "index.js",
   "proxy": "http://127.0.0.1:8000/",