Update model to accept missing scores for mined publications

gene2phenotype_project/gene2phenotype_app/management/commands/load_mined_publications_scores.py

@@ -24,6 +24,7 @@
 - medium
 - low
 - disputed
+- N/A (no access to publication)
 
 How to run the command:
 python manage.py load_mined_publications_scores --data_file <json data file> --email <user account email>
@@ -71,17 +72,22 @@ def handle(self, *args, **options):
             for record_data in data_reader:
                 g2p_id = record_data["id"]
                 for publication in record_data["publications"]:
-                    if publication["status"] and publication["status"] != "incomplete":
+                    if publication["status"]:
                         pmid = publication["id"]
                         score = publication["status"]
-                        score_comment = publication["comment"]
-                        full_text = publication["fulltext"]
                         n_scores += 1
 
-                        if full_text:
-                            score_comment += " (Score based on full text)"
+                        if publication["status"] == "incomplete":
+                            score = "N/A" # Overwrite score for incomplete publications
+                            score_comment = "No access to this publication"
                         else:
-                            score_comment += " (Score based on abstract only)"
+                            score_comment = publication["comment"]
+                            full_text = publication["fulltext"]
+
+                            if full_text:
+                                score_comment += " (Score based on full text)"
+                            else:
+                                score_comment += " (Score based on abstract only)"
 
                         try:
                             lgd_mined_pub_obj = LGDMinedPublication.objects.get(
@@ -100,6 +106,6 @@ def handle(self, *args, **options):
                                 lgd_mined_pub_obj._history_user = user_obj
                                 lgd_mined_pub_obj.save()
                                 n_scores_updated += 1
-        
+
         print(f"\nTotal scores in the input file: {n_scores}")
         print(f"Total scores updated in the database: {n_scores_updated}\n")

gene2phenotype_project/gene2phenotype_app/migrations/0016_remove_lgdminedpublication_score_valid_and_more.py

@@ -0,0 +1,29 @@
+# Generated by Django 5.2.9 on 2026-01-23 11:30
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "gene2phenotype_app",
+            "0015_curationdata_status_historicalcurationdata_status",
+        ),
+    ]
+
+    operations = [
+        migrations.RemoveConstraint(
+            model_name="lgdminedpublication",
+            name="score_valid",
+        ),
+        migrations.AddConstraint(
+            model_name="lgdminedpublication",
+            constraint=models.CheckConstraint(
+                condition=models.Q(
+                    ("score__in", ["high", "medium", "low", "disputed", "N/A", None])
+                ),
+                name="score_valid",
+            ),
+        ),
+    ]

gene2phenotype_project/gene2phenotype_app/models.py

@@ -806,7 +806,7 @@ class Meta:
                 name="status_valid",
             ),
             models.CheckConstraint(
-                condition=Q(score__in=["high", "medium", "low", "disputed", None]),
+                condition=Q(score__in=["high", "medium", "low", "disputed", "N/A", None]),
                 name="score_valid",
             ),
         ]