Merge pull request PGScatalog#354 from fyvon/improve/embargoed_import

Improving import of embargoed studies

curation/imports/curation.py

@@ -150,7 +150,11 @@ def run_curation_import(self):
                         self.failed_studies[study_import.study_name] = 'curation tracker error'
 
                 if curation_pub != None:
-                    curation_pub.curation_status = 'Imported - Awaiting Release'
+                    curation_pub.pgp_id = study_import.study_publication.id
+                    if study_import.study_publication.curation_status == 'E':
+                        curation_pub.curation_status = 'Embargo Imported - Awaiting Publication'
+                    else:
+                        curation_pub.curation_status = 'Imported - Awaiting Release'
                     curation_pub.save()
                     print("  > Curation status updated in the Curation Tracker")
 

curation_tracker/admin.py

@@ -448,7 +448,7 @@ def save_model(self, request, obj, form, change):
 
             # Desembargo the study
             if obj.embargoed == False and (not db_obj or db_obj.embargoed == True):
-                if obj.curation_status == 'Embargo Imported - Awaiting Release':
+                if obj.curation_status == 'Embargo Imported - Awaiting Publication':
                     if obj.doi or obj.PMID:
                         obj.curation_status = 'Imported - Awaiting Release'
                 elif obj.curation_status == 'Embargo Curated - Awaiting Import':
@@ -465,7 +465,7 @@ def save_model(self, request, obj, form, change):
                 if obj.curation_status == 'Curated - Awaiting Import':
                     obj.curation_status = 'Embargo Curated - Awaiting Import'
                 elif obj.curation_status == 'Imported - Awaiting Release':
-                    obj.curation_status == 'Embargo Imported - Awaiting Release'
+                    obj.curation_status = 'Embargo Imported - Awaiting Publication'
 
             # Eligibility - part 2
             if obj.curation_status == 'Abandoned/Ineligible':

curation_tracker/migrations/0005_alter_curationpublicationannotation_curation_status.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.10 on 2024-04-19 14:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('curation_tracker', '0004_emailtemplate'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='curationpublicationannotation',
+            name='curation_status',
+            field=models.CharField(blank=True, choices=[('Abandoned/Ineligible', 'Abandoned/Ineligible'), ('Pending author response', 'Pending author response'), ('Awaiting L1', 'Awaiting L1'), ('Awaiting L2', 'Awaiting L2'), ('Curated - Awaiting Import', 'Curated - Awaiting Import'), ('Imported - Awaiting Release', 'Imported - Awaiting Release'), ('Released', 'Released'), ('Embargo Curated - Awaiting Import', 'Embargo Curated - Awaiting Import'), ('Embargo Imported - Awaiting Publication', 'Embargo Imported - Awaiting Publication'), ('Embargo Lifted - Awaiting Release', 'Embargo Lifted - Awaiting Release'), ('Retired', 'Retired')], default='Awaiting L1', max_length=50, null=True, verbose_name='Curation Status'),
+        ),
+    ]

curation_tracker/models.py

@@ -83,7 +83,7 @@ class CurationPublicationAnnotation(models.Model):
         ('Imported - Awaiting Release','Imported - Awaiting Release'),
         ('Released','Released'),
         ('Embargo Curated - Awaiting Import','Embargo Curated - Awaiting Import'),
-        ('Embargo Imported - Awaiting Release','Embargo Imported - Awaiting Release'),
+        ('Embargo Imported - Awaiting Publication','Embargo Imported - Awaiting Publication'),
         ('Embargo Lifted - Awaiting Release','Embargo Lifted - Awaiting Release'),
         ('Retired','Retired')
     ]

curation_tracker/views.py

@@ -37,10 +37,10 @@ def browse_release_ready(request):
         import_ready = CurationPublicationAnnotation.objects.using(curation_tracker).filter(curation_status='Curated - Awaiting Import')
         context['table_to_import'] = Browse_CurationPublicationAnnotationReleaseReady(import_ready)
 
-    release_ready_count = CurationPublicationAnnotation.objects.using(curation_tracker).filter(curation_status='Imported - Awaiting Release').count()
+    release_ready_count = CurationPublicationAnnotation.objects.using(curation_tracker).filter(curation_status__in=('Imported - Awaiting Release', 'Embargo Lifted - Awaiting Release')).count()
     context['studies_to_release_count'] = release_ready_count
     if release_ready_count:
-        release_ready = CurationPublicationAnnotation.objects.using(curation_tracker).filter(curation_status='Imported - Awaiting Release')
+        release_ready = CurationPublicationAnnotation.objects.using(curation_tracker).filter(curation_status__in=('Imported - Awaiting Release', 'Embargo Lifted - Awaiting Release'))
         context['table_to_release'] = Browse_CurationPublicationAnnotationReleaseReady(release_ready)
 
     if context:

release/scripts/run_release_script.py

@@ -205,7 +205,7 @@ def update_curation_tracker():
                 curation_pub.pgp_id = pgp_id
                 print('  - Updating curation_status on the Curation Tracker')
                 if publication.curation_status == 'E':
-                    curation_pub.curation_status = 'Embargo Imported - Awaiting Release'
+                    curation_pub.curation_status = 'Embargo Imported - Awaiting Publication'
                 else:
                     curation_pub.curation_status = 'Released'
                     curation_pub.release_date = new_release_date