Suppression state propagation (#328)

Co-authored-by: Martín Beracochea <[email protected]>
Co-authored-by: Mahfouz <[email protected]>

emgapi/admin.py

@@ -463,21 +463,21 @@ class AnalysisMetadataVariableNamesAdmin(admin.ModelAdmin):
     ]
 
 
-@admin.register(emg_models.AnalysisJobAnn)
-class AnalysisJobAnnAdmin(admin.ModelAdmin):
-    readonly_fields = [
-        'job',
-        'var',
-    ]
-    list_display = [
-        'job',
-        'var'
-    ]
-    search_fields = [
-        'job__job_id',
-        'var__var_name',
-        'var__description',
-    ]
+# @admin.register(emg_models.AnalysisJobAnn)
+# class AnalysisJobAnnAdmin(admin.ModelAdmin):
+#     readonly_fields = [
+#         'job',
+#         'var',
+#     ]
+#     list_display = [
+#         'job',
+#         'var'
+#     ]
+#     search_fields = [
+#         'job__job_id',
+#         'var__var_name',
+#         'var__description',
+#     ]
 
 
 @admin.register(emg_models.CogCat)

emgapi/management/commands/clean_empty_studies.py

@@ -56,5 +56,5 @@ def handle(self, *args, **kwargs):
                 run.ena_study_accession = study.secondary_accession
                 run.study = None
             Run.objects.bulk_update(runs, ["ena_study_accession", "study"])
-            study.suppress()
+            study.suppress(propagate=False)
             logger.info(f"{study} suppressed")

emgapi/migrations/0013_delete_analysisjobann.py

@@ -0,0 +1,25 @@
+# Generated by Django 3.2.18 on 2023-09-29 19:59
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('emgapi', '0012_alter_publication_pub_type'),
+    ]
+
+    operations = [
+        # migrations.SeparateDatabaseAndState(
+        #     state_operations=[
+        #         migrations.RenameField(
+        #             model_name='analysisjob',
+        #             old_name='analysis_summary_json',
+        #             new_name='analysis_summary',
+        #         ),
+        #     ],
+        # ),
+        migrations.DeleteModel(
+            name='AnalysisJobAnn',
+        ),
+    ]

emgapi/migrations/0014_suppression_reason_ancestor_suppressed.py

@@ -0,0 +1,44 @@
+# Generated by Django 3.2.18 on 2023-09-14 07:16
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('emgapi', '0013_delete_analysisjobann'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='analysisjob',
+            name='suppression_reason',
+            field=models.IntegerField(blank=True, choices=[(1, 'Draft'), (3, 'Cancelled'), (5, 'Suppressed'), (6, 'Killed'), (7, 'Temporary Suppressed'), (8, 'Temporary Killed'), (100, 'Ancestor Suppressed')], db_column='SUPPRESSION_REASON', null=True),
+        ),
+        migrations.AlterField(
+            model_name='assembly',
+            name='study',
+            field=models.ForeignKey(blank=True, db_column='STUDY_ID', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='assemblies', to='emgapi.study'),
+        ),
+        migrations.AlterField(
+            model_name='assembly',
+            name='suppression_reason',
+            field=models.IntegerField(blank=True, choices=[(1, 'Draft'), (3, 'Cancelled'), (5, 'Suppressed'), (6, 'Killed'), (7, 'Temporary Suppressed'), (8, 'Temporary Killed'), (100, 'Ancestor Suppressed')], db_column='SUPPRESSION_REASON', null=True),
+        ),
+        migrations.AlterField(
+            model_name='run',
+            name='suppression_reason',
+            field=models.IntegerField(blank=True, choices=[(1, 'Draft'), (3, 'Cancelled'), (5, 'Suppressed'), (6, 'Killed'), (7, 'Temporary Suppressed'), (8, 'Temporary Killed'), (100, 'Ancestor Suppressed')], db_column='SUPPRESSION_REASON', null=True),
+        ),
+        migrations.AlterField(
+            model_name='sample',
+            name='suppression_reason',
+            field=models.IntegerField(blank=True, choices=[(1, 'Draft'), (3, 'Cancelled'), (5, 'Suppressed'), (6, 'Killed'), (7, 'Temporary Suppressed'), (8, 'Temporary Killed'), (100, 'Ancestor Suppressed')], db_column='SUPPRESSION_REASON', null=True),
+        ),
+        migrations.AlterField(
+            model_name='study',
+            name='suppression_reason',
+            field=models.IntegerField(blank=True, choices=[(1, 'Draft'), (3, 'Cancelled'), (5, 'Suppressed'), (6, 'Killed'), (7, 'Temporary Suppressed'), (8, 'Temporary Killed'), (100, 'Ancestor Suppressed')], db_column='SUPPRESSION_REASON', null=True),
+        ),
+    ]