Merge pull request #4567 from broadinstitute/loading-failed-status

"Loading Failed" analysis status

seqr/management/commands/check_for_new_samples_from_pipeline.py

@@ -166,6 +166,11 @@ def _load_new_samples(cls, metadata_path, genome_version, dataset_type, run_vers
         failed_families_by_guid = {f['guid']: f for f in Family.objects.filter(
             guid__in={family for families in failed_family_samples.values() for family in families}
         ).values('guid', 'family_id', 'project__name')}
+        if failed_families_by_guid:
+            Family.bulk_update(
+                user=None, update_json={'analysis_status': Family.ANALYSIS_STATUS_LOADING_FAILED},
+                guid__in=failed_families_by_guid, analysis_status=Family.ANALYSIS_STATUS_WAITING_FOR_DATA
+            )
         failures_by_project_check = defaultdict(lambda: defaultdict(list))
         for check, check_failures in failed_family_samples.items():
             for family_guid, failure_data in check_failures.items():

seqr/management/tests/check_for_new_samples_from_pipeline_tests.py

@@ -462,6 +462,10 @@ def test_command(self, mock_email, mock_airtable_utils):
             {'analysis_status': 'I', 'analysis_status_last_modified_date': None},
             {'analysis_status': 'I', 'analysis_status_last_modified_date': None},
         ])
+        self.assertSetEqual(
+            set(Family.objects.filter(guid__in=['F000001_1', 'F000002_2', 'F000003_3']).values_list('analysis_status', flat=True)),
+            {'F'},
+        )
         self.assertEqual(Family.objects.get(guid='F000014_14').analysis_status, 'Rncc')
 
         # Test airtable PDO updates

seqr/migrations/0079_alter_family_analysis_status.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.16 on 2025-01-03 19:55
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('seqr', '0078_rename_submit_to_clinvar_variantnote_report'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='family',
+            name='analysis_status',
+            field=models.CharField(choices=[('S', 'S'), ('S_kgfp', 'S'), ('S_kgdp', 'S'), ('S_ng', 'S'), ('ES', 'E'), ('Sc_kgfp', 'S'), ('Sc_kgdp', 'S'), ('Sc_ng', 'S'), ('Rcpc', 'R'), ('Rncc', 'R'), ('C', 'C'), ('PB', 'P'), ('P', 'P'), ('I', 'A'), ('Q', 'W'), ('F', 'L'), ('N', 'N')], default='Q', max_length=10),
+        ),
+    ]

seqr/models.py

@@ -286,6 +286,7 @@ class Family(ModelWithGUID):
     ANALYSIS_STATUS_PARTIAL_SOLVE = 'P'
     ANALYSIS_STATUS_PROBABLE_SOLVE = 'PB'
     ANALYSIS_STATUS_WAITING_FOR_DATA='Q'
+    ANALYSIS_STATUS_LOADING_FAILED = 'F'
     SOLVED_ANALYSIS_STATUS_CHOICES = (
         ('S', 'Solved'),
         ('S_kgfp', 'Solved - known gene for phenotype'),
@@ -308,6 +309,7 @@ class Family(ModelWithGUID):
         (ANALYSIS_STATUS_PARTIAL_SOLVE, 'Partial Solve - Analysis in Progress'),
         (ANALYSIS_STATUS_ANALYSIS_IN_PROGRESS, 'Analysis in Progress'),
         (ANALYSIS_STATUS_WAITING_FOR_DATA, 'Waiting for data'),
+        (ANALYSIS_STATUS_LOADING_FAILED, 'Loading failed'),
         ('N', 'No data expected'),
     )
     SOLVED_ANALYSIS_STATUSES = [status for status, _ in SOLVED_ANALYSIS_STATUS_CHOICES]

seqr/views/utils/dataset_utils.py

@@ -216,7 +216,8 @@ def match_and_update_search_samples(
     updated_samples = Sample.objects.filter(guid__in=activated_sample_guids)
 
     family_guids_to_update = [
-        family_guid for family_guid, analysis_status in included_families.items() if analysis_status == Family.ANALYSIS_STATUS_WAITING_FOR_DATA
+        family_guid for family_guid, analysis_status in included_families.items()
+        if analysis_status in {Family.ANALYSIS_STATUS_WAITING_FOR_DATA, Family.ANALYSIS_STATUS_LOADING_FAILED}
     ]
     Family.bulk_update(
         user, {'analysis_status': Family.ANALYSIS_STATUS_ANALYSIS_IN_PROGRESS}, guid__in=family_guids_to_update)

ui/shared/utils/constants.js

@@ -164,6 +164,7 @@ const FAMILY_STATUS_CLOSED = 'C'
 const FAMILY_STATUS_PARTIAL_SOLVE = 'P'
 const FAMILY_STATUS_ANALYSIS_IN_PROGRESS = 'I'
 const FAMILY_STATUS_WAITING_FOR_DATA = 'Q'
+const FAMILY_STATUS_LOADING_FAILED = 'F'
 const FAMILY_STATUS_NO_DATA = 'N'
 
 const DEPRECATED_FAMILY_ANALYSIS_STATUS_OPTIONS = [
@@ -184,6 +185,7 @@ export const SELECTABLE_FAMILY_ANALYSIS_STATUS_OPTIONS = [
   { value: FAMILY_STATUS_PARTIAL_SOLVE, color: '#288582', name: 'Partial Solve - Analysis in Progress' },
   { value: FAMILY_STATUS_ANALYSIS_IN_PROGRESS, color: '#4682B4', name: 'Analysis in Progress' },
   { value: FAMILY_STATUS_WAITING_FOR_DATA, color: '#FFC107', name: 'Waiting for data' },
+  { value: FAMILY_STATUS_LOADING_FAILED, color: '#ba4c12', name: 'Loading failed' },
   { value: FAMILY_STATUS_NO_DATA, color: '#646464', name: 'No data expected' },
 ]
 export const ALL_FAMILY_ANALYSIS_STATUS_OPTIONS = [