Fix metadata key (#3878)

broadinstitute · Feb 13, 2024 · f6e32f9 · f6e32f9
1 parent 9c35fe4
commit f6e32f9
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/seqr/management/commands/check_for_new_samples_from_pipeline.py b/seqr/management/commands/check_for_new_samples_from_pipeline.py
@@ -41,14 +41,14 @@ def handle(self, *args, **options):
                 raise CommandError(f'Run failed for {path}: {version}, unable to load data')
 
         metadata = json.loads(next(line for line in file_iter(gs_path + 'metadata.json')))
-        families = Family.objects.filter(guid__in=metadata['families'].keys())
-        if len(families) < len(metadata['families']):
-            invalid = metadata['families'].keys() - set(families.values_list('guid', flat=True))
+        families = Family.objects.filter(guid__in=metadata['family_samples'].keys())
+        if len(families) < len(metadata['family_samples']):
+            invalid = metadata['family_samples'].keys() - set(families.values_list('guid', flat=True))
             raise CommandError(f'Invalid families in run metadata {path}: {version} - {", ".join(invalid)}')
 
         family_project_map = {f.guid: f.project for f in families.select_related('project')}
         samples_by_project = defaultdict(list)
-        for family_guid, sample_ids in metadata['families'].items():
+        for family_guid, sample_ids in metadata['family_samples'].items():
             samples_by_project[family_project_map[family_guid]] += sample_ids
 
         sample_project_tuples = []

diff --git a/seqr/management/tests/check_for_new_samples_from_pipeline_tests.py b/seqr/management/tests/check_for_new_samples_from_pipeline_tests.py
@@ -64,7 +64,7 @@ def test_command(self, mock_logger, mock_send_email, mock_send_slack, mock_subpr
         metadata = {
             'callsets': ['1kg.vcf.gz'],
             'sample_type': 'WES',
-            'families': {
+            'family_samples': {
                 'F0000123_ABC': ['NA22882', 'NA20885'],
                 'F000012_12': ['NA20888', 'NA20889'],
                 'F000014_14': ['NA21234'],
@@ -79,7 +79,7 @@ def test_command(self, mock_logger, mock_send_email, mock_send_slack, mock_subpr
             str(ce.exception), 'Invalid families in run metadata GRCh38/SNV_INDEL: auto__2023-08-08 - F0000123_ABC')
         mock_logger.warning.assert_called_with('Loading for failed run GRCh38/SNV_INDEL: auto__2023-08-08')
 
-        metadata['families']['F000011_11'] = metadata['families'].pop('F0000123_ABC')
+        metadata['family_samples']['F000011_11'] = metadata['family_samples'].pop('F0000123_ABC')
         mock_subprocess.return_value.stdout = [json.dumps(metadata).encode()]
         mock_subprocess.return_value.wait.return_value = 0
         with self.assertRaises(CommandError) as ce:
@@ -96,7 +96,7 @@ def test_command(self, mock_logger, mock_send_email, mock_send_slack, mock_subpr
             call_command('check_for_new_samples_from_pipeline', 'GRCh38/SNV_INDEL', 'auto__2023-08-08')
         self.assertEqual(str(ce.exception), 'Matches not found for sample ids: NA22882')
 
-        metadata['families']['F000011_11'] = metadata['families']['F000011_11'][1:]
+        metadata['family_samples']['F000011_11'] = metadata['family_samples']['F000011_11'][1:]
         mock_subprocess.return_value.stdout = [json.dumps(metadata).encode()]
 
         # Test success