single loading error per project

seqr/management/commands/check_for_new_samples_from_pipeline.py

@@ -166,27 +166,28 @@ 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')}
+        failures_by_project_check = defaultdict(lambda: defaultdict(list))
         for check, check_failures in failed_family_samples.items():
-            failures_by_project = defaultdict(list)
             for family_guid, failure_data in check_failures.items():
                 family = failed_families_by_guid[family_guid]
-                failures_by_project[family['project__name']].append(
+                failures_by_project_check[family['project__name']][check].append(
                     f'- {family["family_id"]}: {"; ".join(failure_data["reasons"])}'
                 )
-            for project, failures in failures_by_project.items():
+        for project, failures_by_check in failures_by_project_check.items():
+            messages = [f'Encountered the following errors loading {project}:']
+            for check, failures in failures_by_check.items():
                 summary = '\n'.join(sorted(failures))
-                split_pdos = split_project_pdos.get(project)
-                if split_pdos:
-                    summary += f'\n\nSkipped samples in this project have been moved to {", ".join(split_pdos)}'
-
+                messages.append(f"The following {len(failures)} families failed {check.replace('_', ' ')}:\n{summary}")
                 if check == RELATEDNESS_CHECK_NAME and relatedness_check_file_path:
                     downloadable_link = f'https://storage.cloud.google.com/{relatedness_check_file_path[5:]}'
-                    summary += f'\n\nRelatedness check results: {downloadable_link}'
+                    messages.append(f'Relatedness check results: {downloadable_link}')
 
-                safe_post_to_slack(
-                    SEQR_SLACK_LOADING_NOTIFICATION_CHANNEL,
-                    f'The following {len(failures)} families failed {check.replace("_", " ")} in {project}:\n{summary}'
-                )
+            split_pdos = split_project_pdos.get(project)
+            if split_pdos:
+                messages.append(f'Skipped samples in this project have been moved to {", ".join(split_pdos)}')
+            safe_post_to_slack(
+                SEQR_SLACK_LOADING_NOTIFICATION_CHANNEL, '\n\n'.join(messages),
+            )
 
         # Reload saved variant JSON
         updated_variants_by_id = update_projects_saved_variant_json(

seqr/management/tests/check_for_new_samples_from_pipeline_tests.py

@@ -540,7 +540,7 @@ def test_command(self, mock_email, mock_airtable_utils):
         ])
 
         # Test notifications
-        self.assertEqual(self.mock_send_slack.call_count, 9)
+        self.assertEqual(self.mock_send_slack.call_count, 7)
         self.mock_send_slack.assert_has_calls([
             mock.call(
                 'seqr-data-loading',
@@ -567,24 +567,24 @@ def test_command(self, mock_email, mock_airtable_utils):
             ),
             mock.call(
                 'seqr_loading_notifications',
-                """The following 1 families failed relatedness check in 1kg project nåme with uniçøde:
-- 1: Sample NA19679 has expected relation "parent" to NA19675 but has coefficients [0.0, 0.8505002045292791, 0.14949979547072176, 0.5747498977353613]; Sample NA19678 has expected relation "sibling" to NA19675 but has coefficients [0.17424888135104177, 0.6041745754450025, 0.22157654320395614, 0.5236638309264574]\n\nRelatedness check results: https://storage.cloud.google.com/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/relatedness_check/test_callset_hash.tsv""",
-            ),
-            mock.call(
-                'seqr_loading_notifications',
-                """The following 1 families failed sex check in 1kg project nåme with uniçøde:
-- 1: Sample NA19679 has pedigree sex F but imputed sex M""",
+                """Encountered the following errors loading 1kg project nåme with uniçøde:
+
+The following 1 families failed relatedness check:
+- 1: Sample NA19679 has expected relation "parent" to NA19675 but has coefficients [0.0, 0.8505002045292791, 0.14949979547072176, 0.5747498977353613]; Sample NA19678 has expected relation "sibling" to NA19675 but has coefficients [0.17424888135104177, 0.6041745754450025, 0.22157654320395614, 0.5236638309264574]\n\nRelatedness check results: https://storage.cloud.google.com/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/relatedness_check/test_callset_hash.tsv
+
+The following 1 families failed sex check:
+- 1: Sample NA19679 has pedigree sex F but imputed sex M
+
+The following 2 families failed missing samples:
+- 2: Missing samples: {'HG00732', 'HG00733'}
+- 3: Missing samples: {'NA20870'}""",
             ),
             mock.call(
                 'seqr_loading_notifications',
-                """The following 1 families failed sex check in Non-Analyst Project:
+                """Encountered the following errors loading Non-Analyst Project:
+
+The following 1 families failed sex check:
 - 14: Sample NA21987 has pedigree sex M but imputed sex F""",
-            ),
-            mock.call(
-                'seqr_loading_notifications',
-                """The following 2 families failed missing samples in 1kg project nåme with uniçøde:
-- 2: Missing samples: {'HG00732', 'HG00733'}
-- 3: Missing samples: {'NA20870'}""",
             ),
             mock.call(
                 'seqr-data-loading',