Merge branch 'dev' of https://github.com/broadinstitute/seqr into sho…

…w-all-consequence-terms

seqr/management/commands/check_for_new_samples_from_pipeline.py

@@ -51,7 +51,11 @@ def handle(self, *args, **options):
         success_runs = {path: re.match(path_regex, path).groupdict() for path in list_files(path, user=None)}
         if not success_runs:
             user_args = [f'{k}={options[k]}' for k in RUN_PATH_FIELDS if options[k]]
-            raise CommandError(f'No successful runs found for {", ".join(user_args)}')
+            if user_args:
+                raise CommandError(f'No successful runs found for {", ".join(user_args)}')
+            else:
+                logger.info('No loaded data available')
+                return
 
         loaded_runs = set(Sample.objects.filter(data_source__isnull=False).values_list('data_source', flat=True))
         new_runs = {path: run for path, run in success_runs.items() if run['run_version'] not in loaded_runs}

seqr/management/tests/check_for_new_samples_from_pipeline_tests.py

@@ -326,6 +326,12 @@ def test_command(self, mock_email, mock_airtable_utils):
         self.mock_glob.assert_called_with('/seqr/seqr-hail-search-data/GRCh37/MITO/runs/*/_SUCCESS')
         self.mock_subprocess.assert_not_called()
 
+        call_command('check_for_new_samples_from_pipeline')
+        self.mock_logger.info.assert_called_with('No loaded data available')
+        self.mock_subprocess.assert_not_called()
+        mock_email.assert_not_called()
+        self.mock_send_slack.assert_not_called()
+
         local_files = [
             '/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL/runs/auto__2023-08-09/_SUCCESS',
             '/seqr/seqr-hail-search-data/GRCh37/SNV_INDEL/runs/manual__2023-11-02/_SUCCESS',