Sync with #596

googlegenomics · May 19, 2020 · 924ff45 · 924ff45
1 parent d54adb8
commit 924ff45
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Showing 3 changed files with 5 additions and 7 deletions.
diff --git a/cloudbuild_CI.yaml b/cloudbuild_CI.yaml
@@ -42,9 +42,7 @@ steps:
       - '--project ${PROJECT_ID}'
       - '--image_tag ${COMMIT_SHA}'
       - '--run_unit_tests'
-      - '--run_preprocessor_tests'
-      - '--run_bq_to_vcf_tests'
-      - '--run_all_tests'
+      - '--run_presubmit_tests'
       - '--test_name_prefix cloud-ci-'
     id: 'test-gcp-variant-transforms-docker'
     entrypoint: '/opt/gcp_variant_transforms/src/deploy_and_run_tests.sh'

diff --git a/gcp_variant_transforms/libs/bigquery_util.py b/gcp_variant_transforms/libs/bigquery_util.py
@@ -676,7 +676,7 @@ def get_flatten_table_schema(self, schema_file_path):
                     bq_command)
     else:
       logging.info('Successfully extracted the schema of flatten table.')
-    if _delete_table(full_table_id) == 0:
+    if delete_table(full_table_id) == 0:
       logging.info('Successfully deleted temporary table: %s', full_table_id)
     else:
       logging.error('Was not able to delete temporary table: %s', full_table_id)

diff --git a/gcp_variant_transforms/vcf_to_bq.py b/gcp_variant_transforms/vcf_to_bq.py
@@ -536,7 +536,7 @@ def run(argv=None):
     load_avro = bigquery_util.LoadAvro(avro_root_path,
                                        known_args.output_table,
                                        suffixes, not known_args.append)
-    _ = load_avro.start_loading()
+    not_empty_variant_suffixes = load_avro.start_loading()
   except Exception as e:
     logging.error('Something unexpected happened during the loading of AVRO '
                   'files to BigQuery: %s', str(e))
@@ -561,14 +561,14 @@ def run(argv=None):
 
   if known_args.sample_lookup_optimized_output_table:
     flatten_call_column = bigquery_util.FlattenCallColumn(
-        known_args.output_table, suffixes)
+        known_args.output_table, not_empty_variant_suffixes)
     try:
       flatten_schema_file = tempfile.mkstemp(suffix=_BQ_SCHEMA_FILE_SUFFIX)[1]
       if not flatten_call_column.get_flatten_table_schema(flatten_schema_file):
         raise ValueError('Failed to extract schema of flatten table')
       # Create output flatten tables if needed
       if not known_args.append:
-        for suffix in suffixes:
+        for suffix in not_empty_variant_suffixes:
           output_table_id = bigquery_util.compose_table_name(
               known_args.sample_lookup_optimized_output_table, suffix)
           bigquery_util.create_output_table(output_table_id,