Remove WRITE_TRUNCATE option when writing to BQ.

Author: tneymanov

gcp_variant_transforms/transforms/sample_info_to_bigquery.py

@@ -73,14 +73,11 @@ def __init__(self, output_table_prefix, sample_name_encoding, append=False):
   def expand(self, pcoll):
     return (pcoll
             | 'ConvertSampleInfoToBigQueryTableRow' >> beam.ParDo(
-                ConvertSampleInfoToRow(self._sample_name_encoding))
-            | 'WriteSampleInfoToBigQuery' >> beam.io.Write(beam.io.BigQuerySink(
+                ConvertSampleInfoToRow(self.sample_name_encoding))
+            | 'WriteSampleInfoToBigQuery' >> beam.io.WriteToBigQuery(
                 self._output_table,
                 schema=self._schema,
                 create_disposition=(
                     beam.io.BigQueryDisposition.CREATE_IF_NEEDED),
-                write_disposition=(
-                    beam.io.BigQueryDisposition.WRITE_APPEND
-                    if self._append
-                    else beam.io.BigQueryDisposition.WRITE_TRUNCATE),
+                write_disposition=beam.io.BigQueryDisposition.WRITE_APPEND,
                 method=beam.io.WriteToBigQuery.Method.FILE_LOADS))

gcp_variant_transforms/transforms/variant_to_bigquery.py

@@ -63,8 +63,7 @@ def __init__(
       update_schema_on_append=False,  # type: bool
       allow_incompatible_records=False,  # type: bool
       omit_empty_sample_calls=False,  # type: bool
-      null_numeric_value_replacement=None  # type: int,
-
+      null_numeric_value_replacement=None  # type: int
       ):
     # type: (...) -> None
     """Initializes the transform.
@@ -115,8 +114,5 @@ def expand(self, pcoll):
                 schema=self._schema,
                 create_disposition=(
                     beam.io.BigQueryDisposition.CREATE_IF_NEEDED),
-                write_disposition=(
-                    beam.io.BigQueryDisposition.WRITE_APPEND
-                    if self._append
-                    else beam.io.BigQueryDisposition.WRITE_TRUNCATE),
+                write_disposition=beam.io.BigQueryDisposition.WRITE_APPEND,
                 method=beam.io.WriteToBigQuery.Method.FILE_LOADS))

gcp_variant_transforms/vcf_to_bq.py

@@ -389,7 +389,7 @@ def _run_annotation_pipeline(known_args, pipeline_args):
 
 def _create_sample_info_table(pipeline,  # type: beam.Pipeline
                               pipeline_mode,  # type: PipelineModes
-                              known_args,  # type: argparse.Namespace,
+                              known_args  # type: argparse.Namespace
                              ):
   # type: (...) -> None
   headers = pipeline_common.read_headers(