def test_convert_variant_to_bigquery_row_omit_empty_calls(self): variant, row, header_num_dict = self._get_sample_variant_with_empty_calls() header_fields = vcf_header_util.make_header(header_num_dict) proc_var = processed_variant.ProcessedVariantFactory( header_fields).create_processed_variant(variant) pipeline = TestPipeline(blocking=True) bigquery_rows = ( pipeline | Create([proc_var]) | 'ConvertToRow' >> ParDo(ConvertToBigQueryTableRow( self._row_generator, omit_empty_sample_calls=True))) assert_that(bigquery_rows, equal_to([row])) pipeline.run()
def test_convert_variant_to_bigquery_row_allow_incompatible_recoreds(self): variant, row = self._get_sample_variant_with_incompatible_records() header_fields = vcf_header_io.VcfHeader() proc_var = processed_variant.ProcessedVariantFactory( header_fields).create_processed_variant(variant) pipeline = TestPipeline(blocking=True) bigquery_rows = ( pipeline | Create([proc_var]) | 'ConvertToRow' >> ParDo( ConvertToBigQueryTableRow(self._row_generator, allow_incompatible_records=True))) assert_that(bigquery_rows, equal_to([row])) pipeline.run()
def test_convert_variant_to_bigquery_row(self): variant_1, row_1 = self._get_sample_variant_1() variant_2, row_2 = self._get_sample_variant_2() variant_3, row_3 = self._get_sample_variant_3() header_fields = vcf_header_io.VcfHeader() proc_var_1 = processed_variant.ProcessedVariantFactory( header_fields).create_processed_variant(variant_1) proc_var_2 = processed_variant.ProcessedVariantFactory( header_fields).create_processed_variant(variant_2) proc_var_3 = processed_variant.ProcessedVariantFactory( header_fields).create_processed_variant(variant_3) pipeline = TestPipeline(blocking=True) bigquery_rows = (pipeline | Create([proc_var_1, proc_var_2, proc_var_3]) | 'ConvertToRow' >> ParDo( ConvertToBigQueryTableRow(self._row_generator))) assert_that(bigquery_rows, equal_to([row_1, row_2, row_3])) pipeline.run()
def test_convert_variant_to_bigquery_row(self): variant_1, row_1 = self._get_sample_variant_1() variant_2, row_2 = self._get_sample_variant_2() variant_3, row_3 = self._get_sample_variant_3() header_fields = vcf_header_parser.HeaderFields({}, {}) proc_var_1 = processed_variant.ProcessedVariantFactory( header_fields).create_processed_variant(variant_1) proc_var_2 = processed_variant.ProcessedVariantFactory( header_fields).create_processed_variant(variant_2) proc_var_3 = processed_variant.ProcessedVariantFactory( header_fields).create_processed_variant(variant_3) pipeline = TestPipeline() bigquery_rows = ( pipeline | Create([proc_var_1, proc_var_2, proc_var_3]) | 'ConvertToRow' >> ParDo( ConvertToBigQueryTableRow( mock_bigquery_schema_descriptor.MockSchemaDescriptor()))) assert_that(bigquery_rows, equal_to([row_1, row_2, row_3])) pipeline.run()