def _add_format_fields(schema, formats, allow_incompatible_schema=False):
# type: (bigquery.TableFieldSchema, Dict[str, _Format], bool) -> None
for field in schema.fields:
if field.name in _CONSTANT_CALL_FIELDS:
continue
if (field.name in list(vcf_reserved_fields.FORMAT_FIELDS.keys())
and not allow_incompatible_schema):
reserved_definition = vcf_reserved_fields.FORMAT_FIELDS.get(
field.name)
_validate_reserved_field(field, reserved_definition)
formats.update({
field.name:
vcf_header_io.CreateFormatField(
field.name, reserved_definition.num,
reserved_definition.type,
_remove_special_characters(field.description
or reserved_definition.desc))
})
else:
formats.update({
field.name:
vcf_header_io.CreateFormatField(
field.name,
bigquery_util.get_vcf_num_from_bigquery_schema(
field.mode, field.type),
bigquery_util.get_vcf_type_from_bigquery_type(field.type),
_remove_special_characters(field.description))
})
def _add_info_fields(field, infos, allow_incompatible_schema=False):
# type: (bigquery.TableFieldSchema, Dict[str, _Info], bool) -> None
if field.name == bigquery_util.ColumnKeyConstants.ALTERNATE_BASES:
_add_info_fields_from_alternate_bases(field, infos,
allow_incompatible_schema)
elif (field.name in list(vcf_reserved_fields.INFO_FIELDS.keys())
and not allow_incompatible_schema):
reserved_definition = vcf_reserved_fields.INFO_FIELDS.get(field.name)
_validate_reserved_field(field, reserved_definition)
infos.update({
field.name:
vcf_header_io.CreateInfoField(
field.name, reserved_definition.num, reserved_definition.type,
_remove_special_characters(field.description
or reserved_definition.desc))
})
else:
infos.update({
field.name:
vcf_header_io.CreateInfoField(
field.name,
bigquery_util.get_vcf_num_from_bigquery_schema(
field.mode, field.type),
bigquery_util.get_vcf_type_from_bigquery_type(field.type),
_remove_special_characters(field.description))
})
def test_get_vcf_num_from_bigquery_schema(self):
self.assertEqual('.',
bigquery_util.get_vcf_num_from_bigquery_schema(
bigquery_util.TableFieldConstants.MODE_REPEATED,
bigquery_util.TableFieldConstants.TYPE_INTEGER))
self.assertEqual(1,
bigquery_util.get_vcf_num_from_bigquery_schema(
bigquery_util.TableFieldConstants.MODE_NULLABLE,
bigquery_util.TableFieldConstants.TYPE_INTEGER))
self.assertEqual(0,
bigquery_util.get_vcf_num_from_bigquery_schema(
bigquery_util.TableFieldConstants.MODE_NULLABLE,
bigquery_util.TableFieldConstants.TYPE_BOOLEAN))
self.assertEqual(
0,
bigquery_util.get_vcf_num_from_bigquery_schema(
bigquery_mode=None,
bigquery_type=bigquery_util.TableFieldConstants.TYPE_BOOLEAN))
