def _create_sample_from_row(row, biobank_id_prefix):
"""Creates a new BiobankStoredSample object from a CSV row.
Raises:
DataError if the row is invalid.
Returns:
A new BiobankStoredSample, or None if the row should be skipped.
"""
biobank_id_str = row[_Columns.EXTERNAL_PARTICIPANT_ID]
if not biobank_id_str.startswith(biobank_id_prefix):
# This is a biobank sample for another environment. Ignore it.
return None
if _Columns.BIOBANK_ORDER_IDENTIFIER not in row:
return None
biobank_id = from_client_biobank_id(biobank_id_str)
sample = BiobankStoredSample(
biobankStoredSampleId=row[_Columns.SAMPLE_ID],
biobankId=biobank_id,
biobankOrderIdentifier=row[_Columns.BIOBANK_ORDER_IDENTIFIER],
test=row[_Columns.TEST_CODE])
if row[_Columns.PARENT_ID]:
# Skip child samples.
return None
sample.confirmed = _parse_timestamp(row, _Columns.CONFIRMED_DATE, sample)
sample.created = _parse_timestamp(row, _Columns.CREATE_DATE, sample)
return sample
def make_query_filter(self, field_name, value):
"""Handle HPO and code values when parsing filter values."""
if field_name == 'biobankId':
value = from_client_biobank_id(value, log_exception=True)
if field_name == 'hpoId' or field_name == 'awardee':
hpo = self.hpo_dao.get_by_name(value)
if not hpo:
raise BadRequest('No HPO found with name %s' % value)
if field_name == 'awardee':
field_name = 'hpoId'
return super(ParticipantSummaryDao,
self).make_query_filter(field_name, hpo.hpoId)
if field_name == 'organization':
organization = self.organization_dao.get_by_external_id(value)
if not organization:
raise BadRequest('No organization found with name %s' % value)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id',
organization.organizationId)
if field_name in _SITE_FIELDS:
if value == UNSET:
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id', None)
site = self.site_dao.get_by_google_group(value)
if not site:
raise BadRequest('No site found with google group %s' % value)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id',
site.siteId)
if field_name in _CODE_FILTER_FIELDS:
if value == UNSET:
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id', None)
# Note: we do not at present support querying for UNMAPPED code values.
code = self.code_dao.get_code(PPI_SYSTEM, value)
if not code:
raise BadRequest('No code found: %s' % value)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name + 'Id',
code.codeId)
if field_name == 'patientStatus':
return self._make_patient_status_field_filter(field_name, value)
return super(ParticipantSummaryDao,
self).make_query_filter(field_name, value)
