def _insert_genomic_set_from_row(row, csv_filename, timestamp):
"""Creates a new GenomicSet object from a CSV row.
Raises:
DataError if the row is invalid.
Returns:
A new GenomicSet.
"""
genomic_set_name = row[CsvColumns.GENOMIC_SET_NAME],
set_dao = GenomicSetDao()
genomic_set_version = set_dao.get_new_version_number(genomic_set_name)
kwargs = dict(
genomicSetName=genomic_set_name,
genomicSetCriteria=row[CsvColumns.GENOMIC_SET_CRITERIA],
genomicSetFile=csv_filename,
genomicSetFileTime=timestamp,
genomicSetStatus=GenomicSetStatus.UNSET,
genomicSetVersion=genomic_set_version,
)
genomic_set = GenomicSet(**kwargs)
set_dao.insert(genomic_set)
return genomic_set
def _create_fake_genomic_set(self, genomic_set_name, genomic_set_criteria,
genomic_set_filename):
now = clock.CLOCK.now()
genomic_set = GenomicSet()
genomic_set.genomicSetName = genomic_set_name
genomic_set.genomicSetCriteria = genomic_set_criteria
genomic_set.genomicSetFile = genomic_set_filename
genomic_set.genomicSetFileTime = now
genomic_set.genomicSetStatus = GenomicSetStatus.INVALID
set_dao = GenomicSetDao()
genomic_set.genomicSetVersion = set_dao.get_new_version_number(
genomic_set.genomicSetName)
set_dao.insert(genomic_set)
return genomic_set
class GenomicSetValidationBaseTestCase(SqlTestBase):
def setUp(self, with_data=True, use_mysql=False):
super(GenomicSetValidationBaseTestCase,
self).setUp(with_data=with_data, use_mysql=use_mysql)
self.participant_dao = ParticipantDao()
self.summary_dao = ParticipantSummaryDao()
self.genomic_set_dao = GenomicSetDao()
self.genomic_member_dao = GenomicSetMemberDao()
self._participant_i = 0
self.setup_data()
def setup_data(self):
pass
def make_participant(self, **kwargs):
"""
Make a participant with custom settings.
default should create a valid participant.
"""
i = self._participant_i
self._participant_i += 1
participant = Participant(participantId=i, biobankId=i, **kwargs)
self.participant_dao.insert(participant)
return participant
def make_summary(self, participant, **override_kwargs):
"""
Make a summary with custom settings.
default should create a valid summary.
"""
valid_kwargs = dict(participantId=participant.participantId,
biobankId=participant.biobankId,
withdrawalStatus=participant.withdrawalStatus,
dateOfBirth=datetime.datetime(2000, 1, 1),
firstName='foo',
lastName='bar',
zipCode='12345',
sampleStatus1ED04=SampleStatus.RECEIVED,
sampleStatus1SAL2=SampleStatus.RECEIVED,
samplesToIsolateDNA=SampleStatus.RECEIVED,
consentForStudyEnrollmentTime=datetime.datetime(
2019, 1, 1))
kwargs = dict(valid_kwargs, **override_kwargs)
summary = self._participant_summary_with_defaults(**kwargs)
self.summary_dao.insert(summary)
return summary
def make_genomic_set(self, **override_kwargs):
"""
Make a genomic set with custom settings.
default should create a valid set.
"""
valid_kwargs = dict(genomicSetName='foo',
genomicSetCriteria='something',
genomicSetVersion=1,
genomicSetStatus=GenomicSetStatus.UNSET)
kwargs = dict(valid_kwargs, **override_kwargs)
genomic_set = GenomicSet(**kwargs)
self.genomic_set_dao.insert(genomic_set)
return genomic_set
def make_genomic_member(self, genomic_set, participant, **override_kwargs):
"""
Make a genomic member with custom settings.
default should create a valid member.
"""
valid_kwargs = dict(genomicSetId=genomic_set.id,
participantId=participant.participantId,
sexAtBirth='F',
biobankId=participant.biobankId,
biobankOrderClientId='12345678')
kwargs = dict(valid_kwargs, **override_kwargs)
member = GenomicSetMember(**kwargs)
self.genomic_member_dao.insert(member)
return member