def test_register_custom_factory(self):
## registering GA4GH variant factory
GenericFactoryAvro.register_factory(Variant,
GA4GHVariantFactory,
version="4.0.0")
factory = GenericFactoryAvro.get_factory_avro(Variant, "4.0.0")
instances = factory.create_batch(5)
for instance in instances:
self.assertTrue(instance.validate(instance.toJsonDict()))
self.assertTrue(instance.referenceBases in ["A", "C", "G", "T"])
## register CancerReportedVariantsFactory
GenericFactoryAvro.register_factory(
protocols.reports_3_0_0.ReportedVariantCancer,
CancerReportedVariantsFactory,
version="3.0.0")
factory = GenericFactoryAvro.get_factory_avro(
protocols.reports_3_0_0.CancerInterpretationRequest, "3.0.0")
instances = factory.create_batch(5)
for instance in instances:
self.assertTrue(instance.validate(instance.toJsonDict()))
for tiered_variant in instance.TieredVariants:
self.assertTrue(tiered_variant.reportedVariantCancer.reference
in ["A", "C", "G", "T"])
self.assertTrue(tiered_variant.reportedVariantCancer.alternate
in ["A", "C", "G", "T"])
def setUp(self):
# avoids infinite recursion in mocked data
# now creates another factory generating values for nullable fields
file_factory = GenericFactoryAvro.get_factory_avro(
protocols.reports_3_0_0.File, VERSION_300, False, False)
GenericFactoryAvro.register_factory(protocols.reports_3_0_0.File,
file_factory, VERSION_300, True)
def setUp(self):
GenericFactoryAvro.register_factory(reports_4_0_0.Actions,
ActionFactory,
VERSION_400,
fill_nullables=True)
GenericFactoryAvro.register_factory(reports_4_0_0.Actions,
ActionFactory,
VERSION_400,
fill_nullables=False)
def setUp(self):
GenericFactoryAvro.register_factory(reports_3_0_0.File,
self.FileFactory300,
self.version_3_0_0,
fill_nullables=True)
GenericFactoryAvro.register_factory(reports_3_0_0.File,
self.FileFactory300,
self.version_3_0_0,
fill_nullables=False)
def test_batch(self):
# builds a batch of 5 interpretation requests
interpretation_request_factory = GenericFactoryAvro.get_factory_avro(
protocols.reports_4_2_0.InterpretationRequestRD,
version=VERSION_500
)
instances = interpretation_request_factory.create_batch(5)
for instance in instances:
self.assertTrue(instance.validate(instance.toJsonDict()))
self.assertTrue(instances[0].interpretationRequestId != instances[1].interpretationRequestId)
GenericFactoryAvro.register_factory(protocols.ga4gh_3_0_0.Variant, GA4GHVariantFactory)
GenericFactoryAvro.get_factory_avro(protocols.ga4gh_3_0_0.Variant)
def test_nullable_fields(self):
# creates a factory for File not filling nullable fields and registers it in cache
# as a factory that fill nullable fields
# NOTE: this is the workaround to circumvent the loop in model definition
file_factory = GenericFactoryAvro.get_factory_avro(
protocols.reports_4_2_0.File, VERSION_500, False, False)
GenericFactoryAvro.register_factory(protocols.reports_4_2_0.File,
file_factory, VERSION_500, True)
# get an interpretation request RD for reports 4.2.0
interpretation_request_factory = GenericFactoryAvro.get_factory_avro(
protocols.reports_4_2_0.InterpretationRequestRD,
version=VERSION_500,
fill_nullables=True)
instance = interpretation_request_factory()
self.assertTrue(instance.validate(instance.toJsonDict()))
def setUp(self):
GenericFactoryAvro.register_factory(
reports_4_0_0.Actions, self.ActionFactory, self.version_4_0_0, fill_nullables=True)
GenericFactoryAvro.register_factory(
reports_4_0_0.Actions, self.ActionFactory, self.version_4_0_0, fill_nullables=False)
GenericFactoryAvro.register_factory(
participant_1_0_0.CancerParticipant, self.CancerParticipantFactory, self.version_4_0_0, fill_nullables=False)
GenericFactoryAvro.register_factory(
participant_1_0_0.CancerParticipant, self.CancerParticipantFactoryNulls, self.version_4_0_0, fill_nullables=True)
def test_migrate_cancer_participant(self):
GenericFactoryAvro.register_factory(
clazz=participant_1_0_0.CancerParticipant,
factory=CancerParticipantFactory)
old_participant = GenericFactoryAvro.get_factory_avro(
clazz=participant_1_0_0.CancerParticipant, version=VERSION_400)()
matched_samples = self.old_model.MatchedSamples(
germlineSampleId='test_germline_id',
tumourSampleId='test_tumour_id')
old_participant.matchedSamples = [matched_samples]
old_participant.LDPCode = 'test_LDP_code'
self.assertIsInstance(old_participant,
self.old_model.CancerParticipant)
self._validate(old_participant)
migrated_participant = MigrationParticipants100To103(
).migrate_cancer_participant(old_instance=old_participant)
self.assertIsInstance(migrated_participant,
self.new_model.CancerParticipant)
self._validate(migrated_participant)
self.assertIsInstance(migrated_participant.versionControl,
self.new_model.VersionControl)
self.assertDictEqual(migrated_participant.versionControl.toJsonDict(),
{"GitVersionControl": "1.0.3"})
for germline_sample in migrated_participant.germlineSamples:
self.assertEqual(germline_sample.LDPCode, old_participant.LDPCode)
for tumour_sample in migrated_participant.tumourSamples:
self.assertEqual(tumour_sample.LDPCode, old_participant.LDPCode)
for matched_sample in migrated_participant.matchedSamples:
self.assertIsInstance(matched_sample,
self.new_model.MatchedSamples)
for old_matched_sample, new_matched_sample in zip(
old_participant.matchedSamples,
migrated_participant.matchedSamples):
self.assertDictEqual(old_matched_sample.toJsonDict(),
new_matched_sample.toJsonDict())
def test_register_custom_factory(self):
# creates a custom factory and registers it
class ReportVersionControlFactory(FactoryAvro):
def __init__(self, *args, **kwargs):
super(ReportVersionControlFactory, self).__init__(*args, **kwargs)
class Meta:
model = protocols.reports_4_2_0.ReportVersionControl
_version = VERSION_500
gitVersionControl = "4.3.0-SNAPSHOT"
GenericFactoryAvro.register_factory(
protocols.reports_4_2_0.ReportVersionControl,
ReportVersionControlFactory,
version=VERSION_500
)
interpretation_request_factory = GenericFactoryAvro.get_factory_avro(
protocols.reports_4_2_0.InterpretationRequestRD,
version=VERSION_500
)
instance_ir = interpretation_request_factory()
self.assertTrue(instance_ir.validate(instance_ir.toJsonDict()))
self.assertTrue(instance_ir.versionControl.gitVersionControl == "4.3.0-SNAPSHOT")
# now creates another factory generating values for nullable fields
file_factory = GenericFactoryAvro.get_factory_avro(
protocols.reports_4_2_0.File,
VERSION_500,
False,
False
)
GenericFactoryAvro.register_factory(
protocols.reports_4_2_0.File,
file_factory,
VERSION_500,
True
)
interpretation_request_factory2 = GenericFactoryAvro.get_factory_avro(
protocols.reports_4_2_0.InterpretationRequestRD,
version=VERSION_500,
fill_nullables=True
)
instance_ir2 = interpretation_request_factory2()
self.assertTrue(instance_ir2.validate(instance_ir2.toJsonDict()))
self.assertFalse(instance_ir2.versionControl.gitVersionControl == "4.3.0-SNAPSHOT")
# now registers the factory for ReportVersionControl when filling nullables
GenericFactoryAvro.register_factory(
protocols.reports_4_2_0.ReportVersionControl,
ReportVersionControlFactory,
version=VERSION_500,
fill_nullables=True
)
instance_ir3 = interpretation_request_factory2()
self.assertTrue(instance_ir3.validate(instance_ir3.toJsonDict()))
self.assertTrue(instance_ir3.versionControl.gitVersionControl == "4.3.0-SNAPSHOT")
def setUp(self):
GenericFactoryAvro.register_factory(
reports_4_0_0.Actions, ActionFactory400, VERSION_400, fill_nullables=True)
GenericFactoryAvro.register_factory(
reports_3_0_0.Actions, ActionFactory300, VERSION_300, fill_nullables=True)
GenericFactoryAvro.register_factory(
reports_3_0_0.File, FileFactory300, VERSION_300, fill_nullables=True)
GenericFactoryAvro.register_factory(
reports_2_1_0.File, FileFactory210, VERSION_210, fill_nullables=True)
GenericFactoryAvro.register_factory(
reports_4_0_0.Actions, ActionFactory400, VERSION_400, fill_nullables=False)
GenericFactoryAvro.register_factory(
reports_3_0_0.Actions, ActionFactory300, VERSION_300, fill_nullables=False)
GenericFactoryAvro.register_factory(
reports_3_0_0.File, FileFactory300, VERSION_300, fill_nullables=False)
GenericFactoryAvro.register_factory(
reports_2_1_0.File, FileFactory210, VERSION_210, fill_nullables=False)
def setUp(self):
GenericFactoryAvro.register_factory(reports_3_0_0.File,
self.FileFactory300,
self.version_3_0_0,
fill_nullables=True)
GenericFactoryAvro.register_factory(reports_3_0_0.File,
self.FileFactory300,
self.version_3_0_0,
fill_nullables=False)
GenericFactoryAvro.register_factory(reports_3_0_0.CalledGenotype,
self.CalledGenotypeFactory300,
self.version_3_0_0,
fill_nullables=True)
GenericFactoryAvro.register_factory(reports_3_0_0.RDParticipant,
self.RDParticipantFactory300,
self.version_3_0_0,
fill_nullables=False)
GenericFactoryAvro.register_factory(reports_3_0_0.RDParticipant,
self.RDParticipantFactory300Nulls,
self.version_3_0_0,
fill_nullables=True)
GenericFactoryAvro.register_factory(reports_3_0_0.Pedigree,
self.PedigreeFactory300,
self.version_3_0_0,
fill_nullables=False)
GenericFactoryAvro.register_factory(reports_3_0_0.Pedigree,
self.PedigreeFactory300Nulls,
self.version_3_0_0,
fill_nullables=True)
GenericFactoryAvro.register_factory(reports_3_0_0.HpoTerm,
self.HpoTermFactory,
self.version_3_0_0,
fill_nullables=True)
def setUp(self):
valid_tiers = [self.old_model.Tier.TIER1, self.old_model.Tier.TIER2,
self.old_model.Tier.TIER3, self.old_model.Tier.NONE]
# registers factories to ensure that tiers in report events are only valid ones
class ReportEventFactoryNulls(FactoryAvro):
def __init__(self, *args, **kwargs):
super(ReportEventFactoryNulls, self).__init__(*args, **kwargs)
class Meta:
model = self.old_model.ReportEvent
_version = VERSION_61
_fill_nullables = True
tier = factory.fuzzy.FuzzyChoice(valid_tiers)
GenericFactoryAvro.register_factory(self.old_model.ReportEvent, ReportEventFactoryNulls, VERSION_61, True)
class ReportEventFactory(FactoryAvro):
def __init__(self, *args, **kwargs):
super(ReportEventFactory, self).__init__(*args, **kwargs)
class Meta:
model = self.old_model.ReportEvent
_version = VERSION_61
_fill_nullables = False
tier = factory.fuzzy.FuzzyChoice(valid_tiers)
GenericFactoryAvro.register_factory(self.old_model.ReportEvent, ReportEventFactory, VERSION_61, False)
valid_genomic_features = [self.old_model.GenomicEntityType.regulatory_region,
self.old_model.GenomicEntityType.gene, self.old_model.GenomicEntityType.transcript]
class GenomicEntityFactoryNulls(FactoryAvro):
def __init__(self, *args, **kwargs):
super(GenomicEntityFactoryNulls, self).__init__(*args, **kwargs)
class Meta:
model = self.old_model.GenomicEntity
_version = VERSION_61
_fill_nullables = True
type = factory.fuzzy.FuzzyChoice(valid_genomic_features)
GenericFactoryAvro.register_factory(self.old_model.GenomicEntity, GenomicEntityFactoryNulls, VERSION_61, True)
class GenomicEntityFactory(FactoryAvro):
def __init__(self, *args, **kwargs):
super(GenomicEntityFactory, self).__init__(*args, **kwargs)
class Meta:
model = self.old_model.GenomicEntity
_version = VERSION_61
_fill_nullables = False
type = factory.fuzzy.FuzzyChoice(valid_genomic_features)
GenericFactoryAvro.register_factory(self.old_model.GenomicEntity, GenomicEntityFactory, VERSION_61, False)
valid_genotypes = [
self.old_model.Zygosity.reference_homozygous,
self.old_model.Zygosity.heterozygous,
self.old_model.Zygosity.alternate_homozygous,
self.old_model.Zygosity.missing,
self.old_model.Zygosity.half_missing_reference,
self.old_model.Zygosity.half_missing_alternate,
self.old_model.Zygosity.alternate_hemizigous,
self.old_model.Zygosity.reference_hemizigous,
self.old_model.Zygosity.unk,
]
class VariantCallFactoryNulls(FactoryAvro):
def __init__(self, *args, **kwargs):
super(VariantCallFactoryNulls, self).__init__(*args, **kwargs)
class Meta:
model = self.old_model.VariantCall
_version = VERSION_61
_fill_nullables = True
zygosity = factory.fuzzy.FuzzyChoice(valid_genotypes)
GenericFactoryAvro.register_factory(self.old_model.VariantCall, VariantCallFactoryNulls, VERSION_61, True)
class VariantCallFactory(FactoryAvro):
def __init__(self, *args, **kwargs):
super(VariantCallFactory, self).__init__(*args, **kwargs)
class Meta:
model = self.old_model.VariantCall
_version = VERSION_61
_fill_nullables = False
zygosity = factory.fuzzy.FuzzyChoice(valid_genotypes)
GenericFactoryAvro.register_factory(self.old_model.VariantCall, VariantCallFactory, VERSION_61, False)
# ensures that IR RD always have a pedigree
class InterpretationRequestRDFactory(FactoryAvro):
def __init__(self, *args, **kwargs):
super(InterpretationRequestRDFactory, self).__init__(*args, **kwargs)
class Meta:
model = self.old_model.InterpretationRequestRD
_version = VERSION_61
_fill_nullables = False
pedigree = GenericFactoryAvro.get_factory_avro(
self.old_model.Pedigree, VERSION_61, fill_nullables=_fill_nullables).create()
GenericFactoryAvro.register_factory(
self.old_model.InterpretationRequestRD, InterpretationRequestRDFactory, VERSION_61, False)