def test_migrate_reported_variant_with_consequence(self,
fill_nullables=True):
old_reported_variant = GenericFactoryAvro.get_factory_avro(
self.old_model.ReportedVariant,
VERSION_61,
fill_nullables=fill_nullables).create()
old_reported_variant.additionalTextualVariantAnnotations = {
'ConsequenceType':
"initiator_codon_variant,incomplete_terminal_codon_variant"
}
old_reported_variant.reportEvents[0].tier = self.old_model.Tier.TIER1
old_reported_variant.reportEvents[1].tier = self.old_model.Tier.TIER2
new_small_variant = BaseMigration.convert_class(
reports_6_0_0.SmallVariant, old_reported_variant)
new_small_variant = MigrateReports500To600()._migrate_variant(
(old_reported_variant, new_small_variant))
self._validate(new_small_variant)
self.assertIsInstance(new_small_variant, self.new_model.SmallVariant)
self.assertEqual(
len(new_small_variant.reportEvents[0].variantConsequences), 1)
self.assertTrue(
new_small_variant.reportEvents[0].variantConsequences[0].name ==
'initiator_codon_variant')
self.assertEqual(
len(new_small_variant.reportEvents[1].variantConsequences), 1)
self.assertTrue(
new_small_variant.reportEvents[1].variantConsequences[0].name ==
'incomplete_terminal_codon_variant')
def test_migrate_reported_variant(self, fill_nullables=True):
old_reported_variant = GenericFactoryAvro.get_factory_avro(
self.old_model.ReportedVariant, VERSION_61, fill_nullables=fill_nullables
).create()
new_small_variant = BaseMigration.convert_class(reports_6_0_0.SmallVariant, old_reported_variant)
new_small_variant = MigrateReports500To600()._migrate_variant((old_reported_variant, new_small_variant))
self._validate(new_small_variant)
self.assertIsInstance(new_small_variant, self.new_model.SmallVariant)
for attribute in ["dbSnpId", "cosmicIds", "clinVarIds"]:
if getattr(old_reported_variant, attribute) is not None:
self.assertEqual(
getattr(old_reported_variant, attribute),
getattr(new_small_variant.variantAttributes.variantIdentifiers, attribute)
)
attributes = [
"genomicChanges", "cdnaChanges", "proteinChanges", "additionalTextualVariantAnnotations", "references",
"additionalNumericVariantAnnotations", "comments"
]
for attribute in attributes:
if getattr(old_reported_variant, attribute) is not None:
self.assertEqual(
getattr(old_reported_variant, attribute),
getattr(new_small_variant.variantAttributes, attribute)
)
if old_reported_variant.alleleFrequencies is not None:
old_frequencies = old_reported_variant.alleleFrequencies
new_frequencies = new_small_variant.variantAttributes.alleleFrequencies
for old, new in zip(old_frequencies, new_frequencies):
self.assertIsInstance(new, self.new_model.AlleleFrequency)
if old_reported_variant.alleleOrigins is not None:
old_origins = old_reported_variant.alleleOrigins
new_origins = new_small_variant.variantAttributes.alleleOrigins
for old, new in zip(old_origins, new_origins):
self.assertEqual(new, old)
old_calls = old_reported_variant.variantCalls
new_calls = new_small_variant.variantCalls
for old, new in zip(old_calls, new_calls):
self.assertIsInstance(new, self.new_model.VariantCall)
self.assertEqual(new, MigrateReports500To600()._migrate_variant_call((old, new)))
old_events = old_reported_variant.reportEvents
new_events = new_small_variant.reportEvents
for old, new in zip(old_events, new_events):
self.assertIsInstance(new, self.new_model.ReportEvent)
self.assertEqual(new.toJsonDict(), MigrateReports500To600()._migrate_report_event((old, new)).toJsonDict())
self.assertIsInstance(new_small_variant.variantAttributes, self.new_model.VariantAttributes)
self.assertEqual(
new_small_variant.variantAttributes,
MigrateReports500To600()._migrate_variant_attributes(old_variant=old_reported_variant)
)
def test_migrate_report_event(self, fill_nullables=True):
re_rd_6 = self.get_valid_object(object_type=old_model.ReportEvent,
version=self.version_7_0,
fill_nullables=fill_nullables)
re_rd_6.eventJustification = None
re_rd_6.segregationPattern = old_model.SegregationPattern.CompoundHeterozygous
re_rd_5 = BaseMigration.convert_class(
target_klass=new_model.ReportEvent, instance=re_rd_6)
re_rd_5 = MigrateReports600To500()._migrate_report_event(
(re_rd_6, re_rd_5))
self.assertIsInstance(re_rd_5, new_model.ReportEvent)
self.assertTrue(re_rd_5.validate(re_rd_5.toJsonDict()))
self.assertTrue(old_model.SegregationPattern.CompoundHeterozygous in
re_rd_5.eventJustification)
re_rd_6 = self.get_valid_object(object_type=old_model.ReportEvent,
version=self.version_7_0,
fill_nullables=fill_nullables)
re_rd_6.eventJustification = "I have an event justification"
re_rd_6.segregationPattern = old_model.SegregationPattern.CompoundHeterozygous
re_rd_5 = BaseMigration.convert_class(
target_klass=new_model.ReportEvent, instance=re_rd_6)
re_rd_5 = MigrateReports600To500()._migrate_report_event(
(re_rd_6, re_rd_5))
self.assertIsInstance(re_rd_5, new_model.ReportEvent)
self.assertTrue(re_rd_5.validate(re_rd_5.toJsonDict()))
self.assertTrue(re_rd_5.eventJustification is not None)
self.assertTrue(old_model.SegregationPattern.CompoundHeterozygous
not in re_rd_5.eventJustification)
re_rd_6 = self.get_valid_object(object_type=old_model.ReportEvent,
version=self.version_7_0,
fill_nullables=fill_nullables)
re_rd_6.eventJustification = None
re_rd_6.segregationPattern = None
re_rd_5 = BaseMigration.convert_class(
target_klass=new_model.ReportEvent, instance=re_rd_6)
re_rd_5 = MigrateReports600To500()._migrate_report_event(
(re_rd_6, re_rd_5))
self.assertIsInstance(re_rd_5, new_model.ReportEvent)
self.assertTrue(re_rd_5.validate(re_rd_5.toJsonDict()))
self.assertTrue(re_rd_5.eventJustification is None)
def _validate(self, instance):
return BaseMigration.validate_object(instance, type(instance))
def test_migrate_report_event(self):
old_report_event = GenericFactoryAvro.get_factory_avro(self.old_model.ReportEvent, VERSION_61, fill_nullables=True).create()
new_report_event = BaseMigration.convert_class(reports_4_0_0.ReportEvent, old_report_event)
new_report_event = MigrateReports500To400()._migrate_report_event((old_report_event, new_report_event))
self.assertTrue(isinstance(new_report_event, self.new_model.ReportEvent))
self._validate(new_report_event)