def test_interpretation_request(self):
# 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)
instance = interpretation_request_factory()
self.assertTrue(instance.validate(instance.toJsonDict()))
# get an interpretation request RD for reports 4.0.0
interpretation_request_factory = GenericFactoryAvro.get_factory_avro(
protocols.reports_4_0_0.InterpretationRequestRD,
version=VERSION_400)
instance = interpretation_request_factory()
self.assertTrue(instance.validate(instance.toJsonDict()))
# get an interpretation request RD for reports 3.1.0
interpretation_request_factory = GenericFactoryAvro.get_factory_avro(
protocols.reports_3_0_0.InterpretationRequestRD,
version=VERSION_300)
instance = interpretation_request_factory()
self.assertTrue(instance.validate(instance.toJsonDict()))
def test_migrate_rd_clinical_report(self):
# creates a random clinical report cancer for testing filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.ClinicalReportRD, VERSION_400,
fill_nullables=True).create(
interpretationRequestVersion='1'
) # we need to enforce that it can be cast to int
self._validate(old_instance)
self._check_non_empty_fields(old_instance)
assembly = 'grch38'
new_instance = MigrateReports400To500().migrate_clinical_report_rd(
old_instance, assembly=assembly)
self._validate(new_instance)
self._check_non_empty_fields(
new_instance,
exclusions=[
"alleleFrequencies", "genomicChanges", "proteinChanges",
"cdnaChanges", "dbSnpId", "cosmicIds", "clinVarIds",
"variantConsequences", "drugResponseClassification",
"functionalEffect", "traitAssociation",
"tumorigenesisClassification", "clinicalSignificance",
"variantAttributes", "vaf"
])
self._check_variant_coordinates(old_instance.candidateVariants,
new_instance.variants,
reports_5_0_0.Assembly.GRCh38)
# creates a random clinical report cancer for testing not filling null values
cr_c_400 = GenericFactoryAvro.get_factory_avro(
self.old_model.ClinicalReportRD, VERSION_400,
fill_nullables=False).create(interpretationRequestVersion='1')
self._validate(cr_c_400)
assembly = 'hg19'
new_instance = MigrateReports400To500().migrate_clinical_report_rd(
cr_c_400, assembly=assembly)
self._validate(new_instance)
self.assertTrue(cr_c_400.candidateVariants is None)
self.assertTrue(new_instance.variants is None)
def test_json_serialization(self):
from protocols.util.dependency_manager import VERSION_400
from protocols.util.factories.avro_factory import GenericFactoryAvro
from protocols.reports_4_0_0 import CancerInterpretationRequest as CancerInterpretationRequest_4_0_0
cir_v4 = GenericFactoryAvro.get_factory_avro(clazz=CancerInterpretationRequest_4_0_0,
version=VERSION_400, fill_nullables=True).create()
cir_v4.validate(cir_v4.toJsonDict())
cir_v4_json = cir_v4.toJsonDict()
cir_v4_from_json = CancerInterpretationRequest_4_0_0.fromJsonDict(cir_v4_json)
cir_v4_from_json.validate(cir_v4_from_json.toJsonDict())
def _test_post(self, clazz, post_function):
model = GenericFactoryAvro.get_factory_avro(
clazz=clazz,
version=dependency_manager.VERSION_73,
fill_nullables=False,
).create()
response = post_function(model)
# this is stronger than it looks because post checks for errors
self.assertIsNotNone(response)
return response
def test_migrate_interpretation_request_rd_to_interpreted_genome_210_600(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_2_1_0.InterpretationRequestRD, VERSION_210, fill_nullables=fill_nullables
).create()
self._validate(old_instance)
migrated_instance = MigrationHelpers.migrate_interpretation_request_rd_to_interpreted_genome_latest(
old_instance.toJsonDict(), assembly='GRCh38'
)
self.assertIsInstance(migrated_instance, reports_6_0_0.InterpretedGenome)
self._validate(migrated_instance)
def test_migrate_interpreted_genome_rd_600_300(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_6_0_0.InterpretedGenome, VERSION_70, fill_nullables=fill_nullables
).create()
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.reverse_migrate_interpreted_genome_rd_to_v3(old_instance.toJsonDict())
self.assertIsInstance(migrated_instance, reports_3_0_0.InterpretedGenomeRD)
self._validate(migrated_instance)
def test_migrate_pedigree_110_110(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
participant_1_1_0.Pedigree,
VERSION_61,
fill_nullables=fill_nullables).create()
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.migrate_pedigree_to_latest(
old_instance.toJsonDict())
self._validate(migrated_instance)
def test_migrate_interpreted_genome_rd(self):
""" Test passing on 3000 real cases"""
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretedGenomeRD,
VERSION_300,
fill_nullables=False).create()
self._validate(old_instance)
migrated_instance = MigrateReports3To4().migrate_interpreted_genome_rd(
old_instance=old_instance)
self._validate(migrated_instance)
# fill all nullables
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretedGenomeRD,
VERSION_300,
fill_nullables=True).create()
self._validate(old_instance)
migrated_instance = MigrateReports3To4().migrate_interpreted_genome_rd(
old_instance=old_instance)
self._validate(migrated_instance)
def test_reverse_migrate_clinical_report_cancer_600_400(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_6_0_0.ClinicalReport, VERSION_70, fill_nullables=fill_nullables
).create()
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.reverse_migrate_clinical_report_cancer_to_v4(old_instance.toJsonDict())
self.assertIsInstance(migrated_instance, reports_4_0_0.ClinicalReportCancer)
self._validate(migrated_instance)
def test_migrate_interpretation_request_rd(self):
"""Also tested with real data"""
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretationRequestRD,
VERSION_210,
fill_nullables=False).create(
) # reports_3_0_0.InterpretationRequestRD
self._validate(old_instance)
migrated_instance = Migration21To3().migrate_interpretation_request(
old_instance)
self._validate(migrated_instance)
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretationRequestRD,
VERSION_210,
fill_nullables=True).create(
) # reports_3_0_0.InterpretationRequestRD
self._validate(old_instance)
migrated_instance = Migration21To3().migrate_interpretation_request(
old_instance)
self._validate(migrated_instance)
def test_migrate_interpreted_genome_rd_500_600(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_5_0_0.InterpretedGenomeRD, VERSION_61, fill_nullables=fill_nullables
).create()
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.migrate_interpreted_genome_rd_to_latest(
old_instance.toJsonDict()
)
self._validate(migrated_instance)
def test_migrate_pedigree_300_110(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_3_0_0.Pedigree, VERSION_300, fill_nullables=fill_nullables
).create()
for participant in old_instance.participants:
for disorder in participant.disorderList:
disorder.ageOfOnset = str(factory.fuzzy.FuzzyFloat(0.0).fuzz())
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.migrate_pedigree_to_latest(old_instance.toJsonDict())
self._validate(migrated_instance)
def test_migrate_cancer_interpreted_genome(self, fill_nullables=True):
# creates a random clinical report RD for testing filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.CancerInterpretedGenome, VERSION_61, fill_nullables=fill_nullables
).create(interpretationRequestVersion=1)
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
new_instance = MigrateReports500To400().migrate_cancer_interpreted_genome(old_instance=old_instance)
self.assertTrue(isinstance(new_instance, self.new_model.CancerInterpretedGenome))
self._validate(new_instance)
def test_migrate_cancer_participant(self):
old_participant = GenericFactoryAvro.get_factory_avro(
clazz=participant_1_0_3.CancerParticipant,
version=VERSION_500,
fill_nullables=True)()
migrated_participant = MigrationParticipants103To110(
).migrate_cancer_participant(old_participant)
self.assertIsInstance(migrated_participant,
self.new_model.CancerParticipant)
self._validate(migrated_participant)
old_participant = GenericFactoryAvro.get_factory_avro(
clazz=participant_1_0_3.CancerParticipant,
version=VERSION_500,
fill_nullables=False)()
migrated_participant = MigrationParticipants103To110(
).migrate_cancer_participant(old_participant)
self.assertIsInstance(migrated_participant,
self.new_model.CancerParticipant)
self._validate(migrated_participant)
def test_migrate_interpretation_request_rd(self):
"""Also tested with real data"""
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretationRequestRD,
VERSION_300,
fill_nullables=False).create(
) # reports_3_0_0.InterpretationRequestRD
self._validate(old_instance)
migrated_instance = MigrateReports3To4(
).migrate_interpretation_request_rd(old_instance=old_instance)
self._validate(migrated_instance)
old_big_wigs = old_instance.bigWigs
new_big_wigs = migrated_instance.bigWigs
if old_big_wigs is not None:
for old_big_wig, new_big_wig in zip(old_big_wigs, new_big_wigs):
self.assertIsInstance(new_big_wig, self.new_model.File)
self.assertEqual(new_big_wig.sampleId, old_big_wig.SampleId)
self.assertEqual(new_big_wig.uriFile, old_big_wig.URIFile)
self.assertEqual(new_big_wig.fileType, old_big_wig.fileType)
self.assertEqual(new_big_wig.md5Sum, None)
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretationRequestRD,
VERSION_300,
fill_nullables=True).create(
) # reports_3_0_0.InterpretationRequestRD
self._validate(old_instance)
migrated_instance = MigrateReports3To4(
).migrate_interpretation_request_rd(old_instance=old_instance)
for old_variant, new_variant in zip(old_instance.TieredVariants,
migrated_instance.tieredVariants):
for old_re, new_re in zip(old_variant.reportEvents,
new_variant.reportEvents):
self.assertEqual(old_re.genomicFeature.HGNC,
new_re.genomicFeature.hgnc)
self._validate(migrated_instance)
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 test_reverse_migrate_cancer_exit_questionnaire_to_v5(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_6_0_0.CancerExitQuestionnaire, VERSION_70, fill_nullables=fill_nullables
).create()
old_instance = self.populate_c_eq_variant_level_questions_variant_details(old_c_eq=old_instance)
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.reverse_migrate_cancer_exit_questionnaire_to_v5(
json_dict=old_instance.toJsonDict()
)
self.assertIsInstance(migrated_instance, reports_5_0_0.CancerExitQuestionnaire)
self._validate(migrated_instance)
def test_migrate_clinical_report_cancer_500_600(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_5_0_0.ClinicalReportCancer, VERSION_61, fill_nullables=fill_nullables
).create()
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.migrate_clinical_report_cancer_to_latest(
json_dict=old_instance.toJsonDict(),
)
self.assertIsInstance(migrated_instance, reports_6_0_0.ClinicalReport)
self._validate(migrated_instance)
def test_migrate_genomic_entity_to_feature(self):
old_entity = GenericFactoryAvro.get_factory_avro(self.old_model.GenomicEntity, VERSION_61, fill_nullables=True).create()
entity_type = old_entity.type
feature_type_map = {
self.old_model.GenomicEntityType.regulatory_region: self.new_model.FeatureTypes.RegulatoryRegion,
self.old_model.GenomicEntityType.gene: self.new_model.FeatureTypes.Gene,
self.old_model.GenomicEntityType.transcript: self.new_model.FeatureTypes.Transcript,
}
expected_feature_type = feature_type_map.get(entity_type)
new_feature = MigrateReports500To400()._migrate_genomic_entity_to_feature(old_entity)
self.assertTrue(isinstance(new_feature, self.new_model.GenomicFeature))
self._validate(new_feature)
self.assertEqual(new_feature.featureType, expected_feature_type)
def test_migrate_clinical_report_cancer_300_600(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_3_0_0.ClinicalReportCancer, VERSION_300, fill_nullables=fill_nullables
).create()
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance, exclusions=["md5Sum"])
with self.assertRaises(MigrationError):
MigrationHelpers.migrate_clinical_report_cancer_to_latest(
json_dict=old_instance.toJsonDict(), sample_ids={
'somatic_variant': 'somatic1', 'germline_variant': 'germline1'}, assembly='GRCh38', participant_id='456'
)
def test_migrate_cancer_participant_100_110(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
participant_1_0_0.CancerParticipant,
VERSION_400,
fill_nullables=fill_nullables).create(
) # type: participant_1_0_0.CancerParticipant
old_instance.LDPCode = "fakedLDP"
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.migrate_cancer_participant_to_latest(
old_instance.toJsonDict())
self._validate(migrated_instance)
def test_migrate_interpretation_request_rd(self, fill_nullables=True):
old_ir_rd = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretationRequestRD,
VERSION_61,
fill_nullables=fill_nullables).create()
new_ir_rd = MigrateReports500To600().migrate_interpretation_request_rd(
old_instance=old_ir_rd)
self._validate(new_ir_rd)
self.assertIsInstance(new_ir_rd,
self.new_model.InterpretationRequestRD)
self.assertIsInstance(new_ir_rd.versionControl,
self.new_model.ReportVersionControl)
self.assertEqual(new_ir_rd.versionControl.gitVersionControl, '6.0.0')
def test_migrate_rd_clinical_report_210_600(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_2_1_0.ClinicalReportRD, VERSION_210, fill_nullables=fill_nullables
).create()
old_instance.interpretationRequestVersion = str(factory.fuzzy.FuzzyInteger(0).fuzz())
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.migrate_clinical_report_rd_to_latest(
old_instance.toJsonDict(), assembly='GRCh38')
self.assertIsInstance(migrated_instance, reports_6_0_0.ClinicalReport)
self._validate(migrated_instance)
def test_migrate_interpreted_genome_rd_400_600(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_4_0_0.InterpretedGenomeRD, VERSION_400, fill_nullables=fill_nullables
).create()
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.migrate_interpreted_genome_rd_to_latest(
old_instance.toJsonDict(), assembly='GRCh38', interpretation_request_version=1
)
self.assertIsInstance(migrated_instance, reports_6_0_0.InterpretedGenome)
self._validate(migrated_instance)
def test_migrate_cancer_exit_questionnaire(self, fill_nullables=True):
old_c_eq = GenericFactoryAvro.get_factory_avro(
self.old_model.CancerExitQuestionnaire,
VERSION_61,
fill_nullables=fill_nullables).create()
old_c_eq = self.populate_c_eq_variant_level_questions_variant_details(
old_c_eq=old_c_eq)
new_c_eq = MigrateReports500To600().migrate_cancer_exit_questionnaire(
old_instance=old_c_eq,
assembly="GRCh38",
)
self.assertIsInstance(new_c_eq, self.new_model.CancerExitQuestionnaire)
self._validate(new_c_eq)
def test_migrate_interpretation_request_rd_500_600(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_5_0_0.InterpretationRequestRD, VERSION_61, fill_nullables=fill_nullables
).create()
self.assertIsInstance(old_instance, reports_5_0_0.InterpretationRequestRD)
self._validate(old_instance)
migrated_instance = MigrationHelpers.migrate_interpretation_request_rd_to_latest(
json_dict=old_instance.toJsonDict()
)
self.assertIsInstance(migrated_instance, reports_6_0_0.InterpretationRequestRD)
self._validate(migrated_instance)
self.assertEqual(migrated_instance.versionControl.gitVersionControl, '6.0.0')
def test_migrate_germline_variant_level_questions(self,
fill_nullables=True):
old_q = GenericFactoryAvro.get_factory_avro(
self.old_model.CancerGermlineVariantLevelQuestions,
VERSION_61,
fill_nullables=fill_nullables).create()
old_q = self.populate_variant_level_questions_variant_details(q=old_q)
new_q = MigrateReports500To600(
)._migrate_germline_variant_level_question(question=old_q,
assembly="GRCh38")
self.assertIsInstance(
new_q, self.new_model.CancerGermlineVariantLevelQuestions)
self._validate(new_q)
def test_migrate_cancer_interpretation_request(self):
"""
Test passing with ILMN-8308-1 cancer IR
"""
# tests with all nullable fields being filled
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.CancerInterpretationRequest,
VERSION_400,
fill_nullables=True).create(
) # we need to enforce that it can be cast to int
valid_cancer_origins = ['germline_variant', 'somatic_variant']
for tiered_variant in old_instance.tieredVariants:
if tiered_variant.alleleOrigins[0] not in valid_cancer_origins:
tiered_variant.alleleOrigins[0] = random.choice(
valid_cancer_origins)
self._validate(old_instance)
self._check_non_empty_fields(old_instance)
migrated_instance = MigrateReports400To500(
).migrate_cancer_interpretation_request(old_instance=old_instance,
assembly='GRCh38')
self._validate(migrated_instance)
# test with all nullable fields being null
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.CancerInterpretationRequest,
VERSION_400,
fill_nullables=False).create(
) # we need to enforce that it can be cast to int
for tiered_variant in old_instance.tieredVariants:
if tiered_variant.alleleOrigins[0] not in valid_cancer_origins:
tiered_variant.alleleOrigins[0] = random.choice(
valid_cancer_origins)
old_instance.cancerParticipant.LDPCode = "needs to be filled"
self._validate(old_instance)
migrated_instance = MigrateReports400To500(
).migrate_cancer_interpretation_request(old_instance=old_instance,
assembly='GRCh38')
self._validate(migrated_instance)
def test_migrate_questionnaire_rd_500_600(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_5_0_0.RareDiseaseExitQuestionnaire, VERSION_61, fill_nullables=fill_nullables
).create()
old_instance = self.populate_exit_questionnaire_variant_details(eq=old_instance)
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
migrated_instance = MigrationHelpers.migrate_exit_questionnaire_rd_to_latest(
json_dict=old_instance.toJsonDict(), assembly="GRCh38"
)
self.assertIsInstance(migrated_instance, reports_6_0_0.RareDiseaseExitQuestionnaire)
self._validate(migrated_instance)
def test_migrate_interpreted_genome_cancer_300_500(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
reports_3_0_0.CancerInterpretedGenome, VERSION_300, fill_nullables=fill_nullables
).create()
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance, exclusions=["md5Sum"])
with self.assertRaises(MigrationError):
MigrationHelpers.migrate_interpreted_genome_cancer_to_latest(
old_instance.toJsonDict(), assembly='GRCh38', participant_id='123', sample_ids={
'somatic_variant': 'somatic1', 'germline_variant': 'germline1'},
interpretation_request_version=5, interpretation_service='congenica')
self.assertTrue(False)
