def test_migrate_interpretation_request_rd(self):
# tests with all nullable fields being filled
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretationRequestRD, VERSION_400, fill_nullables=True
).create()
if old_instance.pedigree.members:
for member in old_instance.pedigree.members:
if member.disorderList:
for disorder in member.disorderList:
disorder.ageOfOnset = "1.5"
self._validate(old_instance)
self._check_non_empty_fields(old_instance)
migrated_instance = MigrateReports400To500().migrate_interpretation_request_rd(
old_instance=old_instance, assembly='GRCh38'
)
self._validate(migrated_instance)
for other_file in migrated_instance.otherFiles.values():
self.assertIsInstance(other_file, self.new_model.File)
# test with all nullable fields being null
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretationRequestRD, VERSION_400, fill_nullables=False
).create()
self._validate(old_instance)
migrated_instance = MigrateReports400To500().migrate_interpretation_request_rd(
old_instance=old_instance, assembly='GRCh38'
)
self._validate(migrated_instance)
if migrated_instance.otherFiles is not None:
for other_file in migrated_instance.otherFiles.values():
self.assertIsInstance(other_file, self.new_model.File)
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_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
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
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_cancer_clinical_report(self):
# creates a random clinical report cancer for testing filling null values
cr_c_400 = GenericFactoryAvro.get_factory_avro(
self.old_model.ClinicalReportCancer, VERSION_400, fill_nullables=True
).create(interpretationRequestVersion='1') # we need to enforce that it can be cast to int
valid_cancer_origins = ['germline_variant', 'somatic_variant']
if cr_c_400.candidateVariants:
for candidate_variant in cr_c_400.candidateVariants:
if candidate_variant.alleleOrigins[0] not in valid_cancer_origins:
candidate_variant.alleleOrigins[0] = random.choice(valid_cancer_origins)
self._validate(cr_c_400)
self._check_non_empty_fields(cr_c_400)
assembly = 'grch38'
participant_id = "no_one"
sample_ids = {
'germline_variant': 'germline1',
'somatic_variant': 'somatic1'
}
migrated_cir_500 = MigrateReports400To500().migrate_cancer_clinical_report(
cr_c_400, assembly=assembly, participant_id=participant_id, sample_ids=sample_ids
)
self._validate(migrated_cir_500)
self._check_non_empty_fields(migrated_cir_500,
exclusions=["genomicChanges", "references", "actionType", "otherIds",
"groupOfVariants", "score", "vendorSpecificScores",
"variantClassification", "fdp50", "recurrentlyReported", "others",
"phaseSet"])
self._check_variant_coordinates(
[variant.reportedVariantCancer for variant in cr_c_400.candidateVariants],
migrated_cir_500.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.ClinicalReportCancer, VERSION_400, fill_nullables=False
).create(interpretationRequestVersion='1')
if cr_c_400.candidateVariants:
for candidate_variant in cr_c_400.candidateVariants:
if candidate_variant.alleleOrigins[0] not in valid_cancer_origins:
candidate_variant.alleleOrigins[0] = random.choice(valid_cancer_origins)
self._validate(cr_c_400)
assembly = 'hg19'
participant_id = "no_one"
sample_ids = {
'germline_variant': 'germline1',
'somatic_variant': 'somatic1'
}
migrated_cir_500 = MigrateReports400To500().migrate_cancer_clinical_report(
cr_c_400, assembly=assembly, participant_id=participant_id, sample_ids=sample_ids
)
self._validate(migrated_cir_500)
self.assertTrue(cr_c_400.candidateVariants is None)
self.assertTrue(migrated_cir_500.variants is None)
def test_migrate_interpretation_request_rd_to_interpreted_genome_rd(self):
# creates a random clinical report cancer for testing filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretationRequestRD, VERSION_400, fill_nullables=True
).create() # we need to enforce that it can be cast to int
self._validate(old_instance)
self._check_non_empty_fields(old_instance)
assembly = 'grch38'
interpretation_service = "testing"
new_instance = MigrateReports400To500().migrate_interpretation_request_rd_to_interpreted_genome_rd(
old_instance, assembly=assembly, interpretation_service=interpretation_service,
reference_database_versions={'dbSnp': 'rs12345'},
software_versions={'intogen': '1.5'},
report_url="blablabla.blah",
comments=["bla", "bla!", "bla?"]
)
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.tieredVariants,
new_instance.variants,
reports_5_0_0.Assembly.GRCh38
)
self.assertEqual(old_instance.tieringVersion, new_instance.softwareVersions['tiering'])
# creates a random clinical report cancer for testing not filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretationRequestRD, VERSION_400, fill_nullables=False
).create()
self._validate(old_instance)
assembly = 'hg19'
new_instance = MigrateReports400To500().migrate_interpretation_request_rd_to_interpreted_genome_rd(
old_instance, assembly=assembly, interpretation_service=interpretation_service,
reference_database_versions={'dbSnp': 'rs12345'},
software_versions={'intogen': '1.5'},
report_url="blablabla.blah",
comments=["bla", "bla!", "bla?"]
)
self._validate(new_instance)
self._check_variant_coordinates(
old_instance.tieredVariants,
new_instance.variants,
reports_5_0_0.Assembly.GRCh37
)
def migrate_clinical_report_cancer_to_v6(json_dict,
sample_id=None,
assembly=None,
participant_id=None):
"""
Migration from reports 3.0.0 is not supported as we have no data in that version
:type json_dict: dict
:type sample_id: str
:type assembly: Assembly
:type participant_id: str
:rtype: ClinicalReport_6_0_0
"""
types = [
ClinicalReport_6_0_0, ClinicalReportCancer_5_0_0,
ClinicalReportCancer_4_0_0
]
migrations = [
lambda x: x,
MigrateReports500To600().migrate_cancer_clinical_report,
lambda x: MigrateReports400To500().migrate_cancer_clinical_report(
old_instance=x,
assembly=assembly,
participant_id=participant_id,
sample_id=sample_id)
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def migrate_interpretation_request_rd_to_interpreted_genome_v6(
json_dict, assembly):
"""
:type json_dict: dict
:type assembly: Assembly
:rtype: InterpretedGenomeRD_6_0_0
"""
types = [
InterpretationRequestRD_6_0_0, InterpretationRequestRD_5_0_0,
InterpretationRequestRD_4_0_0, InterpretationRequestRD_3_0_0,
InterpretationRequestRD_2_1_0
]
migrations = [
lambda x: x,
MigrateReports500To600().migrate_interpreted_genome_rd,
lambda x: MigrateReports400To500(
).migrate_interpretation_request_rd_to_interpreted_genome_rd(
old_instance=x,
assembly=assembly,
interpretation_service="tiering",
reference_database_versions={},
software_versions={}),
MigrateReports3To4().migrate_interpretation_request_rd,
Migration21To3().migrate_interpretation_request
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def migrate_interpreted_genome_cancer_to_v6(
json_dict,
assembly=None,
participant_id=None,
sample_id=None,
interpretation_request_version=None,
interpretation_service=None):
"""
Migration from reports 3.0.0 is not supported as we have no data in that version
:type json_dict: dict
:type assembly: Assembly
:type participant_id: str
:type sample_id: str
:type interpretation_request_version: int
:type interpretation_service: str
:rtype: InterpretedGenome_6_0_0
"""
types = [
InterpretedGenome_6_0_0, CancerInterpretedGenome_5_0_0,
CancerInterpretedGenome_4_0_0
]
migrations = [
lambda x: x,
MigrateReports500To600().migrate_cancer_interpreted_genome, lambda
x: MigrateReports400To500().migrate_cancer_interpreted_genome(
old_instance=x,
assembly=assembly,
participant_id=participant_id,
sample_id=sample_id,
interpretation_request_version=interpretation_request_version,
interpretation_service=interpretation_service)
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def migrate_interpreted_genome_rd_to_v6(
json_dict,
assembly=None,
interpretation_request_version=None,
panel_source='panelapp'):
"""
:type json_dict: dict
:type assembly: Assembly
:type interpretation_request_version: int
:type panel_source: str
:rtype: InterpretedGenome_6_0_0
"""
types = [
InterpretedGenome_6_0_0, InterpretedGenomeRD_5_0_0,
InterpretedGenomeRD_4_0_0, InterpretedGenomeRD_3_0_0,
InterpretedGenomeRD_2_1_0
]
migrations = [
lambda x: x, lambda x: MigrateReports500To600(
).migrate_interpreted_genome_rd(x, panel_source=panel_source),
lambda x: MigrateReports400To500().migrate_interpreted_genome_rd(
x,
assembly=assembly,
interpretation_request_version=interpretation_request_version),
MigrateReports3To4().migrate_interpreted_genome_rd,
Migration21To3().migrate_interpreted_genome
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def test_migrate_reported_variants(self):
old_ig = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretedGenomeRD, VERSION_400, fill_nullables=True
).create()
self._validate(old_ig)
reported_variants_5 = MigrateReports400To500().convert_collection(
old_ig.reportedVariants, MigrateReports400To500()._migrate_reported_variant, assembly="GRCh37"
)
old_hgnc_symbols = [re.genomicFeature.hgnc for rv in old_ig.reportedVariants for re in rv.reportEvents]
new_hgnc_symbols = [ge.geneSymbol for rv in reported_variants_5 for re in rv.reportEvents for ge in re.genomicEntities]
[self.assertIsNotNone(symbol) for symbol in old_hgnc_symbols]
[self.assertIsNotNone(symbol) for symbol in new_hgnc_symbols]
self.assertEqual(old_hgnc_symbols, new_hgnc_symbols)
def migrate_interpretation_request_cancer_to_interpreted_genome_v6(
json_dict, assembly, interpretation_service, reference_database_versions, software_versions,
report_url, comments):
"""
:type json_dict: dict
:type assembly: Assembly
:type interpretation_service: str
:type reference_database_versions: dict
:type software_versions: dict
:type report_url: str
:type comments: list
:rtype: CancerInterpretationRequest_6_0_0
"""
if CancerInterpretationRequest_5_0_0.validate(CancerInterpretationRequest_5_0_0.fromJsonDict(json_dict)):
raise MigrationError(
"Cannot transform a cancer interpretation request in version 5.0.0 into an interpreted genome")
if CancerInterpretationRequest_6_0_0.validate(CancerInterpretationRequest_6_0_0.fromJsonDict(json_dict)):
raise MigrationError(
"Cannot transform a cancer interpretation request in version 6.0.0 into an interpreted genome")
types = [
InterpretedGenome_6_0_0,
CancerInterpretedGenome_5_0_0,
CancerInterpretationRequest_4_0_0
]
migrations = [
lambda x: x,
MigrateReports500To600().migrate_cancer_interpreted_genome,
lambda x: MigrateReports400To500().migrate_cancer_interpretation_request_to_cancer_interpreted_genome(
old_instance=x, assembly=assembly, interpretation_service=interpretation_service,
reference_database_versions=reference_database_versions, software_versions=software_versions,
report_url=report_url, comments=comments)
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def test_migrate_rd_interpreted_genome(self):
# creates a random clinical report cancer for testing filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretedGenomeRD,
VERSION_400,
fill_nullables=True).create(
) # 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_interpreted_genome_rd(
old_instance, assembly=assembly, interpretation_request_version=1)
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.reportedVariants,
new_instance.variants,
reports_5_0_0.Assembly.GRCh38)
# creates a random clinical report cancer for testing not filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretedGenomeRD,
VERSION_400,
fill_nullables=False).create()
self._validate(old_instance)
assembly = 'hg19'
new_instance = MigrateReports400To500().migrate_interpreted_genome_rd(
old_instance, assembly=assembly, interpretation_request_version=1)
self._validate(new_instance)
self._check_variant_coordinates(old_instance.reportedVariants,
new_instance.variants,
reports_5_0_0.Assembly.GRCh37)
def migrate_interpretation_request_cancer_to_v6(json_dict, assembly):
"""
:type json_dict: dict
:type assembly: Assembly
:rtype: CancerInterpretationRequest_6_0_0
"""
types = [
CancerInterpretationRequest_6_0_0,
CancerInterpretationRequest_5_0_0,
CancerInterpretationRequest_4_0_0
]
migrations = [
MigrationHelpers.set_version_to_6_0_0,
MigrateReports500To600().migrate_interpretation_request_cancer,
lambda x: MigrateReports400To500().migrate_cancer_interpretation_request(old_instance=x, assembly=assembly)
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def migrate_clinical_report_rd_to_v6(json_dict, assembly=None):
"""
:type json_dict: dict
:type assembly: Assembly
:rtype: ClinicalReportRD_6_0_0
"""
types = [
ClinicalReport_6_0_0, ClinicalReportRD_5_0_0,
ClinicalReportRD_4_0_0, ClinicalReportRD_3_0_0,
ClinicalReportRD_2_1_0
]
migrations = [
lambda x: x,
MigrateReports500To600().migrate_clinical_report_rd,
lambda x: MigrateReports400To500().migrate_clinical_report_rd(
old_instance=x, assembly=assembly),
MigrateReports3To4().migrate_clinical_report_rd,
Migration21To3().migrate_clinical_report
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def migrate_interpretation_request_rd_to_v6(json_dict, assembly=None):
"""
:type json_dict: dict
:type assembly: Assembly
:rtype: InterpretationRequestRD_6_0_0
"""
types = [
InterpretationRequestRD_6_0_0,
InterpretationRequestRD_5_0_0,
InterpretationRequestRD_4_0_0,
InterpretationRequestRD_3_0_0,
InterpretationRequestRD_2_1_0
]
migrations = [
MigrationHelpers.set_version_to_6_0_0, # needed because 5 is valid as 6
MigrateReports500To600().migrate_interpretation_request_rd,
lambda x: MigrateReports400To500().migrate_interpretation_request_rd(old_instance=x, assembly=assembly),
MigrateReports3To4().migrate_interpretation_request_rd,
Migration21To3().migrate_interpretation_request
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def test_migrate_cancer_interpretation_request_to_cancer_interpreted_genome(
self):
# creates a random clinical report cancer for testing filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.CancerInterpretationRequest,
VERSION_400,
fill_nullables=True).create()
old_instance.cancerParticipant.tumourSamples = [
old_instance.cancerParticipant.tumourSamples[0]
]
self._validate(old_instance)
self._check_non_empty_fields(old_instance)
assembly = 'grch38'
interpretation_service = 'testing'
new_instance = MigrateReports400To500(
).migrate_cancer_interpretation_request_to_cancer_interpreted_genome(
old_instance,
assembly=assembly,
interpretation_service=interpretation_service,
reference_database_versions={'dbSnp': 'rs12345'},
software_versions={'intogen': '1.5'},
report_url="blablabla.blah",
comments=["bla", "bla!", "bla?"])
self._validate(new_instance)
self._check_non_empty_fields(
new_instance,
exclusions=[
"genomicChanges", "references", "actionType", "otherIds",
"groupOfVariants", "score", "vendorSpecificScores",
"variantClassification", "fdp50", "recurrentlyReported",
"others", "phaseSet"
])
self._check_variant_coordinates([
variant.reportedVariantCancer
for variant in old_instance.tieredVariants
], new_instance.variants, reports_5_0_0.Assembly.GRCh38)
# creates a random clinical report cancer for testing not filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.CancerInterpretationRequest,
VERSION_400,
fill_nullables=False).create()
old_instance.cancerParticipant.tumourSamples = [
old_instance.cancerParticipant.tumourSamples[0]
]
self._validate(old_instance)
assembly = 'grCH37'
interpretation_service = 'testing'
new_instance = MigrateReports400To500(
).migrate_cancer_interpretation_request_to_cancer_interpreted_genome(
old_instance,
assembly=assembly,
interpretation_service=interpretation_service,
reference_database_versions={},
software_versions={})
self._validate(new_instance)
self._check_variant_coordinates([
variant.reportedVariantCancer
for variant in old_instance.tieredVariants
], new_instance.variants, reports_5_0_0.Assembly.GRCh37)
def test_migrate_cancer_interpreted_genome(self):
# creates a random clinical report cancer for testing filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.CancerInterpretedGenome,
VERSION_400,
fill_nullables=True).create()
self._validate(old_instance)
self._check_non_empty_fields(old_instance)
assembly = 'grch38'
participant_id = "no_one"
sample_id = 'some'
interpretation_request_version = 1
interpretation_service = 'testing'
new_instance = MigrateReports400To500(
).migrate_cancer_interpreted_genome(
old_instance,
assembly=assembly,
participant_id=participant_id,
sample_id=sample_id,
interpretation_request_version=interpretation_request_version,
interpretation_service=interpretation_service)
self._validate(new_instance)
self._check_non_empty_fields(
new_instance,
exclusions=[
"genomicChanges", "references", "actionType", "otherIds",
"groupOfVariants", "score", "vendorSpecificScores",
"variantClassification", "fdp50", "recurrentlyReported",
"others", "phaseSet"
])
self._check_variant_coordinates([
variant.reportedVariantCancer
for variant in old_instance.reportedVariants
], new_instance.variants, reports_5_0_0.Assembly.GRCh38)
# creates a random clinical report cancer for testing not filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.CancerInterpretedGenome,
VERSION_400,
fill_nullables=False).create()
self._validate(old_instance)
assembly = 'hg19'
participant_id = "no_one"
sample_id = 'some'
interpretation_request_version = 1
interpretation_service = 'testing'
new_instance = MigrateReports400To500(
).migrate_cancer_interpreted_genome(
old_instance,
assembly=assembly,
participant_id=participant_id,
sample_id=sample_id,
interpretation_request_version=interpretation_request_version,
interpretation_service=interpretation_service)
self._validate(new_instance)
self._check_variant_coordinates([
variant.reportedVariantCancer
for variant in old_instance.reportedVariants
], new_instance.variants, reports_5_0_0.Assembly.GRCh37)
