def reverse_migrate_interpretation_request_rd_to_v3(
json_dict, ig_json_dict):
ig_types = [InterpretedGenomeRD_5_0_0, InterpretedGenome_6_0_0]
ig_migrations = [
lambda x: x,
MigrateReports600To500().
migrate_interpreted_genome_to_interpreted_genome_rd
]
part_migrated_ig = MigrationHelpers.migrate(ig_json_dict, ig_types,
ig_migrations)
types = [
InterpretationRequestRD_3_0_0, InterpretationRequestRD_4_0_0,
InterpretationRequestRD_5_0_0, InterpretationRequestRD_6_0_0,
InterpretationRequestRD_6_0_1
]
migrations = [
lambda x: x,
MigrateReports400To300().migrate_interpretation_request_rd,
lambda x: MigrateReports500To400(
).migrate_interpretation_request_rd(x, old_ig=part_migrated_ig),
MigrateReports600To500().migrate_interpretation_request_rd,
MigrateReports601To600().migrate_interpretation_request_rd
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def reverse_migrate_interpretation_request_cancer_to_v4(
json_dict, ig_json_dict):
"""
:type json_dict: dict
:type ig_json_dict: dict
:type assembly: Assembly
:rtype: CancerInterpretationRequest_4_0_0
"""
ig_types = [CancerInterpretedGenome_5_0_0, InterpretedGenome_6_0_0]
ig_migrations = [
lambda x: x,
MigrateReports600To500().migrate_cancer_interpreted_genome,
]
part_migrated_ig = MigrationHelpers.migrate(ig_json_dict, ig_types,
ig_migrations)
types = [
CancerInterpretationRequest_4_0_0,
CancerInterpretationRequest_5_0_0,
CancerInterpretationRequest_6_0_0
]
migrations = [
lambda x: x,
lambda x: MigrateReports500To400().
migrate_interpretation_request_cancer_plus_cancer_interpreted_genome(
x, part_migrated_ig),
MigrateReports600To500().migrate_interpretation_request_cancer,
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def test_migrate_variant_call_to_called_genotype(self):
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.VariantCall, VERSION_61, fill_nullables=True
).create()
new_instance = MigrateReports500To400()._migrate_variant_call_to_called_genotype(variant_call=old_instance)
self.assertTrue(isinstance(new_instance, self.new_model.CalledGenotype))
self._validate(new_instance)
def test_migrate_rd_interpretation_request(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretationRequestRD, VERSION_61, fill_nullables=fill_nullables
).create(interpretationRequestVersion=1)
old_instance.additionalInfo = {}
old_instance.additionalInfo['cellbaseVersion'] = '1.0'
old_instance.additionalInfo['tieringVersion'] = '1.0'
old_instance.additionalInfo['analysisReturnUri'] = 'uri.com'
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
old_ig = GenericFactoryAvro.get_factory_avro(
self.old_model.InterpretedGenomeRD, VERSION_61, fill_nullables=fill_nullables
).create(interpretationRequestVersion=1, interpretationRequestId=old_instance.interpretationRequestId)
self._validate(old_ig)
if fill_nullables:
self._check_non_empty_fields(old_ig)
new_instance = MigrateReports500To400().migrate_interpretation_request_rd(
old_instance=old_instance, old_ig=old_ig)
self.assertTrue(isinstance(new_instance, self.new_model.InterpretationRequestRD))
self._validate(new_instance)
if fill_nullables:
self._check_variant_coordinates(
old_variants=old_ig.variants,
new_variants=new_instance.tieredVariants,
)
def test_migrate_variant_consequence_to_so_term(self):
vc_5 = self.get_valid_object(object_type=self.old_model.VariantConsequence, version=self.version_6_1)
so_4 = MigrateReports500To400()._migrate_variant_consequence_to_so_term(vc=vc_5)
self.assertIsInstance(so_4, self.new_model.SoTerm)
self.assertTrue(so_4.validate(so_4.toJsonDict()))
self.assertEqual(so_4.name, vc_5.name)
self.assertEqual(so_4.id, vc_5.id)
def test_migrate_rd_exit_questionnaire(self, fill_nullables=True):
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.RareDiseaseExitQuestionnaire, VERSION_61, fill_nullables=fill_nullables
).create()
self._validate(old_instance)
if fill_nullables:
self._check_non_empty_fields(old_instance)
new_instance = MigrateReports500To400().migrate_exit_questionnaire_rd(old_instance=old_instance)
self.assertTrue(isinstance(new_instance, self.new_model.RareDiseaseExitQuestionnaire))
self._validate(new_instance)
def test_migrate_genomic_entities_to_genomic_feature_cancer(self):
ge_5 = self.get_valid_object(object_type=self.old_model.GenomicEntity, version=self.version_6_1)
test_ref_seq_transcript_id = "test_refSeqTranscriptId"
test_ref_seq_protein_id = "test_refSeqProteinId"
ge_5.otherIds["refSeqTranscriptId"] = test_ref_seq_transcript_id
ge_5.otherIds["refSeqProteinId"] = test_ref_seq_protein_id
gfc_4 = MigrateReports500To400()._migrate_genomic_entities_to_genomic_feature_cancer(genomic_entities=[ge_5])
self.assertIsInstance(gfc_4, self.new_model.GenomicFeatureCancer)
self.assertTrue(gfc_4.validate(gfc_4.toJsonDict()))
self.assertEqual(gfc_4.refSeqProteinId, test_ref_seq_protein_id)
self.assertEqual(gfc_4.refSeqTranscriptId, test_ref_seq_transcript_id)
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 reverse_migrate_interpreted_genome_cancer_to_v4(json_dict):
types = [
CancerInterpretedGenome_4_0_0, CancerInterpretedGenome_5_0_0,
InterpretedGenome_6_0_0
]
migrations = [
lambda x: x,
MigrateReports500To400().migrate_cancer_interpreted_genome,
MigrateReports600To500().migrate_cancer_interpreted_genome
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def reverse_migrate_clinical_report_cancer_to_v4(json_dict):
types = [
ClinicalReportCancer_4_0_0, ClinicalReportCancer_5_0_0,
ClinicalReport_6_0_0
]
migrations = [
lambda x: x,
MigrateReports500To400().migrate_cancer_clinical_report,
MigrateReports600To500().migrate_clinical_report_cancer
]
return MigrationHelpers.migrate(json_dict, types, migrations)
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 reverse_migrate_exit_questionnaire_rd_to_v3(json_dict):
types = [
RareDiseaseExitQuestionnaire_3_0_0,
RareDiseaseExitQuestionnaire_4_0_0,
RareDiseaseExitQuestionnaire_5_0_0,
RareDiseaseExitQuestionnaire_6_0_0
]
migrations = [
lambda x: x,
MigrateReports400To300().migrate_exit_questionnaire_rd,
MigrateReports500To400().migrate_exit_questionnaire_rd,
MigrateReports600To500().migrate_exit_questionnaire_rd
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def test_migrate_interpretation_request_cancer_plus_cancer_interpreted_genome(self, fill_nullables=True):
ir_c_5 = self.get_valid_object(object_type=self.old_model.CancerInterpretationRequest,
version=self.version_6_1, fill_nullables=fill_nullables)
ir_c_5.additionalInfo = {
'interpretGenome': 'True',
'analysisUri': 'blah.com',
'analysisVersion': '1',
'tieringVersion': '1'
}
ig_c_5 = self.get_valid_object(object_type=self.old_model.CancerInterpretedGenome,
version=self.version_6_1, fill_nullables=fill_nullables)
ir_c_4 = MigrateReports500To400().migrate_interpretation_request_cancer_plus_cancer_interpreted_genome(
old_instance=ir_c_5, old_interpreted_genome=ig_c_5
)
self.assertIsInstance(ir_c_4, self.new_model.CancerInterpretationRequest)
self.assertTrue(ir_c_4.validate(ir_c_4.toJsonDict()))
def test_migrate_rd_clinical_report(self, fill_nullables=True):
# creates a random clinical report RD for testing filling null values
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.ClinicalReportRD, 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_clinical_report_rd(old_instance=old_instance)
self.assertTrue(isinstance(new_instance, self.new_model.ClinicalReportRD))
self._validate(new_instance)
if fill_nullables:
self._check_variant_coordinates(
old_variants=old_instance.variants,
new_variants=new_instance.candidateVariants,
)
def reverse_migrate_clinical_report_rd_to_v3(json_dict):
"""
Whether html or json, the clinical report data needs to be migrated from v5 to v3 for RD
:param json_dict: ClinicalReport RD v(6 to 3) json
:return: ClinicalReport model object with cr.clinical_report_data migrated to v3
"""
types = [
ClinicalReportRD_3_0_0, ClinicalReportRD_4_0_0,
ClinicalReportRD_5_0_0, ClinicalReport_6_0_0
]
migrations = [
lambda x: x,
MigrateReports400To300().migrate_clinical_report_rd,
MigrateReports500To400().migrate_clinical_report_rd,
MigrateReports600To500().migrate_clinical_report_rd
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def reverse_migrate_interpreted_genome_rd_to_v3(json_dict):
"""
:type json_dict: dict
:rtype: InterpretedGenomeRD_3_0_0
"""
types = [
InterpretedGenomeRD_3_0_0, InterpretedGenomeRD_4_0_0,
InterpretedGenomeRD_5_0_0, InterpretedGenome_6_0_0
]
migrations = [
lambda x: x,
MigrateReports400To300().migrate_interpreted_genome_rd,
MigrateReports500To400().migrate_interpreted_genome_rd,
MigrateReports600To500().
migrate_interpreted_genome_to_interpreted_genome_rd
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def test_migrate_analysis_panel(self):
old_panel = GenericFactoryAvro.get_factory_avro(
self.old_model.AdditionalAnalysisPanel, VERSION_61, fill_nullables=True
).create()
new_panel = MigrateReports500To400()._migrate_analysis_panel(old_panel=old_panel)
self.assertTrue(new_panel.validate(new_panel.toJsonDict()))
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)
def test_migrate_reported_variant(self):
old_reported_variant = GenericFactoryAvro.get_factory_avro(self.old_model.ReportedVariant, VERSION_61, fill_nullables=True).create()
new_reported_variant = MigrateReports500To400()._migrate_reported_variant(old_reported_variant=old_reported_variant)
self.assertTrue(isinstance(new_reported_variant, self.new_model.ReportedVariant))
self._validate(new_reported_variant)
def test_migrate_cancer_clinical_report(self, fill_nullables=True):
cr_c_5 = self.get_valid_object(object_type=self.old_model.ClinicalReportCancer, version=self.version_6_1, fill_nullables=fill_nullables)
cr_c_4 = MigrateReports500To400().migrate_cancer_clinical_report(old_instance=cr_c_5)
self.assertIsInstance(cr_c_4, self.new_model.ClinicalReportCancer)
self.assertTrue(cr_c_4.validate(cr_c_4.toJsonDict()))
def test_migrate_reported_variant_cancer(self):
rvc_5 = self.get_valid_object(object_type=self.old_model.ReportedVariantCancer, version=self.version_6_1)
rvc_4 = MigrateReports500To400()._migrate_reported_variant_cancer(old_rvc=rvc_5)
self.assertIsInstance(rvc_4, self.new_model.ReportedVariantCancer)
self.assertTrue(rvc_4.validate(rvc_4.toJsonDict()))
