def test_migrate_rd_interpretation_request(self, fill_nullables=True):
# get original IR in version 3.0.0
assembly = Assembly.GRCh38
original_ir = self.get_valid_object(
object_type=reports_3_0_0.InterpretationRequestRD,
version=self.version_3_0_0,
fill_nullables=fill_nullables,
genomeAssemblyVersion=assembly,
versionControl=reports_3_0_0.VersionControl(
)) # type: reports_3_0_0.InterpretationRequestRD
for p in original_ir.pedigree.participants:
p.gelFamilyId = original_ir.pedigree.gelFamilyId
p.yearOfBirth
for p in original_ir.pedigree.participants:
for hpo in p.hpoTermList:
hpo.modifiers = self._get_random_hpo_modifiers()
migrated, round_tripped = MigrationRunner().roundtrip_rd_ir(
original_ir, assembly)
self.assertFalse(
self.diff_round_tripped(original_ir,
round_tripped,
ignore_fields=[
"ageOfOnset",
"consanguineousPopulation",
"additionalInfo", "analysisVersion"
]))
def test_migrate_cancer_clinical_report(self, fill_nullables=True):
assembly = Assembly.GRCh38
original_cr = self.get_valid_object(
object_type=reports_4_0_0.ClinicalReportCancer, version=self.version_4_0_0,
fill_nullables=fill_nullables, genomeAssemblyVersion=assembly,
interpretGenome=True, candidateStructuralVariants=[],
versionControl=reports_4_0_0.ReportVersionControl(gitVersionControl='4.0.0'),
interpretationRequestVersion='123'
)
migrated, round_tripped = MigrationRunner().roundtrip_cancer_cr(original_cr, assembly)
self.assertFalse(self.diff_round_tripped(original_cr, round_tripped, ignore_fields=[
"analysisId", "actions", "additionalTextualVariantAnnotations", "commonAf", "genePanelsCoverage"]))
# NOTE: not all fields in actions are kept and the order is not maintained, thus we ignore it in the
# dictionary comparison and then here manually check them
if original_cr.candidateVariants:
expected_report_events = chain.from_iterable(
map(lambda v: [re for re in v.reportedVariantCancer.reportEvents], original_cr.candidateVariants))
else:
expected_report_events = []
if round_tripped.candidateVariants:
observed_report_events = chain.from_iterable(
map(lambda v: [re for re in v.reportedVariantCancer.reportEvents], round_tripped.candidateVariants))
else:
observed_report_events = []
self.assertFalse(self.diff_actions(chain(expected_report_events, observed_report_events)))
def test_migrate_rd_exit_questionnaire(self, fill_nullables=True):
original = self.get_valid_object(
object_type=reports_3_0_0.RareDiseaseExitQuestionnaire,
version=self.version_3_0_0,
fill_nullables=fill_nullables
) # type: reports_3_0_0.RareDiseaseExitQuestionnaire
for g in original.variantGroupLevelQuestions:
for v in g.variantLevelQuestions:
v.variant_details = self._get_random_variant_details()
migrated, round_tripped = MigrationRunner().roundtrip_rd_eq(
original, Assembly.GRCh38)
self.assertFalse(
self.diff_round_tripped(original, round_tripped, ignore_fields=[]))
def test_migrate_rd_clinical_report(self, fill_nullables=True):
# get original IR in version 3.0.0
original = self.get_valid_object(
object_type=reports_3_0_0.ClinicalReportRD,
version=self.version_3_0_0,
fill_nullables=fill_nullables,
interpretationRequestVersion='1',
candidateStructuralVariants=None)
migrated, round_tripped = MigrationRunner().roundtrip_rd_cr(
original, Assembly.GRCh38)
self.assertFalse(
self.diff_round_tripped(
original,
round_tripped,
ignore_fields=["interpretationRequestAnalysisVersion"]))
def __init__(self, log_file, program, data_folder=None, use_data=False):
# configures logging to get only logs about the failed cases
self.log_file = log_file
self.program = program
self.data_folder = data_folder
self.use_data = use_data
logging.basicConfig(filename=self.log_file, level=logging.ERROR,
format='%(asctime)s.%(msecs)03d\t%(message)s',
datefmt='%H:%M:%S' ,)
if not use_data:
gel_user = raw_input("User:"******"Password:"******"URL:")
self.cipapi_client = CipApiClient(cipapi_url, user=gel_user, password=gel_password, retries=-1)
self.migration_runner = MigrationRunner()
def test_migrate_rd_interpreted_genome(self, fill_nullables=True):
# get original IG in version 3.0.0
# NOTE: we do not want to structural variants and we remove them to avoid noise
original_ig = self.get_valid_object(
object_type=reports_3_0_0.InterpretedGenomeRD,
version=self.version_3_0_0,
fill_nullables=fill_nullables,
reportedStructuralVariants=None,
versionControl=reports_3_0_0.VersionControl(),
analysisId='1',
reportURI='')
migrated, round_tripped = MigrationRunner().roundtrip_rd_ig(
original_ig, Assembly.GRCh38)
self.assertFalse(
self.diff_round_tripped(
original_ig,
round_tripped,
ignore_fields=['additionalNumericVariantAnnotations']))
def test_migrate_cancer_exit_questionnaire(self, fill_nullables=True):
assembly = Assembly.GRCh38
original_eq = self.get_valid_object(
object_type=reports_5_0_0.CancerExitQuestionnaire, version=self.version_6_1,
fill_nullables=fill_nullables,
versionControl=reports_5_0_0.ReportVersionControl()
)
if original_eq.somaticVariantLevelQuestions:
for q in original_eq.somaticVariantLevelQuestions:
q.variantDetails = self._get_random_variant_details()
if original_eq.germlineVariantLevelQuestions:
for q in original_eq.germlineVariantLevelQuestions:
q.variantDetails = self._get_random_variant_details()
if original_eq.otherActionableVariants:
for q in original_eq.otherActionableVariants:
q.variantDetails = self._get_random_variant_details()
migrated, round_tripped = MigrationRunner().roundtrip_cancer_eq(original_eq, assembly)
self.diff_round_tripped(original_eq, round_tripped, ignore_fields=[])
def test_migrate_cancer_interpretation_request(self, fill_nullables=True):
# get original IR in version 4.0.0
assembly = Assembly.GRCh38
original_ir = self.get_valid_object(
object_type=reports_4_0_0.CancerInterpretationRequest,
version=self.version_4_0_0,
fill_nullables=fill_nullables,
genomeAssemblyVersion=assembly,
structuralTieredVariants=[],
versionControl=reports_4_0_0.ReportVersionControl(
gitVersionControl='4.0.0'))
valid_cancer_origins = ['germline_variant', 'somatic_variant']
for tiered_variant in original_ir.tieredVariants:
if tiered_variant.alleleOrigins[0] not in valid_cancer_origins:
tiered_variant.alleleOrigins[0] = random.choice(
valid_cancer_origins)
# # migration requires there is exactly one tumour sample
original_ir.cancerParticipant.tumourSamples = [
original_ir.cancerParticipant.tumourSamples[0]
]
migrated, round_tripped = MigrationRunner().roundtrip_cancer_ir(
original_ir, assembly)
self.assertFalse(
self.diff_round_tripped(original_ir,
round_tripped,
ignore_fields=[
"TNMStageVersion", "TNMStageGrouping",
"actions",
"additionalTextualVariantAnnotations",
"matchedSamples", "commonAf",
"additionalInfo"
]))
# NOTE: not all fields in actions are kept and the order is not maintained, thus we ignore it in the
# dictionary comparison and then here manually check them
expected_report_events = chain.from_iterable(
map(lambda v: [re for re in v.reportedVariantCancer.reportEvents],
original_ir.tieredVariants))
observed_report_events = chain.from_iterable(
map(lambda v: [re for re in v.reportedVariantCancer.reportEvents],
round_tripped.tieredVariants))
self.assertFalse(
self.diff_actions(
chain(expected_report_events, observed_report_events)))
def test_migrate_cancer_interpreted_genome(self, fill_nullables=True):
assembly = Assembly.GRCh38
original_ig = self.get_valid_object(
object_type=reports_4_0_0.CancerInterpretedGenome, version=self.version_4_0_0,
fill_nullables=fill_nullables, genomeAssemblyVersion=assembly,
interpretGenome=True, reportedStructuralVariants=[],
versionControl=reports_4_0_0.ReportVersionControl(gitVersionControl='4.0.0')
)
# migration requires there is exactly one tumour sample
migrated, round_tripped = MigrationRunner().roundtrip_cancer_ig(original_ig, assembly)
self.assertFalse(self.diff_round_tripped(original_ig, round_tripped, ignore_fields=[
"analysisId", "actions", "additionalTextualVariantAnnotations", "commonAf"]))
# NOTE: not all fields in actions are kept and the order is not maintained, thus we ignore it in the
# dictionary comparison and then here manually check them
expected_report_events = chain.from_iterable(
map(lambda v: [re for re in v.reportedVariantCancer.reportEvents], original_ig.reportedVariants))
observed_report_events = chain.from_iterable(
map(lambda v: [re for re in v.reportedVariantCancer.reportEvents], round_tripped.reportedVariants))
self.assertFalse(self.diff_actions(chain(expected_report_events, observed_report_events)))
def test_migrate_rd_interpretation_request(self, fill_nullables=True):
# get original IR in version 3.0.0
assembly = Assembly.GRCh38
original_ir = self.get_valid_object(
object_type=reports_2_1_0.InterpretationRequestRD,
version=self.version_2_1_0,
fill_nullables=fill_nullables,
genomeAssemblyVersion=assembly,
versionControl=reports_2_1_0.VersionControl())
for p in original_ir.pedigree.participants:
p.gelFamilyId = original_ir.pedigree.gelFamilyId
original_ir = Migration21To3().migrate_interpretation_request(
original_ir)
migrated, round_tripped = MigrationRunner().roundtrip_rd_ir(
original_ir, assembly)
self.assertFalse(
self.diff_round_tripped(original_ir,
round_tripped,
ignore_fields=[
"ageOfOnset",
"consanguineousPopulation",
"modifiers", "copyNumber",
"additionalInfo"
]))