def _migrate_pedigree_member(self, member, family_id):
new_instance = self.convert_class(self.new_model.RDParticipant, member)
new_instance.versionControl = participant_old.VersionControl()
new_instance.gelId = str(member.participantId)
new_instance.gelFamilyId = family_id
new_instance.sex = self._migrate_enumerations('Sex', member.sex)
new_instance.lifeStatus = self._migrate_enumerations(
'LifeStatus', member.lifeStatus)
new_instance.adoptedStatus = self._migrate_enumerations(
'AdoptedStatus', member.adoptedStatus)
new_instance.affectionStatus = self._migrate_enumerations(
'AffectionStatus', member.affectionStatus)
if new_instance.affectionStatus == 'uncertain':
new_instance.affectionStatus = 'unknown'
new_instance.hpoTermList = self.convert_collection(
member.hpoTermList, self._migrate_hpo_terms, default=[])
if member.yearOfBirth is not None:
new_instance.yearOfBirth = str(member.yearOfBirth)
new_instance.samples = self.convert_collection(member.samples,
lambda s: s.sampleId,
default=[])
new_instance.disorderList = self.convert_collection(
member.disorderList, self._migrate_disorders, default=[])
if member.ancestries is None:
new_instance.ancestries = participant_old.Ancestries()
return new_instance
def migrate_interpretation_request(self, interpretation_request):
"""
:type interpretation_request: reports_2_1_0.InterpretationRequestRD
:rtype: reports_3_0_0.InterpretationRequestRD
"""
new_instance = self.convert_class(
self.new_model.InterpretationRequestRD, interpretation_request)
new_instance.pedigree = self.migrate_pedigree(
interpretation_request.pedigree)
new_instance.versionControl = reports_3_0_0.VersionControl()
new_instance.TieredVariants = self.convert_collection(
list(
zip(interpretation_request.TieredVariants,
new_instance.TieredVariants)),
self._migrate_reported_variant)
new_instance.BAMs = self.convert_collection(
list(zip(interpretation_request.BAMs, new_instance.BAMs)),
self._migrate_file)
new_instance.VCFs = self.convert_collection(
list(zip(interpretation_request.VCFs, new_instance.VCFs)),
self._migrate_file)
if interpretation_request.bigWigs is not None:
new_instance.bigWigs = self.convert_collection(
list(zip(interpretation_request.bigWigs,
new_instance.bigWigs)), self._migrate_file)
if interpretation_request.pedigreeDiagram:
new_instance.pedigreeDiagram = self._migrate_file(
(interpretation_request.pedigreeDiagram,
new_instance.pedigreeDiagram))
if interpretation_request.annotationFile:
new_instance.annotationFile = self._migrate_file(
(interpretation_request.annotationFile,
new_instance.annotationFile))
return self.validate_object(new_instance,
self.new_model.InterpretationRequestRD)
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 migrate_interpreted_genome(self, interpreted_genome):
"""
:type interpreted_genome: reports_2_1_0.InterpretedGenomeRD
:rtype: reports_3_0_0.InterpretedGenomeRD
"""
new_interpreted_genome = self.new_model.InterpretedGenomeRD.fromJsonDict(
interpreted_genome.toJsonDict())
new_interpreted_genome.reportedVariants = []
new_interpreted_genome.ReportedStructuralVariant = []
interpreted_genome.versionControl = reports_3_0_0.VersionControl()
for reported_variant in interpreted_genome.reportedVariants:
new_interpreted_genome.reportedVariants.append(
self.migrate_reported_variant(reported_variant))
if interpreted_genome.reportedStructuralVariants:
for reported_structural_variant in interpreted_genome.reportedStructuralVariants:
new_interpreted_genome.ReportedStructuralVariant.append(
self.migrate_reported_structural_variant(
reported_structural_variant))
new_interpreted_genome.softwareVersions = {}
new_interpreted_genome.referenceDatabasesVersions = {}
if new_interpreted_genome.validate(
new_interpreted_genome.toJsonDict()):
return new_interpreted_genome
else:
raise Exception('This model can not be converted')
class PedigreeFactory300Nulls(FactoryAvro):
class Meta:
model = reports_3_0_0.Pedigree
_version = dependency_manager.VERSION_300
versionControl = reports_3_0_0.VersionControl()
_fill_nullables = True
def _migrate_rd_participant(self, members):
old_instance = members[0]
new_instance = members[1]
new_instance.versionControl = reports_3_0_0.VersionControl()
if old_instance.additionalInformation:
if 'yearOfBirth' in old_instance.additionalInformation:
new_instance.yearOfBirth = old_instance.additionalInformation[
'yearOfBirth']
return new_instance
class RDParticipantFactory300Nulls(FactoryAvro):
class Meta:
model = reports_3_0_0.RDParticipant
_version = dependency_manager.VERSION_300
versionControl = reports_3_0_0.VersionControl()
yearOfBirth = str(
factory.fuzzy.FuzzyInteger(low=1900, high=2018).fuzz())
_fill_nullables = True
def migrate_pedigree_member(self, member, family_id):
"""
:type member: participant_1_0_1.PedigreeMember
:rtype: participant_old.RDParticipant
"""
new_pedigree_member = self.new_model.RDParticipant.fromJsonDict(
member.toJsonDict())
new_pedigree_member.versionControl = participant_old.VersionControl()
new_pedigree_member.gelId = str(member.participantId)
new_pedigree_member.gelFamilyId = family_id
new_pedigree_member.sex = self.migrate_enumerations('Sex', member.sex)
new_pedigree_member.lifeStatus = self.migrate_enumerations(
'LifeStatus', member.lifeStatus)
new_pedigree_member.adoptedStatus = self.migrate_enumerations(
'AdoptedStatus', member.adoptedStatus)
new_pedigree_member.affectionStatus = self.migrate_enumerations(
'AffectionStatus', member.affectionStatus)
if new_pedigree_member.affectionStatus == 'uncertain':
new_pedigree_member.affectionStatus = 'unknown'
if member.hpoTermList:
new_pedigree_member.hpoTermList = [
self.migrate_hpo_terms(hpo) for hpo in member.hpoTermList
]
else:
new_pedigree_member.hpoTermList = []
try:
new_pedigree_member.yearOfBirth = str(int(member.yearOfBirth))
except TypeError:
new_pedigree_member.yearOfBirth = None
if member.samples:
new_pedigree_member.samples = [
sample.sampleId for sample in member.samples
]
else:
new_pedigree_member.samples = []
if member.disorderList:
new_pedigree_member.disorderList = [
self.migrate_disorders(d) for d in member.disorderList
]
else:
new_pedigree_member.disorderList = []
if member.ancestries is None:
new_pedigree_member.ancestries = participant_old.Ancestries()
if new_pedigree_member.validate(new_pedigree_member.toJsonDict()):
return new_pedigree_member
else:
print new_pedigree_member.validate_parts()
raise Exception('This model can not be converted')
def migrate_pedigree(self, pedigree):
"""
:type pedigree: reports_2_1_0.Pedigree
:rtype: reports_3_0_0.Pedigree
"""
new_instance = self.convert_class(self.new_model.Pedigree, pedigree)
new_instance.versionControl = reports_3_0_0.VersionControl()
new_instance.participants = self.convert_collection(
list(zip(pedigree.participants, new_instance.participants)),
self._migrate_rd_participant)
return self.validate_object(object_to_validate=new_instance,
object_type=self.new_model.Pedigree)
def migrate_rd_participant(self, member):
"""
:type member: reports_2_1_0.RDParticipant
:rtype: reports_3_0_0.RDParticipant
"""
new_rd_participant = self.new_model.RDParticipant.fromJsonDict(
member.toJsonDict())
new_rd_participant.versionControl = reports_3_0_0.VersionControl()
if 'yearOfBirth' in member.additionalInformation:
new_rd_participant.yearOfBirth = member.additionalInformation[
'yearOfBirth']
if new_rd_participant.validate(new_rd_participant.toJsonDict()):
return new_rd_participant
else:
raise Exception('This model can not be converted')
def migrate_interpreted_genome(self, interpreted_genome):
"""
:type interpreted_genome: reports_2_1_0.InterpretedGenomeRD
:rtype: reports_3_0_0.InterpretedGenomeRD
"""
new_instance = self.convert_class(self.new_model.InterpretedGenomeRD,
interpreted_genome)
new_instance.reportedVariants = self.convert_collection(
list(
zip(interpreted_genome.reportedVariants,
new_instance.reportedVariants)),
self._migrate_reported_variant)
new_instance.reportedStructuralVariants = []
interpreted_genome.versionControl = reports_3_0_0.VersionControl()
new_instance.softwareVersions = {}
new_instance.referenceDatabasesVersions = {}
return self.validate_object(new_instance,
self.new_model.InterpretedGenomeRD)
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 migrate_pedigree(self, pedigree):
"""
:type pedigree: reports_2_1_0.Pedigree
:rtype: reports_3_0_0.Pedigree
"""
new_pedigree = self.new_model.Pedigree()
new_pedigree.analysisPanels = pedigree.analysisPanels
new_pedigree.diseasePenetrances = None
new_pedigree.versionControl = reports_3_0_0.VersionControl()
new_pedigree.gelFamilyId = pedigree.gelFamilyId
new_pedigree.participants = []
for member in pedigree.participants:
new_pedigree.participants.append(
self.migrate_rd_participant(member))
if new_pedigree.validate(new_pedigree.toJsonDict()):
return new_pedigree
else:
raise Exception('This model can not be converted')
def migrate_interpretation_request(self, interpretation_request):
"""
:type interpretation_request: reports_2_1_0.InterpretationRequestRD
:rtype: reports_3_0_0.InterpretationRequestRD
"""
new_interpretation_request = self.new_model.InterpretationRequestRD.fromJsonDict(
interpretation_request.toJsonDict())
new_interpretation_request.TieredVariants = []
new_interpretation_request.pedigree = self.migrate_pedigree(
interpretation_request.pedigree)
new_interpretation_request.versionControl = reports_3_0_0.VersionControl(
)
for tiered_variant in interpretation_request.TieredVariants:
new_interpretation_request.TieredVariants.append(
self.migrate_reported_variant(tiered_variant))
if new_interpretation_request.validate(
new_interpretation_request.toJsonDict()):
return new_interpretation_request
else:
raise Exception('This model can not be converted')