def create(cls,
experiment,
sample,
file,
analysisId=None,
study=None,
analysisState="UNPUBLISHED",
info=None):
check_type(experiment, VariantCall)
check_state(
sample is not None and isinstance(sample, list)
and len(sample) > 0, "Atleast one sample must be defined")
check_state(
file is not None and isinstance(file, list) and len(file) > 0,
"Atleast one file must be defined")
for s in sample:
check_type(s, CompositeEntity)
for f in file:
check_type(f, File)
s = VariantCallAnalysis()
s.experiment = experiment
s.analysisId = analysisId
s.study = study
s.analysisState = analysisState
s.sample = sample
s.file = file
s.info = default_value(info, {})
return s
def create(cls,
donorSubmitterId,
studyId,
donorGender,
donorId=None,
info=None):
d = Donor()
d.donorId = donorId
d.info = default_value(info, {})
d.studyId = studyId
d.donorSubmitterId = donorSubmitterId
d.donorGender = donorGender
return d
def create(cls,
specimenId,
sampleSubmitterId,
sampleType,
sampleId=None,
info=None):
s = Sample()
s.info = default_value(info, {})
s.specimenId = specimenId
s.sampleType = sampleType
s.sampleSubmitterId = sampleSubmitterId
s.sampleId = sampleId
return s
def create(cls,
donorId,
specimenSubmitterId,
specimenClass,
specimenType,
specimenId=None,
info=None):
s = Specimen()
s.info = default_value(info, {})
s.specimenId = specimenId
s.donorId = donorId
s.specimenType = specimenType
s.specimenClass = specimenClass
s.specimenSubmitterId = specimenSubmitterId
return s
def create(cls,
fileName,
fileSize,
fileType,
fileMd5sum,
fileAccess,
studyId=None,
analysisId=None,
objectId=None,
info=None):
f = File()
f.objectId = objectId
f.analysisId = analysisId
f.studyId = studyId
f.fileType = fileType
f.fileSize = fileSize
f.info = default_value(info, {})
f.fileMd5sum = fileMd5sum
f.fileAccess = fileAccess
f.fileName = fileName
return f
def non_null(exclude=None):
exclude = default_value(exclude, [])
def wrap(func):
inspected_args = OrderedDict.fromkeys(
inspect.signature(func).parameters.keys(), True)
is_self = False
if "self" in inspected_args.keys():
is_self = True
inspected_args.pop("self")
def new_func(*args, **kwargs):
count = 1 if is_self else 0
for a in inspected_args.keys():
if a not in exclude:
check_state(args[count] is not None,
"The argument '{}' must be non-null", a)
count += 1
return func(*args, **kwargs)
return new_func
return wrap
def __init__(self, analysis_id, manifest_entries=None):
self.analysis_id = analysis_id
self.entries = default_value(manifest_entries, [])