def storeFile(syn,
fileName,
parentId,
center,
fileFormat,
dataSubType,
platform=None,
cBioFileFormat=None,
used=None):
logger.info("STORING FILES")
fileEnt = File(fileName, parent=parentId)
fileEnt.center = center
fileEnt.species = "Human"
fileEnt.consortium = 'GENIE'
fileEnt.dataType = "genomicVariants"
fileEnt.fundingAgency = "AACR"
fileEnt.assay = 'targetGeneSeq'
fileEnt.fileFormat = fileFormat
fileEnt.dataSubType = dataSubType
fileEnt.fileStage = "staging"
fileEnt.platform = platform
if platform is not None:
fileEnt.platform = platform
if cBioFileFormat is not None:
fileEnt.cBioFileFormat = cBioFileFormat
ent = syn.store(fileEnt, used=used)
return (ent)
def storeFile(fileName, stagingID, used, center, annotations, meta=False):
print("STORING FILES")
fileEnt = File(fileName, parent = stagingID)
fileEnt.center = center
fileEnt.dataSubType = annotations.get("dataSubType",'')
fileEnt.dataType = annotations.get("dataType",'')
fileEnt.disease = 'cancer'
fileEnt.fileType = annotations.get("fileType",'')
fileEnt.organism = 'H**o Sapiens'
fileEnt.platform = annotations.get("platform",'')
fileEnt.tissueSource = annotations.get("tissueSource",'')
fileEnt.consortium = 'GENIE'
if meta:
fileEnt.fileType = "txt"
fileEnt.dataType = "meta"
fileEnt.fileStage = "staging"
ent = syn.store(fileEnt,annotations = used)
return(ent)
