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)