def upload(args,syn): if args.dataType == "rnaseq": parentId = "syn6034916" pipeline = "syn6126122" dataType = "RNASeq" elif args.dataType == "dnaseq": parentId = "syn6034751" pipeline = "syn6126123" dataType = "TargDNASeq" elif args.dataType == "snparray": parentId = "syn6038475" pipeline = "syn6126121" dataType = "SNParray" elif args.dataType == "exparray": parentId = "syn6038915" pipeline = "syn6126120" dataType = "expression_microarray" elif args.dataType == "exome": parentId = "syn6115597" dataType = "exome" pipeline = "" else: raise ValueError("dataType needs to be rnaseq/dnaseq/snparray/exparray/exome") if args.workflow is not None: workflow = syn.get(pipeline,downloadFile=False) workflow.path = args.workflow workflow.name = os.path.basename(args.workflow) workflow = syn.store(workflow) pipeline = workflow.id fileEnt = File(args.input,parent=parentId) #fileEnt.annotations = temp.to_dict('index').values()[0] fileEnt.dataType = dataType fileEnt.sampleId = sampleId fileEnt = syn.store(fileEnt,used = pipeline) return(fileEnt.id)
def upload(args, syn): if args.dataType == "rnaseq": parentId = "syn6034916" pipeline = "syn6126122" dataType = "RNASeq" elif args.dataType == "dnaseq": parentId = "syn6034751" pipeline = "syn6126123" dataType = "TargDNASeq" elif args.dataType == "snparray": parentId = "syn6038475" pipeline = "syn6126121" dataType = "SNParray" elif args.dataType == "exparray": parentId = "syn6038915" pipeline = "syn6126120" dataType = "expression_microarray" elif args.dataType == "exome": parentId = "syn6115597" dataType = "exome" pipeline = "" else: raise ValueError( "dataType needs to be rnaseq/dnaseq/snparray/exparray/exome") if args.workflow is not None: workflow = syn.get(pipeline, downloadFile=False) workflow.path = args.workflow workflow.name = os.path.basename(args.workflow) workflow = syn.store(workflow) pipeline = workflow.id fileEnt = File(args.input, parent=parentId) #fileEnt.annotations = temp.to_dict('index').values()[0] fileEnt.dataType = dataType fileEnt.sampleId = sampleId fileEnt = syn.store(fileEnt, used=pipeline) return (fileEnt.id)