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)
