Mercurial > repos > melissacline > ucsc_xena_platform

comparison xenaGetDataset.py @ 41:02b0824c7d60

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Download data from any hub in the federated xena platform
author jingchunzhu <jingchunzhu@gmail.com>
date Mon, 27 Jul 2015 10:05:22 -0700
parents 8bb037f88ed2
children 3167c1a26101
comparison
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40:fd24e220f240 41:02b0824c7d60
7 7
8 def main(): 8 def main():
9 parser = argparse.ArgumentParser() 9 parser = argparse.ArgumentParser()
10 parser.add_argument("dataHub", type=str) 10 parser.add_argument("dataHub", type=str)
11 parser.add_argument("datasetId", type=str) 11 parser.add_argument("datasetId", type=str)
12 parser.add_argument("metadatafile", type=str) 12 #parser.add_argument("metadatafile", type=str)
13 parser.add_argument("datafile", type=str) 13 parser.add_argument("datafile", type=str)
14 args = parser.parse_args() 14 args = parser.parse_args()
15 15
16 datasetUrlHost = re.sub("/proj/", "/download/", args.dataHub) 16 datasetUrlHost = re.sub("/proj/", "/download/", args.dataHub)
17 datasetIdTokens = re.split("/", args.datasetId) 17 datasetIdTokens = re.split("/", args.datasetId)
18 datasetUrl = datasetUrlHost + "/" + "/".join(datasetIdTokens[1:]) 18 datasetUrl = datasetUrlHost + "/" + "/".join(datasetIdTokens[1:])
19 print datasetUrl 19 print datasetUrl
20 """
20 metadataUrl = datasetUrl + ".json" 21 metadataUrl = datasetUrl + ".json"
21 mm = urllib2.urlopen(metadataUrl) 22 mm = urllib2.urlopen(metadataUrl)
22 with open(args.metadatafile, "w") as metadata: 23 with open(args.metadatafile, "w") as metadata:
23 metadata.write(mm.read()) 24 metadata.write(mm.read())
24 mm.close() 25 mm.close()
26 """
25 dd = urllib2.urlopen(datasetUrl) 27 dd = urllib2.urlopen(datasetUrl)
26 with open(args.datafile, "w") as data: 28 with open(args.datafile, "w") as data:
27 data.write(dd.read()) 29 data.write(dd.read())
28 dd.close() 30 dd.close()
29 31