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1 #!/usr/bin/env python
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2 """Download a dataset from Synapse into Galaxy"""
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3
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4 import argparse
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5 import json
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6 import synapseclient
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7 import sys
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8
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9 def saveMetadata(entity, metadataPathname):
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10 fp = open(metadataPathname, "w")
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11 entityMetadata = dict(entity.properties.items()
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12 + entity.annotations.items())
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13 jsonMetadata = json.dumps(entityMetadata)
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14 fp.write("%s\n" % (jsonMetadata))
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15 fp.close()
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16
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17 def saveData(entity, dataPathname):
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18 fpIn = open(entity.path)
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19 fpOut = open(dataPathname, "w")
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20 for row in fpIn:
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21 fpOut.write(row)
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22 fpIn.close()
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23 fpOut.close()
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24
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25 def main():
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26 parser = argparse.ArgumentParser()
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27 parser.add_argument("entityId", type=str)
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28 parser.add_argument("email", type=str)
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29 parser.add_argument("outputMetadataFile", type=str)
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30 parser.add_argument("outputDataFile", type=str)
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31 parser.add_argument("--apiKey", type=str, default=None)
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32 parser.add_argument("--password", type=str, default=None)
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33 args = parser.parse_args()
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34
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35 syn = synapseclient.Synapse()
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36 assert(args.apiKey != None or args.password != None)
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37 try:
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38 if args.apiKey is not None:
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39 syn.login(email=args.email, apiKey=args.apiKey)
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40 else:
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41 syn.login(email=args.email, password = args.password)
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42 except:
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43 print "Login Unsuccessful\n"
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44 sys.exit(-1)
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45 else:
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46 try:
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47 entity=syn.get(args.entityId)
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48 except:
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49 exc_type, exc_value, exc_traceback = sys.exc_info()
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50 lines = traceback.format_exception(exc_type, exc_value,
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51 exc_traceback)
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52 allLines = ''.join('!! ' + line for line in lines)
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53 print "Unsuccessful: error %s\n" % allLines
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54 sys.exit(-1)
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55 else:
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56 saveMetadata(entity, args.outputMetadataFile)
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57 saveData(entity, args.outputDataFile)
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58 sys.exit(0)
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59
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60 if __name__ == "__main__":
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61 main()
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62
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63
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