Mercurial > repos > melissacline > ucsc_cancer_utilities
comparison synapseGetDataset.py @ 24:1d83dbbee373
Fixing a merge conflict
| author | melissacline |
|---|---|
| date | Mon, 20 Jul 2015 15:41:22 -0700 |
| parents | d1104ad3646a |
| children | e81019e3ac99 |
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| 23:7346e5bab4ec | 24:1d83dbbee373 |
|---|---|
| 1 #!/usr/bin/env python | 1 #!/usr/bin/env python |
| 2 """Download a dataset from Synapse into Galaxy""" | 2 """Download a dataset from Synapse into Galaxy """ |
| 3 | 3 |
| 4 import argparse | 4 import argparse |
| 5 import json | 5 import json |
| 6 import synapseclient | 6 import synapseclient |
| 7 import sys | 7 import sys |
| 8 import zipfile | |
| 9 | |
| 10 class InputError(Exception): | |
| 11 def __init__(self, value): | |
| 12 self.value = value | |
| 13 def __str__(self): | |
| 14 return repr(self.value) | |
| 15 | |
| 8 | 16 |
| 9 def saveMetadata(entity, metadataPathname): | 17 def saveMetadata(entity, metadataPathname): |
| 10 fp = open(metadataPathname, "w") | 18 fp = open(metadataPathname, "w") |
| 11 entityMetadata = dict(entity.properties.items() | 19 entityMetadata = dict(entity.properties.items() |
| 12 + entity.annotations.items()) | 20 + entity.annotations.items()) |
| 13 jsonMetadata = json.dumps(entityMetadata) | 21 jsonMetadata = json.dumps(entityMetadata) |
| 14 fp.write("%s\n" % (jsonMetadata)) | 22 fp.write("%s\n" % (jsonMetadata)) |
| 15 fp.close() | 23 fp.close() |
| 16 | 24 |
| 17 def saveData(entity, dataPathname): | 25 def saveData(entity, dataPathname): |
| 18 fpIn = open(entity.path) | 26 if entity.properties['contentType'] == "application/zip": |
| 19 fpOut = open(dataPathname, "w") | 27 zf = zipfile.ZipFile(entity.path) |
| 20 for row in fpIn: | 28 if len(zf.namelist()) > 1: |
| 21 fpOut.write(row) | 29 raise InputError(len(zf.namelist())), "Error: more than one input file" |
| 22 fpIn.close() | 30 else: |
| 23 fpOut.close() | 31 data = zf.read(zf.namelist()[0]) |
| 32 fpOut = open(dataPathname, "w") | |
| 33 fpOut.write(data) | |
| 34 fpOut.close() | |
| 35 else: | |
| 36 fpIn = open(entity.path) | |
| 37 fpOut = open(dataPathname, "w") | |
| 38 for row in fpIn: | |
| 39 fpOut.write(row) | |
| 40 fpIn.close() | |
| 41 fpOut.close() | |
| 24 | 42 |
| 25 def main(): | 43 def main(): |
| 26 parser = argparse.ArgumentParser() | 44 parser = argparse.ArgumentParser() |
| 27 parser.add_argument("entityId", type=str) | 45 parser.add_argument("entityId", type=str) |
| 28 parser.add_argument("email", type=str) | 46 parser.add_argument("email", type=str) |