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4
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1 import sys
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2 import shutil
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20
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3 import gzip
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22
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4 import tempfile
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4
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5 from py_ts import TrustStoreClient, ts_utils
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20
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6 from galaxy.datatypes.checkers import *
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4
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7
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5
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8 def printNice(elem, f, depth):
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9 try:
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10 f.write('\t'*depth + elem.name + " (" + str(len(elem.fragments)) + " parts)\n")
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11 except AttributeError:
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12 f.write('\t'*depth + elem.name + "\n")
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13 for child in elem.children:
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14 printNice(child, f, depth+1)
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15
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4
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16 if __name__ == '__main__':
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17
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18 kms_url = sys.argv[1]
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19 ims_url = sys.argv[2]
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20 username = sys.argv[3]
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21 password = sys.argv[4]
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22 client_key = sys.argv[5]
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23 client_secret = sys.argv[6]
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24 storename = sys.argv[7]
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25 path = sys.argv[8]
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5
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26 filename = ""
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27 outputFile = ""
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28 if len(sys.argv) > 10:
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29 filename = sys.argv[9]
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30 outputFile = sys.argv[10]
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31 else:
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32 outputFile = sys.argv[9]
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4
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33
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34 config = TrustStoreClient.Config(ims_url, kms_url, client_key, client_secret)
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35 ts = TrustStoreClient.TrustStoreClient(headless=True, config=config)
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36 try:
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37 ts.authenticate(username, password)
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38 except TrustStoreClient.TrustStoreClientAuthenticationException as e:
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39 print e
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40 sys.exit(5)
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41 ts.getPrivateKey('privkey.pem')
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42 listing = ts.listStores()
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43 found = False
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44 for store in listing:
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45 if store.friendly_name == storename:
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46 found = True
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47 root = ts.listDirectory(store)
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48 location = None
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49 if path != "/":
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50 location = ts_utils.ts_utils.dirAtPath(root, path)
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51 if not location:
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52 print "Path not found"
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53 sys.exit(3)
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54 else:
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55 location = root
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5
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56 if filename and filename != "":
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57 downloadMe = ts_utils.ts_utils.recurseToChildNamed(location, filename)
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58 if downloadMe:
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59 download = ts.getFile(store, downloadMe)
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20
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60 is_gzipped, is_valid = check_gzip(download)
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61
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62 if is_gzipped and not is_valid:
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63 print "File is compressed (gzip) but not valid."
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64 sys.exit(4)
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65 elif is_gzipped and is_valid:
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21
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66 # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format
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67 CHUNK_SIZE = 2**20 # 1Mb
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68 fd, uncompressed = tempfile.mkstemp(prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname(outputFile), text=False )
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69 gzipped_file = gzip.GzipFile(download, 'rb')
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70 while 1:
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71 try:
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72 chunk = gzipped_file.read(CHUNK_SIZE)
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73 except IOError:
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74 os.close(fd)
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75 os.remove(uncompressed)
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76 print 'Problem decompressing gzipped data', dataset, json_file
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77 sys.exit(4)
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78 if not chunk:
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79 break
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80 os.write(fd, chunk)
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81 os.close(fd)
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82 gzipped_file.close()
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20
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83
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84 shutil.copy(uncompressed, outputFile)
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85 else:
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86 shutil.copy(download, outputFile)
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5
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87 else:
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88 print "File not found"
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89 sys.exit(4)
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4
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90 else:
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5
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91 with open(outputFile, 'w+') as f:
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92 try:
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93 for child in root.children:
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94 printNice(child, f, 0)
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95 except AttributeError as e:
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96 print e
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97 print root
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4
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98 if not found:
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99 print "Store not found"
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100 sys.exit(2)
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