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