Mercurial > repos > cathywise > truststore_browse_testing
annotate TrustStoreGalaxyBrowse.py @ 14:589f9250e30f
Fix son reading.
| author | Catherine Wise <catherine.wise@csiro.au> |
|---|---|
| date | Wed, 13 May 2015 10:54:07 +1000 |
| parents | 11344d545e88 |
| children | 7b3039ccf50f |
| rev | line source |
|---|---|
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1 """TrustStore downloaded for Galaxy.""" |
| 0 | 2 from __future__ import division, absolute_import, print_function, unicode_literals |
| 3 import sys | |
| 4 import shutil | |
| 5 import gzip | |
| 6 import tempfile | |
| 7 import os | |
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8 import json |
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9 import operator |
| 0 | 10 from py_ts import TrustStoreClient, utils |
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11 from galaxy.datatypes.checkers import util |
| 0 | 12 |
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13 CLIENT_KEY = "desktop" |
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14 CLIENT_SECRET = "cpU92F1PT7VOCANjSknuCDp4DrubmujoBaF6b0miz8OpKNokEbGMHCaSFK5/lISbBmaaGVCgeADI2A39F3Hkeg==" |
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15 CHUNK_SIZE = 2**20 # 1Mb |
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16 SAFE_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ ' |
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17 |
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18 def print_nice(elem, f, depth): |
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19 """Print the file name.""" |
| 0 | 20 try: |
| 21 f.write('\t'*depth + elem.name + " (" + str(len(elem.fragments)) + " parts)\n") | |
| 22 except AttributeError: | |
| 23 f.write('\t'*depth + elem.name + "\n") | |
| 24 for child in elem.children: | |
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25 print_nice(child, f, depth+1) |
| 0 | 26 |
| 27 def check_gzip(file_path): | |
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28 """Check if file is gziped.""" |
| 0 | 29 try: |
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30 temp = open(file_path, "U") |
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31 magic_check = temp.read(2) |
| 0 | 32 temp.close() |
| 33 if magic_check != util.gzip_magic: | |
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34 return (False, False) |
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35 except Exception: |
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36 return (False, False) |
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37 return (True, True) |
| 0 | 38 |
| 39 def ungzip(download, outputFile): | |
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40 """Uncompress file.""" |
| 0 | 41 is_gzipped, is_valid = check_gzip(download) |
| 42 | |
| 43 if is_gzipped and not is_valid: | |
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44 print("File is compressed (gzip) but not valid.") |
| 0 | 45 sys.exit(4) |
| 46 elif is_gzipped and is_valid: | |
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47 # We need to uncompress the temp_name file, but BAM files must |
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48 # remain compressed in the BGZF format |
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49 file_handle, uncompressed = tempfile.mkstemp(prefix='data_id_upload_gunzip_', dir=os.path.dirname(outputFile), text=False ) |
| 0 | 50 gzipped_file = gzip.GzipFile(download, 'rb') |
| 51 while 1: | |
| 52 try: | |
| 53 chunk = gzipped_file.read(CHUNK_SIZE) | |
| 54 except IOError: | |
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55 os.close(file_handle) |
| 0 | 56 os.remove(uncompressed) |
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57 print('Problem decompressing gzipped data %s %s' % (download, outputFile)) |
| 0 | 58 sys.exit(4) |
| 59 if not chunk: | |
| 60 break | |
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61 os.write(file_handle, chunk) |
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62 os.close(file_handle) |
| 0 | 63 gzipped_file.close() |
| 64 | |
| 65 shutil.copy(uncompressed, outputFile) | |
| 66 try: | |
| 67 os.remove(uncompressed) | |
| 68 os.remove(download) | |
| 69 except OSError: | |
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70 pass |
| 0 | 71 else: |
| 72 shutil.copy(download, outputFile) | |
| 73 | |
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74 def construct_multi_filename(id, name, file_type): |
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75 """ Implementation of *Number of Output datasets cannot be determined until |
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76 tool run* from documentation_. |
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77 .. _documentation: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files |
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78 From https://github.com/mdshw5/galaxy-json-data-source/blob/master/json_data_source.py |
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79 """ |
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80 filename = "%s_%s_%s_%s_%s" % ('primary', id, name, 'visible', file_type) |
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81 return filename |
| 0 | 82 |
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83 def metadata_to_json(dataset_id, filename, name, extesion, ds_type='dataset', primary=False): |
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84 """ Return line separated JSON |
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85 From https://github.com/mdshw5/galaxy-json-data-source/blob/master/json_data_source.py |
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86 """ |
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87 meta_dict = dict(type=ds_type, |
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88 ext=extesion, |
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89 filename=filename, |
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90 name=name, |
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91 metadata={}) |
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92 if primary: |
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93 meta_dict['base_dataset_id'] = dataset_id |
| 0 | 94 else: |
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95 meta_dict['dataset_id'] = dataset_id |
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96 return "%s\n" % json.dumps(meta_dict) |
| 0 | 97 |
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98 def main(): |
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99 properties_file = sys.argv[1] |
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100 json_params = None |
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101 metadata_path = None |
| 14 | 102 all_params = None |
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103 with open(properties_file, 'r') as file_: |
| 13 | 104 settings = file_.read() |
| 105 print(settings) | |
| 106 all_params = json.loads(settings) | |
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107 json_params = all_params.get("param_dict") |
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108 metadata_path = all_params["job_config"]["TOOL_PROVIDED_JOB_METADATA_FILE"] |
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109 |
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110 output_filename = json_params.get('output', None) |
| 14 | 111 output_data = all_params.get('output_data') |
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112 extra_files_path, file_name, ext, out_data_name, hda_id, dataset_id = \ |
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113 operator.itemgetter('extra_files_path', 'file_name', 'ext', 'out_data_name', 'hda_id', 'dataset_id')(output_data[0]) |
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114 |
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115 url_params = json_params['URL'].split(";") |
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116 if len(url_params) < 3: |
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117 print("The url we got back is malformed: "+ url_params) |
| 0 | 118 sys.exit(5) |
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119 short_url = url_params[0] |
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120 username = url_params[1] |
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121 password = url_params[2] |
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122 if "/short" not in short_url: |
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123 print("The url we got back is malformed: " + url_params) |
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124 sys.exit(5) |
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125 kms_url = short_url.split("/short")[0] |
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126 |
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127 config = TrustStoreClient.Config( |
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128 None, kms_url, CLIENT_KEY, CLIENT_SECRET, tmpDir='/mnt/galaxy/tmp') |
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129 truststore = TrustStoreClient.TrustStoreClient(headless=False, config=config) |
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130 try: |
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131 truststore.authenticate(username, password) |
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132 except TrustStoreClient.TrustStoreClientAuthenticationException as err: |
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133 print(err) |
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134 sys.exit(5) |
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135 truststore.getPrivateKey('privkey.pem') |
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136 |
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137 path_texts = truststore.lengthenPath(short_url) |
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138 if len(path_texts) < 2: |
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139 print("The path we got was malformed.") |
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140 sys.exit(3) |
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141 paths = path_texts[1:] |
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142 store_id = path_texts[0] |
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143 |
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144 store = truststore.getStoreByID(store_id) |
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145 if store is None: |
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146 print("Coudn't find store with that ID, or don't have access.") |
| 0 | 147 sys.exit(2) |
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148 root = truststore.listDirectory(store) |
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149 |
| 14 | 150 first = True |
| 151 | |
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152 with open(metadata_path, 'wb') as metadata_file: |
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153 for path in paths: |
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154 locations = utils.Navigation.files_at_path(root, path) |
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155 for location in locations: |
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156 if not locations: |
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157 print("Path not found: " + path) |
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158 continue |
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159 filename = "".join(c in SAFE_CHARS and c or '-' for c in location.name) |
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160 extension = os.path.splitext(filename)[1] |
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161 name = construct_multi_filename(hda_id, filename, extension) |
| 14 | 162 target_output_filename = None |
| 163 if first: | |
| 164 target_output_filename = file_name | |
| 165 first = False | |
| 166 else: | |
| 167 target_output_filename = os.path.normpath("/".join([extra_files_path, name])) | |
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168 metadata_file.write( |
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169 metadata_to_json(dataset_id, filename, name, extension, target_output_filename)) |
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170 download = truststore.getFile(store, location) |
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171 if download is None: |
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172 print("File %s not found." % location.name) |
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173 sys.exit(4) |
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174 ungzip(download, target_output_filename) |
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175 |
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176 |
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177 if __name__ == '__main__': |
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178 main() |