truststore_browse_testing: TrustStoreGalaxyBrowse.py annotate

annotate TrustStoreGalaxyBrowse.py @ 15:7b3039ccf50f

Un-quote url.

author	Catherine Wise <catherine.wise@csiro.au>
date	Wed, 13 May 2015 10:59:48 +1000
parents	589f9250e30f
children	10ce45af14dd

rev	line source
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	1 """TrustStore downloaded for Galaxy."""
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	2 from __future__ import division, absolute_import, print_function, unicode_literals
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	3 import sys
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	4 import shutil
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	5 import gzip
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	6 import tempfile
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	7 import os
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	8 import json
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	9 import operator
15 7b3039ccf50f Un-quote url. Catherine Wise <catherine.wise@csiro.au> parents: 14 diff changeset	10 import urlparse
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	11 from py_ts import TrustStoreClient, utils
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	12 from galaxy.datatypes.checkers import util
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	13
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	14 CLIENT_KEY = "desktop"
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	15 CLIENT_SECRET = "cpU92F1PT7VOCANjSknuCDp4DrubmujoBaF6b0miz8OpKNokEbGMHCaSFK5/lISbBmaaGVCgeADI2A39F3Hkeg=="
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	16 CHUNK_SIZE = 2**20 # 1Mb
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	17 SAFE_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	18
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	19 def print_nice(elem, f, depth):
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	20 """Print the file name."""
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	21 try:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	22 f.write('\t'*depth + elem.name + " (" + str(len(elem.fragments)) + " parts)\n")
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	23 except AttributeError:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	24 f.write('\t'*depth + elem.name + "\n")
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	25 for child in elem.children:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	26 print_nice(child, f, depth+1)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	27
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	28 def check_gzip(file_path):
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	29 """Check if file is gziped."""
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	30 try:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	31 temp = open(file_path, "U")
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	32 magic_check = temp.read(2)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	33 temp.close()
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	34 if magic_check != util.gzip_magic:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	35 return (False, False)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	36 except Exception:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	37 return (False, False)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	38 return (True, True)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	39
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	40 def ungzip(download, outputFile):
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	41 """Uncompress file."""
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	42 is_gzipped, is_valid = check_gzip(download)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	43
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	44 if is_gzipped and not is_valid:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	45 print("File is compressed (gzip) but not valid.")
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	46 sys.exit(4)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	47 elif is_gzipped and is_valid:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	48 # We need to uncompress the temp_name file, but BAM files must
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	49 # remain compressed in the BGZF format
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	50 file_handle, uncompressed = tempfile.mkstemp(prefix='data_id_upload_gunzip_', dir=os.path.dirname(outputFile), text=False )
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	51 gzipped_file = gzip.GzipFile(download, 'rb')
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	52 while 1:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	53 try:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	54 chunk = gzipped_file.read(CHUNK_SIZE)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	55 except IOError:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	56 os.close(file_handle)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	57 os.remove(uncompressed)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	58 print('Problem decompressing gzipped data %s %s' % (download, outputFile))
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	59 sys.exit(4)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	60 if not chunk:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	61 break
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	62 os.write(file_handle, chunk)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	63 os.close(file_handle)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	64 gzipped_file.close()
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	65
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	66 shutil.copy(uncompressed, outputFile)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	67 try:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	68 os.remove(uncompressed)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	69 os.remove(download)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	70 except OSError:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	71 pass
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	72 else:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	73 shutil.copy(download, outputFile)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	74
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	75 def construct_multi_filename(id, name, file_type):
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	76 """ Implementation of *Number of Output datasets cannot be determined until
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	77 tool run* from documentation_.
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	78 .. _documentation: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	79 From https://github.com/mdshw5/galaxy-json-data-source/blob/master/json_data_source.py
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	80 """
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	81 filename = "%s_%s_%s_%s_%s" % ('primary', id, name, 'visible', file_type)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	82 return filename
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	83
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	84 def metadata_to_json(dataset_id, filename, name, extesion, ds_type='dataset', primary=False):
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	85 """ Return line separated JSON
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	86 From https://github.com/mdshw5/galaxy-json-data-source/blob/master/json_data_source.py
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	87 """
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	88 meta_dict = dict(type=ds_type,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	89 ext=extesion,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	90 filename=filename,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	91 name=name,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	92 metadata={})
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	93 if primary:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	94 meta_dict['base_dataset_id'] = dataset_id
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	95 else:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	96 meta_dict['dataset_id'] = dataset_id
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	97 return "%s\n" % json.dumps(meta_dict)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	98
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	99 def main():
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	100 properties_file = sys.argv[1]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	101 json_params = None
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	102 metadata_path = None
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	103 all_params = None
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	104 with open(properties_file, 'r') as file_:
13 11344d545e88 Debug Catherine Wise <catherine.wise@csiro.au> parents: 10 diff changeset	105 settings = file_.read()
11344d545e88 Debug Catherine Wise <catherine.wise@csiro.au> parents: 10 diff changeset	106 print(settings)
11344d545e88 Debug Catherine Wise <catherine.wise@csiro.au> parents: 10 diff changeset	107 all_params = json.loads(settings)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	108 json_params = all_params.get("param_dict")
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	109 metadata_path = all_params["job_config"]["TOOL_PROVIDED_JOB_METADATA_FILE"]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	110
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	111 output_filename = json_params.get('output', None)
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	112 output_data = all_params.get('output_data')
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	113 extra_files_path, file_name, ext, out_data_name, hda_id, dataset_id = \
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	114 operator.itemgetter('extra_files_path', 'file_name', 'ext', 'out_data_name', 'hda_id', 'dataset_id')(output_data[0])
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	115
15 7b3039ccf50f Un-quote url. Catherine Wise <catherine.wise@csiro.au> parents: 14 diff changeset	116 url_params = urlparse.unquote(json_params['URL']).split(";")
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	117 if len(url_params) < 3:
15 7b3039ccf50f Un-quote url. Catherine Wise <catherine.wise@csiro.au> parents: 14 diff changeset	118 print("The url we got back is malformed: "+ json_params['URL'])
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	119 sys.exit(5)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	120 short_url = url_params[0]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	121 username = url_params[1]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	122 password = url_params[2]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	123 if "/short" not in short_url:
15 7b3039ccf50f Un-quote url. Catherine Wise <catherine.wise@csiro.au> parents: 14 diff changeset	124 print("The url we got back is malformed: " + json_params['URL'])
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	125 sys.exit(5)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	126 kms_url = short_url.split("/short")[0]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	127
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	128 config = TrustStoreClient.Config(
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	129 None, kms_url, CLIENT_KEY, CLIENT_SECRET, tmpDir='/mnt/galaxy/tmp')
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	130 truststore = TrustStoreClient.TrustStoreClient(headless=False, config=config)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	131 try:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	132 truststore.authenticate(username, password)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	133 except TrustStoreClient.TrustStoreClientAuthenticationException as err:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	134 print(err)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	135 sys.exit(5)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	136 truststore.getPrivateKey('privkey.pem')
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	137
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	138 path_texts = truststore.lengthenPath(short_url)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	139 if len(path_texts) < 2:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	140 print("The path we got was malformed.")
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	141 sys.exit(3)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	142 paths = path_texts[1:]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	143 store_id = path_texts[0]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	144
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	145 store = truststore.getStoreByID(store_id)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	146 if store is None:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	147 print("Coudn't find store with that ID, or don't have access.")
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	148 sys.exit(2)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	149 root = truststore.listDirectory(store)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	150
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	151 first = True
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	152
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	153 with open(metadata_path, 'wb') as metadata_file:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	154 for path in paths:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	155 locations = utils.Navigation.files_at_path(root, path)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	156 for location in locations:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	157 if not locations:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	158 print("Path not found: " + path)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	159 continue
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	160 filename = "".join(c in SAFE_CHARS and c or '-' for c in location.name)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	161 extension = os.path.splitext(filename)[1]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	162 name = construct_multi_filename(hda_id, filename, extension)
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	163 target_output_filename = None
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	164 if first:
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	165 target_output_filename = file_name
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	166 first = False
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	167 else:
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	168 target_output_filename = os.path.normpath("/".join([extra_files_path, name]))
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	169 metadata_file.write(
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	170 metadata_to_json(dataset_id, filename, name, extension, target_output_filename))
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	171 download = truststore.getFile(store, location)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	172 if download is None:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	173 print("File %s not found." % location.name)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	174 sys.exit(4)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	175 ungzip(download, target_output_filename)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	176
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	177
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	178 if __name__ == '__main__':
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	179 main()

Mercurial > repos > cathywise > truststore_browse_testing

annotate TrustStoreGalaxyBrowse.py @ 15:7b3039ccf50f