truststore_browse_testing: TrustStoreGalaxyBrowse.py annotate

annotate TrustStoreGalaxyBrowse.py @ 18:c0deddf8a9ad

Attempt 2

author	Catherine Wise <catherine.wise@csiro.au>
date	Thu, 14 May 2015 08:50:16 +1000
parents	10ce45af14dd
children	f4585bf75a8a

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
16 10ce45af14dd Use pyopenssl Catherine Wise <catherine.wise@csiro.au> parents: 15 diff changeset	14 # Tell urllib3 to use pyOpenSSL because we are on old Python stdlib.
10ce45af14dd Use pyopenssl Catherine Wise <catherine.wise@csiro.au> parents: 15 diff changeset	15 import urllib3.contrib.pyopenssl
10ce45af14dd Use pyopenssl Catherine Wise <catherine.wise@csiro.au> parents: 15 diff changeset	16 urllib3.contrib.pyopenssl.inject_into_urllib3()
10ce45af14dd Use pyopenssl Catherine Wise <catherine.wise@csiro.au> parents: 15 diff changeset	17
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	18 CLIENT_KEY = "desktop"
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	19 CLIENT_SECRET = "cpU92F1PT7VOCANjSknuCDp4DrubmujoBaF6b0miz8OpKNokEbGMHCaSFK5/lISbBmaaGVCgeADI2A39F3Hkeg=="
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	20 CHUNK_SIZE = 2**20 # 1Mb
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	21 SAFE_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	22
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	23 def print_nice(elem, f, depth):
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	24 """Print the file name."""
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	25 try:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	26 f.write('\t'*depth + elem.name + " (" + str(len(elem.fragments)) + " parts)\n")
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	27 except AttributeError:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	28 f.write('\t'*depth + elem.name + "\n")
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	29 for child in elem.children:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	30 print_nice(child, f, depth+1)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	31
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	32 def check_gzip(file_path):
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	33 """Check if file is gziped."""
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	34 try:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	35 temp = open(file_path, "U")
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	36 magic_check = temp.read(2)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	37 temp.close()
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	38 if magic_check != util.gzip_magic:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	39 return (False, False)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	40 except Exception:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	41 return (False, False)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	42 return (True, True)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	43
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	44 def ungzip(download, outputFile):
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	45 """Uncompress file."""
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	46 is_gzipped, is_valid = check_gzip(download)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	47
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	48 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	49 print("File is compressed (gzip) but not valid.")
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	50 sys.exit(4)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	51 elif is_gzipped and is_valid:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	52 # 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	53 # remain compressed in the BGZF format
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	54 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	55 gzipped_file = gzip.GzipFile(download, 'rb')
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	56 while 1:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	57 try:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	58 chunk = gzipped_file.read(CHUNK_SIZE)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	59 except IOError:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	60 os.close(file_handle)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	61 os.remove(uncompressed)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	62 print('Problem decompressing gzipped data %s %s' % (download, outputFile))
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	63 sys.exit(4)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	64 if not chunk:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	65 break
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	66 os.write(file_handle, chunk)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	67 os.close(file_handle)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	68 gzipped_file.close()
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	69
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	70 shutil.copy(uncompressed, outputFile)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	71 try:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	72 os.remove(uncompressed)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	73 os.remove(download)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	74 except OSError:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	75 pass
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	76 else:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	77 shutil.copy(download, outputFile)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	78
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	79 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	80 """ 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	81 tool run* from documentation_.
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	82 .. _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	83 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	84 """
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	85 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	86 return filename
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	87
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	88 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	89 """ Return line separated JSON
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	90 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	91 """
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	92 meta_dict = dict(type=ds_type,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	93 ext=extesion,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	94 filename=filename,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	95 name=name,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	96 metadata={})
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	97 if primary:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	98 meta_dict['base_dataset_id'] = dataset_id
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	99 else:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	100 meta_dict['dataset_id'] = dataset_id
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	101 return "%s\n" % json.dumps(meta_dict)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	102
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	103 def main():
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	104 properties_file = sys.argv[1]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	105 json_params = None
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	106 metadata_path = None
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	107 all_params = None
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	108 with open(properties_file, 'r') as file_:
13 11344d545e88 Debug Catherine Wise <catherine.wise@csiro.au> parents: 10 diff changeset	109 settings = file_.read()
11344d545e88 Debug Catherine Wise <catherine.wise@csiro.au> parents: 10 diff changeset	110 print(settings)
11344d545e88 Debug Catherine Wise <catherine.wise@csiro.au> parents: 10 diff changeset	111 all_params = json.loads(settings)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	112 json_params = all_params.get("param_dict")
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	113 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	114
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	115 output_filename = json_params.get('output', None)
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	116 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	117 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	118 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	119
15 7b3039ccf50f Un-quote url. Catherine Wise <catherine.wise@csiro.au> parents: 14 diff changeset	120 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	121 if len(url_params) < 3:
15 7b3039ccf50f Un-quote url. Catherine Wise <catherine.wise@csiro.au> parents: 14 diff changeset	122 print("The url we got back is malformed: "+ json_params['URL'])
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	123 sys.exit(5)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	124 short_url = url_params[0]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	125 username = url_params[1]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	126 password = url_params[2]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	127 if "/short" not in short_url:
15 7b3039ccf50f Un-quote url. Catherine Wise <catherine.wise@csiro.au> parents: 14 diff changeset	128 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	129 sys.exit(5)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	130 kms_url = short_url.split("/short")[0]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	131
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	132 config = TrustStoreClient.Config(
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	133 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	134 truststore = TrustStoreClient.TrustStoreClient(headless=False, config=config)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	135 try:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	136 truststore.authenticate(username, password)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	137 except TrustStoreClient.TrustStoreClientAuthenticationException as err:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	138 print(err)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	139 sys.exit(5)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	140 truststore.getPrivateKey('privkey.pem')
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	141
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	142 path_texts = truststore.lengthenPath(short_url)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	143 if len(path_texts) < 2:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	144 print("The path we got was malformed.")
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	145 sys.exit(3)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	146 paths = path_texts[1:]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	147 store_id = path_texts[0]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	148
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	149 store = truststore.getStoreByID(store_id)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	150 if store is None:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	151 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	152 sys.exit(2)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	153 root = truststore.listDirectory(store)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	154
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	155 first = True
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	156
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	157 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	158 for path in paths:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	159 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	160 for location in locations:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	161 if not locations:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	162 print("Path not found: " + path)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	163 continue
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	164 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	165 extension = os.path.splitext(filename)[1]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	166 name = construct_multi_filename(hda_id, filename, extension)
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	167 target_output_filename = None
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	168 if first:
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	169 target_output_filename = file_name
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	170 first = False
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	171 else:
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	172 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	173 metadata_file.write(
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	174 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	175 download = truststore.getFile(store, location)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	176 if download is None:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	177 print("File %s not found." % location.name)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	178 sys.exit(4)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	179 ungzip(download, target_output_filename)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	180
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	181
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	182 if __name__ == '__main__':
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	183 main()

Mercurial > repos > cathywise > truststore_browse_testing

annotate TrustStoreGalaxyBrowse.py @ 18:c0deddf8a9ad