truststore_browse_testing: TrustStoreGalaxyBrowse.py annotate

annotate TrustStoreGalaxyBrowse.py @ 29:157062f5c547

Fix temporary dir.

author	Catherine Wise <catherine.wise@csiro.au>
date	Mon, 18 May 2015 11:17:03 +1000
parents	901b359bb74a
children	e4c13ce69e25

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.
24 f4585bf75a8a Give up, try to update Python instead. Catherine Wise <catherine.wise@csiro.au> parents: 16 diff changeset	15 # import urllib3.contrib.pyopenssl
f4585bf75a8a Give up, try to update Python instead. Catherine Wise <catherine.wise@csiro.au> parents: 16 diff changeset	16 # urllib3.contrib.pyopenssl.inject_into_urllib3()
25 18fe446f2d02 Tell requests about the new cert bundle. FFS. Catherine Wise <catherine.wise@csiro.au> parents: 24 diff changeset	17 #
26 463b024b53ff The path was wrong. UUUUGH. Catherine Wise <catherine.wise@csiro.au> parents: 25 diff changeset	18 os.environ["REQUESTS_CA_BUNDLE"] = "/etc/ssl/certs/ca-certificates.crt"
16 10ce45af14dd Use pyopenssl Catherine Wise <catherine.wise@csiro.au> parents: 15 diff changeset	19
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	20 CLIENT_KEY = "desktop"
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	21 CLIENT_SECRET = "cpU92F1PT7VOCANjSknuCDp4DrubmujoBaF6b0miz8OpKNokEbGMHCaSFK5/lISbBmaaGVCgeADI2A39F3Hkeg=="
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	22 CHUNK_SIZE = 2**20 # 1Mb
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	23 SAFE_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	24
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	25 def print_nice(elem, f, depth):
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	26 """Print the file name."""
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	27 try:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	28 f.write('\t'*depth + elem.name + " (" + str(len(elem.fragments)) + " parts)\n")
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	29 except AttributeError:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	30 f.write('\t'*depth + elem.name + "\n")
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	31 for child in elem.children:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	32 print_nice(child, f, depth+1)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	33
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	34 def check_gzip(file_path):
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	35 """Check if file is gziped."""
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	36 try:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	37 temp = open(file_path, "U")
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	38 magic_check = temp.read(2)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	39 temp.close()
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	40 if magic_check != util.gzip_magic:
9 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 except Exception:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	43 return (False, False)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	44 return (True, True)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	45
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	46 def ungzip(download, outputFile):
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	47 """Uncompress file."""
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	48 is_gzipped, is_valid = check_gzip(download)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	49
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	50 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	51 print("File is compressed (gzip) but not valid.")
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	52 sys.exit(4)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	53 elif is_gzipped and is_valid:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	54 # 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	55 # remain compressed in the BGZF format
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	56 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	57 gzipped_file = gzip.GzipFile(download, 'rb')
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	58 while 1:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	59 try:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	60 chunk = gzipped_file.read(CHUNK_SIZE)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	61 except IOError:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	62 os.close(file_handle)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	63 os.remove(uncompressed)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	64 print('Problem decompressing gzipped data %s %s' % (download, outputFile))
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	65 sys.exit(4)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	66 if not chunk:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	67 break
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	68 os.write(file_handle, chunk)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	69 os.close(file_handle)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	70 gzipped_file.close()
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	71
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	72 shutil.copy(uncompressed, outputFile)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	73 try:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	74 os.remove(uncompressed)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	75 os.remove(download)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	76 except OSError:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	77 pass
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	78 else:
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	79 shutil.copy(download, outputFile)
2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	80
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	81 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	82 """ 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	83 tool run* from documentation_.
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	84 .. _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	85 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	86 """
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	87 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	88 return filename
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	89
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	90 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	91 """ Return line separated JSON
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	92 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	93 """
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	94 meta_dict = dict(type=ds_type,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	95 ext=extesion,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	96 filename=filename,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	97 name=name,
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	98 metadata={})
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	99 if primary:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	100 meta_dict['base_dataset_id'] = dataset_id
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	101 else:
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	102 meta_dict['dataset_id'] = dataset_id
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	103 return "%s\n" % json.dumps(meta_dict)
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	104
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	105 def main():
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	106 properties_file = sys.argv[1]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	107 json_params = None
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	108 metadata_path = None
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	109 all_params = None
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	110 with open(properties_file, 'r') as file_:
13 11344d545e88 Debug Catherine Wise <catherine.wise@csiro.au> parents: 10 diff changeset	111 settings = file_.read()
11344d545e88 Debug Catherine Wise <catherine.wise@csiro.au> parents: 10 diff changeset	112 print(settings)
11344d545e88 Debug Catherine Wise <catherine.wise@csiro.au> parents: 10 diff changeset	113 all_params = json.loads(settings)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	114 json_params = all_params.get("param_dict")
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	115 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	116
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	117 output_filename = json_params.get('output', None)
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	118 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	119 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	120 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	121
15 7b3039ccf50f Un-quote url. Catherine Wise <catherine.wise@csiro.au> parents: 14 diff changeset	122 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	123 if len(url_params) < 3:
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'])
0 2a996fea49a3 Initial. Catherine Wise <catherine.wise@csiro.au> parents: diff changeset	125 sys.exit(5)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	126 short_url = url_params[0]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	127 username = url_params[1]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	128 password = url_params[2]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	129 if "/short" not in short_url:
15 7b3039ccf50f Un-quote url. Catherine Wise <catherine.wise@csiro.au> parents: 14 diff changeset	130 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	131 sys.exit(5)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	132 kms_url = short_url.split("/short")[0]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	133
29 157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	134 tmp_dir = '/mnt/galaxy/tmp'
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	135 tmp = None
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	136 if os.path.exists(tmp_dir):
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	137 tmp = tmp_dir
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	138
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	139 config = TrustStoreClient.Config(
29 157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	140 None, kms_url, CLIENT_KEY, CLIENT_SECRET, tmpDir=tmp)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	141 truststore = TrustStoreClient.TrustStoreClient(headless=False, config=config)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	142 try:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	143 truststore.authenticate(username, password)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	144 except TrustStoreClient.TrustStoreClientAuthenticationException as err:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	145 print(err)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	146 sys.exit(5)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	147 truststore.getPrivateKey('privkey.pem')
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 path_texts = truststore.lengthenPath(short_url)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	150 if len(path_texts) < 2:
27 901b359bb74a We are getting closer. Catherine Wise <catherine.wise@csiro.au> parents: 26 diff changeset	151 print("The path we got was malformed: " + str(path_texts))
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	152 sys.exit(3)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	153 paths = path_texts[1:]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	154 store_id = path_texts[0]
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	155
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	156 store = truststore.getStoreByID(store_id)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	157 if store is None:
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	158 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	159 sys.exit(2)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	160 root = truststore.listDirectory(store)
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	161
14 589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	162 first = True
589f9250e30f Fix son reading. Catherine Wise <catherine.wise@csiro.au> parents: 13 diff changeset	163
29 157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	164 if root is not None:
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	165 with open(metadata_path, 'wb') as metadata_file:
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	166 for path in paths:
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	167 locations = utils.Navigation.files_at_path(root, path)
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	168 for location in locations:
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	169 if not locations:
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	170 print("Path not found: " + path)
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	171 continue
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	172 filename = "".join(c in SAFE_CHARS and c or '-' for c in location.name)
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	173 extension = os.path.splitext(filename)[1]
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	174 name = construct_multi_filename(hda_id, filename, extension)
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	175 target_output_filename = None
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	176 if first:
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	177 target_output_filename = file_name
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	178 first = False
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	179 else:
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	180 target_output_filename = os.path.normpath("/".join([extra_files_path, name]))
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	181 metadata_file.write(
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	182 metadata_to_json(dataset_id, filename, name, extension, target_output_filename))
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	183 download = truststore.getFile(store, location)
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	184 if download is None:
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	185 print("File %s not found." % location.name)
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	186 sys.exit(4)
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	187 ungzip(download, target_output_filename)
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	188 else:
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	189 print("Store is damaged or we don't have sufficient access.")
157062f5c547 Fix temporary dir. Catherine Wise <catherine.wise@csiro.au> parents: 27 diff changeset	190 sys.exit(4)
9 0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	191
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	192
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	193 if __name__ == '__main__':
0f2a5664c9eb Actually update downloader (probably not working). Catherine Wise <catherine.wise@csiro.au> parents: 0 diff changeset	194 main()

Mercurial > repos > cathywise > truststore_browse_testing

annotate TrustStoreGalaxyBrowse.py @ 29:157062f5c547