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