Mercurial > repos > rhohensinner > galaxy_irods_interface

comparison irods_upload.py @ 3:d2be2eb8350f draft

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"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author rhohensinner
date Mon, 19 Jul 2021 13:11:45 +0000
parents 0641ea2f75b1
children 84f685c067ad
comparison
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2:0641ea2f75b1 3:d2be2eb8350f
7 7
8 import errno 8 import errno
9 import os 9 import os
10 import shutil 10 import shutil
11 import sys 11 import sys
12 sys.path.append("/home/richard/galaxy/lib") 12 import main
13 from json import dump, load, loads 13 from json import dump, load, loads
14 14 global python_path
15 sys.path = python_path
15 from galaxy.datatypes import sniff 16 from galaxy.datatypes import sniff
16 from galaxy.datatypes.registry import Registry 17 from galaxy.datatypes.registry import Registry
17 from galaxy.datatypes.upload_util import handle_upload, UploadProblemException 18 from galaxy.datatypes.upload_util import handle_upload, UploadProblemException
18 from galaxy.util import ( 19 from galaxy.util import (
19 bunch, 20 bunch,
305 306
306 if len(sys.argv) < 4: 307 if len(sys.argv) < 4:
307 print('usage: upload.py <root> <datatypes_conf> <json paramfile> <output spec> ...', file=sys.stderr) 308 print('usage: upload.py <root> <datatypes_conf> <json paramfile> <output spec> ...', file=sys.stderr)
308 sys.exit(1) 309 sys.exit(1)
309 310
311 sys.path.append(argv[5])
310 output_paths = parse_outputs(sys.argv[4:]) 312 output_paths = parse_outputs(sys.argv[4:])
311 313
312 registry = Registry() 314 registry = Registry()
313 registry.load_datatypes(root_dir=sys.argv[1], config=sys.argv[2]) 315 registry.load_datatypes(root_dir=sys.argv[1], config=sys.argv[2])
314 316