Mercurial > repos > rhohensinner > galaxy_irods_interface

comparison irods_upload.py @ 4:84f685c067ad draft default tip

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"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author rhohensinner
date Wed, 04 Aug 2021 12:01:55 +0000
parents d2be2eb8350f
children
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3:d2be2eb8350f 4:84f685c067ad
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 import main
13 from json import dump, load, loads 12 from json import dump, load, loads
14 global python_path 13 with open("python__path.txt", "r") as pp:
15 sys.path = python_path 14 ppstr = pp.read()
15 temp = ppstr.split(",")[:-1]
16 for it in temp:
17 sys.path.append(it)
18
16 from galaxy.datatypes import sniff 19 from galaxy.datatypes import sniff
17 from galaxy.datatypes.registry import Registry 20 from galaxy.datatypes.registry import Registry
18 from galaxy.datatypes.upload_util import handle_upload, UploadProblemException 21 from galaxy.datatypes.upload_util import handle_upload, UploadProblemException
19 from galaxy.util import ( 22 from galaxy.util import (
20 bunch, 23 bunch,
306 309
307 if len(sys.argv) < 4: 310 if len(sys.argv) < 4:
308 print('usage: upload.py <root> <datatypes_conf> <json paramfile> <output spec> ...', file=sys.stderr) 311 print('usage: upload.py <root> <datatypes_conf> <json paramfile> <output spec> ...', file=sys.stderr)
309 sys.exit(1) 312 sys.exit(1)
310 313
311 sys.path.append(argv[5])
312 output_paths = parse_outputs(sys.argv[4:]) 314 output_paths = parse_outputs(sys.argv[4:])
313 315
314 registry = Registry() 316 registry = Registry()
315 registry.load_datatypes(root_dir=sys.argv[1], config=sys.argv[2]) 317 registry.load_datatypes(root_dir=sys.argv[1], config=sys.argv[2])
316 318