Data Libraries: Unable to Link to Files When Paths Contain Spaces
Hi All, We're having problems adding files to data libraries. We'd like to create links to files instead of copying them into Galaxy. We can create links if there aren't spaces in the paths. Also, we can copy files into libraries even if there are spaces in the paths. Unfortunately, we cannot create links to files when their paths contain spaces. The job standard error and miscellaneous information are: Miscellaneous information:uploaded RAW file Traceback (most recent call last): File "/share/galaxy/working/002/2615/set_metadata_hnsR90.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/home/galaxy/Galaxy/galaxy-dist Job Standard Error Traceback (most recent call last): File "/share/galaxy/working/002/2615/set_metadata_hnsR90.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/home/galaxy/Galaxy/galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py", line 80, in set_metadata filename_out = fields.pop( 0 ) IndexError: pop from empty list error We've set allow_library_path_paste = True in galaxy.ini. We've also tried adding "" or '' around the path and get the following error message: Invalid paths: "home/galaxy/Galaxy/galaxy-dist/"/share/projects/2014 Test"" Any help or suggestions would be great. Thanks, Joe Greer Proteomics Center of Excellence Northwestern University
This is a good news, bad news sort of thing. I have opened a PR to fix the actual uploads here - https://github.com/galaxyproject/galaxy/pull/474. But I think many tools don't properly quote file paths with names in them - so I suspect you will find a lot of tool bugs using these files. Thanks for the bug report. -John On Mon, Jul 6, 2015 at 10:11 PM, Joseph Brent Greer <joseph.greer@northwestern.edu> wrote:
Hi All,
We’re having problems adding files to data libraries.
We’d like to create links to files instead of copying them into Galaxy. We can create links if there aren’t spaces in the paths. Also, we can copy files into libraries even if there are spaces in the paths.
Unfortunately, we cannot create links to files when their paths contain spaces.
The job standard error and miscellaneous information are:
Miscellaneous information:uploaded RAW file Traceback (most recent call last): File "/share/galaxy/working/002/2615/set_metadata_hnsR90.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/home/galaxy/Galaxy/galaxy-dist
Job Standard Error
Traceback (most recent call last):
File "/share/galaxy/working/002/2615/set_metadata_hnsR90.py", line 1, in <module>
from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
File "/home/galaxy/Galaxy/galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py", line 80, in set_metadata
filename_out = fields.pop( 0 )
IndexError: pop from empty list
error
We’ve set allow_library_path_paste = True in galaxy.ini.
We’ve also tried adding “” or ‘’ around the path and get the following error message:
Invalid paths: “home/galaxy/Galaxy/galaxy-dist/”/share/projects/2014 Test””
Any help or suggestions would be great.
Thanks,
Joe Greer
Proteomics Center of Excellence
Northwestern University
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participants (2)
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John Chilton -
Joseph Brent Greer