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
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 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
>
>
> 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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