Testing using paths with spaces

[peterjc]

Spin out from discussion on #455 where is is good practice to defensively quote path and filenames in the <command> template (etc?) when wrapping tools. This intended to cope with the corner case where Galaxy or one of the working folders has been setup using a directory name with a space.

While we recognise using spaces in directories is a bad idea given how command line parsing works, and expect that many Galaxy tools will break in this situation (perhaps also parts of Galaxy), it would be nice for tools-iuc to illustrate best practise guidelines by quoting filenames/paths.

This issue is about deliberately including such paths in any automated testing for tools-iuc, e.g. using Travis https://github.com/galaxyproject/tools-iuc/tree/travis

Assuming Galaxy copes, we could tweak the Travis (etc) setup to install all of Galaxy on a path with a space. Otherwise we could try just set a few key paths, e.g. maybe:

job_working_directory = database/job working directory

[bgruening]

@peterjc is it feasible to make this part of Galaxy lint? Searching for all data and text parameters and ensure that these are quoted in the command section?

[peterjc]

It should be easy to spot $name (with white space before and after, including special case of at the end of the line) in planemo lint, and variants like ${name}, within the <command> tag. That would help and seems like a good idea in itself. I like that idea :)

In general however, there is no substitute for actually running the entire stack on a path with spaces.

[nsoranzo]

:+1:

[bernt-matthias]

Like that idea Maybe adding --file_path to the planemo t calls is a good first step.

Otherwise I guess cloning galaxy in a directory with a space and using this via --galaxy_root is the ultimative solution which would also catch errors like scripts shipped with the tool ($__tool_directory__)

[bernt-matthias]

LOL: https://github.com/galaxyproject/galaxy/pull/9222

I tried planemo --file_path .. locally on maxbin2 and it failed .. I think having spaces in path will often require upstream fixes (e.g. for pipelines that don't quote properly internally).

Not sure if we really want to have this globally... my first Idea was that it might be better to have a check in Galaxy

• if its installed in a path with spaces
• filepath contains spaces
• jobwrokingdir contains spaces

and just dont start / print a big warning if one of these applies.