WIP: library_upload_dir: improvements

[bernt-matthias]

major improvement: when using upload_from_galaxy_filesystem the PATH needed to be given absolute and the script generates the complete hierarchy in Galaxy library (i.e. starting from root). Now the script has an additional parameter --root_folder ROOT which allows to upload ROOT/PATH into the library folder PATH.

minor improvements:

• added --library_name which allows to specify the library by name
• fixed --folder which now works as documented, ie the root folder of the library is used if not given
• added preserve dir and tag using files names
• also started a bit with documentation

Questions:

• maybe there is also a better way to add filesystem folders to a library folder
• maybe a mechanism like the one I implemented with --root should be in the API .. then this would also be possible with parsec
• should this script stay here or is it better to integrate into (e.g.) ephemeris ... ?

[jmchilton]

should this script stay here or is it better to integrate into (e.g.) ephemeris ... ?

This script since it is here for demonstration purposes - I'm not sure it is designed to actually be used. I' rather see enhancements to https://github.com/galaxyproject/ephemeris/blob/master/src/ephemeris/setup_data_libraries.py or a second data library script there. But I'm not going to abandon this so I'll merge the PR.

[jmchilton]

Actually, there are linting problems - will you fix those?

./scripts/api/library_upload_dir.py:25:56: W291 trailing whitespace

[bernt-matthias]

I'm fine with adding the script to ephemeris. I thought that it would fit better there. I will test this a bit more and then PR to ephemeris.

[martenson]

@bernt-matthias how do you see the future of this PR?

[mvdbeek]

I've dropped the milestone here, but I also agree with John that this should probably go as an enhancement to ephemeris (if that didn't already happen?).