test: check if extra files were created in Galaxy's file_path

[bernt-matthias]

This is an attempt to automatize galaxyproject/tools-iuc#3986 (comment)

fixes #1189

Seems difficult / impossible to find out which tool / test generates the extra files, so I just set all tests for failure and add some note to the stderr .. (but IUC style tests run 1 planemo test per repo)

I guess this will create quite a bit of noise in the IUC style repos weekly CI tests .. but maybe its a good thing.

[bernt-matthias]

It would be a nice alternative to configure Galaxy that executes the jobs in planemo such that jobs run as real user. Then jobs writing to the files dir would just fail.

[bgruening]

@bernt-matthias wouldn't it be easier to configure Galaxy a little bit. We are running already test with containers. We could now say that all inputs are just mounted in RO.

We did something similar here: https://github.com/bgruening/galaxytools/blob/master/job_conf.xml_condor
https://github.com/bgruening/galaxytools/pull/1022/files

[bernt-matthias]

@bernt-matthias wouldn't it be easier to configure Galaxy a little bit. We are running already test with containers. We could now say that all inputs are just mounted in RO.

We did something similar here: https://github.com/bgruening/galaxytools/blob/master/job_conf.xml_condor https://github.com/bgruening/galaxytools/pull/1022/files

Thanks for sharing. Looks pretty simple. What was the original intention of using htcondor in CI?

Is there somewhere an example for a param that sets up the a directory RO.

I guess we can add this either to the planemo-ci-action .. or the separate repos, preferences?

[bernt-matthias]

Ah I see https://github.com/galaxyproject/galaxy/blob/5dc9111f45b4ed5012575b31e199a591cfad6d7a/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L502

Is there a way to refer to the Galaxy root when specifying the paths?

Do we actually need htcondor? Local docker might be sufficient as well.

...

While reading the docs again wouldnt simply outputs_to_working_directory do the trick without any configuration?

[bernt-matthias]

See here https://github.com/galaxyproject/galaxy/blob/5dc9111f45b4ed5012575b31e199a591cfad6d7a/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L483

[bernt-matthias]

Hah. It does :) .. problem is that there might be tools that try to write and if impossible choose some different branch in the code. But as soon as the tools find a config that allows them to write then they will.

So this PR might serve as a backup...

Still the update_test_data should be implemented .. give me a sec :)