Fix #46 to have netcdf format for outputs in collection in Galaxy FATES tool

[annefou]

Thanks Wolfgang, Marius, and Simon for helping me out fixing this problem. And thanks Beatriz for hosting the Galaxy papercut!

[bgruening]

@annefou I think you can add ftype="netcdf" to the test outputs as well.

[annefou]

@annefou I think you can add ftype="netcdf" to the test outputs as well.

For tests we do not generate netCDF outputs (it would generate too large files for a test) because we only run a few days of simulation.

[bgruening]

For tests we do not generate netCDF outputs (it would generate too large files for a test) because we only run a few days of simulation.

We can by now, latest Galaxy release, test for file-size without storing the netcdf in this repo. https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-tests-test-output-assert-contents --> has_size

[annefou]

Interesting! Let me have a look and add a new test. Many thanks for the tip.

[annefou]

@bgruening I think I need help for writing the output checks. I would like to grep for end of main integration loop (if we have this string anywhere in the file then it means it worked) and I had:

            <output name="atm_log" ftype="txt" file="atm_1m.log" compare="sim_size" delta="1000">
              <assert_contents>
                  <has_text text="end of main integration loop" />
              </assert_contents>
            </output>

And it works locally (with planemo and --docker) but it does not work online.

Now I tried to remove compare and it fails everywhere:

            <output name="atm_log" ftype="txt" file="atm_1m.log">
              <assert_contents>
                  <has_text text="end of main integration loop" />
              </assert_contents>
            </output>

And because I cannot get atm_1m.log I cannot really see what is wrong (if anything is wrong).