I have no issue with supporting this in general - but the
implementation I think is a bit more tricky than it would seem. The
test framework doesn't know if Galaxy would uncompress zipped files or
not - I think the only way to reason about that in the abstract is to
actually upload the file to Galaxy unfortunately. So I guess we could
try something like compare the contents - if not matching and the test
target is compressed - decompress and retry. I've created a Trello
card - https://trello.com/c/ebdBkezi.

Thanks for the suggestion,

On Thu, Nov 6, 2014 at 12:32 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hello all,
> Because Galaxy uses the upload tool internally for the inputs for
> function tests, it is possible to bundle gzipped versions of test
> inputs which saves space. For example,
> https://github.com/peterjc/pico_galaxy/blob/master/tools/clc_assembly_cell/clc_mapper.xml
> However, what I have just found is that this does not work for
> gzipped files as test outputs. Rather Galaxy seems to compare
> the (uncompressed) output from the tool to the expected output
> file as it is (i.e. still compressed). e.g.
> https://github.com/peterjc/pico_galaxy/commit/c8adfdf5d1f48c00ac72df967d2be3c828400d45
> (I have only tested adding/removing the gzip compression on the
> output file locally)
> Is this deliberate?
> Peter
> P.S.
> I wanted point at the TravisCI output for that commit and its parent
> to show the output,
> - https://travis-ci.org/peterjc/pico_galaxy/builds/40203652
> - https://travis-ci.org/peterjc/pico_galaxy/builds/40202182
> However there appears to be an egg issue with the current
> galaxy-central branch:
> $ python scripts/fetch_eggs.py
> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> Traceback (most recent call last):
>   File "scripts/fetch_eggs.py", line 46, in <module>
>     c.resolve() # Only fetch eggs required by the config
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
> line 347, in resolve
>     egg.resolve()
>   File 
> "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py",
> line 192, in resolve
>     if e.args[1].key != e.args[0].key:
> IndexError: tuple index out of range
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