Thanks John,

The technical reasons behind this behaviour are clearer to me now:

For test inputs, Galaxy runs the upload tool which will automatically
decompress gzipped files. This means functional tests can use gzipped
files as inputs.

However, for the expected test output files, Galaxy currently compares
the files directly (without applying the upload tool) and therefore
currently gzipped files cannot (currently) be used in the functional
test definitions.

Thanks,

Peter

On Mon, Nov 10, 2014 at 2:41 PM, John Chilton <jmchil...@gmail.com> wrote:
> 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,
> -John
>
> 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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