Thanks John,
That sounds like quite a subtle root cause - well done. I've
reverted my workaround and the TravisCI tests pass again:
Regards,
Peter
On Wed, Dec 17, 2014 at 2:45 PM, John Chilton <jmchilton(a)gmail.com> wrote:
Hey Peter,
Thanks for the very detailed bug report - it really helped track things down.
I have pushed a fix to next-stable and default (the bug never reached stable).
https://bitbucket.org/galaxy/galaxy-central/commits/a74d32014b0512613042c...
The commit also includes a test case so hopefully this won't break again.
-John
On Wed, Dec 17, 2014 at 6:56 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
> Hi all,
>
> Using gzipped input files in tool functional tests (which would be
> decompressed by the upload tool) used to work, e.g.
>
>
https://travis-ci.org/peterjc/pico_galaxy/builds/42395911
>
https://github.com/peterjc/pico_galaxy/blob/539260fa4348ed454ce464e48c9db...
>
> But with more recent versions of Galaxy this has broken, e.g.
>
>
https://travis-ci.org/peterjc/pico_galaxy/builds/44038046
>
https://github.com/peterjc/pico_galaxy/blob/e3064cc8f42253efd1f8eed56844d...
>
> According to the TravisCI failure, the command run was:
>
> python
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/tools/seq_filter_by_mapping/seq_filter_by_mapping.py
> -i "None" -f "data" -m lax -p
> /tmp/tmpaCsMm5/tmpEpBIX1/database/files/000/dataset_50.dat
> /tmp/tmpaCsMm5/tmpEpBIX1/database/files/000/dataset_49.dat
>
> In this case the -i argument was $input_file, and -f was its
> extension/datatype. Somehow the gzipped FASTQ was
> not found, which is why the filename is just "None" and
> its datatype the default "data".
>
> My tool is sensibly returning error code 1, and:
>
> Missing input file: 'None'
>
> I have made some minor changes to this tool between those
> TravisCI tests, but the test is the same:
>
> <tests>
> <test>
> <param name="input_file"
value="SRR639755_mito_pairs.fastq.gz"
> ftype="fastqsanger" />
> <param name="mapping_file"
> value="SRR639755_sample_by_coord.sam" ftype="sam" />
> <param name="pair_mode" value="lax" />
> <param name="output_choice" value="pos" />
> <output name="output_pos"
file="SRR639755_sample_lax.fastq"
> ftype="fastqsanger" />
> </test>
> <test>
> <param name="input_file"
value="SRR639755_mito_pairs.fastq.gz"
> ftype="fastqsanger" />
> <param name="mapping_file"
> value="SRR639755_sample_by_coord.sam" ftype="sam" />
> <param name="pair_mode" value="strict" />
> <param name="output_choice" value="pos" />
> <output name="output_pos"
file="SRR639755_sample_strict.fastq"
> ftype="fastqsanger" />
> </test>
> </tests>
>
> --
>
> I could reproduce this on my development machine running an
> older Galaxy:
>
> $ hg log | head
> changeset: 16732:212e1d5e9be5
> branch: stable
> tag: tip
> parent: 16716:2db0fb9594d6
> parent: 16731:7adac1842adf
> user: John Chilton <jmchilton(a)gmail.com>
> date: Wed Dec 10 12:20:55 2014 -0500
> summary: Merged in dannon/galaxy-central/stable (pull request #602)
>
> And again updating to the current tip,
>
> $ hg log | head
> changeset: 16850:e614c7c1e0e9
> tag: tip
> parent: 16848:1cf0af0a6324
> parent: 16849:d13f2b265dbf
> user: Dannon Baker <dannon.baker(a)gmail.com>
> date: Tue Dec 16 15:48:44 2014 -0500
> summary: Merged in nitesh1989/galaxy-central3 (pull request #615)
>
> I can "fix" it by swapping the gzipped test input_file
> SRR639755_mito_pairs.fastq.gz to the uncompressed
> SRR639755_mito_pairs.fastq instead, as in this commit:
>
>
https://github.com/peterjc/pico_galaxy/commit/126e3e716965016808ec2ba3a4b...
>
https://travis-ci.org/peterjc/pico_galaxy/builds/44317785
>
> I would like to revert this workaround since the uncompressed
> FASTQ file is a bit large to bundle as a test case - so I hope
> this is simply due to an accidental regression in Galaxy itself.
>
> Thanks,
>
> Peter
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