Gzipped input to functional tests with multiple="true"

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Gzipped input to functional tests with multiple="true"

Peter Cock
Hi all,

I think I've found a bug in the Galaxy test framework :(

With most file inputs, a gzipped input file works fine (Galaxy's upload code
handles unzipping it). However, with multiple="true" this seems to break
(with the Twill backend, the API test framework is OK), e.g.

<param name="filenames" type="data" format="fastq,mira"
multiple="true" required="true" label="Read file(s)"
                  help="Multiple files allowed, for example paired
reads can be given as two files (MIRA looks at read names to identify
pairs)." />


Fails:

<param name="filenames" value="SRR639755_mito_pairs_sample.fastq.gz"
ftype="fastqsanger" />

e.g.  https://travis-ci.org/peterjc/pico_galaxy/builds/27426318

Excerpt from log:

======================================================================
FAIL: test_tool_000000 (functional.test_toolbox.TestForTool_mira_4_0_de_novo)
MIRA v4.0 de novo assember ( mira_4_0_de_novo ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py",
line 108, in test_tool
self.do_it( td )
File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py",
line 32, in do_it
data_list = galaxy_interactor.run_tool( testdef, test_history )
File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py",
line 449, in run_tool
self.twill_test_case.run_tool( testdef.tool.id,
repeat_name=repeat_name, **page_inputs )
File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py",
line 1789, in run_tool
self.submit_form( **kwd )
File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py",
line 1999, in submit_form
raise AssertionError( errmsg )
AssertionError: Attempting to set field 'read_group_0|filenames' to
value '['SRR639755_mito_pairs_sample.fastq.gz']' in form 'tool_form'
threw exception: id=None name=None
label='SRR639755_mito_pairs_sample.fastq.gz'
control: <SelectControl(read_group_0|filenames=[80])>
If the above control is a DataToolparameter whose data type class does
not include a sniff() method,
make sure to include a proper 'ftype' attribute to the tag for the
control within the <test> tag set.


This works,

<param name="filenames" value="SRR639755_mito_pairs_sample.fastq"
ftype="fastqsanger" />

e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/27426336

See: https://github.com/peterjc/pico_galaxy/commit/e6967767535ca29debcdc19d7f0502d73276b6a0

Regards,

Peter
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Re: Gzipped input to functional tests with multiple="true"

Peter Cock
I've filed this bug in the Twill test framework on Trello:
https://trello.com/c/XG3KemZE/1732-gzipped-input-to-twill-functional-tests-fails-with-multiple-true

Peter

On Fri, Jun 13, 2014 at 10:12 AM, Peter Cock <[hidden email]> wrote:

> Hi all,
>
> I think I've found a bug in the Galaxy test framework :(
>
> With most file inputs, a gzipped input file works fine (Galaxy's upload code
> handles unzipping it). However, with multiple="true" this seems to break
> (with the Twill backend, the API test framework is OK), e.g.
>
> <param name="filenames" type="data" format="fastq,mira"
> multiple="true" required="true" label="Read file(s)"
>                   help="Multiple files allowed, for example paired
> reads can be given as two files (MIRA looks at read names to identify
> pairs)." />
>
>
> Fails:
>
> <param name="filenames" value="SRR639755_mito_pairs_sample.fastq.gz"
> ftype="fastqsanger" />
>
> e.g.  https://travis-ci.org/peterjc/pico_galaxy/builds/27426318
>
> Excerpt from log:
>
> ======================================================================
> FAIL: test_tool_000000 (functional.test_toolbox.TestForTool_mira_4_0_de_novo)
> MIRA v4.0 de novo assember ( mira_4_0_de_novo ) > Test-1
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py",
> line 108, in test_tool
> self.do_it( td )
> File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py",
> line 32, in do_it
> data_list = galaxy_interactor.run_tool( testdef, test_history )
> File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py",
> line 449, in run_tool
> self.twill_test_case.run_tool( testdef.tool.id,
> repeat_name=repeat_name, **page_inputs )
> File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py",
> line 1789, in run_tool
> self.submit_form( **kwd )
> File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py",
> line 1999, in submit_form
> raise AssertionError( errmsg )
> AssertionError: Attempting to set field 'read_group_0|filenames' to
> value '['SRR639755_mito_pairs_sample.fastq.gz']' in form 'tool_form'
> threw exception: id=None name=None
> label='SRR639755_mito_pairs_sample.fastq.gz'
> control: <SelectControl(read_group_0|filenames=[80])>
> If the above control is a DataToolparameter whose data type class does
> not include a sniff() method,
> make sure to include a proper 'ftype' attribute to the tag for the
> control within the <test> tag set.
>
>
> This works,
>
> <param name="filenames" value="SRR639755_mito_pairs_sample.fastq"
> ftype="fastqsanger" />
>
> e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/27426336
>
> See: https://github.com/peterjc/pico_galaxy/commit/e6967767535ca29debcdc19d7f0502d73276b6a0
>
> Regards,
>
> Peter
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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