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 <p.j.a.c...@googlemail.com> 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
