Hello Peter,

Thanks for reporting this - I've added the following Trello card for this issue.

https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1

Greg Von Kuster

On Nov 12, 2013, at 7:07 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> Hi guys,
> 
> I have a new wrapper for samtools idxstats with a working
> unit test via run_functional_tests.sh run locally or on TravisCI:
> https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html
> 
> However, this tool's test is failing on the Test Tool Shed:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/6564815949e0
> 
> Tool test results
> Automated test environment
> Time tested: ~ 11 hours ago
> System: Linux 3.8.0-30-generic
> Architecture: x86_64
> Python version: 2.7.4
> Galaxy revision: 11284:28469a503b56
> Galaxy database version: 117
> Tool shed revision:
> Tool shed database version:
> Tool shed mercurial version:
> Tests that failed
> Tool id: samtools_idxstats
> Tool version: samtools_idxstats
> Test: test_tool_000000
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_idxstats/samtools_idxstats/0.0.1)
> Stderr:
> Fatal error: Exit code 1 ()
> Input BAI file not found: None
> Traceback:
> Traceback (most recent call last):
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 216, in test_tool
>    self.do_it( td, shed_tool_id=shed_tool_id )
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 28, in do_it
>    self.__verify_outputs( testdef, shed_tool_id, data_list )
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 134, in __verify_outputs
>    self.__verify_output( output_tuple, shed_tool_id, elem,
> maxseconds=maxseconds )
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 141, in __verify_output
>    self.verify_dataset_correctness( outfile, hid=elem_hid,
> attributes=attributes, shed_tool_id=shed_tool_id )
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> line 782, in verify_dataset_correctness
>    self._assert_dataset_state( elem, 'ok' )
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> line 606, in _assert_dataset_state
>    raise AssertionError( errmsg )
> AssertionError: Expecting dataset state 'ok', but state is 'error'.
> Dataset blurb: error
> 
> It appears that the upload has not generated the *.bai index and
> assigned it to the variable input_bam.metadata.bam_index
> (but this works via run_functional_tests.sh for me):
> 
> $ ls test-data/ex1.*
> test-data/ex1.bam  test-data/ex1.idxstats.tabular
> 
> $ ./run_functional_tests.sh -id samtools_idxstats
> ...
> Ran 1 test in 32.400s
> 
> OK
> ...
> (all fine)
> 
> (Note that the bai file does not seem to be needed)
> 
> Tested with this revision, which works:
> 
> $ hg branch
> default
> $ hg log | head
> changeset:   12309:1df960b4892a
> tag:         tip
> user:        John Chilton <jmchil...@gmail.com>
> date:        Sun Nov 10 23:37:56 2013 -0600
> summary:     PEP-8 cleanups of lib/galaxy/security/__init__.py.
> 
> Updated to current tip, also works:
> 
> $ hg branch
> default
> [galaxy@ppserver galaxy-central]$ hg log | head
> changeset:   12321:e12a10e5418d
> tag:         tip
> user:        guerler
> date:        Mon Nov 11 16:00:10 2013 -0500
> summary:     UI: Fix tooltip placement for masthead icons
> 
> Are there anyone known differences on the Test Tool Shed
> which could explain this failure?
> 
> Thanks,
> 
> Peter
> ___________________________________________________________
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