Hi Peter,

This was due to a bug I introduced last week, which I've just fixed
in d1f6d05. Sorry for the trouble.

--nate

On Tue, Sep 9, 2014 at 9:50 AM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:

> Hi all,
>
> I'm wondering why my samtools_depad repository tests have
> failed, and since I have not changed this recently presume this
> is due to a Galaxy change or general TestToolShed problem
> not specific to my tool:
>
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>
> Tests that failed
> Tool id: samtools_depad
> Tool version: samtools_depad
> Test: test_tool_000000
> (
> functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1
> )
> Stderr:
> 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 114, in test_tool
>     self.do_it( td )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 35, in do_it
>     self._verify_outputs( testdef, test_history, shed_tool_id,
> data_list, galaxy_interactor )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 75, in _verify_outputs
>     galaxy_interactor.verify_output( history, output_data,
> output_testdef=output_testdef, shed_tool_id=shed_tool_id,
> maxseconds=maxseconds )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> line 82, in verify_output
>     self._verify_metadata( history_id, hid, attributes )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> line 103, in _verify_metadata
>     raise Exception( msg )
> Exception: Dataset metadata verification for [file_ext] failed,
> expected [bam] but found [None].
> Traceback (most recent call last):
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/web/framework/decorators.py",
> line 243, in decorator
>     rval = func( self, trans, *args, **kwargs)
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/webapps/galaxy/api/history_contents.py",
> line 188, in show
>     return self.__show_dataset( trans, id, **kwd )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/webapps/galaxy/api/history_contents.py",
> line 214, in __show_dataset
>     hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/web/base/controller.py",
> line 855, in get_display_apps
>     for display_app in hda.get_display_applications( trans ).itervalues():
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/model/__init__.py",
> line 1754, in get_display_applications
>     return self.datatype.get_display_applications_by_dataset( self, trans )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/data.py",
> line 445, in get_display_applications_by_dataset
>     value = value.filter_by_dataset( dataset, trans )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/display_applications/application.py",
> line 200, in filter_by_dataset
>     if link_value.filter_by_dataset( data, trans ):
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/display_applications/application.py",
> line 78, in filter_by_dataset
>     if fill_template( filter_elem.text, context = context ) !=
> filter_elem.get( 'value', 'True' ):
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/util/template.py",
> line 9, in fill_template
>     return str( Template( source=template_text, searchList=[context] ) )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 1004, in __str__
>     return getattr(self, mainMethName)()
>   File "cheetah_DynamicallyCompiledCheetahTemplate_1410263883_33_43576.py",
> line 82, in respond
> NotFound: cannot find 'ucsc_display_sites' while searching for
> 'APP.config.ucsc_display_sites'
> requests.packages.urllib3.connectionpool: DEBUG: "GET
>
> /api/histories/993bad2fe35335db/contents/7fbe67cfae825002?key=edc04240db9605fb7edc7bab44d3404c
> HTTP/1.1" 500 None
> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
> connection (1): 127.0.0.1
> requests.packages.urllib3.connectionpool: DEBUG: "GET
>
> /api/histories/993bad2fe35335db/contents/7fbe67cfae825002/provenance?key=edc04240db9605fb7edc7bab44d3404c
> HTTP/1.1" 200 None
> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
> connection (1): 127.0.0.1
> requests.packages.urllib3.connectionpool: DEBUG: "GET
>
> /api/histories/993bad2fe35335db/contents/7fbe67cfae825002/provenance?key=edc04240db9605fb7edc7bab44d3404c
> HTTP/1.1" 200 None
>
> Any thoughts?
>
> Thanks,
>
> Peter
> ___________________________________________________________
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