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.cock@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 ___________________________________________________________ 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/
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