ToolShed test failure: NotFound: cannot find 'ucsc_display_sites' while searching for 'APP.config.ucsc_display_sites' - galaxy-dev

9 Sep 2014


      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