Dave,
Thanks for your reply. I already had my tool shed specified in
tool_sheds_conf.xml, which is why I omitted the
GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF environment variable. I just tried
it with,
GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF=install_and_test_tool_sheds_conf.xml
The contents of the install_and_test_tool_sheds_conf.xml is as follows:
<?xml version="1.0"?>
<tool_sheds>
<tool_shed name="My tool shed"
url="http://toolshed.galaxy.domain.org/ "/>
</tool_sheds>
But it results in the exact same error:
AssertionError: Invalid HTTP return code 404, allowed codes: 200
Do you have any other ideas?
Regards,
Serrano
On 09/16/2013 08:37 PM, Dave Bouvier wrote:
> Serrano,
>
> The GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF environment variable should be
> set to an XML file that specifies the tool shed you're installing
> from. I've updated the wiki page to be clearer on that point.
>
> --Dave B.
>
> On 09/16/2013 12:32 PM, Serrano Pereira wrote:
>> Dear Galaxy hackers,
>>
>> I'm having trouble with the tool test framework. I have a local
>> installation of a Galaxy Tool Shed (latest stable from the repository)
>> on my Linux server. I have an Apache proxy to my tool shed (per
>> http://wiki.galaxyproject.org/HostingALocalToolShed). The Tool Shed
>> seems to work fine. I'm able to create and maintain repositories and I'm
>> able to install tools from the Tool Shed from remote Galaxy instances.
>>
>> Now I want to run the functional tests of the tools in the Tool Shed. I
>> do that by following the instructions on the wiki
>> (http://wiki.galaxyproject.org/AutomatedToolTests). It comes down to the
>> following commands:
>>
>> ----------------------------------------------------------------------
>> cd /opt/galaxy/galaxy-dist/
>> export
>> GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY=2aeecfe2d9f28d0c5b6959a41886b5fd
>> export
>> GALAXY_INSTALL_TEST_TOOL_SHED_URL=http://toolshed.galaxy.domain.org/
>> python lib/tool_shed/scripts/check_repositories_for_functional_tests.py
>> tool_shed_wsgi.ini
>> sh install_and_test_tool_shed_repositories.sh
>> ----------------------------------------------------------------------
>>
>> The second script (install_and_test_tool_shed_repositories.sh) fails
>> with the following error:
>>
>> ======================================================================
>> FAIL: install_repository_usearch
>> (install_and_test_tool_shed_repositories.functional.test_install_repositories.TestInstallRepository_usearch)
>>
>> Install the repository usearch from http://toolshed.galaxy.domain.org/.
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File
>> "/opt/galaxy/galaxy-dist/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py",
>>
>> line 48, in test_install_repository
>> self.do_installation( repository_dict )
>> File
>> "/opt/galaxy/galaxy-dist/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py",
>>
>> line 17, in do_installation
>> self.install_repository( repository_info_dict )
>> File
>> "/opt/galaxy/galaxy-dist/test/install_and_test_tool_shed_repositories/base/twilltestcase.py",
>>
>> line 61, in install_repository
>> self.visit_url( '%s/repository/preview_tools_in_changeset?%s' % (
>> tool_shed_url, preview_params ) )
>> File
>> "/opt/galaxy/galaxy-dist/test/install_and_test_tool_shed_repositories/base/twilltestcase.py",
>>
>> line 112, in visit_url
>> ( return_code, url, ', '.join( str( code ) for code in
>> allowed_codes ) )
>> AssertionError: Invalid HTTP return code 404 for
>> http://toolshed.galaxy.domain.org//repository/preview_tools_in_changeset?repository_id=3651c288c4818b12&changeset_revision=095baaf5d877,
>>
>> allowed codes: 200
>> ----------------------------------------------------------------------
>>
>> (I've changed twilltestcase.py to also print the URL that is being
>> browsed.) This is were it get's weird. The HTTP 404 response code
>> indicates that the page was not found. However, when I browse to that
>> URL, it works fine! What's more, when I try to access that page with
>> `wget` from the same machine the HTTP response code is 200:
>>
>> ----------------------------------------------------------------------
>> wget
>> http://toolshed.galaxy.domain.org//repository/preview_tools_in_changeset?repository_id=3651c288c4818b12&changeset_revision=095baaf5d877
>>
>> ...
>> HTTP request sent, awaiting response... 200 OK
>> ...
>> ----------------------------------------------------------------------
>>
>> When I use the Tool Shed URL http://localhost:9009/ instead, I get a
>> similar error, only the return code is 500 instead of 404. I suspect
>> that the HTTP return code returned by the Python module that returns it
>> (Mechanize?) is invalid. I found a note about this error on the wiki
>> (http://wiki.galaxyproject.org/Admin/Running%20Tests):
>>
>> "Note: If you have another version of paste installed in your
>> PYTHONPATH, it can cause problems running the functional tests. Many
>> tests will error (instead of passing/failing) because of an HTML code
>> 500 where a 200 was expected. There are two workarounds for this:
>> uninstall paste or use virtualenv. "
>>
>> The thing is, I do not have another version of Paste installed. What can
>> I do to fix this error?
>>
>> Regards,
>> Serrano Pereira
>> ___________________________________________________________
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>
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