On Mon, May 5, 2014 at 2:30 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Peter,
Just looking at the travis job, it looks like there's not a fetch_eggs step at the start, but rather that it's fetching as they're require()'d. Is that correct?
Yes, https://github.com/peterjc/pico_galaxy/blob/master/.travis.yml does not (currently) attempt to fetch any eggs explicitly - it lets the different bits of Galaxy do this on demand. Is there a simple command line instruction to tell Galaxy to fetch all the eggs it might want?
In any event, I'm changing the order of those requires in 13302:92519a9bfa32, which may resolve your issue. They work fine like that in production with eggs fetched ahead of time, but I could see how that'd cause the failure you're seeing.
https://bitbucket.org/galaxy/galaxy-central/commits/92519a9bfa32a42ce47a63fd... It looks like John has his Galaxy mirror automatically updates (or he did a push just now), so I could ask TravisCI to retest immediately. [In earlier testing GitHub was faster than BitBucket for fetching Galaxy]: https://github.com/jmchilton/galaxy-central/commit/9e72c14ef176e494a611bee64... Unfortunately, no real change: ... functional_tests.py INFO 2014-05-05 13:44:46,611 Embedded Universe application started galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,684 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,685 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,758 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,762 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,765 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,773 Enabling 'tool_runner' controller, class: ToolRunner galaxy.eggs DEBUG 2014-05-05 13:44:46,958 Fetched http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,116 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,116 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,189 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,190 Enabling 'search' controller, class: SearchController galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,202 Enabling 'data_admin' controller, class: DataAdmin galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,246 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,256 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,260 Enabling 'ucsc_proxy' controller, class: UCSCProxy Traceback (most recent call last): File "./scripts/functional_tests.py", line 601, in <module> sys.exit( main() ) File "./scripts/functional_tests.py", line 417, in main use_translogger=False, static_enabled=STATIC_ENABLED ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/web/framework/__init__.py", line 441, in add_ui_controllers module = import_module( module_name ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module __import__(name) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", line 18, in <module> eggs.require('pyyaml') File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py", line 412, in require return pkg_resources.working_set.require( req_str ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py", line 666, in require needed = self.resolve(parse_requirements(requirements)) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: pyyaml galaxy.jobs.handler INFO 2014-05-05 13:44:47,295 sending stop signal to worker thread galaxy.jobs.handler INFO 2014-05-05 13:44:47,296 job handler queue stopped ... Peter