Hi all,
Recently my TravisCI tests have started failing during the tool functional tests due to what looks like a missing dependency: e.g. https://travis-ci.org/peterjc/pico_galaxy/jobs/24444682
... galaxy.eggs DEBUG 2014-05-05 11:26:47,387 Fetched http://eggs.galaxyproject.org/boto/boto-2.27.0-py2.7.egg galaxy.eggs DEBUG 2014-05-05 11:26:47,753 Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg 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 20, 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
Is there a missing egg declaration for pyyaml?
I found this commit about a PyYAML 3.10 egg., perhaps linked? https://bitbucket.org/galaxy/galaxy-central/commits/c36dc4155beb0ae5e117ca33...
Thanks,
Peter
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? 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.
-Dannon
On Mon, May 5, 2014 at 9:14 AM, Peter Cock p.j.a.cock@googlemail.comwrote:
Hi all,
Recently my TravisCI tests have started failing during the tool functional tests due to what looks like a missing dependency: e.g. https://travis-ci.org/peterjc/pico_galaxy/jobs/24444682
... galaxy.eggs DEBUG 2014-05-05 11:26:47,387 Fetched http://eggs.galaxyproject.org/boto/boto-2.27.0-py2.7.egg galaxy.eggs DEBUG 2014-05-05 11:26:47,753 Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg 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 20, 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
Is there a missing egg declaration for pyyaml?
I found this commit about a PyYAML 3.10 egg., perhaps linked?
https://bitbucket.org/galaxy/galaxy-central/commits/c36dc4155beb0ae5e117ca33...
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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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
Can you add a `python scripts/fetch_eggs.py` to your travis config just after the stop-daemon? That should parse eggs.ini and fetch all of the eggs.
On Mon, May 5, 2014 at 9:51 AM, Peter Cock p.j.a.cock@googlemail.comwrote:
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
Change made: https://github.com/peterjc/pico_galaxy/commit/19d24c71b5c24cb908907f25e5d992... https://travis-ci.org/peterjc/pico_galaxy/builds/24455410
That worked in one sense:
$ python scripts/fetch_eggs.py Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg Fetched http://eggs.galaxyproject.org/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-li... Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.7.0-py2.7.egg Fetched http://eggs.galaxyproject.org/Babel/Babel-1.3-py2.7.egg Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg Fetched http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.... Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg Fetched http://eggs.galaxyproject.org/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.7.2-py... Fetched http://eggs.galaxyproject.org/NoseHTML/NoseHTML-0.4.1-py2.7.egg Fetched http://eggs.galaxyproject.org/pexpect/pexpect-2.4-py2.7.egg Fetched http://eggs.galaxyproject.org/amqp/amqp-1.4.3-py2.7.egg Fetched http://eggs.galaxyproject.org/bx_python/bx_python-0.7.2-py2.7-linux-x86_64-u... Fetched http://eggs.galaxyproject.org/WebHelpers/WebHelpers-1.3-py2.7.egg Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg Fetched http://eggs.galaxyproject.org/kombu/kombu-3.0.12-py2.7.egg Fetched http://eggs.galaxyproject.org/numpy/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.galaxyproject.org/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.7-li... Fetched http://eggs.galaxyproject.org/mock/mock-1.0.1-py2.7.egg Fetched http://eggs.galaxyproject.org/raven/raven-3.1.8-py2.7.egg Fetched http://eggs.galaxyproject.org/Beaker/Beaker-1.4-py2.7.egg Fetched http://eggs.galaxyproject.org/PyYAML/PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.galaxyproject.org/SQLAlchemy/SQLAlchemy-0.7.9-py2.7-linux-x86_64... Fetched http://eggs.galaxyproject.org/simplejson/simplejson-2.1.1-py2.7-linux-x86_64... Fetched http://eggs.galaxyproject.org/NoseTestDiff/NoseTestDiff-0.1-py2.7.egg Fetched http://eggs.galaxyproject.org/poster/poster-0.8.1-py2.7.egg Fetched http://eggs.galaxyproject.org/python_lzo/python_lzo-1.08_2.03_static-py2.7-l... Fetched http://eggs.galaxyproject.org/Tempita/Tempita-0.5.1-py2.7.egg Fetched http://eggs.galaxyproject.org/MarkupSafe/MarkupSafe-0.12-py2.7-linux-x86_64-... Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg Fetched http://eggs.galaxyproject.org/Routes/Routes-1.12.3-py2.7.egg Fetched http://eggs.galaxyproject.org/decorator/decorator-3.1.2-py2.7.egg Fetched http://eggs.galaxyproject.org/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998... Fetched http://eggs.galaxyproject.org/WebOb/WebOb-0.8.5-py2.7.egg Fetched http://eggs.galaxyproject.org/pycrypto/pycrypto-2.5-py2.7-linux-x86_64-ucs4.... Fetched http://eggs.galaxyproject.org/boto/boto-2.27.0-py2.7.egg Fetched http://eggs.galaxyproject.org/python_daemon/python_daemon-1.5.5-py2.7.egg Fetched http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-u... Fetched http://eggs.galaxyproject.org/wsgiref/wsgiref-0.1.2-py2.7.egg Fetched http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg Fetched http://eggs.galaxyproject.org/pytz/pytz-2013.9-py2.7.egg Fetched http://eggs.galaxyproject.org/nose/nose-0.11.1-py2.7.egg Fetched http://eggs.galaxyproject.org/requests/requests-2.2.1-py2.7.egg Fetched http://eggs.galaxyproject.org/anyjson/anyjson-0.3.3-py2.7.egg Fetched http://eggs.galaxyproject.org/WebError/WebError-0.8a-py2.7.egg Fetched http://eggs.galaxyproject.org/twill/twill-0.9-py2.7.egg
However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg the old error persists. Is there a case-sensitivity issue here (PyYAML versus pyyaml)?
...
functional_tests.py INFO 2014-05-05 14:23:11,383 Embedded Universe application started galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,385 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,386 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,432 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,438 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,440 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,489 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,490 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,673 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,673 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,673 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,673 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,676 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,194 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,204 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,208 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,219 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,238 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,252 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,260 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,272 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,272 Enabling 'search' controller, class: SearchController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,274 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,282 Enabling 'data_admin' controller, class: DataAdmin galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,284 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,293 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,321 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,323 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,323 Enabling 'admin' controller, class: AdminGalaxy 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 14:23:12,343 sending stop signal to worker thread ...
Thanks!
Peter
On Mon, May 5, 2014 at 3:10 PM, Dannon Baker dannon.baker@gmail.com wrote:
Can you add a `python scripts/fetch_eggs.py` to your travis config just after the stop-daemon? That should parse eggs.ini and fetch all of the eggs.
On Mon, May 5, 2014 at 9:51 AM, Peter Cock wrote:
On Mon, May 5, 2014 at 2:30 PM, Dannon Baker 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?
On Mon, May 5, 2014 at 10:32 AM, Peter Cock p.j.a.cock@googlemail.comwrote:
However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg the old error persists. Is there a case-sensitivity issue here (PyYAML versus pyyaml)?
Yep, I've adjusted that now and my guess is it'll work next time.
Let me know if it doesn't, and thanks for finding the issue!
On Mon, May 5, 2014 at 3:47 PM, Dannon Baker dannon.baker@gmail.com wrote:
On Mon, May 5, 2014 at 10:32 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg the old error persists. Is there a case-sensitivity issue here (PyYAML versus pyyaml)?
Yep, I've adjusted that now and my guess is it'll work next time.
Let me know if it doesn't, and thanks for finding the issue!
On Mon, May 5, 2014 at 3:47 PM, Dannon Baker dannon.baker@gmail.com wrote:
On Mon, May 5, 2014 at 10:32 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg the old error persists. Is there a case-sensitivity issue here (PyYAML versus pyyaml)?
Yep, I've adjusted that now and my guess is it'll work next time.
Let me know if it doesn't, and thanks for finding the issue!
Green light :) https://travis-ci.org/peterjc/pico_galaxy/builds/24456751
I'm checking if I actually did need the fetch eggs or not...
Thank you,
Peter
(Apologies for previous blank email, slip of the mouse)
If they're fetching as it runs the tests, you may not need to do it up front explicitly. It's worth noting, though, that this is how galaxy normally runs (checking for and fetching eggs up front -- except when using the --stop-daemon argument) under run.sh.
On Mon, May 5, 2014 at 11:15 AM, Peter Cock p.j.a.cock@googlemail.comwrote:
On Mon, May 5, 2014 at 3:47 PM, Dannon Baker dannon.baker@gmail.com wrote:
On Mon, May 5, 2014 at 10:32 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg the old error persists. Is there a case-sensitivity issue here (PyYAML versus pyyaml)?
Yep, I've adjusted that now and my guess is it'll work next time.
Let me know if it doesn't, and thanks for finding the issue!
Green light :) https://travis-ci.org/peterjc/pico_galaxy/builds/24456751
I'm checking if I actually did need the fetch eggs or not...
Thank you,
Peter
(Apologies for previous blank email, slip of the mouse)
galaxy-dev@lists.galaxyproject.org
-
Dannon Baker -
Peter Cock