[galaxy-dev] Galaxy is not running
Hi,
I am new to Galaxy, so am probably doing something silly.
My jobs do not finish and sometimes do not start. Here is the error message:
Details
user
usernamewatterber
quota_percent3
total_disk_usage10295907343
nice_total_disk_usage9.6 GB
emailatter...@unlv.nevada.edu
is_adminfalse
tags_used
model_classUser
ide2b7da49063484ac
sourceHDACollection(d686c5fd139f68f1,190)
xhr
readyState4
responseText{"err_msg": "Uncaught exception in exposed API method:",
"err_code": 0}
responseJSON
err_msgUncaught exception in exposed API method:
err_code0
status500
statusTextInternal Server Error
responseHeaders
Servernginx/1.4.7
DateThu, 22 May 2014 16:23:06 GMT
Content-Typeapplication/json
Transfer-Encodingchunked
Connectionkeep-alive
Cache-Controlmax-age=0,no-cache,no-store
options
data
parsetrue
emulateHTTPfalse
emulateJSONfalse
Any information would be awesome.
Thank you,
Wally
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Re: [galaxy-dev] download workflow error
Yep, your guess looks correct. We enforced creation of a public username at registration a long while back, but it looks like the API doesn't do the same enforcement (and neither does the web interface, anymore -- d'oh). I'll get a bugfix out shortly. On Thu, May 22, 2014 at 11:12 AM, Evan Bollig wrote: > I have a fresh instance of galaxy-dist#stable. I create users and > upload a workflow via the internal python api, and then I attempt to > edit and download the workflow from the workflow editor tab. I click > the direct download link and get the attached exception. > > I found that the exception is avoided if I instead share/export the > workflow and then create a public username when prompted. When I go > back and use the direct download link again, it works. Not sure if > they're directly connected, but something in the share/export seems to > band-aid the other. Presumably the 'None' should be the public > username. > > Cheers, > > -Evan Bollig > Research Associate | Application Developer | User Support Consultant > Minnesota Supercomputing Institute > 599 Walter Library > 612 624 1447 > e...@msi.umn.edu > boll0...@umn.edu > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] TestToolShed NameError: global name 'suc' is not defined
No problem - that was a remarkably quick fix :) Thanks Greg, Peter On Thu, May 22, 2014 at 1:48 PM, Greg Von Kuster wrote: > Hi Peter, > > I've been doing some refactoring in the central branch which caused this > issuee. It's been fixed in 13582:581e7c8e353e, which is now running on > the test tool shed, ao this bad behavior should be resolved. > > Thanks so much for reporting this. > > Greg Von Kuster ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] TestToolShed NameError: global name 'suc' is not defined
Hi Peter, I've been doing some refactoring in the central branch which caused this issuee. It's been fixed in 13582:581e7c8e353e, which is now running on the test tool shed, ao this bad behavior should be resolved. Thanks so much for reporting this. Greg Von Kuster On May 22, 2014, at 8:39 AM, Peter Cock wrote: > Hi all, > > I just hit a bug on the TestToolShed, > > (1) Goto http://testtoolshed.g2.bx.psu.edu/ > (2) Login > (3) Click "Latest revision: failing tool tests" or similar links > (4) Observer error page, NameError: global name 'suc' is not defined > > This is working on the main ToolShed. > > Regards, > > Peter > > -- > > Internal Server Error > > Galaxy was unable to successfully complete your request > > URL: > http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositories_with_failing_tool_tests > Module galaxy.web.framework.middleware.error:149 in __call__ >>> app_iter = self.application(environ, sr_checker) > Module paste.debug.prints:106 in __call__ >>> environ, self.app) > Module paste.wsgilib:543 in intercept_output >>> app_iter = application(environ, replacement_start_response) > Module paste.recursive:84 in __call__ >>> return self.application(environ, start_response) > Module paste.httpexceptions:633 in __call__ >>> return self.application(environ, start_response) > Module galaxy.web.framework.base:132 in __call__ >>> return self.handle_request( environ, start_response ) > Module galaxy.web.framework.base:190 in handle_request >>> body = method( trans, **kwargs ) > Module galaxy.webapps.tool_shed.controllers.repository:239 in > browse_my_writable_repositories_with_failing_tool_tests >>> return self.my_writable_repositories_with_failing_tool_tests_grid( trans, >>> **kwd ) > Module galaxy.web.framework.helpers.grids:80 in __call__ >>> query = self.build_initial_query( trans, **kwargs ) > Module tool_shed.grids.repository_grids:1083 in build_initial_query >>> grids_util.filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests( >>> trans, repository ) > Module tool_shed.grids.util:89 in > filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests >>> repository_metadata = >>> get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, >>> repository ) > Module tool_shed.grids.util:196 in > get_latest_downloadable_repository_metadata_if_it_includes_tools >>> repository_metadata = get_latest_downloadable_repository_metadata( trans, >>> repository ) > Module tool_shed.grids.util:180 in get_latest_downloadable_repository_metadata >>> latest_downloadable_revision = >>> suc.get_previous_metadata_changeset_revision( repository, repo, tip_ctx, >>> downloadable=True ) > NameError: global name 'suc' is not defined > extra data > > > full traceback > > text version > This may be an intermittent problem due to load or other unpredictable > factors, reloading the page may address the problem. > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] TestToolShed NameError: global name 'suc' is not defined
Hi all, I just hit a bug on the TestToolShed, (1) Goto http://testtoolshed.g2.bx.psu.edu/ (2) Login (3) Click "Latest revision: failing tool tests" or similar links (4) Observer error page, NameError: global name 'suc' is not defined This is working on the main ToolShed. Regards, Peter -- Internal Server Error Galaxy was unable to successfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositories_with_failing_tool_tests Module galaxy.web.framework.middleware.error:149 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:239 in browse_my_writable_repositories_with_failing_tool_tests >> return self.my_writable_repositories_with_failing_tool_tests_grid( trans, >> **kwd ) Module galaxy.web.framework.helpers.grids:80 in __call__ >> query = self.build_initial_query( trans, **kwargs ) Module tool_shed.grids.repository_grids:1083 in build_initial_query >> >> grids_util.filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests( >> trans, repository ) Module tool_shed.grids.util:89 in filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests >> repository_metadata = >> get_latest_downloadable_repository_metadata_if_it_includes_tools( trans, >> repository ) Module tool_shed.grids.util:196 in get_latest_downloadable_repository_metadata_if_it_includes_tools >> repository_metadata = get_latest_downloadable_repository_metadata( trans, >> repository ) Module tool_shed.grids.util:180 in get_latest_downloadable_repository_metadata >> latest_downloadable_revision = >> suc.get_previous_metadata_changeset_revision( repository, repo, tip_ctx, >> downloadable=True ) NameError: global name 'suc' is not defined extra data full traceback text version This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
