Re: [galaxy-dev] Failed to generate job destination
It looks like you have tools with no matching id in toolbox.tools_by_id. Given the complexity of your job_conf.xml I assume you are using multiple Galaxy processes? Have you installed stuff from the tool shed or migrated tools and not restarted all Galaxy processes, or did you try to restart processes but when failed to shutdown? I assume tool shed installed tools are only available to the web process that installed them, so the handler process must be restarted. If restarting it doesn't work, I have attached a patch with added logging that might help. -John On Thu, Nov 14, 2013 at 5:59 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi John, please find attached my jobs_conf.xml file. I was not able to find any systematic in that error. It seems to happen not so often. Thanks, Bjoern Hey Bjoern, Can you post your job_conf.xml or send it to galaxy-b...@bx.psu.edu if it has something sensitive in it, alternatively your runner urls if you are still using the older format for specifying these things? Is this for every job or just certain tools? -John On Thu, Nov 14, 2013 at 5:14 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, anyone has seen the following bug in Galaxy November release? galaxy.jobs.handler ERROR 2013-11-15 00:07:41,008 Failed to generate job destination Traceback (most recent call last): File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 311, in __check_if_ready_to_run self.job_wrappers[job.id].job_destination File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 620, in job_destination return self.job_runner_mapper.get_job_destination(self.params) File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py, line 163, in get_job_destination self.__cache_job_destination( params ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py, line 148, in __cache_job_destination raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) AttributeError: 'NoneType' object has no attribute 'get_job_destination' Thanks, Bjoern ___ 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/ From 9252a708e000662b045b89f7e6a085dba2ba3e7e Mon Sep 17 00:00:00 2001 From: John Chilton jmchil...@gmail.com Date: Fri, 15 Nov 2013 10:57:51 -0600 Subject: Extra logging to track to job mapping problems. diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index 42fa027..d8c14da 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -559,6 +559,8 @@ class JobWrapper( object ): self.session_id = job.session_id self.user_id = job.user_id self.tool = queue.app.toolbox.tools_by_id.get( job.tool_id, None ) +if self.tool is None: +log.warn(Failed to find tool associated with tool_id %s for job %s % ( job.tool_id, job ) ) self.queue = queue self.app = queue.app self.sa_session = self.app.model.context diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py index e6d5b7c..3fddf93 100644 --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -145,7 +145,12 @@ class JobRunnerMapper( object ): raise Exception( Unhandled dynamic job runner type specified - %s % expand_type ) def __cache_job_destination( self, params ): -raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) +tool = self.job_wrapper.tool +if tool is None: +msg = job_wrapper %s is associated with no tool, job will be in problematic state % ( self.job_wrapper ) +log.warn( msg ) +raise AttributeError( msg ) +raw_job_destination = tool.get_job_destination( params ) #raw_job_destination_id_or_tag = self.job_wrapper.tool.get_job_destination_id_or_tag( params ) if raw_job_destination.runner == DYNAMIC_RUNNER_NAME: job_destination = self.__handle_dynamic_job_destination( raw_job_destination ) -- 1.7.10.4 ___ 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] Failed to generate job destination
Hi, anyone has seen the following bug in Galaxy November release? galaxy.jobs.handler ERROR 2013-11-15 00:07:41,008 Failed to generate job destination Traceback (most recent call last): File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 311, in __check_if_ready_to_run self.job_wrappers[job.id].job_destination File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 620, in job_destination return self.job_runner_mapper.get_job_destination(self.params) File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py, line 163, in get_job_destination self.__cache_job_destination( params ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py, line 148, in __cache_job_destination raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) AttributeError: 'NoneType' object has no attribute 'get_job_destination' Thanks, Bjoern ___ 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] Failed to generate job destination
Hey Bjoern, Can you post your job_conf.xml or send it to galaxy-b...@bx.psu.edu if it has something sensitive in it, alternatively your runner urls if you are still using the older format for specifying these things? Is this for every job or just certain tools? -John On Thu, Nov 14, 2013 at 5:14 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, anyone has seen the following bug in Galaxy November release? galaxy.jobs.handler ERROR 2013-11-15 00:07:41,008 Failed to generate job destination Traceback (most recent call last): File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 311, in __check_if_ready_to_run self.job_wrappers[job.id].job_destination File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 620, in job_destination return self.job_runner_mapper.get_job_destination(self.params) File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py, line 163, in get_job_destination self.__cache_job_destination( params ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py, line 148, in __cache_job_destination raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) AttributeError: 'NoneType' object has no attribute 'get_job_destination' Thanks, Bjoern ___ 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] Failed to generate job destination
Hi John, please find attached my jobs_conf.xml file. I was not able to find any systematic in that error. It seems to happen not so often. Thanks, Bjoern Hey Bjoern, Can you post your job_conf.xml or send it to galaxy-b...@bx.psu.edu if it has something sensitive in it, alternatively your runner urls if you are still using the older format for specifying these things? Is this for every job or just certain tools? -John On Thu, Nov 14, 2013 at 5:14 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, anyone has seen the following bug in Galaxy November release? galaxy.jobs.handler ERROR 2013-11-15 00:07:41,008 Failed to generate job destination Traceback (most recent call last): File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 311, in __check_if_ready_to_run self.job_wrappers[job.id].job_destination File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 620, in job_destination return self.job_runner_mapper.get_job_destination(self.params) File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py, line 163, in get_job_destination self.__cache_job_destination( params ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py, line 148, in __cache_job_destination raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) AttributeError: 'NoneType' object has no attribute 'get_job_destination' Thanks, Bjoern ___ 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/ job_conf.xml Description: XML document ___ 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/
