Hi galaxy devs, We are in the final stages of deploying a new Galaxy instance. We downloaded the galaxy-dist version a month ago aprox. We realized that, when launching a job and deleting it in the middle of the execution (hitting the Delete button in the history bar) will output the following error in the logger: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job 45: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45 in local runner galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in monitor_step Traceback (most recent call last): File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 298, in monitor self.monitor_step() File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 341, in monitor_step self.dispatcher.stop( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 438, in stop self.job_runners[runner_name].stop_job( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 180, in stop_job if job.get_external_output_metadata(): AttributeError: 'Job' object has no attribute 'get_external_output_metadata' By copying the definition of get_external_output_data from the Task class into the Job class, we fixed the problem and now the jobs are terminated successfully. This is the code I added: class Job( object ): ... def get_external_output_metadata( self ): return None ... In this file: https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990f... Do you think this fix is correct, or is it a potential problem? Also, sorry I sent you through this channel, I couldn't find the way of reporting this on BitBucket. Regards, -- Juan González-Vallinas PhD Student Regulatory Genomics Group Research Unit in Biomedical Informatics (GRIB) Universitat Pompeu Fabra (UPF) Barcelona Spain (Currently @ UPenn)
That sounds perfectly reasonable. I'll make the change. Thanks, Juan! -Scott ----- Original Message -----
Hi galaxy devs,
We are in the final stages of deploying a new Galaxy instance. We downloaded the galaxy-dist version a month ago aprox. We realized that, when launching a job and deleting it in the middle of the execution (hitting the Delete button in the history bar) will output the following error in the logger:
galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job 45: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45 in local runner galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in monitor_step Traceback (most recent call last): File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 298, in monitor self.monitor_step() File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 341, in monitor_step self.dispatcher.stop( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 438, in stop self.job_runners[runner_name].stop_job( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 180, in stop_job if job.get_external_output_metadata(): AttributeError: 'Job' object has no attribute 'get_external_output_metadata'
By copying the definition of get_external_output_data from the Task class into the Job class, we fixed the problem and now the jobs are terminated successfully. This is the code I added:
class Job( object ):
... def get_external_output_metadata( self ): return None ...
In this file:
https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990f...
Do you think this fix is correct, or is it a potential problem?
Also, sorry I sent you through this channel, I couldn't find the way of reporting this on BitBucket.
Regards,
-- Juan González-Vallinas PhD Student Regulatory Genomics Group Research Unit in Biomedical Informatics (GRIB) Universitat Pompeu Fabra (UPF) Barcelona Spain (Currently @ UPenn)
___________________________________________________________ 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:
Hi Juan, Thanks for reporting this, it is indeed a bug. The fix below isn't quite correct (if there is an external metadata job, we do actually want to terminate it) but I'll take care of it. For reporting bugs in the future, certainly feel free to message this list or you can also file an issue using http://galaxyproject.org/trello Thanks! -Dannon On Nov 6, 2012, at 11:54 AM, Juan González-Vallinas <juanramongvallinas@gmail.com> wrote:
Hi galaxy devs,
We are in the final stages of deploying a new Galaxy instance. We downloaded the galaxy-dist version a month ago aprox. We realized that, when launching a job and deleting it in the middle of the execution (hitting the Delete button in the history bar) will output the following error in the logger:
galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job 45: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45 in local runner galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in monitor_step Traceback (most recent call last): File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 298, in monitor self.monitor_step() File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 341, in monitor_step self.dispatcher.stop( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 438, in stop self.job_runners[runner_name].stop_job( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 180, in stop_job if job.get_external_output_metadata(): AttributeError: 'Job' object has no attribute 'get_external_output_metadata'
By copying the definition of get_external_output_data from the Task class into the Job class, we fixed the problem and now the jobs are terminated successfully. This is the code I added:
class Job( object ):
... def get_external_output_metadata( self ): return None ...
In this file:
https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990f...
Do you think this fix is correct, or is it a potential problem?
Also, sorry I sent you through this channel, I couldn't find the way of reporting this on BitBucket.
Regards,
-- Juan González-Vallinas PhD Student Regulatory Genomics Group Research Unit in Biomedical Informatics (GRIB) Universitat Pompeu Fabra (UPF) Barcelona Spain (Currently @ UPenn)
___________________________________________________________ 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:
Ok, thanks for the response! On 6 November 2012 12:50, Dannon Baker <dannonbaker@me.com> wrote:
Hi Juan,
Thanks for reporting this, it is indeed a bug. The fix below isn't quite correct (if there is an external metadata job, we do actually want to terminate it) but I'll take care of it.
For reporting bugs in the future, certainly feel free to message this list or you can also file an issue using http://galaxyproject.org/trello
Thanks!
-Dannon
On Nov 6, 2012, at 11:54 AM, Juan González-Vallinas < juanramongvallinas@gmail.com> wrote:
Hi galaxy devs,
We are in the final stages of deploying a new Galaxy instance. We downloaded the galaxy-dist version a month ago aprox. We realized that, when launching a job and deleting it in the middle of the execution (hitting the Delete button in the history bar) will output the following error in the logger:
galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job 45: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45 in local runner galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in monitor_step Traceback (most recent call last): File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 298, in monitor self.monitor_step() File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 341, in monitor_step self.dispatcher.stop( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 438, in stop self.job_runners[runner_name].stop_job( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 180, in stop_job if job.get_external_output_metadata(): AttributeError: 'Job' object has no attribute 'get_external_output_metadata'
By copying the definition of get_external_output_data from the Task class into the Job class, we fixed the problem and now the jobs are terminated successfully. This is the code I added:
class Job( object ):
... def get_external_output_metadata( self ): return None ...
In this file:
https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990f...
Do you think this fix is correct, or is it a potential problem?
Also, sorry I sent you through this channel, I couldn't find the way of
reporting this on BitBucket.
Regards,
-- Juan González-Vallinas PhD Student Regulatory Genomics Group Research Unit in Biomedical Informatics (GRIB) Universitat Pompeu Fabra (UPF) Barcelona Spain (Currently @ UPenn)
___________________________________________________________ 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:
It should have been fixed yesterday - if a job is running locally and the user cancels it, then the job will be stopped immediately. Thanks, Juan! -Scott ----- Original Message -----
Ok, thanks for the response!
On 6 November 2012 12:50, Dannon Baker < dannonbaker@me.com > wrote:
Hi Juan,
Thanks for reporting this, it is indeed a bug. The fix below isn't quite correct (if there is an external metadata job, we do actually want to terminate it) but I'll take care of it.
For reporting bugs in the future, certainly feel free to message this list or you can also file an issue using http://galaxyproject.org/trello
Thanks!
-Dannon
On Nov 6, 2012, at 11:54 AM, Juan González-Vallinas < juanramongvallinas@gmail.com > wrote:
Hi galaxy devs,
We are in the final stages of deploying a new Galaxy instance. We downloaded the galaxy-dist version a month ago aprox. We realized that, when launching a job and deleting it in the middle of the execution (hitting the Delete button in the history bar) will output the following error in the logger:
galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job 45:
galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45 in local runner
galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in monitor_step
Traceback (most recent call last):
File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 298, in monitor
self.monitor_step()
File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 341, in monitor_step
self.dispatcher.stop( job )
File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 438, in stop
self.job_runners[runner_name].stop_job( job )
File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 180, in stop_job
if job.get_external_output_metadata():
AttributeError: 'Job' object has no attribute 'get_external_output_metadata'
By copying the definition of get_external_output_data from the Task class into the Job class, we fixed the problem and now the jobs are terminated successfully. This is the code I added:
class Job( object ):
...
def get_external_output_metadata( self ):
return None
...
In this file:
https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990f...
Do you think this fix is correct, or is it a potential problem?
Also, sorry I sent you through this channel, I couldn't find the way of reporting this on BitBucket.
Regards,
--
Juan González-Vallinas
PhD Student
Regulatory Genomics Group
Research Unit in Biomedical Informatics (GRIB)
Universitat Pompeu Fabra (UPF)
Barcelona
Spain
(Currently @ UPenn)
___________________________________________________________
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:
___________________________________________________________ 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:
participants (3)
-
Dannon Baker -
Juan González-Vallinas -
Scott McManus