Workflow: multiple input errors

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Workflow: multiple input errors

Joachim Jacob
Hi all,

I have fired up an cloud instance of Galaxy, 2 persistent nodes,
scalable up to 10. I have updated the code to the latest stable, after
issues with not being able to select multiple input for workflows (more
background:
http://dev.list.galaxyproject.org/selecting-multiple-inputs-for-workflows-not-possible-anymore-td4659827.html)


Running a workflow on multiple inputs (#=58) gives me - after a very
long page loading - this error:

************************************************


  Internal Server Error


    Galaxy was unable to sucessfully complete your request

URL:
http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910 

Module galaxy.web.framework.middleware.error:*149* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>app_iter
*=* self*.*application*(*environ*,* sr_checker*)*|
Module paste.recursive:*84* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
self*.*application*(*environ*,* start_response*)*|
Module paste.httpexceptions:*633* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.base:*128* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
self*.*handle_request*(* environ*,* start_response *)*|
Module galaxy.web.framework.base:*184* in |handle_request|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>body
*=* method*(* trans*,* ****kwargs *)*|
Module galaxy.webapps.galaxy.controllers.workflow:*1443* in |run|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>job*,*
out_data *=* tool*.*execute*(* trans*,* step*.*state*.*inputs*,*
history*=*target_history*)*|
Module galaxy.tools:*2342* in |execute|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
self*.*tool_action*.*execute*(* self*,* trans*,* incoming*=*incoming*,*
set_output_hid*=*set_output_hid*,* history*=*history*,* ****kwargs *)*|
Module galaxy.tools.actions:*397* in |execute|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>job*.*add_input_dataset*(*
name*,* dataset *)*|
Module galaxy.model:*247* in |add_input_dataset|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*input_datasets*.*append*(*
JobToInputDatasetAssociation*(* name*,* dataset *)* *)*|
Module ?:*4* in |__init__|
Module sqlalchemy.orm.state:*82* in |initialize_instance|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
manager*.*events*.*original_init*(****mixed*[**1**:**]**,* ****kwargs*)*|
Module galaxy.model:*450* in |__init__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*dataset
*=* dataset|
Module sqlalchemy.orm.attributes:*150* in |__set__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*impl*.*set*(*instance_state*(*instance*)**,*
instance_dict*(*instance*)**,* value*,* None*)*|
Module sqlalchemy.orm.attributes:*590* in |set|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>value
*=* self*.*fire_replace_event*(*state*,* dict_*,* value*,* old*,*
initiator*)*|
Module sqlalchemy.orm.attributes:*610* in |fire_replace_event|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>value
*=* ext*.*set*(*state*,* value*,* previous*,* initiator *or* self*)*|
Module sqlalchemy.orm.unitofwork:*69* in |set|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>sess*.*add*(*newvalue*)*|

Module sqlalchemy.orm.session:*1091* in |add|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_save_or_update_state*(*state*)*|

Module sqlalchemy.orm.session:*1100* in |_save_or_update_state|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_save_or_update_impl*(*state*)*|

Module sqlalchemy.orm.session:*1267* in |_save_or_update_impl|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_update_impl*(*state*)*|

Module sqlalchemy.orm.session:*1259* in |_update_impl|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_attach*(*state*)*|

Module sqlalchemy.orm.session:*1286* in |_attach|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*(*mapperutil*.*state_str*(*state*)**,*
state*.*key*)*|
*InvalidRequestError: Can't attach instance <HistoryDatasetAssociation
at 0x8591c50>; another instance with key (<class
'galaxy.model.HistoryDatasetAssociation'>, (200,)) is already present in
this session.*
extra data
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#extra_data>


full traceback
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#full_traceback>


text version
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#text_version>

This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
************************************************

After clicking history refresh, the workflow is actually in progress!  
It completes EXCEPT for the last dataset, which stays gray. Clicking on
rerun on this last dataset, gives me the error:

************************************************


  Internal Server Error


    Galaxy was unable to sucessfully complete your request

URL:
http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe 

Module galaxy.web.framework.middleware.error:*149* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>app_iter
*=* self*.*application*(*environ*,* sr_checker*)*|
Module paste.recursive:*84* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return*
self*.*application*(*environ*,* start_response*)*|
Module paste.httpexceptions:*633* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return*
self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.base:*128* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return*
self*.*handle_request*(* environ*,* start_response *)*|
Module galaxy.web.framework.base:*184* in |handle_request|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>body
*=* method*(* trans*,* ****kwargs *)*|
Module galaxy.webapps.galaxy.controllers.tool_runner:*142* in |rerun|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*raise*
Exception*(*"Failed to get job information for dataset hid %d" *%*
data*.*hid*)*|
*Exception: Failed to get job information for dataset hid 112*
extra data
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#extra_data>



full traceback
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#full_traceback>


text version
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#text_version>

This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
********************************************************


I have to manually rerun the last job with the corresponding workflow.


Thanks,
Joachim

--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


___________________________________________________________
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Re: Workflow: multiple input errors

Joachim Jacob
It is most likely due to the cluster configuration, since on our
non-cluster production machine doesn't have this behaviour.

Cheers,
J

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 05/17/2013 10:16 AM, Joachim Jacob | VIB | wrote:

> Hi all,
>
> I have fired up an cloud instance of Galaxy, 2 persistent nodes,
> scalable up to 10. I have updated the code to the latest stable, after
> issues with not being able to select multiple input for workflows
> (more background:
> http://dev.list.galaxyproject.org/selecting-multiple-inputs-for-workflows-not-possible-anymore-td4659827.html)
>
>
> Running a workflow on multiple inputs (#=58) gives me - after a very
> long page loading - this error:
>
> ************************************************
>
>
>  Internal Server Error
>
>
>    Galaxy was unable to sucessfully complete your request
>
> URL:
> http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910 
>
> Module galaxy.web.framework.middleware.error:*149* in |__call__|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>app_iter
> *=* self*.*application*(*environ*,* sr_checker*)*|
> Module paste.recursive:*84* in |__call__|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
> self*.*application*(*environ*,* start_response*)*|
> Module paste.httpexceptions:*633* in |__call__|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
> self*.*application*(*environ*,* start_response*)*|
> Module galaxy.web.framework.base:*128* in |__call__|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
> self*.*handle_request*(* environ*,* start_response *)*|
> Module galaxy.web.framework.base:*184* in |handle_request|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>body
> *=* method*(* trans*,* ****kwargs *)*|
> Module galaxy.webapps.galaxy.controllers.workflow:*1443* in |run|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>job*,*
> out_data *=* tool*.*execute*(* trans*,* step*.*state*.*inputs*,*
> history*=*target_history*)*|
> Module galaxy.tools:*2342* in |execute|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
> self*.*tool_action*.*execute*(* self*,* trans*,*
> incoming*=*incoming*,* set_output_hid*=*set_output_hid*,*
> history*=*history*,* ****kwargs *)*|
> Module galaxy.tools.actions:*397* in |execute|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>job*.*add_input_dataset*(*
> name*,* dataset *)*|
> Module galaxy.model:*247* in |add_input_dataset|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*input_datasets*.*append*(*
> JobToInputDatasetAssociation*(* name*,* dataset *)* *)*|
> Module ?:*4* in |__init__|
> Module sqlalchemy.orm.state:*82* in |initialize_instance|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
> manager*.*events*.*original_init*(****mixed*[**1**:**]**,* ****kwargs*)*|
> Module galaxy.model:*450* in |__init__|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*dataset
> *=* dataset|
> Module sqlalchemy.orm.attributes:*150* in |__set__|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*impl*.*set*(*instance_state*(*instance*)**,*
> instance_dict*(*instance*)**,* value*,* None*)*|
> Module sqlalchemy.orm.attributes:*590* in |set|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>value
> *=* self*.*fire_replace_event*(*state*,* dict_*,* value*,* old*,*
> initiator*)*|
> Module sqlalchemy.orm.attributes:*610* in |fire_replace_event|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>value
> *=* ext*.*set*(*state*,* value*,* previous*,* initiator *or* self*)*|
> Module sqlalchemy.orm.unitofwork:*69* in |set|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>sess*.*add*(*newvalue*)*|
>
> Module sqlalchemy.orm.session:*1091* in |add|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_save_or_update_state*(*state*)*|
>
> Module sqlalchemy.orm.session:*1100* in |_save_or_update_state|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_save_or_update_impl*(*state*)*|
>
> Module sqlalchemy.orm.session:*1267* in |_save_or_update_impl|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_update_impl*(*state*)*|
>
> Module sqlalchemy.orm.session:*1259* in |_update_impl|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_attach*(*state*)*|
>
> Module sqlalchemy.orm.session:*1286* in |_attach|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*(*mapperutil*.*state_str*(*state*)**,*
> state*.*key*)*|
> *InvalidRequestError: Can't attach instance <HistoryDatasetAssociation
> at 0x8591c50>; another instance with key (<class
> 'galaxy.model.HistoryDatasetAssociation'>, (200,)) is already present
> in this session.*
> extra data
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#extra_data>
>
>
> full traceback
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#full_traceback>
>
>
> text version
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#text_version>
>
> This may be an intermittent problem due to load or other unpredictable
> factors, reloading the page may address the problem.
> ************************************************
>
> After clicking history refresh, the workflow is actually in progress!  
> It completes EXCEPT for the last dataset, which stays gray. Clicking
> on rerun on this last dataset, gives me the error:
>
> ************************************************
>
>
>  Internal Server Error
>
>
>    Galaxy was unable to sucessfully complete your request
>
> URL:
> http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe 
>
> Module galaxy.web.framework.middleware.error:*149* in |__call__|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>app_iter
> *=* self*.*application*(*environ*,* sr_checker*)*|
> Module paste.recursive:*84* in |__call__|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return*
> self*.*application*(*environ*,* start_response*)*|
> Module paste.httpexceptions:*633* in |__call__|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return*
> self*.*application*(*environ*,* start_response*)*|
> Module galaxy.web.framework.base:*128* in |__call__|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return*
> self*.*handle_request*(* environ*,* start_response *)*|
> Module galaxy.web.framework.base:*184* in |handle_request|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>body
> *=* method*(* trans*,* ****kwargs *)*|
> Module galaxy.webapps.galaxy.controllers.tool_runner:*142* in |rerun|
> |>>
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*raise*
> Exception*(*"Failed to get job information for dataset hid %d" *%*
> data*.*hid*)*|
> *Exception: Failed to get job information for dataset hid 112*
> extra data
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#extra_data>
>
>
>
> full traceback
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#full_traceback>
>
>
> text version
> <http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#text_version>
>
> This may be an intermittent problem due to load or other unpredictable
> factors, reloading the page may address the problem.
> ********************************************************
>
>
> I have to manually rerun the last job with the corresponding workflow.
>
>
> Thanks,
> Joachim
>

___________________________________________________________
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/