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upload data error

Beginner TI
Hi,

I'm trying to upload a file to a new galaxy instance for the first time, however an error happened, which never did in the past:

Traceback (most recent call last):
  File "/media/libraryfiles/galaxy/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job
    job_wrapper.prepare()
  File "/media/libraryfiles/galaxy/lib/galaxy/jobs/__init__.py", line 893, in prepare
    tool_evaluator.set_compute_environment( compute_environment, get_special=get_special )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/evaluation.py", line 63, in set_compute_environment
    visit_input_values( self.tool.inputs, incoming, validate_inputs )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 92, in visit_input_values
    visit_input_values( input.inputs, d, callback, new_name_prefix, new_label_prefix, parent_prefix=new_name_prefix, **payload )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 110, in visit_input_values
    callback_helper( input, input_values, name_prefix, label_prefix, parent_prefix=parent_prefix, context=context )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 75, in callback_helper
    new_value = callback( **args )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/evaluation.py", line 62, in validate_inputs
    input.validate( value, request_context )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/basic.py", line 198, in validate
    validator.validate( value, trans )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/validation.py", line 99, in validate
    raise ValueError( message )
ValueError: You will need to reselect the file you specified (/media/8tb/galaxy-data-store/database/tmp/upload_file_data_5wWKi5).
It looks those files were successfuly uploaded, but the dataset files are all empty.

Has anyone seen this? 

Thanks,
Rui

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Re: upload data error

Gildas Le Corguillé
Hi

Do you set some remote destination in the job_conf.xml like run the jobs on a HPC?
If so, we have a similar issue and the solution was to let the upload1 tool run on the local server not on the remote server.

<tool id="upload1" destination="local"/>

But maybe, it’s another problem :P

Gildas

-----------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
------------------------------------------------------------------



Le 21 oct. 2016 à 20:58, Beginner TI <[hidden email]> a écrit :

Hi,

I'm trying to upload a file to a new galaxy instance for the first time, however an error happened, which never did in the past:

Traceback (most recent call last):
  File "/media/libraryfiles/galaxy/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job
    job_wrapper.prepare()
  File "/media/libraryfiles/galaxy/lib/galaxy/jobs/__init__.py", line 893, in prepare
    tool_evaluator.set_compute_environment( compute_environment, get_special=get_special )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/evaluation.py", line 63, in set_compute_environment
    visit_input_values( self.tool.inputs, incoming, validate_inputs )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 92, in visit_input_values
    visit_input_values( input.inputs, d, callback, new_name_prefix, new_label_prefix, parent_prefix=new_name_prefix, **payload )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 110, in visit_input_values
    callback_helper( input, input_values, name_prefix, label_prefix, parent_prefix=parent_prefix, context=context )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 75, in callback_helper
    new_value = callback( **args )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/evaluation.py", line 62, in validate_inputs
    input.validate( value, request_context )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/basic.py", line 198, in validate
    validator.validate( value, trans )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/validation.py", line 99, in validate
    raise ValueError( message )
ValueError: You will need to reselect the file you specified (/media/8tb/galaxy-data-store/database/tmp/upload_file_data_5wWKi5).
It looks those files were successfuly uploaded, but the dataset files are all empty.

Has anyone seen this? 

Thanks,
Rui
___________________________________________________________
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:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


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in your mail client.  To manage your subscriptions to this
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Re: upload data error

Beginner TI
Hi Gildas,

Thanks for the reply! Actually we are only using this as a local instance, so there isn't any remote
server. :-)

Cheers,
Rui

On Mon, Oct 24, 2016 at 3:17 AM, Gildas Le Corguillé <[hidden email]> wrote:
Hi

Do you set some remote destination in the job_conf.xml like run the jobs on a HPC?
If so, we have a similar issue and the solution was to let the upload1 tool run on the local server not on the remote server.

<tool id="upload1" destination="local"/>

But maybe, it’s another problem :P

Gildas

-----------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: <a href="tel:%2B33%202%2098%2029%2023%2081" value="+33298292381" target="_blank">+33 2 98 29 23 81
------------------------------------------------------------------



Le 21 oct. 2016 à 20:58, Beginner TI <[hidden email]> a écrit :

Hi,

I'm trying to upload a file to a new galaxy instance for the first time, however an error happened, which never did in the past:

Traceback (most recent call last):
  File "/media/libraryfiles/galaxy/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job
    job_wrapper.prepare()
  File "/media/libraryfiles/galaxy/lib/galaxy/jobs/__init__.py", line 893, in prepare
    tool_evaluator.set_compute_environment( compute_environment, get_special=get_special )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/evaluation.py", line 63, in set_compute_environment
    visit_input_values( self.tool.inputs, incoming, validate_inputs )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 92, in visit_input_values
    visit_input_values( input.inputs, d, callback, new_name_prefix, new_label_prefix, parent_prefix=new_name_prefix, **payload )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 110, in visit_input_values
    callback_helper( input, input_values, name_prefix, label_prefix, parent_prefix=parent_prefix, context=context )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", line 75, in callback_helper
    new_value = callback( **args )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/evaluation.py", line 62, in validate_inputs
    input.validate( value, request_context )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/basic.py", line 198, in validate
    validator.validate( value, trans )
  File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/validation.py", line 99, in validate
    raise ValueError( message )
ValueError: You will need to reselect the file you specified (/media/8tb/galaxy-data-store/database/tmp/upload_file_data_5wWKi5).
It looks those files were successfuly uploaded, but the dataset files are all empty.

Has anyone seen this? 

Thanks,
Rui
___________________________________________________________
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:
 https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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