Problem downloading HTML datasets

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Problem downloading HTML datasets

Stephanie LE GRAS

Hi there,

 

I’m currently facing several problems with the galaxy instance I’m managing. I’m going to send a mail per problem so sorry in advance : for flooding !

 

The first problem I’m facing is that we can’t download HTML datasets from Galaxy. Here is the error I got when I try to do download an HTML dataset :

 

URL: http://use.galaxeast.fr/datasets/ff16fe18e3db62e7/display?to_ext=html

File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/weberror/evalexception.py', line 431 in respond

  app_iter = self.application(environ, detect_start_response)

File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__

  return self.application(environ, start_response)

File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__

  return self.application(environ, start_response)

File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 131 in __call__

  return self.handle_request( environ, start_response )

File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 190 in handle_request

  body = method( trans, **kwargs )

File '/data2/galaxy/production/galaxy/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 245 in display

  return data.datatype.display_data(trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd)

File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 353 in display_data

  return self._archive_composite_dataset( trans, data, **kwd )

File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 235 in _archive_composite_dataset

  params = util.Params( kwd )

File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 683 in __init__

  self.__dict__[ key ] = sanitize_param( value )

File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 488 in sanitize_param

  raise Exception('Unknown parameter type (%s)' % ( type( value ) ))

Exception: Unknown parameter type (<type 'NoneType'>)

 

We don’t want to disable the sanitize process and we try to add some tools that generate HTML datasets into the whitelist but it didn’t solve our problem.

 

Version of Galaxy : release_16.04

 

Any idea about what the problem can be ?

 

Many thanks in advance for any help,

 

Best regards,

 

Stephanie

 

-- 

Stephanie Le Gras

INSERM
Computational scientist - Bioinformatician
GenomEast platform (former Microarray and Sequencing platform)
IGBMC
1, rue Laurent Fries
67404 ILLKIRCH Cedex
France
Tel. : +33 (0)3 88 65 32 73

 


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Re: Problem downloading HTML datasets

Cristel Thomas
Not that helpful, but we have the same problem with our 16.04 instance.

On Tue, Sep 13, 2016 at 10:21 AM, Stephanie LE GRAS <[hidden email]> wrote:

Hi there,

 

I’m currently facing several problems with the galaxy instance I’m managing. I’m going to send a mail per problem so sorry in advance : for flooding !

 

The first problem I’m facing is that we can’t download HTML datasets from Galaxy. Here is the error I got when I try to do download an HTML dataset :

 

URL: http://use.galaxeast.fr/datasets/ff16fe18e3db62e7/display?to_ext=html

File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/weberror/evalexception.py', line 431 in respond

  app_iter = self.application(environ, detect_start_response)

File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__

  return self.application(environ, start_response)

File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__

  return self.application(environ, start_response)

File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 131 in __call__

  return self.handle_request( environ, start_response )

File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 190 in handle_request

  body = method( trans, **kwargs )

File '/data2/galaxy/production/galaxy/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 245 in display

  return data.datatype.display_data(trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd)

File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 353 in display_data

  return self._archive_composite_dataset( trans, data, **kwd )

File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 235 in _archive_composite_dataset

  params = util.Params( kwd )

File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 683 in __init__

  self.__dict__[ key ] = sanitize_param( value )

File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 488 in sanitize_param

  raise Exception('Unknown parameter type (%s)' % ( type( value ) ))

Exception: Unknown parameter type (<type 'NoneType'>)

 

We don’t want to disable the sanitize process and we try to add some tools that generate HTML datasets into the whitelist but it didn’t solve our problem.

 

Version of Galaxy : release_16.04

 

Any idea about what the problem can be ?

 

Many thanks in advance for any help,

 

Best regards,

 

Stephanie

 

-- 

Stephanie Le Gras

INSERM
Computational scientist - Bioinformatician
GenomEast platform (former Microarray and Sequencing platform)
IGBMC
1, rue Laurent Fries
67404 ILLKIRCH Cedex
France
Tel. : <a href="tel:%2B33%20%280%293%2088%2065%2032%2073" value="+33388653273" target="_blank">+33 (0)3 88 65 32 73

 


___________________________________________________________
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
and other Galaxy lists, please use the interface at:
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Re: Problem downloading HTML datasets

Stephanie LE GRAS

 

Thank you for your feedback ! It seems that we don’t have the problem anymore with our test instance (16.07)

 

Steph

 

 

De : <[hidden email]> au nom de Cristel Thomas <[hidden email]>
Date : mercredi 14 septembre 2016 14:20
À : Stephanie Le Gras <[hidden email]>
Cc : "[hidden email]" <[hidden email]>
Objet : Re: [galaxy-dev] Problem downloading HTML datasets

 

Not that helpful, but we have the same problem with our 16.04 instance.

 

On Tue, Sep 13, 2016 at 10:21 AM, Stephanie LE GRAS <[hidden email]> wrote:

Hi there,

 

I’m currently facing several problems with the galaxy instance I’m managing. I’m going to send a mail per problem so sorry in advance : for flooding !

 

The first problem I’m facing is that we can’t download HTML datasets from Galaxy. Here is the error I got when I try to do download an HTML dataset :

 

URL: http://use.galaxeast.fr/datasets/ff16fe18e3db62e7/display?to_ext=html

File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/weberror/evalexception.py', line 431 in respond

  app_iter = self.application(environ, detect_start_response)

File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__

  return self.application(environ, start_response)

File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__

  return self.application(environ, start_response)

File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 131 in __call__

  return self.handle_request( environ, start_response )

File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 190 in handle_request

  body = method( trans, **kwargs )

File '/data2/galaxy/production/galaxy/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 245 in display

  return data.datatype.display_data(trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd)

File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 353 in display_data

  return self._archive_composite_dataset( trans, data, **kwd )

File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 235 in _archive_composite_dataset

  params = util.Params( kwd )

File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 683 in __init__

  self.__dict__[ key ] = sanitize_param( value )

File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 488 in sanitize_param

  raise Exception('Unknown parameter type (%s)' % ( type( value ) ))

Exception: Unknown parameter type (<type 'NoneType'>)

 

We don’t want to disable the sanitize process and we try to add some tools that generate HTML datasets into the whitelist but it didn’t solve our problem.

 

Version of Galaxy : release_16.04

 

Any idea about what the problem can be ?

 

Many thanks in advance for any help,

 

Best regards,

 

Stephanie

 

-- 

Stephanie Le Gras

INSERM
Computational scientist - Bioinformatician
GenomEast platform (former Microarray and Sequencing platform)
IGBMC
1, rue Laurent Fries
67404 ILLKIRCH Cedex
France
Tel. : <a href="tel:%2B33%20%280%293%2088%2065%2032%2073" target="_blank">+33 (0)3 88 65 32 73

 


___________________________________________________________
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/