Re: [galaxy-dev] Problem downloading HTML datasets
Thank you for your feedback ! It seems that we don’t have the problem anymore
with our test instance (16.07)
Steph
De : au nom de Cristel Thomas
Date : mercredi 14 septembre 2016 14:20
À : Stephanie Le Gras
Cc : "galaxy-dev@lists.galaxyproject.org"
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
mailto:sleg...@igbmc.fr>> 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 ()
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: [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
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 ()
>
>
>
> 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
>
>
>
> ___
> 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/
[galaxy-dev] Problem downloading HTML datasets
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 ()
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
___
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/
