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 (<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
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 <slegras@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 (<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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Thank you for your feedback ! It seems that we don’t have the problem anymore with our test instance (16.07) Steph De : <arthynia@gmail.com> au nom de Cristel Thomas <cristel.thomas@gmail.com> Date : mercredi 14 septembre 2016 14:20 À : Stephanie Le Gras <slegras@igbmc.fr> Cc : "galaxy-dev@lists.galaxyproject.org" <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 <slegras@igbmc.fr<mailto:slegras@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 (<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<tel:%2B33%20%280%293%2088%2065%2032%2073> ___________________________________________________________ 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/
participants (2)
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Cristel Thomas -
Stephanie LE GRAS