Custom Builds Server eroor
Hello I added a custom build to Galaxy, then deleted it and added a new build with the same name. Now whenever I try to acces my custom builds I am getting a server error. Can you point me towards any faults? Do I need to manually remove the custom builds from the database and if so where can I find them? Thanks Shaun Webb Error - <type 'exceptions.KeyError'>: u'ensembl_Current' URL: http://bifx-core.bio.ed.ac.uk:8080/galaxy/display_application/4100358d24a8f6... File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 740 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py', line 189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) File '/storage/home/galaxy/galaxy_env/lib/python2.6/UserDict.py', line 22 in __getitem__ raise KeyError(key) KeyError: u'ensembl_Current' -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Hello I added a custom build to Galaxy, then deleted it and added a new build with the same name. Now whenever I try to acces my custom builds I am getting a server error.
I can't reproduce this issue using the most recent galaxy-dist. Also, the stack trace that you pasted below doesn't relate to custom builds; it relates to visualizing the data with Ensembl. Can you be more specific about what steps you took and what your goal is? Thanks, J.
Can you point me towards any faults? Do I need to manually remove the custom builds from the database and if so where can I find them?
Thanks Shaun Webb
Error - <type 'exceptions.KeyError'>: u'ensembl_Current' URL: http://bifx-core.bio.ed.ac.uk:8080/galaxy/display_application/4100358d24a8f6... File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 740 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py', line 189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) File '/storage/home/galaxy/galaxy_env/lib/python2.6/UserDict.py', line 22 in __getitem__ raise KeyError(key) KeyError: u'ensembl_Current'
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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Hi Shaun I recently run into troubles creating a visualization for a custom build using a fasta file to provide the sequence lengths. In order to continue, I had to remove the entry from the database, ie: changing the value to "{}" for name = 'dbkeys' in the 'user_preference' table. I repeated it by adding the sequence length manually and it worked. I then run into the next problem: I couldn't add new wiggle or bed files to a data library using this custom build. However, once in the data library I could change the genome to the custom one. Regards, Hans-Rudolf On 12/12/2012 08:09 PM, Jeremy Goecks wrote:
Hello I added a custom build to Galaxy, then deleted it and added a new build with the same name. Now whenever I try to acces my custom builds I am getting a server error.
I can't reproduce this issue using the most recent galaxy-dist. Also, the stack trace that you pasted below doesn't relate to custom builds; it relates to visualizing the data with Ensembl.
Can you be more specific about what steps you took and what your goal is?
Thanks, J.
Can you point me towards any faults? Do I need to manually remove the custom builds from the database and if so where can I find them?
Thanks Shaun Webb
Error - <type 'exceptions.KeyError'>: u'ensembl_Current' URL: http://bifx-core.bio.ed.ac.uk:8080/galaxy/display_application/4100358d24a8f6... File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 740 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py', line 189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) File '/storage/home/galaxy/galaxy_env/lib/python2.6/UserDict.py', line 22 in __getitem__ raise KeyError(key) KeyError: u'ensembl_Current'
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
___________________________________________________________ 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:
___________________________________________________________ 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:
I recently run into troubles creating a visualization for a custom build using a fasta file to provide the sequence lengths.
In order to continue, I had to remove the entry from the database, ie: changing the value to "{}" for name = 'dbkeys' in the 'user_preference' table.
If you can provide the steps to reproduce this error, I'd be happy to take a look at the issue.
I couldn't add new wiggle or bed files to a data library using this custom build. However, once in the data library I could change the genome to the custom one.
This is fixed in -central changeset 0ec7f0b6dec8 Best, J.
participants (3)
-
Hans-Rudolf Hotz -
Jeremy Goecks -
Shaun Webb