Hi guys,
we are currently establishing our own local Galaxy instance. However, after we tried to install the “mothur toolsuite” we could not enter the admin pages anymore. Every time we try we we obtain the following error:
"Internal Server Error
Galaxy was unable to successfully complete your request
An error occurred.
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
The error has been logged to our team."
Here is what the paster.log says:
172.31.30.58 - - [26/Jun/2013:11:02:14 +0200] "GET /history/get_display_application_links HTTP/1.0" 200 - "http://galaxy.jki.bund.de/history" "Mozilla/5.0 (Windows NT 6.1; rv:21.0) Gecko/20100101 Firefox/21.0"
172.31.30.58 - - [26/Jun/2013:11:02:33 +0200] "GET /admin HTTP/1.0" 500 - "http://galaxy.jki.bund.de/" "Mozilla/5.0 (Windows NT 6.1; rv:21.0) Gecko/20100101 Firefox/21.0"
Error - <class 'simplejson.decoder.JSONDecodeError'>: Expecting object: line 1 column 65534 (char 65534)
URL: http://galaxy.jki.bund.de/admin
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
app_iter = self.application(environ, sr_checker)
File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
return self.application(environ, start_response)
File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
return self.application(environ, start_response)
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request
body = method( trans, **kwargs )
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator
return func( self, trans, *args, **kwargs )
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', line 31 in index
installing_repository_ids = get_ids_of_tool_shed_repositories_being_installed( trans, as_string=True )
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', line 1080 in get_ids_of_tool_shed_repositories_being_installed
trans.model.ToolShedRepository.status == loading_datatypes_status ) ):
File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2348 in instances
File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2120 in _instance
File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1974 in populate_state
File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 150 in fetch_col
File '/opt/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py', line 658 in process
File '/opt/galaxy/galaxy-dist/lib/galaxy/model/custom_types.py', line 52 in process_result_value
return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) )
File '/opt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py', line 402 in decode
File '/opt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py', line 418 in raw_decode
JSONDecodeError: Expecting object: line 1 column 65534 (char 65534)
CGI Variables
-------------
CONTENT_LENGTH: '0'
HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_ENCODING: 'gzip, deflate'
HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
HTTP_CACHE_CONTROL: 'max-age=0'
HTTP_CONNECTION: 'keep-alive'
HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a29d379ce3a444c9b5d260e535a8d6224324fc4d09af0e63592f8cd6e92ad7996'
HTTP_HOST: 'galaxy.jki.bund.de'
HTTP_REFERER: 'http://galaxy.jki.bund.de/'
HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; rv:21.0) Gecko/20100101 Firefox/21.0'
HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
HTTP_X_FORWARDED_FOR: '172.31.30.58'
ORGINAL_REMOTE_ADDR: '172.16.20.52'
PATH_INFO: '/admin'
REMOTE_ADDR: '172.31.30.58'
REQUEST_METHOD: 'GET'
SERVER_NAME: '0.0.0.0'
SERVER_PORT: '8080'
SERVER_PROTOCOL: 'HTTP/1.0'
WSGI Variables
--------------
application: <paste.recursive.RecursiveMiddleware object at 0x98fb190>
is_api_request: False
paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a29d379ce3a444c9b5d260e535a8d6224324fc4d09af0e63592f8cd6e92ad7996'>, 'galaxysession=c6ca0ddb55be603a29d379ce3a444c9b5d260e535a8d6224324fc4d09af0e63592f8cd6e92ad7996')
paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x9d5ad90>
paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xa33d990>
paste.recursive.forward: <paste.recursive.Forwarder from />
paste.recursive.include: <paste.recursive.Includer from />
paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: '2355c54cde3f11e294120050568d0b1f'
webob._parsed_query_vars: (MultiDict([]), '')
wsgi process: 'Multithreaded'
------------------------------------------------------------
Our system is:
Linux version 2.6.32-5-amd64 (Debian 2.6.32-48squeeze1) (dannf@debian.org) (gcc version 4.3.5 (Debian 4.3.5-4) ) #1 SMP Mon Feb 25 00:26:11 UTC 2013
Thanks for any help.
Regards, Thomas