Hello David, We don't have a workaround yet - but we (Dan did most of the investigating) understand the problem I think. You are using a MySQL database I assume? (Ignore the rest of this e-mail if not). I think MySQL has lower limits on the size of BLOBs that can be stored in the database than postgres - and we think the tool shed is tried to storing a really large blob of metadata in the database and it got truncated and now Galaxy is failing because it cannot load that entry as JSON.
The work around would be something like trying to find the truncated column in the tool_repositories table - deleting it and references - changing that column to a LONGBLOB and reinstalling that tool. I have created a Trello card for this bug report. https://trello.com/c/RbW6pOd2 It is said a lot but we strongly encourage not using MySQL. It might be worth trying this patch (https://bitbucket.org/galaxy/galaxy-central/pull-request/511/allow-model-objects-to-be-loaded-when-they/diff#comment-3288189) from Dan as well. I am not sure what the tool shed would do if it cannot find the metadata though. -John On Mon, Sep 29, 2014 at 11:41 AM, David Bernick <dbern...@soe.ucsc.edu> wrote: > Good morning - > > I have acquired an Internal server error on our local galaxy install. It > seems to be an unterminated string. How do I resolve this? > thanks in advance - > David Bernick > UCSC > > Here is the relevant portion of the log (I hope). > > Error - <type 'exceptions.ValueError'>: Unterminated string starting at: > line 1 column 65528 (char 65528) > URL: http://campusrocks.cse.ucsc.edu:8080/admin/index > File > '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', > line 149 in __call__ > app_iter = self.application(environ, sr_checker) > File > '/projects/galaxy/bin/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 > '/projects/galaxy/bin/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 '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/base.py', > line 132 in __call__ > return self.handle_request( environ, start_response ) > File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/base.py', > line 190 in handle_request > body = method( trans, **kwargs ) > File > '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/__init__.py', > line 383 in decorator > return func( self, trans, *args, **kwargs ) > File > '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', > line 34 in index > installing_repository_ids = > suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, > as_string=True ) > File > '/projects/galaxy/bin/galaxy-dist/lib/tool_shed/util/shed_util_common.py', > line 277 in get_ids_of_tool_shed_repositories_being_installed > app.install_model.ToolShedRepository.status == loading_datatypes_status ) > ): > File > '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', > line 2348 in instances > File > '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', > line 2120 in _instance > File > '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', > line 1974 in populate_state > File > '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', > line 150 in fetch_col > File > '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py', > line 658 in process > File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/model/custom_types.py', > line 52 in process_result_value > return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) > File '/usr/lib64/python2.6/json/decoder.py', line 319 in decode > obj, end = self.raw_decode(s, idx=_w(s, 0).end()) > File '/usr/lib64/python2.6/json/decoder.py', line 336 in raw_decode > obj, end = self._scanner.iterscan(s, **kw).next() > File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan > rval, next_pos = action(m, context) > File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject > value, end = iterscan(s, idx=end, context=context).next() > File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan > rval, next_pos = action(m, context) > File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray > value, end = iterscan(s, idx=end, context=context).next() > File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan > rval, next_pos = action(m, context) > File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject > value, end = iterscan(s, idx=end, context=context).next() > File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan > rval, next_pos = action(m, context) > File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray > value, end = iterscan(s, idx=end, context=context).next() > File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan > rval, next_pos = action(m, context) > File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject > value, end = iterscan(s, idx=end, context=context).next() > File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan > rval, next_pos = action(m, context) > File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray > value, end = iterscan(s, idx=end, context=context).next() > File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan > rval, next_pos = action(m, context) > File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray > value, end = iterscan(s, idx=end, context=context).next() > File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan > rval, next_pos = action(m, context) > File '/usr/lib64/python2.6/json/decoder.py', line 155 in JSONString > return scanstring(match.string, match.end(), encoding, strict) > ValueError: Unterminated string starting at: line 1 column 65528 (char > 65528) > > > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
