Sure, all you need to do is update to at least that revision, you can do that with:
% hg pull -u -r 89190bcd1ccf http://bitbucket.org/galaxy/galaxy-central/
On Mar 24, 2011, at 4:58 AM, Vincent Le Texier wrote:
Hello Dannon, Thanks for your answer. So could you tell me when this issue will be resolved ? Can I apply a patch now and how ? I am facing problem with galaxy-reports and mysql (date_trunc of Postgresql), so it would be better for me to use postgreSQL 9. Vincent
Le 3/22/11 6:13 PM, Dannon Baker a écrit :
Vincent,
This issue should be resolved after changeset 5074:89190bcd1ccf, available in the galaxy-central repository. This change will also be available in the near future in the galaxy-dist repository.
Thanks!
Dannon
On Mar 22, 2011, at 12:59 PM, Vincent Le Texier wrote:
Hello everyone, I am having trouble to save/edit a workflow with postgreSQL 9.0.3. (It works fine if I use MySQL)
Any idea of the problem ?
I get the following error (JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)) :
URL: http://localhost:8080/workflow File '/data-ddn/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/data-ddn/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/workflow.py', line 114 in index return self.list( trans ) File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/workflow.py', line 139 in list .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py', line 1267 in all return list(self) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py', line 1422 in instances rows = [process[0](context, row) for row in fetch] File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py', line 2032 in main return _instance(row, None) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance populate_state(state, dict_, row, isnew, only_load_props) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state populator(state, dict_, row, isnew=isnew, **flags) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py', line 762 in execute dict_[key] = _instance(row, None) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance populate_state(state, dict_, row, isnew, only_load_props) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state populator(state, dict_, row, isnew=isnew, **flags) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py', line 781 in execute _instance(row, result_list) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance populate_state(state, dict_, row, isnew, only_load_props) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state populator(state, dict_, row, isnew=isnew, **flags) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py', line 120 in new_execute dict_[key] = row[col] File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 1348 in __getitem__ return self.__parent._get_col(self.__row, key) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py', line 1620 in _get_col return processor(row[index]) File '/data-ddn/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/types.py', line 288 in process return self.process_result_value(value, dialect) File '/data-ddn/home/galaxy/galaxy-dist/lib/galaxy/model/custom_types.py', line 32 in process_result_value return json_decoder.decode( str( value ) ) File '/data-ddn/home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py', line 402 in decode File '/data-ddn/home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py', line 420 in raw_decode JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) -- Vincent Le Texier Senior Software Engineer Synergie Lyon Cancer Leon Berard Center, Cheney C 28, rue Laennec 69373 LYON Cedex 08 +33 4 26 55 67 85
letexier@lyon.fnclcc.fr ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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-- Vincent Le Texier Senior Software Engineer Synergie Lyon Cancer Leon Berard Center, Cheney C 28, rue Laennec 69373 LYON Cedex 08 +33 4 26 55 67 85 letexier@lyon.fnclcc.fr