Help: History panel of Galaxy interface shows traceback operational error

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Help: History panel of Galaxy interface shows traceback operational error

wenqing zhang-2
Hi;
 
I  tried  new install in linux centos at school and home. I make everything with the same setting.
the difference is that galaxy at home is running well, but the galaxy at school shows the problem, which is the histroy panel of galaxy interface showing the traceback operational error.
 
I didn't change anything else except for modifying the database_connection to local mysql in drupal in universe_wsgi.ini file.
Grag mentioned the data in the galaxy database could be corruptted.  I couldn't understand how the data was corruptted since we didn't change any data and setting in galaxy.
 
if the data is really corruptted, why the galaxy at home is running well?
 
I appreciate anyone could give any idea. 
  
Thanks.
 
wenqing zhang



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Re: Help: History panel of Galaxy interface shows traceback operational error

James Taylor
Please send the specific error that you see. Thanks.

On Jun 14, 2010, at 3:59 PM, wenqing zhang wrote:

> Hi;
>
> I  tried  new install in linux centos at school and home. I make  
> everything with the same setting.
> the difference is that galaxy at home is running well, but the  
> galaxy at school shows the problem, which is the histroy panel of  
> galaxy interface showing the traceback operational error.
>
> I didn't change anything else except for modifying the  
> database_connection to local mysql in drupal in universe_wsgi.ini  
> file.
> Grag mentioned the data in the galaxy database could be corruptted.  
> I couldn't understand how the data was corruptted since we didn't  
> change any data and setting in galaxy.
>
> if the data is really corruptted, why the galaxy at home is running  
> well?
>
> I appreciate anyone could give any idea.
>
> Thanks.
>
> wenqing zhang
>
>
> Hotmail has tools for the New Busy. Search, chat and e-mail from  
> your inbox. Learn more.  
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev

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Re: Help: History panel of Galaxy interface shows traceback operational error

wenqing zhang-2
Hi James;
 
I made the copy of error of histroy panel I can see. It is as following, please give any hints. thanks again
 
Error Traceback:
_________________
 
operational Error:
(operational Error:)
(1054, "Unknown Column 'published' in 'field list' ")
u'INSERT INTO histroy (create_time, update_time, user_id, name, hid_counter, deleteed, purged,
genome_build, importabel, slug, published) VALUES (%s, %s, %s, %s, %s,%s, %s, %s, %s, %s, %s)'
[datetime.datetime(26,14,20,37,36, 399055),  datetime.datetime(206, 14, 20, 37, 36, 399073), None, "Unnamed history', 1, o, 0, '?', 0, None, 0]
 
URL: http://127.0.01:8080//histroy
Module
weberror.evalexception.middleware: 364
in respond
>>  app_iter = self.application(environ, detect_start_response)
____________________________________________________
Module paste.debug.prints:97 in
 __call__         view         threadedprint.register(replacement_stdout)
            try:
                status, headers, body = wsgilib.intercept_output(
                    environ, self.app)
                if status is None:>>  status, headers, body = wsgilib.intercept_output(
Module paste.wsgilib:539 in intercept_output         view
<<          data.append(headers)
            return output.write
        app_iter = application(environ, replacement_start_response)
        if data[0] is None:
            return (None, None, app_iter)>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__         view
<<          environ['paste.recursive.script_name'] = my_script_name
            try:
                return self.application(environ, start_response)
            except ForwardRequestException, e:
                middleware = CheckForRecursionMiddleware(>>  return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__         view
<<                             []).append(HTTPException)
            try:
                return self.application(environ, start_response)
            except HTTPException, exc:
                return exc(environ, start_response)>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:126 in __call__         view
<<          kwargs.pop( '_', None )
            try:
                body = method( trans, **kwargs )
            except Exception, e:
                body = self.handle_controller_exception( e, trans, **kwargs )>>  body = method( trans, **kwargs )
Module galaxy.web.controllers.root:66 in history         view
<<          if trans.app.config.require_login and not trans.user:
                return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' )
            history = trans.get_history( create=True )
            if as_xml:
                trans.response.set_content_type('text/xml')>>  history = trans.get_history( create=True )
Module galaxy.web.framework:504 in get_history         view
<<          if not history:
                if util.string_as_bool( create ):
                    history = self.new_history()
                else:
                    # Perhaps a bot is running a tool without having logged in to get a history
    >>  history = self.new_history()
Module galaxy.web.framework:538 in new_history         view
<<          # Save
            self.sa_session.add_all( ( self.galaxy_session, history ) )
            self.sa_session.flush()
            return history
        def get_user( self ):>>  self.sa_session.flush()
Module sqlalchemy.orm.scoping:127 in do         view
<<  def instrument(name):
        def do(self, *args, **kwargs):
            return getattr(self.registry(), name)(*args, **kwargs)
        return do
    for meth in Session.public_methods:>>  return getattr(self.registry(), name)(*args, **kwargs)
Module sqlalchemy.orm.session:1356 in flush         view
<<          try:
                self._flushing = True
                self._flush(objects)
            finally:
                self._flushing = False>>  self._flush(objects)
Module sqlalchemy.orm.session:1434 in _flush         view
<<              subtransactions=True)
            try:
                flush_context.execute()
  
                for ext in self.extensions:>>  flush_context.execute()
Module sqlalchemy.orm.unitofwork:261 in execute         view
<<          if self._should_log_info:
                self.logger.info("Task dump:\n" + self._dump(tasks))
            UOWExecutor().execute(self, tasks)
            if self._should_log_info:
                self.logger.info("Execute Complete")>>  UOWExecutor().execute(self, tasks)
Module sqlalchemy.orm.unitofwork:753 in execute         view
<<          if isdelete is not True:
                for task in tasks:
                    self.execute_save_steps(trans, task)
            if isdelete is not False:
                for task in reversed(tasks):>>  self.execute_save_steps(trans, task)
Module sqlalchemy.orm.unitofwork:768 in execute_save_steps         view
<<
        def execute_save_steps(self, trans, task):
            self.save_objects(trans, task)
            for dep in task.polymorphic_cyclical_dependencies:
                self.execute_dependency(trans, dep, False)>>  self.save_objects(trans, task)
Module sqlalchemy.orm.unitofwork:759 in save_objects         view
<<
        def save_objects(self, trans, task):
            task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
  
        def delete_objects(self, trans, task):>>  task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
Module sqlalchemy.orm.mapper:1424 in _save_obj         view
<<                  statement = table.insert()
                    for state, params, mapper, connection, value_params in insert:
                        c = connection.execute(statement.values(value_params), params)
                        primary_key = c.last_inserted_ids()>>  c = connection.execute(statement.values(value_params), params)
Module sqlalchemy.engine.base:824 in execute         view
<<          for c in type(object).__mro__:
                if c in Connection.executors:
                    return Connection.executors[c](self, object, multiparams, params)
            else:
                raise exc.InvalidRequestError("Unexecutable object type: " + str(type(object)))>>  return Connection.executors[c](self, object, multiparams, params)
Module sqlalchemy.engine.base:874 in _execute_clauseelement         view
<<                          parameters=params
                        )
            return self.__execute_context(context)
  
        def _execute_compiled(self, compiled, multiparams, params):>>  return self.__execute_context(context)
Module sqlalchemy.engine.base:896 in __execute_context         view
<<              self._cursor_executemany(context.cursor, context.statement, context.parameters, context=context)
            else:
                self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context)
            if context.compiled:
                context.post_exec()>>  self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context)
Module sqlalchemy.engine.base:950 in _cursor_execute         view
<<              self.dialect.do_execute(cursor, statement, parameters, context=context)
            except Exception, e:
                self._handle_dbapi_exception(e, statement, parameters, cursor, context)
                raise
    >>  self._handle_dbapi_exception(e, statement, parameters, cursor, context)
Module sqlalchemy.engine.base:931 in _handle_dbapi_exception         view
<<                  if self.__close_with_result:
                        self.close()
                raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect)
            finally:
                del self._reentrant_error>>  raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect)
OperationalError: (OperationalError) (1054, "Unknown column 'published' in 'field list'") u'INSERT INTO history (create_time, update_time, user_id, name, hid_counter, deleted, purged, genome_build, importable, slug, published) VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s)' [datetime.datetime(2010, 6, 14, 20, 37, 36, 399055), datetime.datetime(2010, 6, 14, 20, 37, 36, 399073), None, 'Unnamed history', 1, 0, 0, '?', 0, None, 0]
URL: http://127.0.0.1:8080/history File '/usr/local/galaxy/galaxy_dist/eggs/WebError-0.8a-py2.4.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/debug/prints.py', line 97 in __call__ status, headers, body = wsgilib.intercept_output( File '/usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy_dist/lib/galaxy/web/controllers/root.py', line 66 in history history = trans.get_history( create=True ) File '/usr/local/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 504 in get_history history = self.new_history() File '/usr/local/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 538 in new_history self.sa_session.flush() File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py', line 127 in do return getattr(self.registry(), name)(*args, **kwargs) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py', line 1356 in flush self._flush(objects) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py', line 1434 in _flush flush_context.execute() File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py', line 261 in execute UOWExecutor().execute(self, tasks) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py', line 753 in execute self.execute_save_steps(trans, task) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py', line 768 in execute_save_steps self.save_objects(trans, task) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py', line 759 in save_objects task.mapper._save_obj(task.polymorphic_tosave_objects, trans) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/mapper.py', line 1424 in _save_obj c = connection.execute(statement.values(value_params), params) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py', line 824 in execute return Connection.executors[c](self, object, multiparams, params) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py', line 874 in _execute_clauseelement return self.__execute_context(context) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py', line 896 in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py', line 950 in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File '/usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) (1054, "Unknown column 'published' in 'field list'") u'INSERT INTO history (create_time, update_time, user_id, name, hid_counter, deleted, purged, genome_build, importable, slug, published) VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s)' [datetime.datetime(2010, 6, 14, 20, 37, 36, 399055), datetime.datetime(2010, 6, 14, 20, 37, 36, 399073), None, 'Unnamed history', 1, 0, 0, '?', 0, None, 0]
<?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.4.3"> Python </language> </sysinfo> <stack> <frame> <module> weberror.evalexception.middleware </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/WebError-0.8a-py2.4.egg/weberror/evalexception/middleware.py </filename> <line> 364 </line> <function> respond </function> <operation> app_iter = self.application(environ, detect_start_response) </operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter) </operation_context> </frame> <frame> <module> paste.debug.prints </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/debug/prints.py </filename> <line> 97 </line> <function> __call__ </function> <operation> status, headers, body = wsgilib.intercept_output( </operation> <operation_context> threadedprint.register(replacement_stdout) try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: </operation_context> </frame> <frame> <module> paste.wsgilib </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/wsgilib.py </filename> <line> 539 </line> <function> intercept_output </function> <operation> app_iter = application(environ, replacement_start_response) </operation> <operation_context> data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter) </operation_context> </frame> <frame> <module> paste.recursive </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py </filename> <line> 80 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware( </operation_context> </frame> <frame> <module> paste.httpexceptions </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py </filename> <line> 632 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response) </operation_context> </frame> <frame> <module> galaxy.web.framework.base </module> <filename> /usr/local/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py </filename> <line> 126 </line> <function> __call__ </function> <operation> body = method( trans, **kwargs ) </operation> <operation_context> kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) </operation_context> </frame> <frame> <module> galaxy.web.controllers.root </module> <filename> /usr/local/galaxy/galaxy_dist/lib/galaxy/web/controllers/root.py </filename> <line> 66 </line> <function> history </function> <operation> history = trans.get_history( create=True ) </operation> <operation_context> if trans.app.config.require_login and not trans.user: return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' ) history = trans.get_history( create=True ) if as_xml: trans.response.set_content_type('text/xml') </operation_context> </frame> <frame> <module> galaxy.web.framework </module> <filename> /usr/local/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py </filename> <line> 504 </line> <function> get_history </function> <operation> history = self.new_history() </operation> <operation_context> if not history: if util.string_as_bool( create ): history = self.new_history() else: # Perhaps a bot is running a tool without having logged in to get a history </operation_context> </frame> <frame> <module> galaxy.web.framework </module> <filename> /usr/local/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py </filename> <line> 538 </line> <function> new_history </function> <operation> self.sa_session.flush() </operation> <operation_context> # Save self.sa_session.add_all( ( self.galaxy_session, history ) ) self.sa_session.flush() return history def get_user( self ): </operation_context> </frame> <frame> <module> sqlalchemy.orm.scoping </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py </filename> <line> 127 </line> <function> do </function> <operation> return getattr(self.registry(), name)(*args, **kwargs) </operation> <operation_context> def instrument(name): def do(self, *args, **kwargs): return getattr(self.registry(), name)(*args, **kwargs) return do for meth in Session.public_methods: </operation_context> </frame> <frame> <module> sqlalchemy.orm.session </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py </filename> <line> 1356 </line> <function> flush </function> <operation> self._flush(objects) </operation> <operation_context> try: self._flushing = True self._flush(objects) finally: self._flushing = False </operation_context> </frame> <frame> <module> sqlalchemy.orm.session </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py </filename> <line> 1434 </line> <function> _flush </function> <operation> flush_context.execute() </operation> <operation_context> subtransactions=True) try: flush_context.execute() for ext in self.extensions: </operation_context> </frame> <frame> <module> sqlalchemy.orm.unitofwork </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py </filename> <line> 261 </line> <function> execute </function> <operation> UOWExecutor().execute(self, tasks) </operation> <operation_context> if self._should_log_info: self.logger.info(&quot;Task dump:\n&quot; + self._dump(tasks)) UOWExecutor().execute(self, tasks) if self._should_log_info: self.logger.info(&quot;Execute Complete&quot;) </operation_context> </frame> <frame> <module> sqlalchemy.orm.unitofwork </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py </filename> <line> 753 </line> <function> execute </function> <operation> self.execute_save_steps(trans, task) </operation> <operation_context> if isdelete is not True: for task in tasks: self.execute_save_steps(trans, task) if isdelete is not False: for task in reversed(tasks): </operation_context> </frame> <frame> <module> sqlalchemy.orm.unitofwork </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py </filename> <line> 768 </line> <function> execute_save_steps </function> <operation> self.save_objects(trans, task) </operation> <operation_context> def execute_save_steps(self, trans, task): self.save_objects(trans, task) for dep in task.polymorphic_cyclical_dependencies: self.execute_dependency(trans, dep, False) </operation_context> </frame> <frame> <module> sqlalchemy.orm.unitofwork </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py </filename> <line> 759 </line> <function> save_objects </function> <operation> task.mapper._save_obj(task.polymorphic_tosave_objects, trans) </operation> <operation_context> def save_objects(self, trans, task): task.mapper._save_obj(task.polymorphic_tosave_objects, trans) def delete_objects(self, trans, task): </operation_context> </frame> <frame> <module> sqlalchemy.orm.mapper </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/mapper.py </filename> <line> 1424 </line> <function> _save_obj </function> <operation> c = connection.execute(statement.values(value_params), params) </operation> <operation_context> statement = table.insert() for state, params, mapper, connection, value_params in insert: c = connection.execute(statement.values(value_params), params) primary_key = c.last_inserted_ids() </operation_context> </frame> <frame> <module> sqlalchemy.engine.base </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py </filename> <line> 824 </line> <function> execute </function> <operation> return Connection.executors[c](self, object, multiparams, params) </operation> <operation_context> for c in type(object).__mro__: if c in Connection.executors: return Connection.executors[c](self, object, multiparams, params) else: raise exc.InvalidRequestError(&quot;Unexecutable object type: &quot; + str(type(object))) </operation_context> </frame> <frame> <module> sqlalchemy.engine.base </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py </filename> <line> 874 </line> <function> _execute_clauseelement </function> <operation> return self.__execute_context(context) </operation> <operation_context> parameters=params ) return self.__execute_context(context) def _execute_compiled(self, compiled, multiparams, params): </operation_context> </frame> <frame> <module> sqlalchemy.engine.base </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py </filename> <line> 896 </line> <function> __execute_context </function> <operation> self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) </operation> <operation_context> self._cursor_executemany(context.cursor, context.statement, context.parameters, context=context) else: self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) if context.compiled: context.post_exec() </operation_context> </frame> <frame> <module> sqlalchemy.engine.base </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py </filename> <line> 950 </line> <function> _cursor_execute </function> <operation> self._handle_dbapi_exception(e, statement, parameters, cursor, context) </operation> <operation_context> self.dialect.do_execute(cursor, statement, parameters, context=context) except Exception, e: self._handle_dbapi_exception(e, statement, parameters, cursor, context) raise </operation_context> </frame> <frame> <module> sqlalchemy.engine.base </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py </filename> <line> 931 </line> <function> _handle_dbapi_exception </function> <operation> raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) </operation> <operation_context> if self.__close_with_result: self.close() raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) finally: del self._reentrant_error </operation_context> </frame> </stack> <exception> <type> OperationalError </type> <value> (OperationalError) (1054, &quot;Unknown column 'published' in 'field list'&quot;) u'INSERT INTO history (create_time, update_time, user_id, name, hid_counter, deleted, purged, genome_build, importable, slug, published) VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s)' [datetime.datetime(2010, 6, 14, 20, 37, 36, 399055), datetime.datetime(2010, 6, 14, 20, 37, 36, 399073), None, 'Unnamed history', 1, 0, 0, '?', 0, None, 0] </value> </exception> </traceback>
<?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.4.3"> Python </language> </sysinfo> <stack> <frame> <module> weberror.evalexception.middleware </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/WebError-0.8a-py2.4.egg/weberror/evalexception/middleware.py </filename> <line> 364 </line> <function> respond </function> <operation> app_iter = self.application(environ, detect_start_response) </operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter) </operation_context> </frame> <frame> <module> paste.debug.prints </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/debug/prints.py </filename> <line> 97 </line> <function> __call__ </function> <operation> status, headers, body = wsgilib.intercept_output( </operation> <operation_context> threadedprint.register(replacement_stdout) try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: </operation_context> </frame> <frame> <module> paste.wsgilib </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/wsgilib.py </filename> <line> 539 </line> <function> intercept_output </function> <operation> app_iter = application(environ, replacement_start_response) </operation> <operation_context> data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter) </operation_context> </frame> <frame> <module> paste.recursive </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py </filename> <line> 80 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware( </operation_context> </frame> <frame> <module> paste.httpexceptions </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py </filename> <line> 632 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response) </operation_context> </frame> <frame> <module> galaxy.web.framework.base </module> <filename> /usr/local/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py </filename> <line> 126 </line> <function> __call__ </function> <operation> body = method( trans, **kwargs ) </operation> <operation_context> kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) </operation_context> </frame> <frame> <module> galaxy.web.controllers.root </module> <filename> /usr/local/galaxy/galaxy_dist/lib/galaxy/web/controllers/root.py </filename> <line> 66 </line> <function> history </function> <operation> history = trans.get_history( create=True ) </operation> <operation_context> if trans.app.config.require_login and not trans.user: return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' ) history = trans.get_history( create=True ) if as_xml: trans.response.set_content_type('text/xml') </operation_context> </frame> <frame> <module> galaxy.web.framework </module> <filename> /usr/local/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py </filename> <line> 504 </line> <function> get_history </function> <operation> history = self.new_history() </operation> <operation_context> if not history: if util.string_as_bool( create ): history = self.new_history() else: # Perhaps a bot is running a tool without having logged in to get a history </operation_context> </frame> <frame> <module> galaxy.web.framework </module> <filename> /usr/local/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py </filename> <line> 538 </line> <function> new_history </function> <operation> self.sa_session.flush() </operation> <operation_context> # Save self.sa_session.add_all( ( self.galaxy_session, history ) ) self.sa_session.flush() return history def get_user( self ): </operation_context> </frame> <frame> <module> sqlalchemy.orm.scoping </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py </filename> <line> 127 </line> <function> do </function> <operation> return getattr(self.registry(), name)(*args, **kwargs) </operation> <operation_context> def instrument(name): def do(self, *args, **kwargs): return getattr(self.registry(), name)(*args, **kwargs) return do for meth in Session.public_methods: </operation_context> </frame> <frame> <module> sqlalchemy.orm.session </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py </filename> <line> 1356 </line> <function> flush </function> <operation> self._flush(objects) </operation> <operation_context> try: self._flushing = True self._flush(objects) finally: self._flushing = False </operation_context> </frame> <frame> <module> sqlalchemy.orm.session </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py </filename> <line> 1434 </line> <function> _flush </function> <operation> flush_context.execute() </operation> <operation_context> subtransactions=True) try: flush_context.execute() for ext in self.extensions: </operation_context> </frame> <frame> <module> sqlalchemy.orm.unitofwork </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py </filename> <line> 261 </line> <function> execute </function> <operation> UOWExecutor().execute(self, tasks) </operation> <operation_context> if self._should_log_info: self.logger.info(&quot;Task dump:\n&quot; + self._dump(tasks)) UOWExecutor().execute(self, tasks) if self._should_log_info: self.logger.info(&quot;Execute Complete&quot;) </operation_context> </frame> <frame> <module> sqlalchemy.orm.unitofwork </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py </filename> <line> 753 </line> <function> execute </function> <operation> self.execute_save_steps(trans, task) </operation> <operation_context> if isdelete is not True: for task in tasks: self.execute_save_steps(trans, task) if isdelete is not False: for task in reversed(tasks): </operation_context> </frame> <frame> <module> sqlalchemy.orm.unitofwork </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py </filename> <line> 768 </line> <function> execute_save_steps </function> <operation> self.save_objects(trans, task) </operation> <operation_context> def execute_save_steps(self, trans, task): self.save_objects(trans, task) for dep in task.polymorphic_cyclical_dependencies: self.execute_dependency(trans, dep, False) </operation_context> </frame> <frame> <module> sqlalchemy.orm.unitofwork </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/unitofwork.py </filename> <line> 759 </line> <function> save_objects </function> <operation> task.mapper._save_obj(task.polymorphic_tosave_objects, trans) </operation> <operation_context> def save_objects(self, trans, task): task.mapper._save_obj(task.polymorphic_tosave_objects, trans) def delete_objects(self, trans, task): </operation_context> </frame> <frame> <module> sqlalchemy.orm.mapper </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/mapper.py </filename> <line> 1424 </line> <function> _save_obj </function> <operation> c = connection.execute(statement.values(value_params), params) </operation> <operation_context> statement = table.insert() for state, params, mapper, connection, value_params in insert: c = connection.execute(statement.values(value_params), params) primary_key = c.last_inserted_ids() </operation_context> </frame> <frame> <module> sqlalchemy.engine.base </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py </filename> <line> 824 </line> <function> execute </function> <operation> return Connection.executors[c](self, object, multiparams, params) </operation> <operation_context> for c in type(object).__mro__: if c in Connection.executors: return Connection.executors[c](self, object, multiparams, params) else: raise exc.InvalidRequestError(&quot;Unexecutable object type: &quot; + str(type(object))) </operation_context> </frame> <frame> <module> sqlalchemy.engine.base </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py </filename> <line> 874 </line> <function> _execute_clauseelement </function> <operation> return self.__execute_context(context) </operation> <operation_context> parameters=params ) return self.__execute_context(context) def _execute_compiled(self, compiled, multiparams, params): </operation_context> </frame> <frame> <module> sqlalchemy.engine.base </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py </filename> <line> 896 </line> <function> __execute_context </function> <operation> self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) </operation> <operation_context> self._cursor_executemany(context.cursor, context.statement, context.parameters, context=context) else: self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) if context.compiled: context.post_exec() </operation_context> </frame> <frame> <module> sqlalchemy.engine.base </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py </filename> <line> 950 </line> <function> _cursor_execute </function> <operation> self._handle_dbapi_exception(e, statement, parameters, cursor, context) </operation> <operation_context> self.dialect.do_execute(cursor, statement, parameters, context=context) except Exception, e: self._handle_dbapi_exception(e, statement, parameters, cursor, context) raise </operation_context> </frame> <frame> <module> sqlalchemy.engine.base </module> <filename> /usr/local/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py </filename> <line> 931 </line> <function> _handle_dbapi_exception </function> <operation> raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) </operation> <operation_context> if self.__close_with_result: self.close() raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) finally: del self._reentrant_error </operation_context> </frame> </stack> <exception> <type> OperationalError </type> <value> (OperationalError) (1054, &quot;Unknown column 'published' in 'field list'&quot;) u'INSERT INTO history (create_time, update_time, user_id, name, hid_counter, deleted, purged, genome_build, importable, slug, published) VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s)' [datetime.datetime(2010, 6, 14, 20, 37, 36, 399055), datetime.datetime(2010, 6, 14, 20, 37, 36, 399073), None, 'Unnamed history', 1, 0, 0, '?', 0, None, 0] </value> </exception> </traceback>
 
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> CC: [hidden email]
> From: [hidden email]
> To: [hidden email]
> Subject: Re: [galaxy-dev] Help: History panel of Galaxy interface shows traceback operational error
> Date: Mon, 14 Jun 2010 16:01:54 -0400
>
> Please send the specific error that you see. Thanks.
>
> On Jun 14, 2010, at 3:59 PM, wenqing zhang wrote:
>
> > Hi;
> >
> > I tried new install in linux centos at school and home. I make
> > everything with the same setting.
> > the difference is that galaxy at home is running well, but the
> > galaxy at school shows the problem, which is the histroy panel of
> > galaxy interface showing the traceback operational error.
> >
> > I didn't change anything else except for modifying the
> > database_connection to local mysql in drupal in universe_wsgi.ini
> > file.
> > Grag mentioned the data in the galaxy database could be corruptted.
> > I couldn't understand how the data was corruptted since we didn't
> > change any data and setting in galaxy.
> >
> > if the data is really corruptted, why the galaxy at home is running
> > well?
> >
> > I appreciate anyone could give any idea.
> >
> > Thanks.
> >
> > wenqing zhang
> >
> >
> > Hotmail has tools for the New Busy. Search, chat and e-mail from
> > your inbox. Learn more.
> > _______________________________________________
> > galaxy-dev mailing list
> > [hidden email]
> > http://lists.bx.psu.edu/listinfo/galaxy-dev
>


The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. Get busy.
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