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("Task dump:\n" + self._dump(tasks)) UOWExecutor().execute(self, tasks) if self._should_log_info: self.logger.info("Execute Complete") </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("Unexecutable object type: " + 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, "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] </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("Task dump:\n" + self._dump(tasks)) UOWExecutor().execute(self, tasks) if self._should_log_info: self.logger.info("Execute Complete") </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("Unexecutable object type: " + 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, "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] </value> </exception> </traceback>
Extra Features
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Re-GET Page
> CC: galaxy-dev@lists.bx.psu.edu
> From: james@bx.psu.edu
> To: wqzhang71@hotmail.com
> 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
> > galaxy-dev@lists.bx.psu.edu
> > 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.