Hi Vipin, Strange, are you running the latest galaxy-dist? That line doesn't exist in e.g. https://bitbucket.org/galaxy/galaxy-dist/src/ebe87051fadff5750ec226490b31e49bdd68b070/templates/webapps/galaxy/root/history.mako?at=default. Can you compare your file to the file in the repository? What is the output of:
hg diff templates/webapps/galaxy/root/history.mako and hg summary and hg config Thanks for using Galaxy, Dan On Aug 9, 2013, at 3:56 PM, Vipin TS wrote: > Hi Dan, > > I deleted the contents from /codebase/database/complied_templates/* and > restarted the instance, still no luck. Sorry. > > Thanks, Vipin > > > On Fri, Aug 9, 2013 at 3:43 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote: > Hi Vipin, > > Can you try deleting the contents of your compiled templates directory (i.e. > /codebase/database/compiled_templates/*)? > > Thanks for using Galaxy, > > Dan > > > On Aug 9, 2013, at 3:22 PM, Vipin TS wrote: > >> Hi Dan, >> >> Thanks for the information, I have updated this to my repository manually. >> Now I can invoke the page but the frames were not loaded correctly. >> >> The log message as follows: >> /codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927: >> SAWarning: The IN-predicate on "request_type.id" was invoked with an empty >> sequence. This results in a contradiction, which nonetheless can be >> expensive to evaluate. Consider alternative strategies for improved >> performance. >> X.X.X.X - - [09/Aug/2013:15:09:55 -0400] "GET / HTTP/1.1" 200 - "-" >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17 >> (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" >> X.X.X.X - - [09/Aug/2013:15:09:56 -0400] "GET /root/tool_menu HTTP/1.1" 404 >> - "https://galaxy.cbio.mskcc.org/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X >> 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 >> Safari/536.26.17" >> X.X.X.X - - [09/Aug/2013:15:09:56 -0400] "GET /history HTTP/1.1" 200 - >> "https://galaxy.cbio.mskcc.org/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X >> 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 >> Safari/536.26.17" >> X.X.X.X - - [09/Aug/2013:15:09:56 -0400] "GET /history HTTP/1.1" 500 - >> "https://galaxy.cbio.mskcc.org/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X >> 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 >> Safari/536.26.17" >> ---------------------------------------- >> Exception happened during processing of request from ('127.0.0.1', 43370) >> Traceback (most recent call last): >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line >> 1068, in process_request_in_thread >> self.finish_request(request, client_address) >> File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request >> self.RequestHandlerClass(request, client_address, self) >> File "/usr/lib64/python2.6/SocketServer.py", line 617, in __init__ >> self.handle() >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line >> 442, in handle >> BaseHTTPRequestHandler.handle(self) >> File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle >> self.handle_one_request() >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line >> 437, in handle_one_request >> self.wsgi_execute() >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line >> 287, in wsgi_execute >> self.wsgi_start_response) >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py", line 203, >> in __call__ >> return app(environ, start_response) >> File "/codebase/lib/galaxy/web/framework/middleware/request_id.py", line >> 12, in __call__ >> return self.app( environ, start_response ) >> File "/codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py", >> line 21, in __call__ >> return self.app( environ, start_response ) >> File "/codebase/lib/galaxy/web/framework/middleware/translogger.py", line >> 68, in __call__ >> return self.application(environ, replacement_start_response) >> File "/codebase/lib/galaxy/web/framework/middleware/error.py", line 159, >> in __call__ >> exc_info) >> File "/codebase/lib/galaxy/web/framework/middleware/translogger.py", line >> 67, in replacement_start_response >> return start_response( status, headers, exc_info ) >> File "/codebase/lib/galaxy/web/framework/middleware/error.py", line 149, >> in __call__ >> app_iter = self.application(environ, sr_checker) >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py", line 84, >> in __call__ >> return self.application(environ, start_response) >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py", >> line 633, in __call__ >> return self.application(environ, start_response) >> File "/codebase/lib/galaxy/web/framework/base.py", line 132, in __call__ >> return self.handle_request( environ, start_response ) >> File "/codebase/lib/galaxy/web/framework/base.py", line 199, in >> handle_request >> return body( environ, start_response ) >> File "/codebase/lib/galaxy/web/framework/__init__.py", line 985, in render >> template.render_context( context ) >> File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/template.py", line 319, in >> render_context >> **kwargs) >> File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", line 692, in >> _render_context >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) >> File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", line 718, in >> _exec_template >> callable_(context, *args, **kwargs) >> File "/codebase/database/compiled_templates/root/history.mako.py", line >> 73, in render_body >> if bool( [ data for data in history.active_datasets if data.state in >> ['running', 'queued', '', None ] ] ): >> AttributeError: 'Undefined' object has no attribute 'active_datasets' >> >> Do you have any quick way to fix the same? Or update to galaxy-central >> stable branch? >> >> Thank you, Vipin >> >> On Fri, Aug 9, 2013 at 2:57 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote: >> Hi Vipin, >> >> This has been fixed in the stable branch of galaxy-central >> https://bitbucket.org/galaxy/galaxy-central/commits/cd6fec2f5cba but has not >> made it on to galaxy-dist yet. >> >> >> Thanks for using Galaxy, >> >> Dan >> >> >> >> On Aug 9, 2013, at 2:33 PM, Vipin TS wrote: >> >>> Hello dev-team, >>> >>> I am experiencing a strange problem with my production instance, after I >>> carefully merged remote changes from galaxy-dist release to my code >>> repository. While restarting, It fails to load the the page properly, the >>> message from log file stating that "serving on 0.0.0.0:8080" >>> >>> Here are some message found in the log file: >>> >>> X.X.X.X - - [09/Aug/2013:14:30:56 -0400] "GET / HTTP/1.1" 500 - "-" >>> "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 (KHTML, like Gecko) >>> rekonq Safari/534.34" >>> Error - <type 'exceptions.ValueError'>: expected only letters, got ' en' >>> URL: https://galaxy.cbio.mskcc.org/ >>> File '/codebase/lib/galaxy/web/framework/middleware/error.py', line 149 in >>> __call__ >>> app_iter = self.application(environ, sr_checker) >>> File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 >>> in __call__ >>> return self.application(environ, start_response) >>> File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line >>> 633 in __call__ >>> return self.application(environ, start_response) >>> File '/codebase/lib/galaxy/web/framework/base.py', line 132 in __call__ >>> return self.handle_request( environ, start_response ) >>> File '/codebase/lib/galaxy/web/framework/base.py', line 159 in >>> handle_request >>> trans = self.transaction_factory( environ ) >>> File '/codebase/lib/galaxy/web/framework/__init__.py', line 238 in <lambda> >>> self.set_transaction_factory( lambda e: self.transaction_chooser( e, >>> galaxy_app, session_cookie ) ) >>> File '/codebase/lib/galaxy/web/framework/__init__.py', line 269 in >>> transaction_chooser >>> return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) >>> File '/codebase/lib/galaxy/web/framework/__init__.py', line 332 in __init__ >>> self.setup_i18n() >>> File '/codebase/lib/galaxy/web/framework/__init__.py', line 370 in >>> setup_i18n >>> locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language ) >>> File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 212 in parse >>> return cls(*parse_locale(identifier, sep=sep)) >>> File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 763 in >>> parse_locale >>> raise ValueError('expected only letters, got %r' % lang) >>> ValueError: expected only letters, got ' en' >>> >>> >>> CGI Variables >>> ------------- >>> CONTENT_LENGTH: '0' >>> HTTP_ACCEPT: >>> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' >>> HTTP_ACCEPT_CHARSET: 'utf-8,*;q=0.5' >>> HTTP_ACCEPT_ENCODING: 'gzip, deflate, x-gzip, x-deflate' >>> HTTP_ACCEPT_LANGUAGE: 'en-US, en-US; q=0.8, en; q=0.6' >>> HTTP_CACHE_CONTROL: 'max-age=0' >>> HTTP_CONNECTION: 'Keep-Alive' >>> HTTP_HOST: 'galaxy.cbio.mskcc.org' >>> HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 >>> (KHTML, like Gecko) rekonq Safari/534.34' >>> HTTP_X_FORWARDED_FOR: '172.21.50.129' >>> HTTP_X_FORWARDED_HOST: 'galaxy.cbio.mskcc.org' >>> HTTP_X_FORWARDED_SERVER: 'galaxy.cbio.mskcc.org' >>> HTTP_X_URL_SCHEME: 'https' >>> ORGINAL_HTTP_HOST: 'localhost:8081' >>> ORGINAL_REMOTE_ADDR: '127.0.0.1' >>> PATH_INFO: '/' >>> REMOTE_ADDR: '172.21.50.129' >>> REQUEST_METHOD: 'GET' >>> SERVER_NAME: '0.0.0.0' >>> SERVER_PORT: '8081' >>> SERVER_PROTOCOL: 'HTTP/1.1' >>> >>> >>> WSGI Variables >>> -------------- >>> application: <paste.recursive.RecursiveMiddleware object at 0x7f78910> >>> is_api_request: False >>> original_wsgi.url_scheme: 'http' >>> paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] >>> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object >>> at 0x7f78210> >>> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at >>> 0x8066d90> >>> 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: 'd4f643a8012111e3819090b11c087d99' >>> wsgi process: 'Multithreaded' >>> ------------------------------------------------------------ >>> >>> Any idea what is going wrong here? Please let me know if you need more get >>> more details. >>> >>> Many thanks, >>> --/Vipin >>> >>> ___________________________________________________________ >>> 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/
