Hi Dan, hg config for our repository is: cat .hg/hgrc [paths] default = http://www.bx.psu.edu/hg/galaxy [ui] username = Galaxy RaetschLab <galaxy@raetschlab.org> verbose = True merge = vimdiff [merge-tools] vimdiff.executable = vim vimdiff.args = -d $base $local $output $other +close +close Thanks, Vipin

Hi Dan,

Thanks for your support, Hmm, I can see that there are changes: but here is the out come from the below commands:

$$ hg diff templates/webapps/galaxy/root/history.mako

empty

$$ hg summary

parent: 10218:ff0bd4a811d9 tip merged the changes from stable release version July 2013 from bx.psu.edu branch: default commit: 5 modified, 5 removed, 452 deleted update: 1663 new changesets, 2 branch heads (merge)

$$hg config

Sorry, it says unknown option.

Do you think I have mixed up something ? Thank you, Vipin

On Fri, Aug 9, 2013 at 4:41 PM, Daniel Blankenberg <dan@bx.psu.edu> wrote:

...

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/ebe87051fadff5750ec226490b31e49.... 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 <dan@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 <dan@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

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