Hi Dan,

hg config for our repository is:

cat .hg/hgrc
[paths]
default = http://www.bx.psu.edu/hg/galaxy
[ui]
username = Galaxy RaetschLab <gal...@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 <d...@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/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/
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>
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