[galaxy-dev] Server error one LefSe
Hi All, When using the Huttenhower LEfSe on the main, online, Galaxy I got a Server Error, (Server Error,An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)) when tried to Format data for LEfSe. Was able to successfully use it yesterday, but now it seems to be down. This happened using three different browsers and on multiple retries.. Any help is appreciated.. (is there a way of getting around that step? Other steps seem to be working fine). Gil ___ 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/
[galaxy-dev] Server Error: UnicodeDecodeError: 'utf8' codec can't decode byte 0xdd in position 29: invalid continuation byte
Hi, I have this problem: I uploaded some data and when I click to display data in browser (the eye) I get this error: Server Error: URL: http://localhost:8080/datasets/d413a19dec13d11e/display/?preview=True Module paste.exceptions.errormiddleware:144 in __call__ app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ environ, self.app) Module paste.wsgilib:543 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:194 in handle_request return body( environ, start_response ) Module galaxy.web.framework:876 in render template.render_context( context ) Module mako.template:319 in render_context **kwargs) Module mako.runtime:692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template callable_(context, *args, **kwargs) Module _base_mako:42 in render_body __M_writer(unicode(next.body())) Module _dataset_large_file_mako:45 in render_body __M_writer(filters.html_escape(unicode( unicode( truncated_data, 'utf-8' ) ))) UnicodeDecodeError: 'utf8' codec can't decode byte 0xdd in position 29: invalid continuation byte ___ 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/
[galaxy-dev] Server Error when creating Quota
My goal is that no user can upload or create a total of more than 100 gb.
So I tried following the instructions here to set up a quota:
http://wiki.galaxyproject.org/Admin/Disk%20Quotas
I turned on these two things in universe_wsgi.ini:
enable_quotas = True
allow_user_dataset_purge = True
And then tried to set up a quota like this:
http://snag.gy/cf4CF.jpg
When I clicked save i got a server error. I see this in the galaxy log file:
WSGI Variables
--
application: paste.recursive.RecursiveMiddleware object at 0x858b8d0
paste.cookies: (SimpleCookie:
galaxysession='040ae2dcc0761ad6d57d3a6c430f4cfc5d1d179e714a38e8623d7c662c791cc00a39bc01fe396534',
'galaxysession=040ae2dcc0761ad6d57d3a6c430f4cfc5d1d179e714a38e8623d7c662c791cc00a39bc01fe396534')
paste.expected_exceptions: [class 'paste.httpexceptions.HTTPException']
paste.httpexceptions: paste.httpexceptions.HTTPExceptionHandler
object at 0x858b550
paste.httpserver.thread_pool: paste.httpserver.ThreadPool object at
0x2265950
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
webob._parsed_post_vars: (MultiDict([('name', 'General'),
('description', 'General User Quota'), ('amount', '100 gb'),
('operation', '='), ('default', 'registered'), ('create_quota_button',
'Save')]), FakeCGIBody at 7f3c3ce18950 viewing
MultiDict([('na...e')]))
webob._parsed_query_vars: (MultiDict([]), '')
wsgi process: 'Multithreaded'
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Re: [galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool
Hi Daniel, In fact, my version needs to be updated : changeset: 6799:40f1816d6857 tag: tip user:Greg Von Kuster g...@bx.psu.edu date:Wed Mar 07 13:35:34 2012 -0500 summary: Fix for populating the tool panel and generating the integrated_tool_panel.xml file. I try and let you know. Sarah Daniel Blankenberg d...@bx.psu.edu a écrit : Hi Sarah, This looks to be due to a non-unicode character in the dataset's info field. Are you using a Galaxy revision = 7563:fca4e12478d6? Thanks for using Galaxy, Dan On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote: Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/edit File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in edit refresh_frames=refresh_frames ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template_mako return template.render( **data ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/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 '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in render_body __M_writer(filters.html_escape(unicode(data.info ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 31: ordinal not in range(128) ___ 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/ -- Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 ___ 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/
Re: [galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool
Hi Sarah, This looks to be due to a non-unicode character in the dataset's info field. Are you using a Galaxy revision = 7563:fca4e12478d6? Thanks for using Galaxy, Dan On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote: Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/edit File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in edit refresh_frames=refresh_frames ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template_mako return template.render( **data ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/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 '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in render_body __M_writer(filters.html_escape(unicode(data.info ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 31: ordinal not in range(128) ___ 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/ ___ 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/
[galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool
Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/edit File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in edit refresh_frames=refresh_frames ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template_mako return template.render( **data ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/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 '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in render_body __M_writer(filters.html_escape(unicode(data.info ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 31: ordinal not in range(128) ___ 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/
Re: [galaxy-dev] Server Error in history framer when debug = False
On Aug 3, 2012, at 10:42 AM, David Roquis wrote: Dear Galaxy community, I have noticed on forums that some users are experiencing this problem too, but no clues on how to fix it. When I set debug = false in universe.wsgi.ini, I get a server error in the history frame (history works perfectly when debug = true). Trying to create a new history, or to upload a saved one, doesn't work either. I use postgresql and nginx, but I this problem also appears on a freshly cloned instance of galaxy-dist. I tried on two machines with Fedora 13 + python 2.6.4 and Fedora 17 + python 2.7.3. As my goal is to use Galaxy in a production environment (with 2 webservers, 1 manager and 2 handlers), I would really like to be able to turn off debug. Here is what I can find in my paster.log when I turn off debug. Thanks a lot if anyone has a solution! David Starting server in PID 4664. serving on 0.0.0.0:8081 view at http://127.0.0.1:8081 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] GET / HTTP/1.0 200 - - Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] GET /root/tool_menu HTTP/1.0 200 - http://127.0.0.1:8080/; Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] GET /history HTTP/1.0 200 - http://127.0.0.1:8080/; Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] GET /history HTTP/1.0 500 - http://127.0.0.1:8080/; Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1 Error - type 'exceptions.TypeError': 'NoneType' object is not callable URL: http://127.0.0.1/history File '/usr/lib/python2.7/site-packages/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/lib/python2.7/site-packages/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/lib/python2.7/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/base.py', line 169 in __call__ return body( environ, start_response ) File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 772 in render template.render_context( context ) File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 319 in render_context **kwargs) File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy2ei/galaxy-dist/database/compiled_templates/root/history.mako.py', line 62 in render_body __M_writer(u'\n\n') File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 769 in write response_write( d.encode( 'utf-8' ) ) TypeError: 'NoneType' object is not callable Hi David, Sorry it took so long to get back to you. The problem appears to be that Galaxy is using a version of Paste from your site-packages rather than the egg bundled with Galaxy. A quick solution to this would be to set up a virtualenv as described in the production server documentation and run Galaxy under that interpreter. --nate CGI Variables - CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-us,en;q=0.5' HTTP_CONNECTION: 'close' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a1a924b5a883eb84f93f9e2c6424cabed485f00c49dc51dd6632e1e679e865175' HTTP_HOST: '127.0.0.1' HTTP_REFERER: 'http://127.0.0.1:8080/' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1' HTTP_X_FORWARDED_FOR: '127.0.0.1' HTTP_X_FORWARDED_HOST: '127.0.0.1' ORGINAL_HTTP_HOST: 'galaxy_app' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/history' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.0' Configuration - __file__: '/home/galaxy2ei/galaxy-dist/universe_wsgi.ini' admin_users: 'david.roq...@yahoo.com, galaxyt...@2ei.com' allow_library_path_paste: 'True' allow_user_dataset_purge: 'True' allow_user_deletion: 'True' allow_user_impersonation: 'True' database_connection: 'postgres://galaxy2ei:galaxy2ei@localhost:5432/galaxyprod' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' datatypes_config_file: 'datatypes_conf.xml' debug: 'False' default_job_handlers: 'handler0' enable_quotas: 'True' file_path:
[galaxy-dev] Server Error in history framer when debug = False
Dear Galaxy community, I have noticed on forums that some users are experiencing this problem too, but no clues on how to fix it. When I set debug = false in universe.wsgi.ini, I get a server error in the history frame (history works perfectly when debug = true). Trying to create a new history, or to upload a saved one, doesn't work either. I use postgresql and nginx, but I this problem also appears on a freshly cloned instance of galaxy-dist. I tried on two machines with Fedora 13 + python 2.6.4 and Fedora 17 + python 2.7.3. As my goal is to use Galaxy in a production environment (with 2 webservers, 1 manager and 2 handlers), I would really like to be able to turn off debug. Here is what I can find in my paster.log when I turn off debug. Thanks a lot if anyone has a solution! David Starting server in PID 4664. serving on 0.0.0.0:8081 view at http://127.0.0.1:8081 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] GET / HTTP/1.0 200 - - Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] GET /root/tool_menu HTTP/1.0 200 - http://127.0.0.1:8080/; Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] GET /history HTTP/1.0 200 - http://127.0.0.1:8080/; Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] GET /history HTTP/1.0 500 - http://127.0.0.1:8080/; Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1 Error - type 'exceptions.TypeError': 'NoneType' object is not callable URL: http://127.0.0.1/history File '/usr/lib/python2.7/site-packages/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/lib/python2.7/site-packages/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/lib/python2.7/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/base.py', line 169 in __call__ return body( environ, start_response ) File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 772 in render template.render_context( context ) File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 319 in render_context **kwargs) File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy2ei/galaxy-dist/database/compiled_templates/root/history.mako.py', line 62 in render_body __M_writer(u'\n\n') File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 769 in write response_write( d.encode( 'utf-8' ) ) TypeError: 'NoneType' object is not callable CGI Variables - CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-us,en;q=0.5' HTTP_CONNECTION: 'close' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a1a924b5a883eb84f93f9e2c6424cabed485f00c49dc51dd6632e1e679e865175' HTTP_HOST: '127.0.0.1' HTTP_REFERER: 'http://127.0.0.1:8080/' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1' HTTP_X_FORWARDED_FOR: '127.0.0.1' HTTP_X_FORWARDED_HOST: '127.0.0.1' ORGINAL_HTTP_HOST: 'galaxy_app' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/history' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.0' Configuration - __file__: '/home/galaxy2ei/galaxy-dist/universe_wsgi.ini' admin_users: 'david.roq...@yahoo.com, galaxyt...@2ei.com' allow_library_path_paste: 'True' allow_user_dataset_purge: 'True' allow_user_deletion: 'True' allow_user_impersonation: 'True' database_connection: 'postgres://galaxy2ei:galaxy2ei@localhost:5432/galaxyprod' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' datatypes_config_file: 'datatypes_conf.xml' debug: 'False' default_job_handlers: 'handler0' enable_quotas: 'True' file_path: 'database/files' here: '/home/galaxy2ei/galaxy-dist' job_handlers: 'handler0' job_manager: 'manager' job_working_directory: 'database/job_working_directory' library_import_dir: '/home/galaxy2ei/Downloads' new_file_path: 'database/tmp' nginx_upload_path: '/_upload' nginx_upload_store: 'database/tmp/upload_store' nginx_x_accel_redirect_base: '/_x_accel_redirect' nglims_config_file: 'tool-data/nglims.yaml' set_metadata_externally: 'True' static_cache_time: '360' static_dir:
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
I am still experiencing issues getting my galaxy server to start since the
upgrade. The logs are all getting this type of error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist cat runner0.log
python path is:
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip,
/usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2,
/usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old,
/usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/Numeric,
/usr/lib64/python2.6/site-packages/gtk-2.0,
/usr/local/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages
galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py,
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py, line
35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options, app=self )
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/check.py,
line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '101' but this code expects version '97'.
Please backup your database and then migrate the schema by running 'sh
manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid
I have not dropped my database and built it fresh. However, I have attempted
the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade' for
both the runner and web app ini files with the following error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist sh manage_db.sh
-c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
File ./scripts/manage_db.py, line 63, in module
main( repository=repo, url=db_url )
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py,
line 150, in main
ret = command_func(**kwargs)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 327, in _migrate
changeset = schema.changeset(version)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 173, in changeset
changeset =
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
It looks like what happened is that you've updated the instance that was
originally connected to this database from galaxy-central at some point
recently. The current tip of galaxy-central is at database version 103.
The first two options that come to mind are:
1) Hook a fresh galaxy-central clone up to this database and `manage_db.sh
downgrade 97` which should set your database back to the version appropriate
for galaxy-dist.
2) Swap to galaxy-central instead of -dist
Taking a brief look at the migrations, #1 looks fairly safe, but as always --
back up the database first.
-Dannon
On Jul 3, 2012, at 1:03 PM, Iry Witham wrote:
I am still experiencing issues getting my galaxy server to start since the
upgrade. The logs are all getting this type of error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist cat runner0.log
python path is:
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchem!
y-0.5.6_dev_r6498-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDe!
ploy-1.3.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy!
-dist/eg
gs/PasteScript-1.7.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip,
/usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2,
/usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old,
/usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/Numeric,
/usr/lib64/python2.6/site-packages/gtk-2.0,
/usr/local/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages
galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py,
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py,
line 35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options, app=self )
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/check.py,
line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '101' but this code expects version
'97'. Please backup your database and then migrate the schema by running 'sh
manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid
I have not dropped my database and built it fresh. However, I have attempted
the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade' for
both the runner and web app ini files with the following error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist sh manage_db.sh
-c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
File ./scripts/manage_db.py, line 63, in module
main( repository=repo, url=db_url )
File
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
Hi Iry, Exception: Your database has version '101' but this code expects version '97'. Please backup your database and then migrate the schema by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'. Removing PID file runner0.pid Your galaxy version seems to be older than your database. It seems you run galaxy-central and afterwards starting galaxy-dist with the same database. That does not work. With your database you should run a newer version of galaxy, e.g. the newest galaxy-central. Hope that helps, Bjoern -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ 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/
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
Thanks Dannon and Bjorn for the assistance. I followed Dannon's
suggestion and that fixed my issue.
Thanks,
Iry
On 7/3/12 1:15 PM, Dannon Baker dannonba...@me.com wrote:
It looks like what happened is that you've updated the instance that was
originally connected to this database from galaxy-central at some point
recently. The current tip of galaxy-central is at database version 103.
The first two options that come to mind are:
1) Hook a fresh galaxy-central clone up to this database and
`manage_db.sh downgrade 97` which should set your database back to the
version appropriate for galaxy-dist.
2) Swap to galaxy-central instead of -dist
Taking a brief look at the migrations, #1 looks fairly safe, but as
always -- back up the database first.
-Dannon
On Jul 3, 2012, at 1:03 PM, Iry Witham wrote:
I am still experiencing issues getting my galaxy server to start since
the upgrade. The logs are all getting this type of error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist cat
runner0.log
python path is:
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linu
x-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10
f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-
linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.eg
g,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-l
inux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_s
tatic-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff
194725-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.eg
g,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r
6498-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-
linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.e
gg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6
-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.eg
g,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_2005
0316-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg
,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.eg
g,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-li
nux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.
6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.
6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib,
/usr/lib/python26.zip, /usr/lib64/python2.6,
/usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk,
/usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload,
/usr/lib64/python2.6/site-packages/Numeric,
/usr/lib64/python2.6/site-packages/gtk-2.0,
/usr/local/lib64/python2.6/site-packages,
/usr/lib64/python2.6/site-packages
galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py
, line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py, line
35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self
)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/c
heck.py, line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest,
config_arg ) )
Exception: Your database has version '101' but this code expects
version '97'. Please backup your database and then migrate the schema
by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid
I have not dropped my database and built it fresh. However, I have
attempted the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini
upgrade' for both the runner and web app ini files with the following
error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist sh
manage_db.sh -c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
File
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
Hi Nate,
I removed to previous instillation just to be safe and performed a new
clone. This time it appears to be less problematic. I am no longer
getting all of the errors. However, I am getting an error due to my
database version. The error is:
galaxy.model.migrate.check DEBUG 2012-06-27 12:39:11,843 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py,
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py,
line 35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self )
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/che
ck.py, line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg
) )
Exception: Your database has version '101' but this code expects version
'97'. Please backup your database and then migrate the schema by running
'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
I have attempted to run sh manage_db.sh -c ./universe_wsgi.runner.ini
upgrade and that fails with the following error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist sh
manage_db.sh -c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
File ./scripts/manage_db.py, line 63, in module
main( repository=repo, url=db_url )
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/shell.py, line 150, in main
ret = command_func(**kwargs)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/api.py, line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err,
**opts)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/api.py, line 327, in _migrate
changeset = schema.changeset(version)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/schema.py, line 173, in changeset
changeset = self.repository.changeset(database, start_ver, version)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/repository.py, line 170, in changeset
changes = [self.version(v).script(database, op) for v in versions]
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/repository.py, line 145, in version
return self.versions.version(*p, **k)
File
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/version.py, line 125, in version
return self.versions[VerNum(vernum)]
KeyError: VerNum(101)
It is getting closer, but I am not quite there yet.
Thanks,
Iry
On 6/22/12 11:50 AM, Nate Coraor n...@bx.psu.edu wrote:
On Jun 20, 2012, at 6:46 PM, Iry Witham wrote:
I have recently performed a fresh installation of Galaxy utilizing the
latest distribution and am getting a sizable number of errors when
attempting to start the server. The issue started when I performed a
merge so I decided to do the clean install as a test. The server
appears to start just fine, but with errors reported in the logs. The
web0.log gives the following errors and warnings (I am truncating the
file for space):
galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database
version 97
galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2
egg successfully loaded for postgres dialect
galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At
migrate_tools version 2
galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg
successfully loaded for postgres dialect
galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
Loading references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
Loaded reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
Loaded reference to tool shed: Galaxy test tool shed
galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading
datatypes from datatypes_conf.xml
galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding
conflicting datatype with extension 'coverage', using datatype from
datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer
for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer
for datatype
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
On Jun 20, 2012, at 6:46 PM, Iry Witham wrote: I have recently performed a fresh installation of Galaxy utilizing the latest distribution and am getting a sizable number of errors when attempting to start the server. The issue started when I performed a merge so I decided to do the clean install as a test. The server appears to start just fine, but with errors reported in the logs. The web0.log gives the following errors and warnings (I am truncating the file for space): galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database version 97 galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2 egg successfully loaded for postgres dialect galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At migrate_tools version 2 galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg successfully loaded for postgres dialect galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded reference to tool shed: Galaxy test tool shed galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding conflicting datatype with extension 'coverage', using datatype from datatypes_conf.xml. galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for datatype 'galaxy.datatypes.xml:BlastXml' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.tools.data DEBUG 2012-06-20 18:29:21,059 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2012-06-20 18:29:21,060 Loaded tool data table 'bfast_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,061 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2012-06-20 18:29:21,062 Loaded tool data table 'blastdb_p' galaxy.tools.data DEBUG 2012-06-20 18:29:21,065 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,066 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG
[galaxy-dev] Server Error when downloading files from history
Hi there, I received the following error when trying to download/save my tabular files with 5k lines: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Please help! Thanks in advance. Cheers, Rathi -- Rathi D. Thiagarajan, PhD Professional Scientific Collaborator UCSD Research Scholar Dept. of Chemical Physiology Center for Regenerative Medicine The Scripps Research Institute 3030 Science Park Rd, La Jolla, CA 92035, USA Mail:SP30-3021 W: 858.784.7753 E: ra...@scripps.edu E: rthiagara...@ucsd.edu ___ 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/
[galaxy-dev] server error
Hi, I have run into a server error, how can I fix it? Thanks, Ashley ___ 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/
Re: [galaxy-dev] server error
Given the information supplied, I suggest a spatula. Many servers are quite adept with a spatula. Your results may vary. Bob H On May 9, 2012, at 4:43 PM, Ashley Tehranchi wrote: Hi, I have run into a server error, how can I fix it? Thanks, Ashley ___ 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/ ___ 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/
Re: [galaxy-dev] server error
I'm not sure what that means. From: Bob Harris rshar...@bx.psu.edu Date: Wednesday, May 9, 2012 1:49 PM To: Ashley Tehranchi a...@stanford.edu Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] server error Given the information supplied, I suggest a spatula. Many servers are quite adept with a spatula. Your results may vary. Bob H On May 9, 2012, at 4:43 PM, Ashley Tehranchi wrote: Hi, I have run into a server error, how can I fix it? Thanks, Ashley ___ 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/ ___ 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/
Re: [galaxy-dev] server error
Ashley: I think he was joking around. Essentially - to provide any help, people here need to know much more detail about what kind of server error occurred, and what input was provided so that the problem can be reproduced or a helpful suggestion can be made. This guide to asking good questions might be of some help to you: http://catb.org/~esr/faqs/smart-questions.html I probably can't help you with your actual problem, but if you can provide more information maybe somebody else can. some examples that might help. if you were running on the public galaxy server or not what you were trying to do what kind of data you where trying to analyze the contents of /var/log/galaxy/galaxy.log (or wherever the log is on your local installation) the results you see when you click on the bug icon in your failing history step Brad On May 9, 2012, at 6:51 PM, Ashley Tehranchi wrote: I'm not sure what that means. From: Bob Harris rshar...@bx.psu.edumailto:rshar...@bx.psu.edu Date: Wednesday, May 9, 2012 1:49 PM To: Ashley Tehranchi a...@stanford.edumailto:a...@stanford.edu Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] server error Given the information supplied, I suggest a spatula. Many servers are quite adept with a spatula. Your results may vary. Bob H On May 9, 2012, at 4:43 PM, Ashley Tehranchi wrote: Hi, I have run into a server error, how can I fix it? Thanks, Ashley ___ 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/ ___ 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/ -- Brad Langhorst langho...@neb.commailto:langho...@neb.com 978-380-7564 ___ 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/
[galaxy-dev] Server Error when downloading files from history
Hi there, I received the following error when trying to download/save my tabular files with 5k lines: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Please help! Thanks in advance. Cheers, Rathi -- Rathi D. Thiagarajan, PhD Professional Scientific Collaborator UCSD Research Scholar Dept. of Chemical Physiology Center for Regenerative Medicine The Scripps Research Institute 3030 Science Park Rd, La Jolla, CA 92035, USA Mail:SP30-3021 W: 858.784.7753 E: ra...@scripps.edu E: rthiagara...@ucsd.edu ___ 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/
[galaxy-dev] server error when installing tool from tool shed repository into local instance
Hello, I have the version 6528:63bc46cc73b7 of galaxy running locally on our server installed from https://bitbucket.org/galaxy/galaxy-dist/. I've tried to bring tabular2html tool from Galaxy main tool shed repository following the wiki information (http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance) without success. Here is what I've done. (1) I've edited my universe_wsgi.ini # -- Files and directories # Tool config files, defines what tools are available in Galaxy. # Tools can be locally developed or installed from Galaxy tool sheds. tool_config_file = tool_conf.xml,shed_tool_conf.xml # Default path to the directory containing the tools defined in tool_conf.xml. # Other tool config files must include the tool_path as an attribute in the toolbox tag. tool_path = tools (2) I've created the directory shed_tools/ above the galaxy-dist/ as recommended (3) I've restarted the server (4) I've logged in as admin user. I've clicked the Admin link in the top Galaxy tool panel to display the Galaxy Administration interface and then Search and browse tool sheds under Tool sheds from the left blue section to display the Accessible Galaxy tool sheds page, click Galaxy main tool shed to display the valid repositories and choose tabular2html and click on Install to local Galaxy, select the panel section and click Install. I get a page with Server Error. Strangely, the tool appears in the list of tools and works in my Galaxy instance. The tool files have been installed on disk at the directory created in (2) but the shed_tool_conf.xml has not been updated. After restarting my Galaxy server, the tool is not visible anymore. Here is what appears in the log related to the installation of the tool: galaxy.util.shed_util DEBUG 2012-01-25 14:20:54,451 Installing repository 'tabular2html' galaxy.util.shed_util DEBUG 2012-01-25 14:20:54,451 Cloning http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html galaxy.util.shed_util DEBUG 2012-01-25 14:20:55,486 Updating cloned repository to revision a5814dd5a11a galaxy.tools DEBUG 2012-01-25 14:20:55,652 Reloading section: My Tools galaxy.tools DEBUG 2012-01-25 14:20:55,673 Loaded tool id: toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, version: 1.0 .0. 143.65.172.178 - - [25/Jan/2012:14:20:54 +0100] POST /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.ps u.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c6573 2066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f74616275 6c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True HTTP/1.1 500 - http://uk-cri-lbio08/galaxy/admin_toolshed/insta ll_repository?tool_shed_url=http://toolshed.g2.bx.psu.edurepo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d 6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e 7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7dincludes_tools=True Mozilla/5.0 ( Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13 Error - type 'exceptions.TypeError': cannot serialize None (type NoneType) URL: http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edurepo_info_dict=3abd2912 9982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c6172206 46174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c202261353 8313464643561313161225d7dincludes_tools=True File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 275 in install_repository new_install=True ) File
Re: [galaxy-dev] Server Error after Update
On Oct 27, 2011, at 8:23 AM, SHAUN WEBB wrote:
Hi, I updated my test server today and everything seemed fine. I added a new
library item via a URL. After that my history panel displays Internal Server
Error and I am getting the error below in paster.log:
Any ideas how this has occurred and if there is a fix?
Hi Shaun,
If you set 'debug = True', you should get a more helpful error message in the
log.
--nate
Shaun
Exception happened during processing of request from ('2.218.9.31', 63227)
Traceback (most recent call last):
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py,
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib/python2.6/SocketServer.py, line 320, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib/python2.6/SocketServer.py, line 615, in __init__
self.handle()
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py,
line 432, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py,
line 427, in handle_one_request
self.wsgi_execute()
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py,
line 290, in wsgi_execute
self.wsgi_write_chunk(chunk)
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py,
line 125, in wsgi_write_chunk
Content returned before start_response called)
RuntimeError: Content returned before start_response called
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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___
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[galaxy-dev] Server Error after Update
Hi, I updated my test server today and everything seemed fine. I added
a new library item via a URL. After that my history panel displays
Internal Server Error and I am getting the error below in paster.log:
Any ideas how this has occurred and if there is a fix?
Shaun
Exception happened during processing of request from ('2.218.9.31', 63227)
Traceback (most recent call last):
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 1053, in
process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib/python2.6/SocketServer.py, line 320, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib/python2.6/SocketServer.py, line 615, in __init__
self.handle()
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 432, in
handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 427, in
handle_one_request
self.wsgi_execute()
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 290, in
wsgi_execute
self.wsgi_write_chunk(chunk)
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 125, in
wsgi_write_chunk
Content returned before start_response called)
RuntimeError: Content returned before start_response called
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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Re: [galaxy-dev] Server Error when trying to upload repository.
David, I looked into this for some time, and although I found strange behavior in the mercurial environment, it is impossible to determine what caused it. Your repository was definitely corrupted in some way, perhaps by a network problem that occurred when you were transferring files, or some other indeterminate issue. In any case, I have recreated your repository from scratch so it is ready for you to upload your files once again. From your change log, it was clear that you had deleted all files in the repository anyway. I'll keep a watch on this. Please let us know if you encounter further problems. Sorry for the inconvenience with this. Greg Von Kuster On Oct 27, 2011, at 9:52 AM, David Murphy wrote: Just realized I didn't reply to all, so the list didn't see this. No problem at all, it would be much appreciated in fact. Is there anything I need to do to do so you can do that? Cheers David On Wed, Oct 26, 2011 at 9:28 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello David, I'm not sure why you're seeing this - do you mind if I try to delete all of the files in your repository whose name ends in '~'? That may help me track down the problem. Greg Von Kuster On Oct 26, 2011, at 3:09 PM, David Murphy wrote: Hi I've been trying to create a repository for a small tool called CodonLogo at http://toolshed.g2.bx.psu.edu/. The problem is that the first zip I uploaded contained a few backup copies of some text files ending with a ~. It now won't allow me to delete them by checking them and clicking delete selected files it then simply gives the error The selected files were deleted from the repository. Change set revision '7ff079013d98' includes no tools or exported workflows for which metadata can be set. but the selected files are not deleted. When I try to upload a new zip without the older files it gives an error Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Am I doing something foolish or is this a bug? Cheers David ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
Re: [galaxy-dev] Server Error when trying to upload repository.
Just realized I didn't reply to all, so the list didn't see this. No problem at all, it would be much appreciated in fact. Is there anything I need to do to do so you can do that? Cheers David On Wed, Oct 26, 2011 at 9:28 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello David, I'm not sure why you're seeing this - do you mind if I try to delete all of the files in your repository whose name ends in '~'? That may help me track down the problem. Greg Von Kuster On Oct 26, 2011, at 3:09 PM, David Murphy wrote: Hi I've been trying to create a repository for a small tool called CodonLogo at http://toolshed.g2.bx.psu.edu/. The problem is that the first zip I uploaded contained a few backup copies of some text files ending with a ~. It now won't allow me to delete them by checking them and clicking delete selected files it then simply gives the error The selected files were deleted from the repository. Change set revision '7ff079013d98' includes no tools or exported workflows for which metadata can be set. but the selected files are not deleted. When I try to upload a new zip without the older files it gives an error Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Am I doing something foolish or is this a bug? Cheers David ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
Re: [galaxy-dev] Server Error when trying to upload repository.
Hello David, I'm not sure why you're seeing this - do you mind if I try to delete all of the files in your repository whose name ends in '~'? That may help me track down the problem. Greg Von Kuster On Oct 26, 2011, at 3:09 PM, David Murphy wrote: Hi I've been trying to create a repository for a small tool called CodonLogo at http://toolshed.g2.bx.psu.edu/. The problem is that the first zip I uploaded contained a few backup copies of some text files ending with a ~. It now won't allow me to delete them by checking them and clicking delete selected files it then simply gives the error The selected files were deleted from the repository. Change set revision '7ff079013d98' includes no tools or exported workflows for which metadata can be set. but the selected files are not deleted. When I try to upload a new zip without the older files it gives an error Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Am I doing something foolish or is this a bug? Cheers David ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
Re: [galaxy-dev] Server Error
Hello Alex, This issue was the result of a configuration error that should now be corrected. Please let us know if you encounter further issues. thanks for reporting this, Greg Von Kuster On Sep 9, 2011, at 12:41 PM, Alex R Bigelow wrote: Hi, I am a new developer interested in writing tools for Galaxy, but when I try to use the tool shed (http://toolshed.g2.bx.psu.edu), every link I click on gives me a Server Error. I have tried in both Google Chrome and Safari; does anyone know what is going on? Thanks, Alex Bigelow ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
Re: [galaxy-dev] Server error from history view
Hi Isabelle, thank you for your help. However filter-with=gzip is disabled in our configuration. I set everything according to the guide on https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer. The gzip option you see in my log is from the Apache server. Sarah On 03/10/2011 07:08 PM, Isabelle Phan wrote: Hello Sarah, (my galaxy-dev account is broken, read your post on nabble) You need to disable filter-with=gzip in order to set debug=False But in any case, I have not seen a difference in the log, so my take is that galaxy only ever runs in debug mode. Isabelle ___ 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/ ___ 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/
