November 2012 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Bug report : JSONDecodeError
by Greg Von Kuster 14 Nov '12

14 Nov '12

Hi Mathieu, It's pretty difficult to tell you where to start looking within your environment for the cause of the problem. You mentioned that you attempted to uninstall the repository name mothur from you local Galaxy instance, and that action produced this problem. What is the result of running the following sql command in your db? select * from tool_shed_repository where name = 'mothur'; Also, have the entries for the mothur tools been eliminated from your shed_tool_conf.xml file? How about the install directory for the mothur repository? Has is been removed from disk? Greg Von Kuster On Nov 12, 2012, at 10:57 AM, Mathieu Bahin wrote: > Hi Greg, > > I kind of forgot a maybe interesting information. We found this message at the end of the paster.log : > > Exception happened during processing of request from ('127.0.0.1', 55428) > Traceback (most recent call last): > File "/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread > self.finish_request(request, client_address) > File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 323, in finish_request > self.RequestHandlerClass(request, client_address, self) > File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 641, in __init__ > self.finish() > File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 694, in finish > self.wfile.flush() > File "/local/python/2.7-bis/lib/python2.7/socket.py", line 301, in flush > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > error: [Errno 32] Broken pipe > > Cheers, > Mathieu > > De: "Mathieu Bahin" <mathieu.bahin(a)irisa.fr> > À: "Greg Von Kuster" <greg(a)bx.psu.edu> > Cc: galaxy-dev(a)bx.psu.edu > Envoyé: Lundi 12 Novembre 2012 15:54:35 > Objet: Re: [galaxy-dev] Bug report : JSONDecodeError > > Hi again, > > I got this with "hg heads" : > > changeset: 7986:12fcd068b12e > tag: tip > user: Daniel Blankenberg <dan(a)bx.psu.edu> > date: Thu Oct 18 11:22:12 2012 -0400 > summary: Do not hide failed datasets with HideDatasetAction post job action. > > changeset: 7152:ffc20445b35e > branch: split_blast2 > parent: 7058:22f545c0d412 > user: Dannon Baker <dannonbaker(a)me.com> > date: Wed Apr 18 07:59:38 2012 -0400 > summary: Branch close. > > changeset: 7151:c94957ac5454 > branch: workflow_import_menu_api > parent: 6834:1a3d01b09f7a > user: Dannon Baker <dannonbaker(a)me.com> > date: Wed Mar 21 09:50:44 2012 -0400 > summary: Branch close for pull request. > > changeset: 7150:314a10ae112d > branch: split_blast > parent: 6757:ebf65c0b1e26 > user: Dannon Baker <dannonbaker(a)me.com> > date: Tue Feb 28 12:32:54 2012 -0500 > summary: Close split_blast branch > > changeset: 7149:1327f2219423 > branch: meme_requirement_on_fimo > parent: 6662:8ba74c17e809 > user: Daniel Blankenberg <dan(a)bx.psu.edu> > date: Fri Feb 03 11:15:29 2012 -0500 > summary: close branch > -------------------------------------------------------- > > And I got this with the debug at : > > JSONDecodeError: Unterminated string starting at: line 1 column 65522 (char 65522) > > URL: http://dev-galaxy.genouest.org/admin_toolshed/browse_repositories > File '/opt/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond > app_iter = self.application(environ, detect_start_response) > File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ > environ, self.app) > File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output > app_iter = application(environ, replacement_start_response) > File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ > return self.application(environ, start_response) > File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ > return self.app( environ, start_response ) > File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ > return self.application(environ, start_response) > File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ > body = method( trans, **kwargs ) > File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 203 in decorator > return func( self, trans, *args, **kwargs ) > File '/opt/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 381 in browse_repositories > return self.installed_repository_grid( trans, **kwd ) > File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 277 in __call__ > kwargs=kwargs ) > File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 765 in fill_template > return self.fill_template_mako( filename, **kwargs ) > File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 776 in fill_template_mako > return template.render( **data ) > File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render > return runtime._render(self, self.callable_, args, data) > File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render > **_kwargs_for_callable(callable_, data)) > File '/opt/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 '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template > callable_(context, *args, **kwargs) > File '/opt/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body > __M_writer(unicode(next.body())) > File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 119 in render_body > __M_writer(unicode(self.grid_body( grid ))) > File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 784 in render_grid_body > __M_writer(unicode(self.make_grid( grid ))) > File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 813 in render_make_grid > __M_writer(unicode(self.render_grid_table( grid, show_item_checkboxes ))) > File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 762 in render_render_grid_table > __M_writer(unicode(render_grid_table_body_contents( grid, show_item_checkboxes ))) > File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 658 in render_grid_table_body_contents > return render_render_grid_table_body_contents(context,grid,show_item_checkboxes) > File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 281 in render_render_grid_table_body_contents > for i, item in enumerate( query ): > File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 1422 in instances > rows = [process[0](context, row) for row in fetch] > File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 2032 in main > return _instance(row, None) > File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance > populate_state(state, dict_, row, isnew, only_load_props) > File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state > populator(state, dict_, row, isnew=isnew, **flags) > File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/strategies.py', line 120 in new_execute > dict_[key] = row[col] > File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 1348 in __getitem__ > return self.__parent._get_col(self.__row, key) > File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 1620 in _get_col > return processor(row[index]) > File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/types.py', line 284 in process > return self.process_result_value(impl_processor(value), dialect) > File '/opt/galaxy-dist/lib/galaxy/model/custom_types.py', line 50 in process_result_value > return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) > File '/opt/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/decoder.py', line 402 in decode > File '/opt/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/decoder.py', line 418 in raw_decode > JSONDecodeError: Unterminated string starting at: line 1 column 65522 (char 65522) > ---------------------------------------------- > > I hope this can help you find the problem ! > > Thanks, > Mathieu > > > > > De: "Greg Von Kuster" <greg(a)bx.psu.edu> > À: "Mathieu Bahin" <mathieu.bahin(a)irisa.fr> > Cc: galaxy-dev(a)bx.psu.edu > Envoyé: Lundi 12 Novembre 2012 12:33:10 > Objet: Re: [galaxy-dev] Bug report : JSONDecodeError > > Hi Matthiew, > > Can you clarify the version of Galaxy you are using? What is the result of typing "hg heads" in your Galaxy installation directory? > > ALso, I noticed the following in your paster log: > > ---------------------------------------- > 131.254.16.26 - - [12/Nov/2012:10:52:26 +0200] "GET /admin_toolshed/browse_repositories HTTP/1.1" 500 - "http://dev-galaxy.genouest.org/admin" "Mozilla/5.0 (X11; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0" > Debug at: http://dev-galaxy.genouest.org/_debug/view/1352713905 > > Directing your browser to the URL in the "Debug at" address will provide a stack trace of the exception thrown due to the problem. What is this this complete stack trace? > > Thanks, > > Greg Von Kuster > > > On Nov 12, 2012, at 4:56 AM, Mathieu Bahin wrote: > > And here is the paster... > > De: "Mathieu Bahin" <mathieu.bahin(a)irisa.fr> > À: "Greg Von Kuster" <greg(a)bx.psu.edu> > Cc: galaxy-dev(a)bx.psu.edu > Envoyé: Lundi 12 Novembre 2012 10:54:21 > Objet: Re: [galaxy-dev] Bug report : JSONDecodeError > > Hi Greg ! > > Thanks for the quick answer. > > I am using the 7720 parent version but I keep it up-to-date without any problems. > Enclosed you'll find the 'paster.log' file generated when I start Galaxy and try to access the manage installed tool shed repositories page. > > Cheers, > Mathieu Bahin > > De: "Greg Von Kuster" <greg(a)bx.psu.edu> > À: "Mathieu Bahin" <mathieu.bahin(a)irisa.fr> > Cc: galaxy-dev(a)bx.psu.edu > Envoyé: Vendredi 9 Novembre 2012 19:28:09 > Objet: Re: [galaxy-dev] Bug report : JSONDecodeError > > Hello Mathieu, > > What version of Galaxy are you running? Also, I cannot read the stack trace from your pasted image, so can you send a text version of the complete stack trace from your paster log? > > Thanks, > > Greg Von Kuster > > > > On Nov 9, 2012, at 11:26 AM, Mathieu Bahin wrote: > > Hi, > > I am using my own Galaxy instance and I had a problem removing a tool from the tool shed : mothur. > The installation was ok and I the mothur tool running without any problem. But when I tried to uninstall the tool, I get an error (screenshot enclosed). And I get the same every time I try to go on the 'Manage tool shed repositories' in the Admin panel. > > I have tried to rebuilt the eggs and to restart Galaxy basically. Actually, I don't really understand the error message. > > Cheers, > Mathieu Bahin > <07.png>___________________________________________________________ > 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/ > > > > <paster.log> > > > >

2 3

Error: updating quotas galaxy_dist
by Bossers, Alex 14 Nov '12

14 Nov '12

Dear all, I have an today up-to-date galaxy-dist running (7986:12fcd068b12e). All seems to work fine. However in the admin panel when I make a quotum it works unless I let it make default at the same time or allocate groups of users to the quota. Just creating the quotem works fine without any options or groups associated... Making the quotem default afterwards gives me the follow error 1 independant of yes/no registered users...; The second when I add a group of users to the quota (errr2); It has worked on our release when used several months ago... Any pointers where to look and how to fix? Thanks Alex ============================== err 1 ============================= Server Error URL: http://galaxy.wur.nl:8082/galaxy/admin/set_quota_default Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin:575 in set_quota_default >> quota, params = self._quota_op( trans, 'set_default_quota_button', self._set_quota_default, kwd ) Module galaxy.webapps.galaxy.controllers.admin:661 in _quota_op >> message = op_method( quota, params ) Module galaxy.actions.admin:111 in _set_quota_default >> self.app.quota_agent.set_default_quota( params.default, quota ) AttributeError: 'NoQuotaAgent' object has no attribute 'set_default_quota' extra data full traceback URL: http://galaxy.wur.nl:8082/galaxy/admin/set_quota_default Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin:575 in set_quota_default >> quota, params = self._quota_op( trans, 'set_default_quota_button', self._set_quota_default, kwd ) Module galaxy.webapps.galaxy.controllers.admin:661 in _quota_op >> message = op_method( quota, params ) Module galaxy.actions.admin:111 in _set_quota_default >> self.app.quota_agent.set_default_quota( params.default, quota ) AttributeError: 'NoQuotaAgent' object has no attribute 'set_default_quota' ============================== err 1 ============================= ============================== err 2 ============================= URL: http://galaxy.wur.nl:8082/galaxy/admin/manage_users_and_groups_for_quota?id… Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin:528 in manage_users_and_groups_for_quota >> quota, params = self._quota_op( trans, 'quota_members_edit_button', self._manage_users_and_groups_for_quota, kwd ) Module galaxy.webapps.galaxy.controllers.admin:661 in _quota_op >> message = op_method( quota, params ) Module galaxy.actions.admin:79 in _manage_users_and_groups_for_quota >> self.app.quota_agent.set_entity_quota_associations( quotas=[ quota ], users=in_users, groups=in_groups ) AttributeError: 'NoQuotaAgent' object has no attribute 'set_entity_quota_associations' extra data full traceback URL: http://galaxy.wur.nl:8082/galaxy/admin/manage_users_and_groups_for_quota?id… Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin:528 in manage_users_and_groups_for_quota >> quota, params = self._quota_op( trans, 'quota_members_edit_button', self._manage_users_and_groups_for_quota, kwd ) Module galaxy.webapps.galaxy.controllers.admin:661 in _quota_op >> message = op_method( quota, params ) Module galaxy.actions.admin:79 in _manage_users_and_groups_for_quota >> self.app.quota_agent.set_entity_quota_associations( quotas=[ quota ], users=in_users, groups=in_groups ) AttributeError: 'NoQuotaAgent' object has no attribute 'set_entity_quota_associations' ============================== err 2 =============================

2 5

Re: [galaxy-dev] Error: updating user hist size (was error updating quotas) galaxy_dist
by Bossers, Alex 14 Nov '12

14 Nov '12

Hhhmmm just tested this and indeed a compressed 10GB export history file of the previous instance (expanded roughly 30GB) does not seem to contribute to the history size used for a user when imported again.... The files are physically there and checking physically on disk it indeed consumes that amount of disk space! Looking at the time-stamps of the files they seem to be the original ones from the past.... Is there a delay for the history size to be updated? In the galaxy reports the counter also stands at zero... Alex -----Oorspronkelijk bericht----- Van: Nate Coraor [mailto:nate@bx.psu.edu] Verzonden: dinsdag 13 november 2012 16:45 Aan: Bossers, Alex CC: Galaxy Dev List Onderwerp: Re: [galaxy-dev] Error: updating quotas galaxy_dist On Nov 12, 2012, at 2:43 PM, Nate Coraor wrote: > On Nov 12, 2012, at 2:35 PM, Bossers, Alex wrote: > >> Nate, >> crap....that fixed it...not sure why that setting didn't show up in the svn diff but anyway...it's working again. >> >> I wonder; if a user is member of two groups with different quota...will the largest be effective? > > It's been a while since I wrote it, but I believe it's the sum of both. The reasoning is that if a user needs quota X for project X and quota Y for project Y, they probably need the total to have enough space for both projects. I had a look at the code and need to correct myself. From the comments: Calculated like so: 1. Anonymous users get the default quota. 2. Logged in users start with the highest of their associated '=' quotas or the default quota, if there are no associated '=' quotas. If an '=' unlimited (-1 in the database) quota is found during this process, the user has no quota (aka unlimited). 3. Quota is increased or decreased by any corresponding '+' or '-' quotas. --nate > > --nate > >> >> Thanks >> Alex >> >> >> ________________________________________ >> Van: Nate Coraor [nate(a)bx.psu.edu] >> Verzonden: maandag 12 november 2012 20:03 >> To: Bossers, Alex >> Cc: Galaxy Dev List >> Onderwerp: Re: [galaxy-dev] Error: updating quotas galaxy_dist >> >> On Nov 12, 2012, at 5:38 AM, Bossers, Alex wrote: >> >>> Dear all, >>> >>> I have an today up-to-date galaxy-dist running (7986:12fcd068b12e). All seems to work fine. >>> However in the admin panel when I make a quotum it works unless I let it make default at the same time or allocate groups of users to the quota. >>> Just creating the quotem works fine without any options or groups associated... >>> Making the quotem default afterwards gives me the follow error 1 >>> independant of yes/no registered users...; The second when I add a >>> group of users to the quota (errr2); >>> >>> It has worked on our release when used several months ago... >>> >>> Any pointers where to look and how to fix? >> >> Hi Alex, >> >> You should only be encountering the NoQuotaAgent if enable_quotas is not set to True in the config file. Can you double check that this config setting has not changed? >> >> Thanks, >> --nate >> >>> >>> Thanks >>> Alex >>> >>> ============================== err 1 ============================= >>> Server Error >>> URL: http://galaxy.wur.nl:8082/galaxy/admin/set_quota_default >>> Module paste.exceptions.errormiddleware:143 in __call__ >>>>> app_iter = self.application(environ, start_response) >>> Module paste.debug.prints:98 in __call__ >>>>> environ, self.app) >>> Module paste.wsgilib:539 in intercept_output >>>>> app_iter = application(environ, replacement_start_response) >>> Module paste.recursive:80 in __call__ >>>>> return self.application(environ, start_response) >>> Module paste.httpexceptions:632 in __call__ >>>>> return self.application(environ, start_response) >>> Module galaxy.web.framework.base:160 in __call__ >>>>> body = method( trans, **kwargs ) >>> Module galaxy.web.framework:206 in decorator >>>>> return func( self, trans, *args, **kwargs ) >>> Module galaxy.webapps.galaxy.controllers.admin:575 in >>> set_quota_default >>>>> quota, params = self._quota_op( trans, 'set_default_quota_button', >>>>> self._set_quota_default, kwd ) >>> Module galaxy.webapps.galaxy.controllers.admin:661 in _quota_op >>>>> message = op_method( quota, params ) >>> Module galaxy.actions.admin:111 in _set_quota_default >>>>> self.app.quota_agent.set_default_quota( params.default, quota ) >>> AttributeError: 'NoQuotaAgent' object has no attribute 'set_default_quota' >>> extra data >>> >>> full traceback >>> URL: http://galaxy.wur.nl:8082/galaxy/admin/set_quota_default >>> Module paste.exceptions.errormiddleware:143 in __call__ >>>>> app_iter = self.application(environ, start_response) >>> Module paste.debug.prints:98 in __call__ >>>>> environ, self.app) >>> Module paste.wsgilib:539 in intercept_output >>>>> app_iter = application(environ, replacement_start_response) >>> Module paste.recursive:80 in __call__ >>>>> return self.application(environ, start_response) >>> Module paste.httpexceptions:632 in __call__ >>>>> return self.application(environ, start_response) >>> Module galaxy.web.framework.base:160 in __call__ >>>>> body = method( trans, **kwargs ) >>> Module galaxy.web.framework:206 in decorator >>>>> return func( self, trans, *args, **kwargs ) >>> Module galaxy.webapps.galaxy.controllers.admin:575 in >>> set_quota_default >>>>> quota, params = self._quota_op( trans, 'set_default_quota_button', >>>>> self._set_quota_default, kwd ) >>> Module galaxy.webapps.galaxy.controllers.admin:661 in _quota_op >>>>> message = op_method( quota, params ) >>> Module galaxy.actions.admin:111 in _set_quota_default >>>>> self.app.quota_agent.set_default_quota( params.default, quota ) >>> AttributeError: 'NoQuotaAgent' object has no attribute 'set_default_quota' >>> ============================== err 1 ============================= >>> >>> ============================== err 2 ============================= >>> URL: >>> http://galaxy.wur.nl:8082/galaxy/admin/manage_users_and_groups_for_q >>> uota?id=06c56fae8b8db405 Module paste.exceptions.errormiddleware:143 >>> in __call__ >>>>> app_iter = self.application(environ, start_response) >>> Module paste.debug.prints:98 in __call__ >>>>> environ, self.app) >>> Module paste.wsgilib:539 in intercept_output >>>>> app_iter = application(environ, replacement_start_response) >>> Module paste.recursive:80 in __call__ >>>>> return self.application(environ, start_response) >>> Module paste.httpexceptions:632 in __call__ >>>>> return self.application(environ, start_response) >>> Module galaxy.web.framework.base:160 in __call__ >>>>> body = method( trans, **kwargs ) >>> Module galaxy.web.framework:206 in decorator >>>>> return func( self, trans, *args, **kwargs ) >>> Module galaxy.webapps.galaxy.controllers.admin:528 in >>> manage_users_and_groups_for_quota >>>>> quota, params = self._quota_op( trans, >>>>> 'quota_members_edit_button', >>>>> self._manage_users_and_groups_for_quota, kwd ) >>> Module galaxy.webapps.galaxy.controllers.admin:661 in _quota_op >>>>> message = op_method( quota, params ) >>> Module galaxy.actions.admin:79 in _manage_users_and_groups_for_quota >>>>> self.app.quota_agent.set_entity_quota_associations( quotas=[ quota >>>>> ], users=in_users, groups=in_groups ) >>> AttributeError: 'NoQuotaAgent' object has no attribute 'set_entity_quota_associations' >>> extra data >>> >>> full traceback >>> URL: >>> http://galaxy.wur.nl:8082/galaxy/admin/manage_users_and_groups_for_q >>> uota?id=06c56fae8b8db405 Module paste.exceptions.errormiddleware:143 >>> in __call__ >>>>> app_iter = self.application(environ, start_response) >>> Module paste.debug.prints:98 in __call__ >>>>> environ, self.app) >>> Module paste.wsgilib:539 in intercept_output >>>>> app_iter = application(environ, replacement_start_response) >>> Module paste.recursive:80 in __call__ >>>>> return self.application(environ, start_response) >>> Module paste.httpexceptions:632 in __call__ >>>>> return self.application(environ, start_response) >>> Module galaxy.web.framework.base:160 in __call__ >>>>> body = method( trans, **kwargs ) >>> Module galaxy.web.framework:206 in decorator >>>>> return func( self, trans, *args, **kwargs ) >>> Module galaxy.webapps.galaxy.controllers.admin:528 in >>> manage_users_and_groups_for_quota >>>>> quota, params = self._quota_op( trans, >>>>> 'quota_members_edit_button', >>>>> self._manage_users_and_groups_for_quota, kwd ) >>> Module galaxy.webapps.galaxy.controllers.admin:661 in _quota_op >>>>> message = op_method( quota, params ) >>> Module galaxy.actions.admin:79 in _manage_users_and_groups_for_quota >>>>> self.app.quota_agent.set_entity_quota_associations( quotas=[ quota >>>>> ], users=in_users, groups=in_groups ) >>> AttributeError: 'NoQuotaAgent' object has no attribute 'set_entity_quota_associations' >>> >>> ============================== err 2 ============================= >>> >>> >>> >>> ___________________________________________________________ >>> 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/

1 0

Errors in creating galaxy DB in MySQL for fresh galaxy-dist
by Bossers, Alex 14 Nov '12

14 Nov '12

Hi All, As posted earlier there were problems with our instance of which some are sorted but one did not. The change attribute failure... Since the instance was empty anyway we decided to do a fresh pull and start all clean (also a clean MySQL db). It all works ok on SQLlight and when adjusting the universe_wsgi.ini file to use MySQL it makes a DB...however there are some errors/warnings! Can these be ignored? I post below the log of the instance making all tables...snipped the last regular startup-part. It seems to work ok (incl the change attributes of datasets) but I do not want to end-up later again with a buggy DB while I can still fix it now when empty... Thanks Alex ============ startup log after FIRST boot using MySQL settings ============ Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/MySQL_python/MySQL_python-1.2.3c1_5.1.41_static-p… Fetch successful. galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-13 12:52:46,485 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-13 12:52:46,485 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-13 12:52:46,485 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2012-11-13 12:52:46,506 MySQL_python egg successfully loaded for mysql dialect galaxy.model.migrate.check INFO 2012-11-13 12:52:46,545 No database, initializing galaxy.model.migrate.check INFO 2012-11-13 12:52:46,561 Migrating 0 -> 1... galaxy.model.migrate.check INFO 2012-11-13 12:52:47,033 galaxy.model.migrate.check INFO 2012-11-13 12:52:47,034 Migrating 1 -> 2... galaxy.model.migrate.check INFO 2012-11-13 12:52:47,112 galaxy.model.migrate.check INFO 2012-11-13 12:52:47,113 Migrating 2 -> 3... galaxy.model.migrate.check INFO 2012-11-13 12:52:48,066 galaxy.model.migrate.check INFO 2012-11-13 12:52:48,066 Migrating 3 -> 4... galaxy.model.migrate.check INFO 2012-11-13 12:52:48,201 galaxy.model.migrate.check INFO 2012-11-13 12:52:48,201 Migrating 4 -> 5... galaxy.model.custom_types DEBUG 2012-11-13 12:52:48,230 Fixing a discrepancy concerning deleted shared history items. galaxy.model.custom_types DEBUG 2012-11-13 12:52:48,511 0 items affected, and restored. galaxy.model.custom_types DEBUG 2012-11-13 12:52:48,511 Time elapsed: 0.281452894211 galaxy.model.custom_types DEBUG 2012-11-13 12:52:48,511 Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs. galaxy.model.custom_types DEBUG 2012-11-13 12:52:48,514 0 items affected, and restored. galaxy.model.custom_types DEBUG 2012-11-13 12:52:48,514 Time elapsed: 0.00216221809387 galaxy.model.migrate.check INFO 2012-11-13 12:52:48,517 galaxy.model.migrate.check INFO 2012-11-13 12:52:48,517 Migrating 5 -> 6... galaxy.model.migrate.check INFO 2012-11-13 12:52:48,637 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:48,637 This migration script changes certain values in the history_dataset_association.extension galaxy.model.migrate.check INFO 2012-11-13 12:52:48,638 column, specifically 'qual' is chaged to be 'qual454'. galaxy.model.migrate.check INFO 2012-11-13 12:52:48,638 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:48,638 galaxy.model.migrate.check INFO 2012-11-13 12:52:48,638 Migrating 6 -> 7... galaxy.model.migrate.check INFO 2012-11-13 12:52:48,750 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:48,750 This migration script creates the new history_user_share_association table, and adds galaxy.model.migrate.check INFO 2012-11-13 12:52:48,750 a new boolean type column to the history table. This provides support for sharing galaxy.model.migrate.check INFO 2012-11-13 12:52:48,750 histories in the same way that workflows are shared. galaxy.model.migrate.check INFO 2012-11-13 12:52:48,750 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:48,750 galaxy.model.migrate.check INFO 2012-11-13 12:52:48,750 Migrating 7 -> 8... galaxy.model.migrate.check INFO 2012-11-13 12:52:49,289 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:49,289 This migration script adds the following new tables for supporting Galaxy forms: galaxy.model.migrate.check INFO 2012-11-13 12:52:49,289 1) form_definition_current galaxy.model.migrate.check INFO 2012-11-13 12:52:49,289 2) form_definition galaxy.model.migrate.check INFO 2012-11-13 12:52:49,289 3) form_values galaxy.model.migrate.check INFO 2012-11-13 12:52:49,289 4) request_type galaxy.model.migrate.check INFO 2012-11-13 12:52:49,289 5) request galaxy.model.migrate.check INFO 2012-11-13 12:52:49,289 6) sample galaxy.model.migrate.check INFO 2012-11-13 12:52:49,290 7) sample_state galaxy.model.migrate.check INFO 2012-11-13 12:52:49,290 8) sample_event galaxy.model.migrate.check INFO 2012-11-13 12:52:49,290 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:49,290 galaxy.model.migrate.check INFO 2012-11-13 12:52:49,290 Migrating 8 -> 9... galaxy.model.migrate.check INFO 2012-11-13 12:52:49,396 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:49,396 This migration script adds a new column to 2 tables: galaxy.model.migrate.check INFO 2012-11-13 12:52:49,396 1) a new boolean type column named 'submitted' to the 'request' table galaxy.model.migrate.check INFO 2012-11-13 12:52:49,396 2) a new string type column named 'bar_code' to the 'sample' table galaxy.model.migrate.check INFO 2012-11-13 12:52:49,396 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:49,396 galaxy.model.migrate.check INFO 2012-11-13 12:52:49,397 Migrating 9 -> 10... galaxy.model.custom_types DEBUG 2012-11-13 12:52:49,501 Creating history_dataset_association_display_at_authorization table failed: (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_display_at_authorization_update_time' is too long") u'CREATE INDEX ix_history_dataset_association_display_at_authorization_update_time ON history_dataset_association_display_at_authorization (update_time)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:49,503 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:49,504 This migration script adds the history_dataset_association_display_at_authorization table, which galaxy.model.migrate.check INFO 2012-11-13 12:52:49,504 allows 'private' datasets to be displayed at external sites without making them public. galaxy.model.migrate.check INFO 2012-11-13 12:52:49,504 galaxy.model.migrate.check INFO 2012-11-13 12:52:49,504 If using mysql, this script will display the following error, which is corrected in the next migration galaxy.model.migrate.check INFO 2012-11-13 12:52:49,504 script: history_dataset_association_display_at_authorization table failed: (OperationalError) galaxy.model.migrate.check INFO 2012-11-13 12:52:49,504 (1059, 'Identifier name 'ix_history_dataset_association_display_at_authorization_update_time' galaxy.model.migrate.check INFO 2012-11-13 12:52:49,504 is too long. galaxy.model.migrate.check INFO 2012-11-13 12:52:49,504 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:49,504 galaxy.model.migrate.check INFO 2012-11-13 12:52:49,504 Migrating 10 -> 11... galaxy.model.migrate.check INFO 2012-11-13 12:52:49,625 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:49,626 This script fixes a problem introduced in the previous migration script ( 9->10 ). MySQL galaxy.model.migrate.check INFO 2012-11-13 12:52:49,626 has a name length limit and thus the index 'ix_hdadaa_history_dataset_association_id' has galaxy.model.migrate.check INFO 2012-11-13 12:52:49,626 to be manually created. galaxy.model.migrate.check INFO 2012-11-13 12:52:49,626 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:49,626 galaxy.model.migrate.check INFO 2012-11-13 12:52:49,626 Migrating 11 -> 12... galaxy.model.migrate.check INFO 2012-11-13 12:52:49,772 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:49,773 This script adds a new user_address table that is currently only used with sample requests, where galaxy.model.migrate.check INFO 2012-11-13 12:52:49,773 a user can select from a list of his addresses to associate with the request. This script also galaxy.model.migrate.check INFO 2012-11-13 12:52:49,773 drops the request.submitted column which was boolean and replaces it with a request.state column galaxy.model.migrate.check INFO 2012-11-13 12:52:49,773 which is a string, allowing for more flexibility with request states. galaxy.model.migrate.check INFO 2012-11-13 12:52:49,773 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:49,773 galaxy.model.migrate.check INFO 2012-11-13 12:52:49,773 Migrating 12 -> 13... 0013_change_lib_item_templates_to_forms DEBUG 2012-11-13 12:52:49,990 Creating library_dataset_dataset_info_association table failed: (OperationalError) (1059, "Identifier name 'ix_library_dataset_dataset_info_association_library_dataset_dataset_association_id' is too long") u'CREATE INDEX ix_library_dataset_dataset_info_association_library_dataset_dataset_association_id ON library_dataset_dataset_info_association (library_dataset_dataset_association_id)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 This migration script eliminates all of the tables that were used for the 1st version of the galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 library templates where template fields and contents were each stored as a separate table row galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 in various library item tables. All of these tables are dropped in this script, eliminating all galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 existing template data. A total of 14 existing tables are dropped. galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 We're now basing library templates on Galaxy forms, so field contents are stored as a jsonified galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 list in the form_values table. This script introduces the following 3 new association tables: galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 1) library_info_association galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 2) library_folder_info_association galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 3) library_dataset_dataset_info_association galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,005 If using mysql, this script will throw an (OperationalError) exception due to a long index name galaxy.model.migrate.check INFO 2012-11-13 12:52:50,006 on the library_dataset_dataset_info_association table, which is OK because the script creates galaxy.model.migrate.check INFO 2012-11-13 12:52:50,006 an index with a shortened name. galaxy.model.migrate.check INFO 2012-11-13 12:52:50,006 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:50,006 0013_change_lib_item_templates_to_forms DEBUG 2012-11-13 12:52:49,990 Creating library_dataset_dataset_info_association table failed: (OperationalError) (1059, "Identifier name 'ix_library_dataset_dataset_info_association_library_dataset_dataset_association_id' is too long") u'CREATE INDEX ix_library_dataset_dataset_info_association_library_dataset_dataset_association_id ON library_dataset_dataset_info_association (library_dataset_dataset_association_id)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:50,006 0013_change_lib_item_templates_to_forms DEBUG 2012-11-13 12:52:49,990 Creating library_dataset_dataset_info_association table failed: (OperationalError) (1059, "Identifier name 'ix_library_dataset_dataset_info_association_library_dataset_dataset_association_id' is too long") u'CREATE INDEX ix_library_dataset_dataset_info_association_library_dataset_dataset_association_id ON library_dataset_dataset_info_association (library_dataset_dataset_association_id)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:50,006 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,006 Migrating 13 -> 14... 0014_pages DEBUG 2012-11-13 12:52:50,110 Could not create page table galaxy.model.migrate.check INFO 2012-11-13 12:52:50,129 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,129 Migration script to add support for "Pages". galaxy.model.migrate.check INFO 2012-11-13 12:52:50,129 1) Creates Page and PageRevision tables galaxy.model.migrate.check INFO 2012-11-13 12:52:50,130 2) Adds username column to User table galaxy.model.migrate.check INFO 2012-11-13 12:52:50,130 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,130 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,130 Migrating 14 -> 15... 0015_tagging DEBUG 2012-11-13 12:52:50,309 Creating history_dataset_association_tag_association table failed: (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_tag_association_history_dataset_association_id' is too long") u'CREATE INDEX ix_history_dataset_association_tag_association_history_dataset_association_id ON history_dataset_association_tag_association (history_dataset_association_id)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:50,311 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 This migration script adds the tables necessary to support tagging of histories, galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 datasets, and history-dataset associations (user views of datasets). galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 If using mysql, this script will display the following error, which is galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 corrected in the next migration script: galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 history_dataset_association_tag_association table failed: galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 (OperationalError) (1059, 'Identifier name galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 'ix_history_dataset_association_tag_association_history_dataset_association_id' galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 is too long) galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_tag_association_history_dataset_association_id' is too long") u'CREATE INDEX ix_history_dataset_association_tag_association_history_dataset_association_id ON history_dataset_association_tag_association (history_dataset_association_id)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,312 Migrating 15 -> 16... galaxy.model.migrate.check INFO 2012-11-13 12:52:50,413 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,413 This script fixes a problem introduced in 0015_tagging.py. MySQL has a galaxy.model.migrate.check INFO 2012-11-13 12:52:50,413 name length limit and thus the index 'ix_hda_ta_history_dataset_association_id' galaxy.model.migrate.check INFO 2012-11-13 12:52:50,413 has to be manually created. galaxy.model.migrate.check INFO 2012-11-13 12:52:50,413 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,413 Migrating 16 -> 17... 0017_library_item_indexes DEBUG 2012-11-13 12:52:50,512 Adding index 'ix_library_folder_name' to library_folder table failed: (OperationalError) (1170, "BLOB/TEXT column 'name' used in key specification without a key length") 'CREATE INDEX ix_library_folder_name ON library_folder (name)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:50,536 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:50,536 This script adds 3 indexes to table columns: library_folder.name, galaxy.model.migrate.check INFO 2012-11-13 12:52:50,536 library_dataset.name, library_dataset_dataset_association.name. galaxy.model.migrate.check INFO 2012-11-13 12:52:50,536 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:50,536 0017_library_item_indexes DEBUG 2012-11-13 12:52:50,512 Adding index 'ix_library_folder_name' to library_folder table failed: (OperationalError) (1170, "BLOB/TEXT column 'name' used in key specification without a key length") 'CREATE INDEX ix_library_folder_name ON library_folder (name)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:50,536 0017_library_item_indexes DEBUG 2012-11-13 12:52:50,512 Adding index 'ix_library_folder_name' to library_folder table failed: (OperationalError) (1170, "BLOB/TEXT column 'name' used in key specification without a key length") 'CREATE INDEX ix_library_folder_name ON library_folder (name)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:50,536 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,536 Migrating 17 -> 18... galaxy.model.migrate.check INFO 2012-11-13 12:52:50,804 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,805 This migration script provides support for (a) ordering tags by recency and galaxy.model.migrate.check INFO 2012-11-13 12:52:50,805 (b) tagging pages. This script deletes all existing tags. galaxy.model.migrate.check INFO 2012-11-13 12:52:50,805 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,805 Migrating 18 -> 19... galaxy.model.migrate.check INFO 2012-11-13 12:52:50,911 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:50,911 This script creates a request.folder_id column which is a foreign galaxy.model.migrate.check INFO 2012-11-13 12:52:50,911 key to the library_folder table. This also adds a 'type' and 'layout' column galaxy.model.migrate.check INFO 2012-11-13 12:52:50,911 to the form_definition table. galaxy.model.migrate.check INFO 2012-11-13 12:52:50,911 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:50,911 galaxy.model.migrate.check INFO 2012-11-13 12:52:50,911 Migrating 19 -> 20... galaxy.model.migrate.check INFO 2012-11-13 12:52:51,277 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,277 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:51,277 This script creates a job_to_output_library_dataset table for allowing library galaxy.model.migrate.check INFO 2012-11-13 12:52:51,277 uploads to run as regular jobs. To support this, a library_folder_id column is galaxy.model.migrate.check INFO 2012-11-13 12:52:51,277 added to the job table, and library_folder/output_library_datasets relations galaxy.model.migrate.check INFO 2012-11-13 12:52:51,277 are added to the Job object. An index is also added to the dataset.state galaxy.model.migrate.check INFO 2012-11-13 12:52:51,277 column. galaxy.model.migrate.check INFO 2012-11-13 12:52:51,277 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:51,278 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,278 Migrating 20 -> 21... galaxy.model.migrate.check INFO 2012-11-13 12:52:51,395 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,395 This migration script adds a user preferences table to Galaxy. galaxy.model.migrate.check INFO 2012-11-13 12:52:51,395 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,395 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,395 Migrating 21 -> 22... 0022_visualization_tables DEBUG 2012-11-13 12:52:51,513 Could not create page table galaxy.model.migrate.check INFO 2012-11-13 12:52:51,529 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,529 Migration script to add support for storing visualizations. galaxy.model.migrate.check INFO 2012-11-13 12:52:51,529 1) Creates Visualization and VisualizationRevision tables galaxy.model.migrate.check INFO 2012-11-13 12:52:51,529 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,530 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,530 Migrating 22 -> 23... galaxy.model.migrate.check INFO 2012-11-13 12:52:51,635 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,635 Migration script to add columns for tracking whether pages are deleted and galaxy.model.migrate.check INFO 2012-11-13 12:52:51,635 publicly accessible. galaxy.model.migrate.check INFO 2012-11-13 12:52:51,635 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,636 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,636 Migrating 23 -> 24... galaxy.model.migrate.check INFO 2012-11-13 12:52:51,740 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,740 Remove unique constraint from page slugs to allow creating a page with galaxy.model.migrate.check INFO 2012-11-13 12:52:51,740 the same slug as a deleted page. galaxy.model.migrate.check INFO 2012-11-13 12:52:51,740 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,740 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,740 Migrating 24 -> 25... galaxy.model.migrate.check INFO 2012-11-13 12:52:51,855 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:51,855 This script adds a foreign key to the form_values table in the galaxy_user table galaxy.model.migrate.check INFO 2012-11-13 12:52:51,855 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:51,855 galaxy.model.migrate.check INFO 2012-11-13 12:52:51,855 Migrating 25 -> 26... galaxy.model.migrate.check INFO 2012-11-13 12:52:52,141 galaxy.model.migrate.check INFO 2012-11-13 12:52:52,141 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:52,141 This script adds tables needed for Galaxy cloud functionality. galaxy.model.migrate.check INFO 2012-11-13 12:52:52,141 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:52,142 galaxy.model.migrate.check INFO 2012-11-13 12:52:52,142 Migrating 26 -> 27... galaxy.model.migrate.check INFO 2012-11-13 12:52:52,287 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:52,287 This migration script adds the request_event table and galaxy.model.migrate.check INFO 2012-11-13 12:52:52,287 removes the state field in the request table galaxy.model.migrate.check INFO 2012-11-13 12:52:52,287 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:52,287 galaxy.model.migrate.check INFO 2012-11-13 12:52:52,287 Migrating 27 -> 28... galaxy.model.migrate.check INFO 2012-11-13 12:52:52,400 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:52,400 This script adds the filename_override_metadata column to the JobExternalOutputMetadata table, galaxy.model.migrate.check INFO 2012-11-13 12:52:52,400 allowing existing metadata files to be written when using external metadata and a cluster galaxy.model.migrate.check INFO 2012-11-13 12:52:52,400 set up with read-only access to database/files galaxy.model.migrate.check INFO 2012-11-13 12:52:52,400 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:52,400 galaxy.model.migrate.check INFO 2012-11-13 12:52:52,400 Migrating 28 -> 29... galaxy.model.migrate.check INFO 2012-11-13 12:52:52,534 galaxy.model.migrate.check INFO 2012-11-13 12:52:52,534 This migration script adds a user actions table to Galaxy. galaxy.model.migrate.check INFO 2012-11-13 12:52:52,534 galaxy.model.migrate.check INFO 2012-11-13 12:52:52,534 galaxy.model.migrate.check INFO 2012-11-13 12:52:52,534 Migrating 29 -> 30... galaxy.model.migrate.check INFO 2012-11-13 12:52:52,649 galaxy.model.migrate.check INFO 2012-11-13 12:52:52,649 Migration script to add column for a history slug. galaxy.model.migrate.check INFO 2012-11-13 12:52:52,650 galaxy.model.migrate.check INFO 2012-11-13 12:52:52,650 galaxy.model.migrate.check INFO 2012-11-13 12:52:52,650 Migrating 30 -> 31... galaxy.model.migrate.check INFO 2012-11-13 12:52:53,266 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,266 Migration script to (a) add and populate necessary columns for doing community tagging of histories, datasets, and pages and (b) add table for doing individual and community tagging of workflows. galaxy.model.migrate.check INFO 2012-11-13 12:52:53,266 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,266 SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so this script will generate error messages when run against SQLite; however, script does execute successfully against SQLite. galaxy.model.migrate.check INFO 2012-11-13 12:52:53,266 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,266 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,266 Migrating 31 -> 32... galaxy.model.migrate.check INFO 2012-11-13 12:52:53,399 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,399 Migration script to add slug column for stored workflow. galaxy.model.migrate.check INFO 2012-11-13 12:52:53,400 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,400 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,400 Migrating 32 -> 33... galaxy.model.migrate.check INFO 2012-11-13 12:52:53,561 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,561 Migration script to add necessary columns for distinguishing between viewing/importing and publishing histories, workflows, and pages. Script adds published column to histories and workflows and importable column to pages. galaxy.model.migrate.check INFO 2012-11-13 12:52:53,561 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,561 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,561 Migrating 33 -> 34... galaxy.model.migrate.check INFO 2012-11-13 12:52:53,701 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,701 Migration script to create a table for page-user share association. galaxy.model.migrate.check INFO 2012-11-13 12:52:53,701 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,701 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,701 Migrating 34 -> 35... 0035_item_annotations_and_workflow_step_tags DEBUG 2012-11-13 12:52:53,851 Creating history_annotation_association table failed: (OperationalError) (1170, "BLOB/TEXT column 'annotation' used in key specification without a key length") u'CREATE INDEX ix_history_annotation_association_annotation ON history_annotation_association (annotation)' () 0035_item_annotations_and_workflow_step_tags DEBUG 2012-11-13 12:52:53,867 Creating history_dataset_association_annotation_association table failed: (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_annotation_association_history_dataset_association_id' is too long") u'CREATE INDEX ix_history_dataset_association_annotation_association_history_dataset_association_id ON history_dataset_association_annotation_association (history_dataset_association_id)' () 0035_item_annotations_and_workflow_step_tags DEBUG 2012-11-13 12:52:53,895 Creating stored_workflow_annotation_association table failed: (OperationalError) (1170, "BLOB/TEXT column 'annotation' used in key specification without a key length") u'CREATE INDEX ix_stored_workflow_annotation_association_annotation ON stored_workflow_annotation_association (annotation)' () 0035_item_annotations_and_workflow_step_tags DEBUG 2012-11-13 12:52:53,923 Creating workflow_step_annotation_association table failed: (OperationalError) (1170, "BLOB/TEXT column 'annotation' used in key specification without a key length") u'CREATE INDEX ix_workflow_step_annotation_association_annotation ON workflow_step_annotation_association (annotation)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:53,989 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,989 Migration script to (a) create tables for annotating objects and (b) create tags for workflow steps. galaxy.model.migrate.check INFO 2012-11-13 12:52:53,990 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,990 (OperationalError) (1170, "BLOB/TEXT column 'annotation' used in key specification without a key length") u'CREATE INDEX ix_history_annotation_association_annotation ON history_annotation_association (annotation)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:53,990 (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_annotation_association_history_dataset_association_id' is too long") u'CREATE INDEX ix_history_dataset_association_annotation_association_history_dataset_association_id ON history_dataset_association_annotation_association (history_dataset_association_id)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:53,990 (OperationalError) (1170, "BLOB/TEXT column 'annotation' used in key specification without a key length") u'CREATE INDEX ix_stored_workflow_annotation_association_annotation ON stored_workflow_annotation_association (annotation)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:53,990 (OperationalError) (1170, "BLOB/TEXT column 'annotation' used in key specification without a key length") u'CREATE INDEX ix_workflow_step_annotation_association_annotation ON workflow_step_annotation_association (annotation)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:53,990 galaxy.model.migrate.check INFO 2012-11-13 12:52:53,990 Migrating 35 -> 36... 0036_add_deleted_column_to_library_template_assoc_tables DEBUG 2012-11-13 12:52:54,124 deleted to false in library_info_association failed: global name 'db_session' is not defined 0036_add_deleted_column_to_library_template_assoc_tables DEBUG 2012-11-13 12:52:54,129 deleted to false in library_folder_info_association failed: global name 'db_session' is not defined 0036_add_deleted_column_to_library_template_assoc_tables DEBUG 2012-11-13 12:52:54,133 deleted to false in library_dataset_dataset_info_association failed: global name 'db_session' is not defined galaxy.model.migrate.check INFO 2012-11-13 12:52:54,135 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,136 Migration script to add a deleted column to the following tables: galaxy.model.migrate.check INFO 2012-11-13 12:52:54,136 library_info_association, library_folder_info_association, library_dataset_dataset_info_association. galaxy.model.migrate.check INFO 2012-11-13 12:52:54,136 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,136 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,136 Migrating 36 -> 37... 0037_samples_library DEBUG 2012-11-13 12:52:54,265 Deleting column 'library_id' to request table failed: (OperationalError) (1025, "Error on rename of './galaxy_dist/#sql-721b_475' to './galaxy_dist/request' (errno: 150)") u'\nALTER TABLE request DROP COLUMN library_id' () 0037_samples_library DEBUG 2012-11-13 12:52:54,270 Deleting column 'folder_id' to request table failed: (OperationalError) (1025, "Error on rename of './galaxy_dist/#sql-721b_475' to './galaxy_dist/request' (errno: 150)") u'\nALTER TABLE request DROP COLUMN folder_id' () galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 This migration script removes the library_id & folder_id fields in the 'request' table and galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 adds the same to the 'sample' table. This also adds a 'datatx' column to request_type table galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 to store the sequencer login information. Finally, this adds a 'dataset_files' column to galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 the sample table. galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 0037_samples_library DEBUG 2012-11-13 12:52:54,265 Deleting column 'library_id' to request table failed: (OperationalError) (1025, "Error on rename of './galaxy_dist/#sql-721b_475' to './galaxy_dist/request' (errno: 150)") u'\nALTER TABLE request DROP COLUMN library_id' () galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 0037_samples_library DEBUG 2012-11-13 12:52:54,265 Deleting column 'library_id' to request table failed: (OperationalError) (1025, "Error on rename of './galaxy_dist/#sql-721b_475' to './galaxy_dist/request' (errno: 150)") u'\nALTER TABLE request DROP COLUMN library_id' () galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 0037_samples_library DEBUG 2012-11-13 12:52:54,270 Deleting column 'folder_id' to request table failed: (OperationalError) (1025, "Error on rename of './galaxy_dist/#sql-721b_475' to './galaxy_dist/request' (errno: 150)") u'\nALTER TABLE request DROP COLUMN folder_id' () galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 0037_samples_library DEBUG 2012-11-13 12:52:54,270 Deleting column 'folder_id' to request table failed: (OperationalError) (1025, "Error on rename of './galaxy_dist/#sql-721b_475' to './galaxy_dist/request' (errno: 150)") u'\nALTER TABLE request DROP COLUMN folder_id' () galaxy.model.migrate.check INFO 2012-11-13 12:52:54,292 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,293 Migrating 37 -> 38... 0038_add_inheritable_column_to_library_template_assoc_tables DEBUG 2012-11-13 12:52:54,417 Setting value of column inheritable to false in library_info_association failed: global name 'db_session' is not defined 0038_add_inheritable_column_to_library_template_assoc_tables DEBUG 2012-11-13 12:52:54,421 Setting value of column inheritable to false in library_folder_info_association failed: global name 'db_session' is not defined galaxy.model.migrate.check INFO 2012-11-13 12:52:54,423 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,423 Migration script to add an inheritable column to the following tables: galaxy.model.migrate.check INFO 2012-11-13 12:52:54,423 library_info_association, library_folder_info_association. galaxy.model.migrate.check INFO 2012-11-13 12:52:54,423 Also, in case of sqlite check if the previous migration script deleted the galaxy.model.migrate.check INFO 2012-11-13 12:52:54,423 request table and if so, restore the table. galaxy.model.migrate.check INFO 2012-11-13 12:52:54,423 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,424 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,424 Migrating 38 -> 39... galaxy.model.migrate.check INFO 2012-11-13 12:52:54,554 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,555 Migration script to add a synopsis column to the library table. galaxy.model.migrate.check INFO 2012-11-13 12:52:54,555 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,555 galaxy.model.migrate.check INFO 2012-11-13 12:52:54,555 Migrating 39 -> 40... 0040_page_annotations DEBUG 2012-11-13 12:52:55,090 Creating page_annotation_association table failed: (OperationalError) (1170, "BLOB/TEXT column 'annotation' used in key specification without a key length") u'CREATE INDEX ix_page_annotation_association_annotation ON page_annotation_association (annotation)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:55,093 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,093 Migration script to (a) create tables for annotating pages. galaxy.model.migrate.check INFO 2012-11-13 12:52:55,094 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,094 (OperationalError) (1170, "BLOB/TEXT column 'annotation' used in key specification without a key length") u'CREATE INDEX ix_page_annotation_association_annotation ON page_annotation_association (annotation)' () galaxy.model.migrate.check INFO 2012-11-13 12:52:55,094 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,094 Migrating 40 -> 41... galaxy.model.migrate.check INFO 2012-11-13 12:52:55,290 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,290 Migration script to create tables for tracking workflow invocations. galaxy.model.migrate.check INFO 2012-11-13 12:52:55,290 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,290 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,290 Migrating 41 -> 42... galaxy.model.migrate.check INFO 2012-11-13 12:52:55,601 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,601 Drop and readd workflow invocation tables, allowing null jobs galaxy.model.migrate.check INFO 2012-11-13 12:52:55,601 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,601 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,601 Migrating 42 -> 43... galaxy.model.migrate.check INFO 2012-11-13 12:52:55,928 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,928 Migration script to create tables and columns for sharing visualizations. galaxy.model.migrate.check INFO 2012-11-13 12:52:55,929 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,929 galaxy.model.migrate.check INFO 2012-11-13 12:52:55,929 Migrating 43 -> 44... galaxy.model.migrate.check INFO 2012-11-13 12:52:56,066 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,066 Migration script to add a notify column to the request table. galaxy.model.migrate.check INFO 2012-11-13 12:52:56,066 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,066 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,066 Migrating 44 -> 45... galaxy.model.migrate.check INFO 2012-11-13 12:52:56,229 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,229 Migration script to add the request_type_permissions table. galaxy.model.migrate.check INFO 2012-11-13 12:52:56,229 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,229 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,229 Migrating 45 -> 46... galaxy.model.migrate.check INFO 2012-11-13 12:52:56,393 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,393 Migration script to create tables for handling post-job actions. galaxy.model.migrate.check INFO 2012-11-13 12:52:56,394 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,394 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,394 Migrating 46 -> 47... galaxy.model.migrate.check INFO 2012-11-13 12:52:56,546 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,546 Add a user_id column to the job table. galaxy.model.migrate.check INFO 2012-11-13 12:52:56,546 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,546 Updating user_id column in job table for 0 rows... galaxy.model.migrate.check INFO 2012-11-13 12:52:56,546 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,546 Updated the user_id column for 0 rows in the job table. galaxy.model.migrate.check INFO 2012-11-13 12:52:56,546 0 rows have no user_id since the value was NULL in the galaxy_session table. galaxy.model.migrate.check INFO 2012-11-13 12:52:56,546 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,546 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,546 Migrating 47 -> 48... galaxy.model.migrate.check INFO 2012-11-13 12:52:56,716 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,717 Add a state column to the history_dataset_association and library_dataset_dataset_association table. galaxy.model.migrate.check INFO 2012-11-13 12:52:56,717 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,717 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,717 Migrating 48 -> 49... galaxy.model.migrate.check INFO 2012-11-13 12:52:56,881 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,881 Migration script to add the api_keys table. galaxy.model.migrate.check INFO 2012-11-13 12:52:56,881 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,881 galaxy.model.migrate.check INFO 2012-11-13 12:52:56,882 Migrating 49 -> 50... 0050_drop_cloud_tables DEBUG 2012-11-13 12:52:57,548 Dropping cloud tables failed: (IntegrityError) (1217, 'Cannot delete or update a parent row: a foreign key constraint fails') '\nDROP TABLE cloud_provider' () galaxy.model.migrate.check INFO 2012-11-13 12:52:57,551 galaxy.model.migrate.check INFO 2012-11-13 12:52:57,551 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:57,551 This script drops tables that were associated with the old Galaxy Cloud functionality. galaxy.model.migrate.check INFO 2012-11-13 12:52:57,551 ======================================== galaxy.model.migrate.check INFO 2012-11-13 12:52:57,551 galaxy.model.migrate.check INFO 2012-11-13 12:52:57,552 Migrating 50 -> 51... galaxy.model.migrate.check INFO 2012-11-13 12:52:57,694 galaxy.model.migrate.check INFO 2012-11-13 12:52:57,695 Migration script to add imported column for jobs table. galaxy.model.migrate.check INFO 2012-11-13 12:52:57,695 galaxy.model.migrate.check INFO 2012-11-13 12:52:57,695 galaxy.model.migrate.check INFO 2012-11-13 12:52:57,695 Migrating 51 -> 52... galaxy.model.migrate.check INFO 2012-11-13 12:52:57,851 galaxy.model.migrate.check INFO 2012-11-13 12:52:57,851 Migration script to add the sample_dataset table and remove the 'dataset_files' column galaxy.model.migrate.check INFO 2012-11-13 12:52:57,851 from the 'sample' table galaxy.model.migrate.check INFO 2012-11-13 12:52:57,851 galaxy.model.migrate.check INFO 2012-11-13 12:52:57,851 galaxy.model.migrate.check INFO 2012-11-13 12:52:57,851 Migrating 52 -> 53... galaxy.model.migrate.check INFO 2012-11-13 12:52:58,141 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,141 Migration script to create tables for rating histories, datasets, workflows, pages, and visualizations. galaxy.model.migrate.check INFO 2012-11-13 12:52:58,141 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,141 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,141 Migrating 53 -> 54... galaxy.model.migrate.check INFO 2012-11-13 12:52:58,298 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,298 Migration script to add dbkey column for visualization. galaxy.model.migrate.check INFO 2012-11-13 12:52:58,299 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,299 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,299 Migrating 54 -> 55... galaxy.model.migrate.check INFO 2012-11-13 12:52:58,465 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,465 Migration script to add the post_job_action_association table. galaxy.model.migrate.check INFO 2012-11-13 12:52:58,465 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,465 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,465 Migrating 55 -> 56... galaxy.model.migrate.check INFO 2012-11-13 12:52:58,646 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,646 Migration script to create tables for adding explicit workflow outputs. galaxy.model.migrate.check INFO 2012-11-13 12:52:58,646 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,646 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,646 Migrating 56 -> 57... galaxy.model.migrate.check INFO 2012-11-13 12:52:58,810 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,810 Migration script to modify the 'notify' field in the 'request' table from a boolean galaxy.model.migrate.check INFO 2012-11-13 12:52:58,810 to a JSONType galaxy.model.migrate.check INFO 2012-11-13 12:52:58,810 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,810 galaxy.model.migrate.check INFO 2012-11-13 12:52:58,811 Migrating 57 -> 58... galaxy.model.migrate.check INFO 2012-11-13 12:52:59,005 galaxy.model.migrate.check INFO 2012-11-13 12:52:59,005 Migration script to create table for exporting histories to archives. galaxy.model.migrate.check INFO 2012-11-13 12:52:59,005 galaxy.model.migrate.check INFO 2012-11-13 12:52:59,005 galaxy.model.migrate.check INFO 2012-11-13 12:52:59,005 Migrating 58 -> 59... galaxy.model.migrate.check INFO 2012-11-13 12:52:59,156 galaxy.model.migrate.check INFO 2012-11-13 12:52:59,156 Migration script to modify the 'file_path' field type in 'sample_dataset' table galaxy.model.migrate.check INFO 2012-11-13 12:52:59,157 to 'TEXT' so that it can support large file paths exceeding 255 characters galaxy.model.migrate.check INFO 2012-11-13 12:52:59,157 galaxy.model.migrate.check INFO 2012-11-13 12:52:59,157 galaxy.model.migrate.check INFO 2012-11-13 12:52:59,157 Migrating 59 -> 60... galaxy.model.migrate.check INFO 2012-11-13 12:52:59,333 galaxy.model.migrate.check INFO 2012-11-13 12:52:59,334 Migration script to create column and table for importing histories from galaxy.model.migrate.check INFO 2012-11-13 12:52:59,334 file archives. galaxy.model.migrate.check INFO 2012-11-13 12:52:59,334 galaxy.model.migrate.check INFO 2012-11-13 12:52:59,334 galaxy.model.migrate.check INFO 2012-11-13 12:52:59,334 Migrating 60 -> 61... galaxy.model.migrate.check INFO 2012-11-13 12:53:00,129 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,129 Migration script to create tables task management. galaxy.model.migrate.check INFO 2012-11-13 12:53:00,129 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,129 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,129 Migrating 61 -> 62... galaxy.model.migrate.check INFO 2012-11-13 12:53:00,320 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,320 Migration script to create table for associating sessions and users with galaxy.model.migrate.check INFO 2012-11-13 12:53:00,320 OpenIDs. galaxy.model.migrate.check INFO 2012-11-13 12:53:00,320 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,320 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,320 Migrating 62 -> 63... galaxy.model.migrate.check INFO 2012-11-13 12:53:00,506 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,506 Migration script to create a new 'sequencer' table galaxy.model.migrate.check INFO 2012-11-13 12:53:00,506 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,506 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,506 Migrating 63 -> 64... galaxy.model.migrate.check INFO 2012-11-13 12:53:00,741 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,741 Migration script to add the run and sample_run_association tables. galaxy.model.migrate.check INFO 2012-11-13 12:53:00,741 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,741 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,741 Migrating 64 -> 65... galaxy.model.migrate.check INFO 2012-11-13 12:53:00,912 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,912 Migration script to add 'name' attribute to the JSON dict which describes galaxy.model.migrate.check INFO 2012-11-13 12:53:00,912 a form definition field and the form values in the database. In the 'form_values' galaxy.model.migrate.check INFO 2012-11-13 12:53:00,912 table, the 'content' column is now a JSON dict instead of a list. galaxy.model.migrate.check INFO 2012-11-13 12:53:00,912 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,912 galaxy.model.migrate.check INFO 2012-11-13 12:53:00,912 Migrating 65 -> 66... galaxy.model.migrate.check INFO 2012-11-13 12:53:01,105 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,105 Migration script to create table for storing deferred job and managed transfer galaxy.model.migrate.check INFO 2012-11-13 12:53:01,105 information. galaxy.model.migrate.check INFO 2012-11-13 12:53:01,105 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,105 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,105 Migrating 66 -> 67... galaxy.model.migrate.check INFO 2012-11-13 12:53:01,293 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,293 Migration script to populate the 'sequencer' table and it is populated using unique galaxy.model.migrate.check INFO 2012-11-13 12:53:01,293 entries in the 'datatx_info' column in the 'request_type' table. It also deletes the 'datatx_info' galaxy.model.migrate.check INFO 2012-11-13 12:53:01,294 column in the 'request_type' table and adds a foreign key to the 'sequencer' table. The galaxy.model.migrate.check INFO 2012-11-13 12:53:01,294 actual contents of the datatx_info column are stored as form_values. galaxy.model.migrate.check INFO 2012-11-13 12:53:01,294 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,294 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,294 Migrating 67 -> 68... 0068_rename_sequencer_to_external_services DEBUG 2012-11-13 12:53:01,500 Deleting column 'sequencer_id' from the 'request_type' table failed: (OperationalError) (1025, "Error on rename of './galaxy_dist/#sql-721b_475' to './galaxy_dist/request_type' (errno: 150)") u'\nALTER TABLE request_type DROP COLUMN sequencer_id' () galaxy.model.migrate.check INFO 2012-11-13 12:53:01,502 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,503 This migration script renames the sequencer table to 'external_service' table and galaxy.model.migrate.check INFO 2012-11-13 12:53:01,503 creates a association table, 'request_type_external_service_association' and galaxy.model.migrate.check INFO 2012-11-13 12:53:01,503 populates it. The 'sequencer_id' foreign_key from the 'request_type' table is removed. galaxy.model.migrate.check INFO 2012-11-13 12:53:01,503 The 'sequencer_type_id' column is renamed to 'external_service_type_id' in the renamed galaxy.model.migrate.check INFO 2012-11-13 12:53:01,503 table 'external_service'. Finally, adds a foreign key to the external_service table in the galaxy.model.migrate.check INFO 2012-11-13 12:53:01,503 sample_dataset table and populates it. galaxy.model.migrate.check INFO 2012-11-13 12:53:01,503 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,503 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,503 Migrating 68 -> 69... galaxy.model.migrate.check INFO 2012-11-13 12:53:01,670 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,671 Migration script to rename the sequencer information form type to external service information form galaxy.model.migrate.check INFO 2012-11-13 12:53:01,671 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,671 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,671 Migrating 69 -> 70... galaxy.model.migrate.check INFO 2012-11-13 12:53:01,838 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,838 Migration script to add 'info' column to the transfer_job table. galaxy.model.migrate.check INFO 2012-11-13 12:53:01,838 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,838 galaxy.model.migrate.check INFO 2012-11-13 12:53:01,838 Migrating 70 -> 71... galaxy.model.migrate.check INFO 2012-11-13 12:53:02,013 galaxy.model.migrate.check INFO 2012-11-13 12:53:02,013 Migration script to add 'workflow' and 'history' columns for a sample. galaxy.model.migrate.check INFO 2012-11-13 12:53:02,014 galaxy.model.migrate.check INFO 2012-11-13 12:53:02,014 galaxy.model.migrate.check INFO 2012-11-13 12:53:02,014 Migrating 71 -> 72... galaxy.model.migrate.check INFO 2012-11-13 12:53:02,181 galaxy.model.migrate.check INFO 2012-11-13 12:53:02,181 Migration script to add 'pid' and 'socket' columns to the transfer_job table. galaxy.model.migrate.check INFO 2012-11-13 12:53:02,181 galaxy.model.migrate.check INFO 2012-11-13 12:53:02,181 galaxy.model.migrate.check INFO 2012-11-13 12:53:02,181 Migrating 72 -> 73... galaxy.model.migrate.check INFO 2012-11-13 12:53:02,373 galaxy.model.migrate.check INFO 2012-11-13 12:53:02,374 Migration script to add 'ldda_parent_id' column to the implicitly_converted_dataset_association table. galaxy.model.migrate.check INFO 2012-11-13 12:53:02,374 galaxy.model.migrate.check INFO 2012-11-13 12:53:02,374 galaxy.model.migrate.check INFO 2012-11-13 12:53:02,374 Migrating 73 -> 74... galaxy.model.migrate.check INFO 2012-11-13 12:53:03,307 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,308 Migration script to add 'purged' column to the library_dataset table. galaxy.model.migrate.check INFO 2012-11-13 12:53:03,308 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,308 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,308 Migrating 74 -> 75... galaxy.model.migrate.check INFO 2012-11-13 12:53:03,494 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,495 Migration script to add a 'subindex' column to the run table. galaxy.model.migrate.check INFO 2012-11-13 12:53:03,495 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,495 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,495 Migrating 75 -> 76... galaxy.model.migrate.check INFO 2012-11-13 12:53:03,654 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,654 This migration script fixes the data corruption caused in the form_values galaxy.model.migrate.check INFO 2012-11-13 12:53:03,654 table (content json field) by migrate script 65. galaxy.model.migrate.check INFO 2012-11-13 12:53:03,654 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,654 No corrupted rows found. galaxy.model.migrate.check INFO 2012-11-13 12:53:03,654 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,654 Migrating 76 -> 77... galaxy.model.migrate.check INFO 2012-11-13 12:53:03,874 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,874 Migration script to create table for storing tool tag associations. galaxy.model.migrate.check INFO 2012-11-13 12:53:03,874 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,874 galaxy.model.migrate.check INFO 2012-11-13 12:53:03,874 Migrating 77 -> 78... galaxy.model.migrate.check INFO 2012-11-13 12:53:04,054 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,055 Migration script to add 'total_size' column to the dataset table, 'purged' galaxy.model.migrate.check INFO 2012-11-13 12:53:04,055 column to the HDA table, and 'disk_usage' column to the User and GalaxySession galaxy.model.migrate.check INFO 2012-11-13 12:53:04,055 tables. galaxy.model.migrate.check INFO 2012-11-13 12:53:04,055 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,055 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,055 Migrating 78 -> 79... galaxy.model.migrate.check INFO 2012-11-13 12:53:04,250 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,250 Migration script to add the job_to_input_library_dataset table. galaxy.model.migrate.check INFO 2012-11-13 12:53:04,250 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,250 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,250 Migrating 79 -> 80... galaxy.model.migrate.check INFO 2012-11-13 12:53:04,517 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,517 Migration script to create tables for disk quotas. galaxy.model.migrate.check INFO 2012-11-13 12:53:04,517 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,517 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,517 Migrating 80 -> 81... galaxy.model.migrate.check INFO 2012-11-13 12:53:04,697 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,698 Migration script to add a 'tool_version' column to the hda/ldda tables. galaxy.model.migrate.check INFO 2012-11-13 12:53:04,698 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,698 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,698 Migrating 81 -> 82... galaxy.model.migrate.check INFO 2012-11-13 12:53:04,916 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,917 Migration script to add the tool_shed_repository table. galaxy.model.migrate.check INFO 2012-11-13 12:53:04,917 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,917 galaxy.model.migrate.check INFO 2012-11-13 12:53:04,917 Migrating 82 -> 83... galaxy.model.migrate.check INFO 2012-11-13 12:53:05,098 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,098 Migration script to add 'prepare_input_files_cmd' column to the task table and to rename a column. galaxy.model.migrate.check INFO 2012-11-13 12:53:05,098 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,099 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,099 Migrating 83 -> 84... galaxy.model.migrate.check INFO 2012-11-13 12:53:05,290 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,290 Migration script to add 'ldda_id' column to the implicitly_converted_dataset_association table. galaxy.model.migrate.check INFO 2012-11-13 12:53:05,290 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,290 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,290 Migrating 84 -> 85... galaxy.model.migrate.check INFO 2012-11-13 12:53:05,466 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,467 Migration script to add 'info' column to the task table. galaxy.model.migrate.check INFO 2012-11-13 12:53:05,467 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,467 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,467 Migrating 85 -> 86... galaxy.model.migrate.check INFO 2012-11-13 12:53:05,673 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,673 Migration script to add the metadata, update_available and includes_datatypes columns to the tool_shed_repository table. galaxy.model.migrate.check INFO 2012-11-13 12:53:05,673 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,673 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,673 Migrating 86 -> 87... 0087_tool_id_guid_map_table DEBUG 2012-11-13 12:53:05,848 Creating tool_id_guid_map table failed: (OperationalError) (1170, "BLOB/TEXT column 'guid' used in key specification without a key length") u'CREATE UNIQUE INDEX ix_tool_id_guid_map_guid ON tool_id_guid_map (guid)' () galaxy.model.migrate.check INFO 2012-11-13 12:53:05,851 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,851 Migration script to create the tool_id_guid_map table. galaxy.model.migrate.check INFO 2012-11-13 12:53:05,851 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,851 0087_tool_id_guid_map_table DEBUG 2012-11-13 12:53:05,848 Creating tool_id_guid_map table failed: (OperationalError) (1170, "BLOB/TEXT column 'guid' used in key specification without a key length") u'CREATE UNIQUE INDEX ix_tool_id_guid_map_guid ON tool_id_guid_map (guid)' () galaxy.model.migrate.check INFO 2012-11-13 12:53:05,851 0087_tool_id_guid_map_table DEBUG 2012-11-13 12:53:05,848 Creating tool_id_guid_map table failed: (OperationalError) (1170, "BLOB/TEXT column 'guid' used in key specification without a key length") u'CREATE UNIQUE INDEX ix_tool_id_guid_map_guid ON tool_id_guid_map (guid)' () galaxy.model.migrate.check INFO 2012-11-13 12:53:05,851 galaxy.model.migrate.check INFO 2012-11-13 12:53:05,851 Migrating 87 -> 88... galaxy.model.migrate.check INFO 2012-11-13 12:53:06,027 galaxy.model.migrate.check INFO 2012-11-13 12:53:06,027 Migration script to add the installed_changeset_revision column to the tool_shed_repository table. galaxy.model.migrate.check INFO 2012-11-13 12:53:06,027 galaxy.model.migrate.check INFO 2012-11-13 12:53:06,027 Updated the installed_changeset_revision column for 0 rows in the tool_shed_repository table. galaxy.model.migrate.check INFO 2012-11-13 12:53:06,027 galaxy.model.migrate.check INFO 2012-11-13 12:53:06,028 Migrating 88 -> 89... galaxy.model.migrate.check INFO 2012-11-13 12:53:07,133 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,134 Migration script to add 'object_store_id' column to various tables galaxy.model.migrate.check INFO 2012-11-13 12:53:07,134 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,134 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,134 Migrating 89 -> 90... galaxy.model.migrate.check INFO 2012-11-13 12:53:07,320 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,320 Migration script to add the uninstalled and dist_to_shed columns to the tool_shed_repository table. galaxy.model.migrate.check INFO 2012-11-13 12:53:07,320 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,320 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,320 Migrating 90 -> 91... galaxy.model.migrate.check INFO 2012-11-13 12:53:07,536 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,536 Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table. galaxy.model.migrate.check INFO 2012-11-13 12:53:07,537 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,537 Added 0 rows to the new tool_version table. galaxy.model.migrate.check INFO 2012-11-13 12:53:07,537 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,537 Migrating 91 -> 92... galaxy.model.migrate.check INFO 2012-11-13 12:53:07,713 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,713 Migration script to create the migrate_tools table. galaxy.model.migrate.check INFO 2012-11-13 12:53:07,713 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,713 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,713 Migrating 92 -> 93... galaxy.model.migrate.check INFO 2012-11-13 12:53:07,895 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,896 Migration script to create "params" column in job table. galaxy.model.migrate.check INFO 2012-11-13 12:53:07,896 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,896 galaxy.model.migrate.check INFO 2012-11-13 12:53:07,896 Migrating 93 -> 94... galaxy.model.migrate.check INFO 2012-11-13 12:53:08,105 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,105 Migration script to create "handler" column in job table. galaxy.model.migrate.check INFO 2012-11-13 12:53:08,105 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,105 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,105 Migrating 94 -> 95... galaxy.model.migrate.check INFO 2012-11-13 12:53:08,333 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,333 Migration script to create table for tracking history_dataset_association subsets. galaxy.model.migrate.check INFO 2012-11-13 12:53:08,333 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,333 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,334 Migrating 95 -> 96... galaxy.model.migrate.check INFO 2012-11-13 12:53:08,510 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,510 Migration script to add column to openid table for provider. galaxy.model.migrate.check INFO 2012-11-13 12:53:08,510 Remove any OpenID entries with nonunique GenomeSpace Identifier galaxy.model.migrate.check INFO 2012-11-13 12:53:08,510 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,511 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,511 Migrating 96 -> 97... galaxy.model.migrate.check INFO 2012-11-13 12:53:08,689 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,689 Migration script to add the ctx_rev column to the tool_shed_repository table. galaxy.model.migrate.check INFO 2012-11-13 12:53:08,689 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,689 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,689 Migrating 97 -> 98... galaxy.model.migrate.check INFO 2012-11-13 12:53:08,930 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,930 Migration script to create the genome_index_tool_data table. galaxy.model.migrate.check INFO 2012-11-13 12:53:08,930 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,930 galaxy.model.migrate.check INFO 2012-11-13 12:53:08,930 Migrating 98 -> 99... galaxy.model.migrate.check INFO 2012-11-13 12:53:09,121 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,121 Migration script to add the tool_dependency table. galaxy.model.migrate.check INFO 2012-11-13 12:53:09,121 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,121 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,121 Migrating 99 -> 100... galaxy.model.migrate.check INFO 2012-11-13 12:53:09,312 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,312 Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text. galaxy.model.migrate.check INFO 2012-11-13 12:53:09,312 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,313 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,313 Migrating 100 -> 101... galaxy.model.migrate.check INFO 2012-11-13 12:53:09,498 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,498 Migration script to drop the installed_changeset_revision column from the tool_dependency table. galaxy.model.migrate.check INFO 2012-11-13 12:53:09,498 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,498 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,498 Migrating 101 -> 102... galaxy.model.migrate.check INFO 2012-11-13 12:53:09,688 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,688 Migration script to add status and error_message columns to the tool_dependency table and drop the uninstalled column from the tool_dependency table. galaxy.model.migrate.check INFO 2012-11-13 12:53:09,688 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,688 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,688 Migrating 102 -> 103... galaxy.model.migrate.check INFO 2012-11-13 12:53:09,902 Migration script to add status and error_message columns to the tool_shed_repository table. galaxy.model.migrate.check INFO 2012-11-13 12:53:09,902 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,903 Migrating 103 -> 104... galaxy.model.migrate.check INFO 2012-11-13 12:53:09,914 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,914 Migration script to update the deferred job parameters for liftover transfer jobs. galaxy.model.migrate.check INFO 2012-11-13 12:53:09,914 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,914 galaxy.model.migrate.check INFO 2012-11-13 12:53:09,914 Migrating 104 -> 105... galaxy.model.migrate.check INFO 2012-11-13 12:53:10,310 galaxy.model.migrate.check INFO 2012-11-13 12:53:10,310 Migration script to add the cleanup_event* tables. galaxy.model.migrate.check INFO 2012-11-13 12:53:10,310 galaxy.model.migrate.check INFO 2012-11-13 12:53:10,310 galaxy.model.migrate.check INFO 2012-11-13 12:53:10,310 Migrating 105 -> 106... 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,520 Creating index 'ix_metadata_file_lda_id' on column 'lda_id' in table 'metadata_file' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,530 Creating index 'ix_history_importable' on column 'importable' in table 'history' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,542 Creating index 'ix_sample_bar_code' on column 'bar_code' in table 'sample' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,553 Creating index 'ix_request_type_deleted' on column 'deleted' in table 'request_type' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,565 Creating index 'ix_galaxy_user_username' on column 'username' in table 'galaxy_user' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,577 Creating index 'ix_form_definition_type' on column 'type' in table 'form_definition' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,589 Creating index 'ix_form_definition_layout' on column 'layout' in table 'form_definition' 0106_add_missing_indexes ERROR 2012-11-13 12:53:10,590 Unable to create index 'ix_form_definition_layout': (OperationalError) (1170, "BLOB/TEXT column 'layout' used in key specification without a key length") 'CREATE INDEX ix_form_definition_layout ON form_definition (layout)' () 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,590 Creating index 'ix_job_library_folder_id' on column 'library_folder_id' in table 'job' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,602 Creating index 'ix_page_published' on column 'published' in table 'page' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,618 Creating index 'ix_page_deleted' on column 'deleted' in table 'page' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,629 Creating index 'ix_galaxy_user_form_values_id' on column 'form_values_id' in table 'galaxy_user' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,642 Creating index 'ix_lia_deleted' on column 'deleted' in table 'library_info_association' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,701 Creating index 'ix_lfia_deleted' on column 'deleted' in table 'library_folder_info_association' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,709 Creating index 'ix_lddia_deleted' on column 'deleted' in table 'library_dataset_dataset_info_association' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,721 Creating index 'ix_sample_library_id' on column 'library_id' in table 'sample' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,730 Creating index 'ix_sample_folder_id' on column 'folder_id' in table 'sample' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,742 Creating index 'ix_lia_inheritable' on column 'inheritable' in table 'library_info_association' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,753 Creating index 'ix_lfia_inheritable' on column 'inheritable' in table 'library_folder_info_association' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,765 Creating index 'ix_job_imported' on column 'imported' in table 'job' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,777 Creating index 'ix_request_notification' on column 'notification' in table 'request' 0106_add_missing_indexes ERROR 2012-11-13 12:53:10,778 Unable to create index 'ix_request_notification': (OperationalError) (1170, "BLOB/TEXT column 'notification' used in key specification without a key length") 'CREATE INDEX ix_request_notification ON request (notification)' () 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,778 Creating index 'ix_sd_external_service_id' on column 'external_service_id' in table 'sample_dataset' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,790 Creating index 'ix_icda_ldda_parent_id' on column 'ldda_parent_id' in table 'implicitly_converted_dataset_association' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,802 Creating index 'ix_library_dataset_purged' on column 'purged' in table 'library_dataset' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,813 Creating index 'ix_run_subindex' on column 'subindex' in table 'run' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,825 Creating index 'ix_history_dataset_association_purged' on column 'purged' in table 'history_dataset_association' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,838 Creating index 'ix_galaxy_user_disk_usage' on column 'disk_usage' in table 'galaxy_user' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,849 Creating index 'ix_galaxy_session_disk_usage' on column 'disk_usage' in table 'galaxy_session' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,861 Creating index 'ix_icda_ldda_id' on column 'ldda_id' in table 'implicitly_converted_dataset_association' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,874 Creating index 'ix_tsr_includes_datatypes' on column 'includes_datatypes' in table 'tool_shed_repository' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,885 Creating index 'ix_dataset_object_store_id' on column 'object_store_id' in table 'dataset' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,897 Creating index 'ix_job_object_store_id' on column 'object_store_id' in table 'job' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,909 Creating index 'ix_metadata_file_object_store_id' on column 'object_store_id' in table 'metadata_file' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,921 Creating index 'ix_job_handler' on column 'handler' in table 'job' 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,933 Creating index 'ix_galaxy_user_email' on column 'email' in table 'galaxy_user' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,948 galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 Migration script to create missing indexes. Adding new columns to existing tables via SQLAlchemy does not create the index, even if the column definition includes index=True. galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,520 Creating index 'ix_metadata_file_lda_id' on column 'lda_id' in table 'metadata_file' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,520 Creating index 'ix_metadata_file_lda_id' on column 'lda_id' in table 'metadata_file' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,530 Creating index 'ix_history_importable' on column 'importable' in table 'history' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,530 Creating index 'ix_history_importable' on column 'importable' in table 'history' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,542 Creating index 'ix_sample_bar_code' on column 'bar_code' in table 'sample' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,542 Creating index 'ix_sample_bar_code' on column 'bar_code' in table 'sample' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,553 Creating index 'ix_request_type_deleted' on column 'deleted' in table 'request_type' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,553 Creating index 'ix_request_type_deleted' on column 'deleted' in table 'request_type' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,565 Creating index 'ix_galaxy_user_username' on column 'username' in table 'galaxy_user' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,565 Creating index 'ix_galaxy_user_username' on column 'username' in table 'galaxy_user' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,577 Creating index 'ix_form_definition_type' on column 'type' in table 'form_definition' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,577 Creating index 'ix_form_definition_type' on column 'type' in table 'form_definition' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,589 Creating index 'ix_form_definition_layout' on column 'layout' in table 'form_definition' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,589 Creating index 'ix_form_definition_layout' on column 'layout' in table 'form_definition' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,949 0106_add_missing_indexes ERROR 2012-11-13 12:53:10,590 Unable to create index 'ix_form_definition_layout': (OperationalError) (1170, "BLOB/TEXT column 'layout' used in key specification without a key length") 'CREATE INDEX ix_form_definition_layout ON form_definition (layout)' () galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes ERROR 2012-11-13 12:53:10,590 Unable to create index 'ix_form_definition_layout': (OperationalError) (1170, "BLOB/TEXT column 'layout' used in key specification without a key length") 'CREATE INDEX ix_form_definition_layout ON form_definition (layout)' () galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,590 Creating index 'ix_job_library_folder_id' on column 'library_folder_id' in table 'job' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,590 Creating index 'ix_job_library_folder_id' on column 'library_folder_id' in table 'job' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,602 Creating index 'ix_page_published' on column 'published' in table 'page' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,602 Creating index 'ix_page_published' on column 'published' in table 'page' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,618 Creating index 'ix_page_deleted' on column 'deleted' in table 'page' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,618 Creating index 'ix_page_deleted' on column 'deleted' in table 'page' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,629 Creating index 'ix_galaxy_user_form_values_id' on column 'form_values_id' in table 'galaxy_user' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,629 Creating index 'ix_galaxy_user_form_values_id' on column 'form_values_id' in table 'galaxy_user' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,642 Creating index 'ix_lia_deleted' on column 'deleted' in table 'library_info_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,642 Creating index 'ix_lia_deleted' on column 'deleted' in table 'library_info_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,701 Creating index 'ix_lfia_deleted' on column 'deleted' in table 'library_folder_info_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,701 Creating index 'ix_lfia_deleted' on column 'deleted' in table 'library_folder_info_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,709 Creating index 'ix_lddia_deleted' on column 'deleted' in table 'library_dataset_dataset_info_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,709 Creating index 'ix_lddia_deleted' on column 'deleted' in table 'library_dataset_dataset_info_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,721 Creating index 'ix_sample_library_id' on column 'library_id' in table 'sample' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,721 Creating index 'ix_sample_library_id' on column 'library_id' in table 'sample' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,730 Creating index 'ix_sample_folder_id' on column 'folder_id' in table 'sample' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,950 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,730 Creating index 'ix_sample_folder_id' on column 'folder_id' in table 'sample' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,742 Creating index 'ix_lia_inheritable' on column 'inheritable' in table 'library_info_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,742 Creating index 'ix_lia_inheritable' on column 'inheritable' in table 'library_info_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,753 Creating index 'ix_lfia_inheritable' on column 'inheritable' in table 'library_folder_info_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,753 Creating index 'ix_lfia_inheritable' on column 'inheritable' in table 'library_folder_info_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,765 Creating index 'ix_job_imported' on column 'imported' in table 'job' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,765 Creating index 'ix_job_imported' on column 'imported' in table 'job' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,777 Creating index 'ix_request_notification' on column 'notification' in table 'request' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,777 Creating index 'ix_request_notification' on column 'notification' in table 'request' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes ERROR 2012-11-13 12:53:10,778 Unable to create index 'ix_request_notification': (OperationalError) (1170, "BLOB/TEXT column 'notification' used in key specification without a key length") 'CREATE INDEX ix_request_notification ON request (notification)' () galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes ERROR 2012-11-13 12:53:10,778 Unable to create index 'ix_request_notification': (OperationalError) (1170, "BLOB/TEXT column 'notification' used in key specification without a key length") 'CREATE INDEX ix_request_notification ON request (notification)' () galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,778 Creating index 'ix_sd_external_service_id' on column 'external_service_id' in table 'sample_dataset' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,778 Creating index 'ix_sd_external_service_id' on column 'external_service_id' in table 'sample_dataset' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,790 Creating index 'ix_icda_ldda_parent_id' on column 'ldda_parent_id' in table 'implicitly_converted_dataset_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,790 Creating index 'ix_icda_ldda_parent_id' on column 'ldda_parent_id' in table 'implicitly_converted_dataset_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,802 Creating index 'ix_library_dataset_purged' on column 'purged' in table 'library_dataset' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,802 Creating index 'ix_library_dataset_purged' on column 'purged' in table 'library_dataset' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,813 Creating index 'ix_run_subindex' on column 'subindex' in table 'run' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,951 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,813 Creating index 'ix_run_subindex' on column 'subindex' in table 'run' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,825 Creating index 'ix_history_dataset_association_purged' on column 'purged' in table 'history_dataset_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,825 Creating index 'ix_history_dataset_association_purged' on column 'purged' in table 'history_dataset_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,838 Creating index 'ix_galaxy_user_disk_usage' on column 'disk_usage' in table 'galaxy_user' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,838 Creating index 'ix_galaxy_user_disk_usage' on column 'disk_usage' in table 'galaxy_user' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,849 Creating index 'ix_galaxy_session_disk_usage' on column 'disk_usage' in table 'galaxy_session' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,849 Creating index 'ix_galaxy_session_disk_usage' on column 'disk_usage' in table 'galaxy_session' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,861 Creating index 'ix_icda_ldda_id' on column 'ldda_id' in table 'implicitly_converted_dataset_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,861 Creating index 'ix_icda_ldda_id' on column 'ldda_id' in table 'implicitly_converted_dataset_association' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,874 Creating index 'ix_tsr_includes_datatypes' on column 'includes_datatypes' in table 'tool_shed_repository' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,874 Creating index 'ix_tsr_includes_datatypes' on column 'includes_datatypes' in table 'tool_shed_repository' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,885 Creating index 'ix_dataset_object_store_id' on column 'object_store_id' in table 'dataset' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,885 Creating index 'ix_dataset_object_store_id' on column 'object_store_id' in table 'dataset' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,897 Creating index 'ix_job_object_store_id' on column 'object_store_id' in table 'job' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,897 Creating index 'ix_job_object_store_id' on column 'object_store_id' in table 'job' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,909 Creating index 'ix_metadata_file_object_store_id' on column 'object_store_id' in table 'metadata_file' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,909 Creating index 'ix_metadata_file_object_store_id' on column 'object_store_id' in table 'metadata_file' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,921 Creating index 'ix_job_handler' on column 'handler' in table 'job' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,921 Creating index 'ix_job_handler' on column 'handler' in table 'job' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,952 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,933 Creating index 'ix_galaxy_user_email' on column 'email' in table 'galaxy_user' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,953 0106_add_missing_indexes DEBUG 2012-11-13 12:53:10,933 Creating index 'ix_galaxy_user_email' on column 'email' in table 'galaxy_user' galaxy.model.migrate.check INFO 2012-11-13 12:53:10,953 galaxy.model.migrate.check INFO 2012-11-13 12:53:10,953 Migrating 106 -> 107... galaxy.model.migrate.check INFO 2012-11-13 12:53:11,160 galaxy.model.migrate.check INFO 2012-11-13 12:53:11,160 Add the exit_code column to the Job and Task tables. galaxy.model.migrate.check INFO 2012-11-13 12:53:11,160 galaxy.model.migrate.check INFO 2012-11-13 12:53:11,160 galaxy.tool_shed.migrate.check DEBUG 2012-11-13 12:53:11,172 MySQL_python egg successfully loaded for mysql dialect galaxy.tool_shed.migrate.check DEBUG 2012-11-13 12:53:11,178 The main Galaxy tool shed is not currently available, so skipped tool migration 1 until next server startup galaxy.model.custom_types DEBUG 2012-11-13 12:53:11,182 MySQL_python egg successfully loaded for mysql dialect galaxy.datatypes.registry DEBUG 2012-11-13 12:53:11,196 Loading datatypes from datatypes_conf.xml

3 3

Warning message
by rolandomantilla1＠gmail.com 14 Nov '12

14 Nov '12

Sent from my Verizon Wireless BlackBerry -----Original Message----- From: Rolando Mantilla <rolandomantilla1(a)gmail.com> Date: Mon, 12 Nov 2012 19:31:20 To: <galaxy-user(a)lists.bx.psu.edu> Subject: Warning message I'm having issues with the FASTQ_Groomer. What I have done it first I downloaded an SRA file created by an Ion torrent sequencer from the NCBI site. Then used the fastq-dump app from the NCBI site to covert the .sra file to .fastq file. When I uploaded the data into galaxy it recognized it as a fastq(as it should) but when I try to run the FASTQ groomer I get the message and warnings below. I also have already downloaded the the blast_datatypes tool from the tool_shed. I truly don't know what the issue is, any help An error occurred running this job: *Groomed 12376 sanger reads into sanger reads. *WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with extension 'blastxml', using datatype from /mnt/galaxyData/tmp/tmpdP_cZ7.

2 1

How to make toolshed tool to create dummy env.sh
by Kevin Y 13 Nov '12

13 Nov '12

Hi dev list, What is the simplest xml I can put into a tool_dependencies.xml for it to create a dummy env.sh in tool-dependency/tool/version/ ..../awef234243/env.sh And will this be sourced each time. Or does the dependency need to be some sort of "successfully install" status for it to be sourced? Ideally I would be elegant if there is a way to create this env.sh easily as it's the best way for a galaxy admin to manage the different versions of dependencies. Thanks, Kevin.

3 3

Improving "New Galaxy tool shed repository alert" emails
by Peter Cock 13 Nov '12

13 Nov '12

Hi all, I would find the "New Galaxy tool shed repository alert" more useful if the important details were at the start of the message, so this is shown in the 'peek' text of my email client (in this case, GoogleMail). Perhaps going further the new repository's name could be in the title? Thanks, Peter

2 2

Can I change the tool runner for set_metadata.sh?
by Luobin Yang 13 Nov '12

13 Nov '12

Hi, guys, I noticed that set_metadata.sh is not in the tools folder as other tools. Can I set a tool runner for set_metadata.sh so that I can use specific resources (like specific compute node in the cluster) to run set_metadata.sh? Thanks, Luobin

2 2

Re: [galaxy-dev] Galaxy at Duke
by Dave Clements 13 Nov '12

13 Nov '12

Hi Alan, I'm CC'ing the Galaxy-Dev list on my response to your question. I talked with Jen Jackson on this. Her suggestion is that the symlink is most likely the problem somehow - this time. When in doubt, getting rid of these good place to start. So recommended starting solution to try - use full paths for everything. Also probably keep all on same partition for the best performance, but that would be hard to defend (there was some debate about this recently). Many thanks to Jen for her (as always) careful consideration. Dave C. On Mon, Nov 5, 2012 at 7:15 AM, Alan V. Cowles <alan.cowles(a)duke.edu> wrote: > Hey Dave, > > Thanks for getting back in touch with me. > > We are running our galaxy instance on a vm... with Centos (RHEL) 6.2, 2 > vcpus, and 2gb vram, with a remote postgresql prod server as our database > instance. > > Our first issue was trying to get it so we could load sequence and larger > files directly from an nfs mounted directory on the server, without > uploading via the web (php vs large files problem.) We accomplished this > via the data libraries interface but it's still not very user intuitive. > > Our first demo user attempted to upload 3 large files and actually filled > up the / partition on the server as galaxy was installed at /usr/local. > > After scrapping and rebuilding that, we now have a several hundred GB nfs > partition, mounted and /usr/local/galaxy is a symlink to a folder on this > volume. > > The issue we are currently seeing is during an upload, or even just > linking files it runs for a while before erroring out and saying there is > no information on the error. The file seems to be there and taking up the > correct amount of disk space but galaxy has a red bar. > > The galaxy server instance is running back grounded in a screen so we can > always switch over and look at the output it shows to standard out as > errors happen, and it seems that it has trouble changing permissions on the > files in the nfs directory, even though, root squash is disabled, and the > entire directory is 777 at the top level and everything underneath is owned > galaxy:galaxy. > > AC > > > > > -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

4 8

Re: [galaxy-dev] Error when running cleanup_datasets.py
by Liisa Koski 13 Nov '12

13 Nov '12

Hi Nate, I'm back to trying to figure this out again as I am running out of disk space. I added the bit of code you suggested below, but I don't think it helped, I'm not so familiar with python. I'm now running Galaxy Reports and it tells me that I have 7479 datasets that were deleted but have not yet been purged. I get the error below when I run cleanup_datasets.py with both the -5 and -4 flag Marking as deleted: LibraryDatasetDatasetAssociation id 6907 (for dataset id 51991) Deleting dataset id 51991 Deleting library dataset id 7225 Traceback (most recent call last): File "scripts/cleanup_datasets/cleanup_datasets.py", line 526, in <module> if __name__ == "__main__": main() File "scripts/cleanup_datasets/cleanup_datasets.py", line 124, in main purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) File "scripts/cleanup_datasets/cleanup_datasets.py", line 247, in purge_folders _purge_folder( folder, app, remove_from_disk, info_only = info_only ) File "scripts/cleanup_datasets/cleanup_datasets.py", line 499, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "scripts/cleanup_datasets/cleanup_datasets.py", line 499, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable File "scripts/cleanup_datasets/cleanup_datasets.py", line 373, in _purge_dataset_instance log.debug( '%s %s has None dataset' % ( type( dataset_instance ), dataset_instance.id ) ) AttributeError: 'NoneType' object has no attribute 'id' Thanks in advance for your help, Liisa From: Nate Coraor <nate(a)bx.psu.edu> To: Liisa Koski <liisa.koski(a)basf.com> Cc: galaxy-dev(a)lists.bx.psu.edu Date: 02/10/2012 10:50 AM Subject: Re: [galaxy-dev] Error when running cleanup_datasets.py On Oct 2, 2012, at 10:44 AM, Liisa Koski wrote: > Hi Nate, > That select statement does not return anything :( Could you add a bit of debugging to the script to see what the id is of the dataset_instance that has a None dataset? if dataset_instance is None: log.debug( '%s %s has None dataset' % ( type( dataset_instance ), dataset_instance.id ) ) Thanks, --nate > > Thanks, > Liisa > > > > > > From: Nate Coraor <nate(a)bx.psu.edu> > To: Liisa Koski <liisa.koski(a)basf.com> > Cc: galaxy-dev(a)lists.bx.psu.edu > Date: 01/10/2012 01:01 PM > Subject: Re: [galaxy-dev] Error when running cleanup_datasets.py > > > > On Sep 24, 2012, at 10:41 AM, Liisa Koski wrote: > > > Hello, > > I am trying to run the cleanup scripts on my local installation but get stuck when trying to run the following: > > > > ./scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 10 -5 -r > > > > Deleting library dataset id 7225 > > Traceback (most recent call last): > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in <module> > > if __name__ == "__main__": main() > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 124, in main > > purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 247, in purge_folders > > _purge_folder( folder, app, remove_from_disk, info_only = info_only ) > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder > > _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder > > _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 495, in _purge_folder > > _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 376, in _purge_dataset_instance > > ( dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id ) > > AttributeError: 'NoneType' object has no attribute 'id' > > Hi Liisa, > > It'd appear that you have a library_dataset_dataset_association in your dataset that lacks an associated dataset. Does 'select id from library_dataset_dataset_association where dataset_id is null' in your database return anything? > > --nate > > > > > > > Any help would be much appreciated. > > > > Thanks, > > Liisa > > ___________________________________________________________ > > 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/ > >

2 2