August 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8fbff1243ec6/ Changeset: 8fbff1243ec6 User: dannon Date: 2014-08-20 18:55:32 Summary: Swap remote user logout to actually follow galaxy internal logout procedure and then redirect. Also fix logic for user dropdown -- it was preventing users from seeing stuff that was actually available before. Affected #: 3 files diff -r 30c4d8730943a40646341e6adf3659cf9fd36985 -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -616,11 +616,14 @@ if biostar_url: # TODO: It would be better if we automatically logged this user out of biostar message += '<br>To logout of Biostar, please click <a href="%s" target="_blank">here</a>.' % ( biostar_url ) - return trans.fill_template( '/user/logout.mako', - refresh_frames=refresh_frames, - message=message, - status='done', - active_view="user" ) + if trans.app.config.use_remote_user and trans.app.config.remote_user_logout_href: + trans.response.send_redirect(trans.app.config.remote_user_logout_href) + else: + return trans.fill_template('/user/logout.mako', + refresh_frames=refresh_frames, + message=message, + status='done', + active_view="user" ) @web.expose def create( self, trans, cntrller='user', redirect_url='', refresh_frames=[], **kwd ): diff -r 30c4d8730943a40646341e6adf3659cf9fd36985 -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -289,34 +289,24 @@ title : "Logged in as " + this.options.user.email }); - // remote user - if (this.options.use_remote_user && this.options.remote_user_logout_href) - { - tab_user.add({ - title : "Logout", - content : this.options.remote_user_logout_href, - target : "_top" - }); - } else { - tab_user.add({ - title : "Preferences", - content : "user?cntrller=user", - target : "galaxy_main" - }); + tab_user.add({ + title : "Preferences", + content : "user?cntrller=user", + target : "galaxy_main" + }); - tab_user.add({ - title : "Custom Builds", - content : "user/dbkeys", - target : "galaxy_main" - }); - - tab_user.add({ - title : "Logout", - content : "user/logout", - target : "_top", - divider : true - }); - } + tab_user.add({ + title : "Custom Builds", + content : "user/dbkeys", + target : "galaxy_main" + }); + + tab_user.add({ + title : "Logout", + content : "user/logout", + target : "_top", + divider : true + }); // default tabs tab_user.add({ diff -r 30c4d8730943a40646341e6adf3659cf9fd36985 -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -19,13 +19,7 @@ %if trans.app.config.enable_openid and not trans.app.config.use_remote_user: <li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller )}">${_('Manage OpenIDs')}</a> linked to your account</li> %endif - %if trans.app.config.use_remote_user: - %if trans.app.config.remote_user_logout_href: - <li><a href="${trans.app.config.remote_user_logout_href}" target="_top">${_('Logout')}</a></li> - %endif - %else: - <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li> - %endif + <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li> %else: <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller )}">${_('Manage your information')}</a></li><li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller )}">${_('Manage your API keys')}</a></li> https://bitbucket.org/galaxy/galaxy-central/commits/871a781a0507/ Changeset: 871a781a0507 User: dannon Date: 2014-08-20 18:56:01 Summary: Strip trailing whitespace from galaxy.menu.js Affected #: 1 file diff -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 -r 871a781a05070d5a227469c55c4249dbe6945e2d static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -10,10 +10,10 @@ { // options options: null, - + // link masthead class masthead: null, - + // initialize initialize: function(options) { @@ -21,7 +21,7 @@ this.masthead = options.masthead; this.create(); }, - + // default menu create: function() { @@ -149,7 +149,7 @@ content : "visualization/list", target : "_frame" }); - } + } this.masthead.append(tab_visualization); // @@ -300,14 +300,14 @@ content : "user/dbkeys", target : "galaxy_main" }); - + tab_user.add({ title : "Logout", content : "user/logout", target : "_top", divider : true }); - + // default tabs tab_user.add({ title : "Saved Histories", @@ -343,7 +343,7 @@ // add to masthead this.masthead.append(tab_user); } - + // identify active tab if (this.options.active_view) this.masthead.highlight(this.options.active_view); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Fix formatting in cloudlaunch.
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/30c4d8730943/ Changeset: 30c4d8730943 User: dannon Date: 2014-08-20 18:33:11 Summary: Fix formatting in cloudlaunch. Affected #: 1 file diff -r fb28ce36133ffcb6a167ba95003f4608b7574942 -r 30c4d8730943a40646341e6adf3659cf9fd36985 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -40,6 +40,7 @@ ("r3.8xlarge", "Memory optimized 8xLarge (32 vCPU/244GB RAM)"), ] + class CloudController(BaseUIController): """Galaxy Cloud Functions""" @@ -56,7 +57,7 @@ share_string=share_string, ami=ami, bucket_default=bucket_default, - instance_types = DEFAULT_INSTANCE_TYPES) + instance_types=DEFAULT_INSTANCE_TYPES) @web.expose def get_account_info(self, trans, key_id, secret): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Update instance types, slim down the options to recommended types. This will (eventually) make it to a single shared resource in bioblend that's used in cloudman + galaxy, but this change gets us in sync for now.
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fb28ce36133f/ Changeset: fb28ce36133f User: dannon Date: 2014-08-20 18:22:38 Summary: Update instance types, slim down the options to recommended types. This will (eventually) make it to a single shared resource in bioblend that's used in cloudman + galaxy, but this change gets us in sync for now. Affected #: 2 files diff -r cb7713c693e73d90731489e267ca52a7b585d580 -r fb28ce36133ffcb6a167ba95003f4608b7574942 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -31,6 +31,14 @@ DEFAULT_KEYPAIR = 'cloudman_keypair' CLOUDMAN_TAG_KEY = 'galaxy:cloudman' +DEFAULT_INSTANCE_TYPES = [ + ("c3.large", "Compute optimized Large (2 vCPU/4GB RAM)"), + ("c3.2xlarge", "Compute optimized 2xLarge (8 vCPU/15GB RAM)"), + ("c3.8xlarge", "Compute optimized 8xLarge (32 vCPU/60GB RAM)"), + ("r3.large", "Memory optimized Large (2 vCPU/15GB RAM)"), + ("r3.2xlarge", "Memory optimized 2xLarge (8 vCPU/61GB RAM)"), + ("r3.8xlarge", "Memory optimized 8xLarge (32 vCPU/244GB RAM)"), +] class CloudController(BaseUIController): """Galaxy Cloud Functions""" @@ -47,7 +55,8 @@ default_keypair=DEFAULT_KEYPAIR, share_string=share_string, ami=ami, - bucket_default=bucket_default) + bucket_default=bucket_default, + instance_types = DEFAULT_INSTANCE_TYPES) @web.expose def get_account_info(self, trans, key_id, secret): diff -r cb7713c693e73d90731489e267ca52a7b585d580 -r fb28ce36133ffcb6a167ba95003f4608b7574942 templates/webapps/galaxy/cloud/index.mako --- a/templates/webapps/galaxy/cloud/index.mako +++ b/templates/webapps/galaxy/cloud/index.mako @@ -238,10 +238,9 @@ <div class="form-row"><label for="id_instance_type">Instance Type</label><select name="instance_type" id="id_instance_type"> - <option value="m1.large">Large</option> - <option value="m1.xlarge">Extra Large</option> - <option value="c3.2xlarge">Compute Optimized Double Extra Large</option> - <option value="m2.4xlarge">High-Memory Quadruple Extra Large</option> + %for (itype, description) in instance_types: + <option value="${itype}">${description}</option> + %endfor </select></div><div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in dan/galaxy-central-prs/stable (pull request #470)
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6445c0fe7612/ Changeset: 6445c0fe7612 Branch: stable User: dannon Date: 2014-08-20 17:03:06 Summary: Merged in dan/galaxy-central-prs/stable (pull request #470) Fix for resetting installed toolshed repository metadata inside of Galaxy. Affected #: 1 file diff -r 354fb22316ef3d259cb81f3af40af8aeb0334187 -r 6445c0fe761258410a17b95ad2f221a9e60fc5c7 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1717,7 +1717,7 @@ else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repositories_select_field = irmm.build_repository_ids_select_field( trans ) + repositories_select_field = irmm.build_repository_ids_select_field() return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/14e588f9674c/ Changeset: 14e588f9674c Branch: stable User: dan Date: 2014-08-20 16:48:48 Summary: Fix for resetting installed toolshed repository metadata inside of Galaxy. Affected #: 1 file diff -r d2fc633d1bcc2d02c5efccf923c4e3ce5336512a -r 14e588f9674ce69d9a8d56f188b26a4e788809be lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1717,7 +1717,7 @@ else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repositories_select_field = irmm.build_repository_ids_select_field( trans ) + repositories_select_field = irmm.build_repository_ids_select_field() return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, https://bitbucket.org/galaxy/galaxy-central/commits/6445c0fe7612/ Changeset: 6445c0fe7612 Branch: stable User: dannon Date: 2014-08-20 17:03:06 Summary: Merged in dan/galaxy-central-prs/stable (pull request #470) Fix for resetting installed toolshed repository metadata inside of Galaxy. Affected #: 1 file diff -r 354fb22316ef3d259cb81f3af40af8aeb0334187 -r 6445c0fe761258410a17b95ad2f221a9e60fc5c7 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1717,7 +1717,7 @@ else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repositories_select_field = irmm.build_repository_ids_select_field( trans ) + repositories_select_field = irmm.build_repository_ids_select_field() return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for resetting installed toolshed repository metadata inside of Galaxy.
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cb7713c693e7/ Changeset: cb7713c693e7 User: dan Date: 2014-08-20 16:48:48 Summary: Fix for resetting installed toolshed repository metadata inside of Galaxy. Affected #: 1 file diff -r a49333fbaf635b37fd4b96ce89ffc50166b2326e -r cb7713c693e73d90731489e267ca52a7b585d580 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1717,7 +1717,7 @@ else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repositories_select_field = irmm.build_repository_ids_select_field( trans ) + repositories_select_field = irmm.build_repository_ids_select_field() return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/69537ff827f3/ Changeset: 69537ff827f3 Branch: tool_list_fix User: natefoo Date: 2014-08-20 16:37:12 Summary: Close merged branch tool_list_fix Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/b17f89fc2f22/ Changeset: b17f89fc2f22 Branch: federation_ids User: natefoo Date: 2014-08-20 16:37:35 Summary: Close merged branch federation_ids Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/4444ee067fb7/ Changeset: 4444ee067fb7 Branch: jjohnson/for-_ensure_valid_session-with-use_remo-1408455181422 User: natefoo Date: 2014-08-20 16:37:54 Summary: Close merged branch jjohnson/for-_ensure_valid_session-with-use_remo-1408455181422 Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Updated tag latest_2014.08.11 for changeset 7748a83f3361
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/354fb22316ef/ Changeset: 354fb22316ef Branch: stable User: natefoo Date: 2014-08-20 16:36:22 Summary: Updated tag latest_2014.08.11 for changeset 7748a83f3361 Affected #: 1 file diff -r 7748a83f33617f450b23557420c753754e54ee4d -r 354fb22316ef3d259cb81f3af40af8aeb0334187 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -7e4d21621ce12e13ebbdf9fd3259df58c3ef124c latest_2014.08.11 +7748a83f33617f450b23557420c753754e54ee4d latest_2014.08.11 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cfbcb00008cb/ Changeset: cfbcb00008cb User: dannon Date: 2014-08-20 15:48:19 Summary: Re-enable administrative job lock, works with multiple handler processes using the internal message queue Affected #: 5 files diff -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -53,6 +53,7 @@ """Start the job manager""" self.app = app self.dispatcher = dispatcher + self.job_lock = False self.sa_session = app.model.context self.track_jobs_in_database = self.app.config.track_jobs_in_database @@ -168,7 +169,10 @@ """ while self.running: try: - self.__monitor_step() + # If jobs are locked, there's nothing to monitor and we skip + # to the sleep. + if not self.job_lock: + self.__monitor_step() except: log.exception( "Exception in monitor_step" ) # Sleep diff -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -105,5 +105,14 @@ table_names = app.tool_data_tables.reload_tables( table_names=params.get('table_name', None)) log.debug("Finished data table reload for %s" % table_names) + +def admin_job_lock(app, **kwargs): + job_lock = kwargs.get('job_lock', False) + # job_queue is exposed in the root app, but this will be 'fixed' at some + # point, so we're using the reference from the handler. + app.job_manager.job_handler.job_queue.job_lock = job_lock + log.debug("Job dispatching is now set to %s" % job_lock) + control_message_to_task = { 'reload_tool': reload_tool, - 'reload_tool_data_tables': reload_tool_data_tables} + 'reload_tool_data_tables': reload_tool_data_tables, + 'admin_job_lock': admin_job_lock} diff -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -27,7 +27,8 @@ Refactor later to actually persist this somewhere instead of building it repeatedly. """ - return [Queue('control.%s' % q, galaxy_exchange, routing_key='control') for q in config.server_names] + return [Queue('control.%s' % q, galaxy_exchange, routing_key='control') for + q in config.server_names] def control_queue_from_config(config): diff -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1037,6 +1037,7 @@ heap = heap.theone return trans.fill_template( '/admin/memdump.mako', heap = heap, ids = ids, sorts = sorts, breadcrumb = breadcrumb, msg = msg ) + @web.expose @web.require_admin def jobs( self, trans, stop = [], stop_msg = None, cutoff = 180, job_lock = None, ajl_submit = None, **kwd ): @@ -1069,6 +1070,17 @@ msg += ', '.join( deleted ) status = 'done' trans.sa_session.flush() + if ajl_submit: + if job_lock == 'on': + galaxy.queue_worker.send_control_task(trans, 'admin_job_lock', + kwargs={'job_lock': True } ) + job_lock = True + else: + galaxy.queue_worker.send_control_task(trans, 'admin_job_lock', + kwargs={'job_lock': False } ) + job_lock = False + else: + job_lock = trans.app.job_manager.job_handler.job_queue.job_lock cutoff_time = datetime.utcnow() - timedelta( seconds=int( cutoff ) ) jobs = trans.sa_session.query( trans.app.model.Job ) \ .filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time, @@ -1089,7 +1101,8 @@ last_updated = last_updated, cutoff = cutoff, msg = msg, - status = status ) + status = status, + job_lock = job_lock) ## ---- Utility methods ------------------------------------------------------- diff -r 25804ca32d9b3a78a022afa580e574cc6713d2b8 -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 templates/admin/jobs.mako --- a/templates/admin/jobs.mako +++ b/templates/admin/jobs.mako @@ -133,3 +133,33 @@ </div></div></form> + +<form name="jobs" action="${h.url_for(controller='admin', action='jobs')}" method="POST"> + <p/> + <div class="toolForm"> + <div class="toolFormTitle"> + Administrative Job Lock + </div> + <div class="toolFormBody"> + <div class="form-row"> + <input type="hidden" name="ajl_submit" value="True"/> + %if job_lock==True: + <p>Job dispatching is currently <strong>locked</strong>.</p> + <label> + <input type='checkbox' name='job_lock' checked='checked' /> + Prevent jobs from dispatching. + </label> + %else: + <p>Job dispatching is currently <strong>unlocked</strong>.</p> + <label> + <input type='checkbox' name='job_lock' /> + Prevent jobs from dispatching. + </label> + %endif + </div> + <div class="form-row"> + <input type="submit" class="primary-button" name="submit" value="Update"> + </div> + </div> + </div> +</form> https://bitbucket.org/galaxy/galaxy-central/commits/b232fa5e0dc4/ Changeset: b232fa5e0dc4 User: dannon Date: 2014-08-20 15:49:00 Summary: Merge. Affected #: 2 files diff -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 -r b232fa5e0dc40ca809ea826a73111e6be8645b95 README.txt --- a/README.txt +++ b/README.txt @@ -1,31 +1,34 @@ -GALAXY -====== -http://galaxyproject.org/ - -The latest information about Galaxy is always available via the Galaxy -website above. - -HOW TO START -============ -Galaxy requires Python 2.6 or 2.7. To check your python version, run: - -% python -V -Python 2.7.3 - -Start Galaxy: - -% sh run.sh - -Once Galaxy completes startup, you should be able to view Galaxy in your -browser at: - -http://localhost:8080 - -You may wish to make changes from the default configuration. This can be done -in the universe_wsgi.ini file. Tools are configured in tool_conf.xml. Details -on adding tools can be found on the Galaxy website (linked above). - -Not all dependencies are included for the tools provided in the sample -tool_conf.xml. A full list of external dependencies is available at: - -https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies +GALAXY +====== +http://galaxyproject.org/ + +The latest information about Galaxy is always available via the Galaxy +website above. + +HOW TO START +============ +Galaxy requires Python 2.6 or 2.7. To check your python version, run: + +% python -V +Python 2.7.3 + +Start Galaxy: + +% sh run.sh + +Once Galaxy completes startup, you should be able to view Galaxy in your +browser at: + +http://localhost:8080 + +You may wish to make changes from the default configuration. This can be done +in the universe_wsgi.ini file. Tools can be either installed from the Tool Shed +or added manually. For details please see the Galaxy wiki: + +https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial. + + +Not all dependencies are included for the tools provided in the sample +tool_conf.xml. A full list of external dependencies is available at: + +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies \ No newline at end of file diff -r cfbcb00008cb49126274695cdb3b5bcad0dd7db9 -r b232fa5e0dc40ca809ea826a73111e6be8645b95 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1268,6 +1268,7 @@ except: error("That history does not exist.") try: # use a try/finally block to restore the user's current history + default_target_history = trans.get_history() if kwargs: # If kwargs were provided, the states for each step should have # been POSTed @@ -1329,7 +1330,7 @@ trans.sa_session.add( new_history ) target_history = new_history else: - target_history = trans.get_history() + target_history = default_target_history # Build replacement dict for this workflow execution. replacement_dict = {} https://bitbucket.org/galaxy/galaxy-central/commits/a49333fbaf63/ Changeset: a49333fbaf63 User: dannon Date: 2014-08-20 16:31:01 Summary: Clarify job lock log statement, swap loglevel from debug to info. Affected #: 1 file diff -r b232fa5e0dc40ca809ea826a73111e6be8645b95 -r a49333fbaf635b37fd4b96ce89ffc50166b2326e lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -54,7 +54,7 @@ if body.get('noop', None) != self.app.config.server_name: try: f = self.task_mapping[body['task']] - log.debug("Instance recieved '%s' task, executing now." % body['task']) + log.info("Instance recieved '%s' task, executing now." % body['task']) f(self.app, **body['kwargs']) except Exception: # this shouldn't ever throw an exception, but... @@ -111,7 +111,8 @@ # job_queue is exposed in the root app, but this will be 'fixed' at some # point, so we're using the reference from the handler. app.job_manager.job_handler.job_queue.job_lock = job_lock - log.debug("Job dispatching is now set to %s" % job_lock) + log.info("Administrative Job Lock is now set to %s. Jobs will %s dispatch." + % (job_lock, "not" if job_lock else "now")) control_message_to_task = { 'reload_tool': reload_tool, 'reload_tool_data_tables': reload_tool_data_tables, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Attempt to ensure batch workflows are all properly assigned to same history.
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/86fd99a90b81/ Changeset: 86fd99a90b81 User: jmchilton Date: 2014-08-20 14:44:02 Summary: Attempt to ensure batch workflows are all properly assigned to same history. ... in case trans.get_history() changes during scheduling. I believe this was what was happening here (http://dev.list.galaxyproject.org/redirecting-to-unnamed-history-td4665414.…) though I have no proof - nonetheless this won't hurt anything. Affected #: 1 file diff -r 481b64dd8dff0d2c52388e906a1632370536ef67 -r 86fd99a90b81c84eb4f7489ce016c6d1ed10496a lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1268,6 +1268,7 @@ except: error("That history does not exist.") try: # use a try/finally block to restore the user's current history + default_target_history = trans.get_history() if kwargs: # If kwargs were provided, the states for each step should have # been POSTed @@ -1329,7 +1330,7 @@ trans.sa_session.add( new_history ) target_history = new_history else: - target_history = trans.get_history() + target_history = default_target_history # Build replacement dict for this workflow execution. replacement_dict = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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