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

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6eeb1ac6b732/ Changeset: 6eeb1ac6b732 Branch: next-stable User: jmchilton Date: 2014-11-19 17:42:17+00:00 Summary: Remove unused code. Affected #: 1 file diff -r 61f42ba042e6eefb830ebc3203cd98a57f47f690 -r 6eeb1ac6b732573552532a6f8baff9610647f2cf test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -270,12 +270,6 @@ pass return wait - def __wait_for_job( self, job_id ): - def wait(): - while not self.__job_ready( job_id ): - pass - return wait - def __job_ready( self, job_id ): job_json = self._get( "jobs/%s" % job_id ).json() state = job_json[ 'state' ] https://bitbucket.org/galaxy/galaxy-central/commits/b81798f94dc0/ Changeset: b81798f94dc0 Branch: next-stable User: jmchilton Date: 2014-11-19 17:42:17+00:00 Summary: Bug fix for 21e3d69. Affected #: 1 file diff -r 6eeb1ac6b732573552532a6f8baff9610647f2cf -r b81798f94dc0fd14de1d585ed7e57f820f998fae test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -59,7 +59,7 @@ attributes = output_testdef.attributes name = output_testdef.name for job in jobs: - self.wait_for_job( job[ 'id' ], maxseconds ) + self.wait_for_job( job[ 'id' ], history_id, maxseconds ) hid = self.__output_id( output_data ) fetcher = self.__dataset_fetcher( history_id ) ## TODO: Twill version verifys dataset is 'ok' in here. @@ -115,8 +115,8 @@ def wait_for_history( self, history_id, maxseconds ): self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) - def wait_for_job( self, job_id, maxseconds ): - self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id ), maxseconds=maxseconds) + def wait_for_job( self, job_id, history_id, maxseconds ): + self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id, history_id ), maxseconds=maxseconds) def get_job_stdio( self, job_id ): job_stdio = self.__get_job_stdio( job_id ).json() @@ -270,14 +270,14 @@ pass return wait - def __job_ready( self, job_id ): + def __job_ready( self, job_id, history_id ): job_json = self._get( "jobs/%s" % job_id ).json() state = job_json[ 'state' ] try: return self._state_ready( state, error_msg="Job in error state." ) except Exception: if VERBOSE_ERRORS: - self._summarize_job_errors( history_id ) + self._summarize_history_errors( history_id ) raise def __history_ready( self, history_id ): https://bitbucket.org/galaxy/galaxy-central/commits/a799879a82c5/ Changeset: a799879a82c5 Branch: next-stable User: jmchilton Date: 2014-11-19 17:42:17+00:00 Summary: Enable more verbose errors for install and test framework(?). Not actually sure if they will show up in the GUI - hopefully. Affected #: 1 file diff -r b81798f94dc0fd14de1d585ed7e57f820f998fae -r a799879a82c54c2d1afec6e33d8918479bbf2373 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -1,5 +1,9 @@ #!/bin/sh +# Enable verbose test errors for install and test framework. +GALAXY_TEST_VERBOSE_ERRORS="True" +export GALAXY_TEST_VERBOSE_ERRORS + # A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/ # The test/install_and_test_tool_shed_repositories/functional_tests.py cannot be executed directly because it must 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 19 Nov '14

19 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/61f42ba042e6/ Changeset: 61f42ba042e6 Branch: next-stable User: guerler Date: 2014-11-19 16:51:53+00:00 Summary: Fix drill down filter if context is missing Affected #: 1 file diff -r bc3f37e266b062a23a38f016bd2f520549c826cf -r 61f42ba042e6eefb830ebc3203cd98a57f47f690 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1446,7 +1446,7 @@ else: options = [] for filter_key, filter_value in self.filtered.iteritems(): - dataset = other_values[filter_key] + dataset = other_values.get(filter_key) if dataset.__class__.__name__.endswith( "DatasetFilenameWrapper" ): # this is a bad way to check for this, but problems importing class ( due to circular imports? ) dataset = dataset.dataset if dataset: https://bitbucket.org/galaxy/galaxy-central/commits/ba2808ad2c77/ Changeset: ba2808ad2c77 User: guerler Date: 2014-11-19 16:52:21+00:00 Summary: Merge Affected #: 1 file diff -r c6cc1b48564682ac96ef7c5915c6f4982d8184fc -r ba2808ad2c779d3b09013aaf56a752fa9993cdfc lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1446,7 +1446,7 @@ else: options = [] for filter_key, filter_value in self.filtered.iteritems(): - dataset = other_values[filter_key] + dataset = other_values.get(filter_key) if dataset.__class__.__name__.endswith( "DatasetFilenameWrapper" ): # this is a bad way to check for this, but problems importing class ( due to circular imports? ) dataset = dataset.dataset if dataset: 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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[galaxyproject/usegalaxy-playbook] f053e3: tracking code for main
by GitHub 19 Nov '14

19 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f053e3e563175d684c44f0c47c2a9ae34305c734 https://github.com/galaxyproject/usegalaxy-playbook/commit/f053e3e563175d68… Author: martenson <cech.marten(a)gmail.com> Date: 2014-11-19 (Wed, 19 Nov 2014) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- tracking code for main Commit: b063436bd2dfd445de3361176adf55ae285de862 https://github.com/galaxyproject/usegalaxy-playbook/commit/b063436bd2dfd445… Author: martenson <cech.marten(a)gmail.com> Date: 2014-11-19 (Wed, 19 Nov 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Merge commit '958e2ddb6a3541e53e40d9ed56c1712a357a07f9' Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/958e2ddb6a35...…

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bc3f37e266b0/ Changeset: bc3f37e266b0 Branch: next-stable User: carlfeberhard Date: 2014-11-19 16:11:47+00:00 Summary: History, options menu: prevent AMD race conditions with Galaxy object by rendering options menu vars server-side Affected #: 4 files diff -r e131cfefca435532efffca4a1ce777216cda1933 -r bc3f37e266b062a23a38f016bd2f520549c826cf client/galaxy/scripts/mvc/history/options-menu.js --- a/client/galaxy/scripts/mvc/history/options-menu.js +++ b/client/galaxy/scripts/mvc/history/options-menu.js @@ -120,8 +120,7 @@ } ]; -function buildMenu( isAnon, purgeAllowed ){ - var urlRoot = Galaxy.options.root; +function buildMenu( isAnon, purgeAllowed, urlRoot ){ return _.clone( menu ).filter( function( menuOption ){ if( isAnon && !menuOption.anon ){ return false; @@ -150,11 +149,13 @@ options = options || {}; var isAnon = options.anonymous === undefined? true : options.anonymous, purgeAllowed = options.purgeAllowed || false, - menu = buildMenu( isAnon, purgeAllowed ); + root = options.root || ( ( Galaxy && Galaxy.options )? Galaxy.options.root: '/' ), + menu = buildMenu( isAnon, purgeAllowed, root ); //console.debug( 'menu:', menu ); return new PopupMenu( $button, menu ); }; + // ============================================================================ return create; }); diff -r e131cfefca435532efffca4a1ce777216cda1933 -r bc3f37e266b062a23a38f016bd2f520549c826cf static/scripts/mvc/history/options-menu.js --- a/static/scripts/mvc/history/options-menu.js +++ b/static/scripts/mvc/history/options-menu.js @@ -120,8 +120,7 @@ } ]; -function buildMenu( isAnon, purgeAllowed ){ - var urlRoot = Galaxy.options.root; +function buildMenu( isAnon, purgeAllowed, urlRoot ){ return _.clone( menu ).filter( function( menuOption ){ if( isAnon && !menuOption.anon ){ return false; @@ -150,11 +149,13 @@ options = options || {}; var isAnon = options.anonymous === undefined? true : options.anonymous, purgeAllowed = options.purgeAllowed || false, - menu = buildMenu( isAnon, purgeAllowed ); + root = options.root || ( ( Galaxy && Galaxy.options )? Galaxy.options.root: '/' ), + menu = buildMenu( isAnon, purgeAllowed, root ); //console.debug( 'menu:', menu ); return new PopupMenu( $button, menu ); }; + // ============================================================================ return create; }); diff -r e131cfefca435532efffca4a1ce777216cda1933 -r bc3f37e266b062a23a38f016bd2f520549c826cf static/scripts/packed/mvc/history/options-menu.js --- a/static/scripts/packed/mvc/history/options-menu.js +++ b/static/scripts/packed/mvc/history/options-menu.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,d){var e=[{html:d("History Lists"),header:true},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("Current History"),header:true,anon:true},{html:d("Create New"),func:function(){if(Galaxy&&Galaxy.currHistoryPanel){Galaxy.currHistoryPanel.createNewHistory()}}},{html:d("Copy History"),href:"history/copy"},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:true},{html:d("Collapse Expanded Datasets"),func:function(){if(Galaxy&&Galaxy.currHistoryPanel){Galaxy.currHistoryPanel.collapseAll()}}},{html:d("Unhide Hidden Datasets"),confirm:d("Really unhide all hidden datasets?"),href:"history/unhide_datasets?current=True",anon:true},{html:d("Delete Hidden Datasets"),confirm:d("Really delete all hidden datasets?"),href:"history/delete_hidden_datasets",anon:true},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:true,anon:true},{html:d("Show Structure"),href:"history/display_structured",anon:true},{html:d("Export Citations"),href:"history/citations",anon:true},{html:d("Export to File"),href:"history/export_archive?preview=True",anon:true},{html:d("Delete"),confirm:d("Really delete the current history?"),href:"history/delete_current"},{html:d("Delete Permanently"),confirm:d("Really delete the current history permanently? This cannot be undone."),href:"history/delete_current?purge=True",purge:true,anon:true},{html:d("Other Actions"),header:true},{html:d("Import from File"),href:"history/import_archive"}];function c(h,g){var f=Galaxy.options.root;return _.clone(e).filter(function(i){if(h&&!i.anon){return false}if(!g&&i.purge){return false}if(i.href){i.href=f+i.href;i.target="galaxy_main"}if(i.confirm){i.func=function(){if(confirm(i.confirm)){galaxy_main.location=i.href}}}return true})}var b=function(h,f){f=f||{};var i=f.anonymous===undefined?true:f.anonymous,g=f.purgeAllowed||false,j=c(i,g);return new PopupMenu(h,j)};return b}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,d){var e=[{html:d("History Lists"),header:true},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("Current History"),header:true,anon:true},{html:d("Create New"),func:function(){if(Galaxy&&Galaxy.currHistoryPanel){Galaxy.currHistoryPanel.createNewHistory()}}},{html:d("Copy History"),href:"history/copy"},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:true},{html:d("Collapse Expanded Datasets"),func:function(){if(Galaxy&&Galaxy.currHistoryPanel){Galaxy.currHistoryPanel.collapseAll()}}},{html:d("Unhide Hidden Datasets"),confirm:d("Really unhide all hidden datasets?"),href:"history/unhide_datasets?current=True",anon:true},{html:d("Delete Hidden Datasets"),confirm:d("Really delete all hidden datasets?"),href:"history/delete_hidden_datasets",anon:true},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:true,anon:true},{html:d("Show Structure"),href:"history/display_structured",anon:true},{html:d("Export Citations"),href:"history/citations",anon:true},{html:d("Export to File"),href:"history/export_archive?preview=True",anon:true},{html:d("Delete"),confirm:d("Really delete the current history?"),href:"history/delete_current"},{html:d("Delete Permanently"),confirm:d("Really delete the current history permanently? This cannot be undone."),href:"history/delete_current?purge=True",purge:true,anon:true},{html:d("Other Actions"),header:true},{html:d("Import from File"),href:"history/import_archive"}];function c(h,g,f){return _.clone(e).filter(function(i){if(h&&!i.anon){return false}if(!g&&i.purge){return false}if(i.href){i.href=f+i.href;i.target="galaxy_main"}if(i.confirm){i.func=function(){if(confirm(i.confirm)){galaxy_main.location=i.href}}}return true})}var b=function(i,g){g=g||{};var j=g.anonymous===undefined?true:g.anonymous,h=g.purgeAllowed||false,f=g.root||((Galaxy&&Galaxy.options)?Galaxy.options.root:"/"),k=c(j,h,f);return new PopupMenu(i,k)};return b}); \ No newline at end of file diff -r e131cfefca435532efffca4a1ce777216cda1933 -r bc3f37e266b062a23a38f016bd2f520549c826cf templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -126,10 +126,12 @@ }); require([ 'mvc/history/options-menu' ], function( optionsMenu ){ $(function(){ + //##TODO: Galaxy is not reliably available here since index doesn't use app var popupmenu = optionsMenu( $( "#history-options-button" ), { - anonymous : Galaxy.currUser.isAnonymous(), - purgeAllowed : Galaxy.config.allow_user_dataset_purge - }); + anonymous : ${ 'true' if not trans.user else 'false' }, + purgeAllowed : ${ 'true' if trans.app.config.allow_user_dataset_purge else 'false' }, + root : '${ h.url_for( "/" ) }' + }); Galaxy.historyOptionsMenu = popupmenu; }); }); https://bitbucket.org/galaxy/galaxy-central/commits/c6cc1b485646/ Changeset: c6cc1b485646 User: carlfeberhard Date: 2014-11-19 16:12:08+00:00 Summary: Merge next-stable Affected #: 4 files diff -r 9aabb1c64eed61a0d9afd367eba6160670c9c8d3 -r c6cc1b48564682ac96ef7c5915c6f4982d8184fc client/galaxy/scripts/mvc/history/options-menu.js --- a/client/galaxy/scripts/mvc/history/options-menu.js +++ b/client/galaxy/scripts/mvc/history/options-menu.js @@ -120,8 +120,7 @@ } ]; -function buildMenu( isAnon, purgeAllowed ){ - var urlRoot = Galaxy.options.root; +function buildMenu( isAnon, purgeAllowed, urlRoot ){ return _.clone( menu ).filter( function( menuOption ){ if( isAnon && !menuOption.anon ){ return false; @@ -150,11 +149,13 @@ options = options || {}; var isAnon = options.anonymous === undefined? true : options.anonymous, purgeAllowed = options.purgeAllowed || false, - menu = buildMenu( isAnon, purgeAllowed ); + root = options.root || ( ( Galaxy && Galaxy.options )? Galaxy.options.root: '/' ), + menu = buildMenu( isAnon, purgeAllowed, root ); //console.debug( 'menu:', menu ); return new PopupMenu( $button, menu ); }; + // ============================================================================ return create; }); diff -r 9aabb1c64eed61a0d9afd367eba6160670c9c8d3 -r c6cc1b48564682ac96ef7c5915c6f4982d8184fc static/scripts/mvc/history/options-menu.js --- a/static/scripts/mvc/history/options-menu.js +++ b/static/scripts/mvc/history/options-menu.js @@ -120,8 +120,7 @@ } ]; -function buildMenu( isAnon, purgeAllowed ){ - var urlRoot = Galaxy.options.root; +function buildMenu( isAnon, purgeAllowed, urlRoot ){ return _.clone( menu ).filter( function( menuOption ){ if( isAnon && !menuOption.anon ){ return false; @@ -150,11 +149,13 @@ options = options || {}; var isAnon = options.anonymous === undefined? true : options.anonymous, purgeAllowed = options.purgeAllowed || false, - menu = buildMenu( isAnon, purgeAllowed ); + root = options.root || ( ( Galaxy && Galaxy.options )? Galaxy.options.root: '/' ), + menu = buildMenu( isAnon, purgeAllowed, root ); //console.debug( 'menu:', menu ); return new PopupMenu( $button, menu ); }; + // ============================================================================ return create; }); diff -r 9aabb1c64eed61a0d9afd367eba6160670c9c8d3 -r c6cc1b48564682ac96ef7c5915c6f4982d8184fc static/scripts/packed/mvc/history/options-menu.js --- a/static/scripts/packed/mvc/history/options-menu.js +++ b/static/scripts/packed/mvc/history/options-menu.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,d){var e=[{html:d("History Lists"),header:true},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("Current History"),header:true,anon:true},{html:d("Create New"),func:function(){if(Galaxy&&Galaxy.currHistoryPanel){Galaxy.currHistoryPanel.createNewHistory()}}},{html:d("Copy History"),href:"history/copy"},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:true},{html:d("Collapse Expanded Datasets"),func:function(){if(Galaxy&&Galaxy.currHistoryPanel){Galaxy.currHistoryPanel.collapseAll()}}},{html:d("Unhide Hidden Datasets"),confirm:d("Really unhide all hidden datasets?"),href:"history/unhide_datasets?current=True",anon:true},{html:d("Delete Hidden Datasets"),confirm:d("Really delete all hidden datasets?"),href:"history/delete_hidden_datasets",anon:true},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:true,anon:true},{html:d("Show Structure"),href:"history/display_structured",anon:true},{html:d("Export Citations"),href:"history/citations",anon:true},{html:d("Export to File"),href:"history/export_archive?preview=True",anon:true},{html:d("Delete"),confirm:d("Really delete the current history?"),href:"history/delete_current"},{html:d("Delete Permanently"),confirm:d("Really delete the current history permanently? This cannot be undone."),href:"history/delete_current?purge=True",purge:true,anon:true},{html:d("Other Actions"),header:true},{html:d("Import from File"),href:"history/import_archive"}];function c(h,g){var f=Galaxy.options.root;return _.clone(e).filter(function(i){if(h&&!i.anon){return false}if(!g&&i.purge){return false}if(i.href){i.href=f+i.href;i.target="galaxy_main"}if(i.confirm){i.func=function(){if(confirm(i.confirm)){galaxy_main.location=i.href}}}return true})}var b=function(h,f){f=f||{};var i=f.anonymous===undefined?true:f.anonymous,g=f.purgeAllowed||false,j=c(i,g);return new PopupMenu(h,j)};return b}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,d){var e=[{html:d("History Lists"),header:true},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("Current History"),header:true,anon:true},{html:d("Create New"),func:function(){if(Galaxy&&Galaxy.currHistoryPanel){Galaxy.currHistoryPanel.createNewHistory()}}},{html:d("Copy History"),href:"history/copy"},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:true},{html:d("Collapse Expanded Datasets"),func:function(){if(Galaxy&&Galaxy.currHistoryPanel){Galaxy.currHistoryPanel.collapseAll()}}},{html:d("Unhide Hidden Datasets"),confirm:d("Really unhide all hidden datasets?"),href:"history/unhide_datasets?current=True",anon:true},{html:d("Delete Hidden Datasets"),confirm:d("Really delete all hidden datasets?"),href:"history/delete_hidden_datasets",anon:true},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:true,anon:true},{html:d("Show Structure"),href:"history/display_structured",anon:true},{html:d("Export Citations"),href:"history/citations",anon:true},{html:d("Export to File"),href:"history/export_archive?preview=True",anon:true},{html:d("Delete"),confirm:d("Really delete the current history?"),href:"history/delete_current"},{html:d("Delete Permanently"),confirm:d("Really delete the current history permanently? This cannot be undone."),href:"history/delete_current?purge=True",purge:true,anon:true},{html:d("Other Actions"),header:true},{html:d("Import from File"),href:"history/import_archive"}];function c(h,g,f){return _.clone(e).filter(function(i){if(h&&!i.anon){return false}if(!g&&i.purge){return false}if(i.href){i.href=f+i.href;i.target="galaxy_main"}if(i.confirm){i.func=function(){if(confirm(i.confirm)){galaxy_main.location=i.href}}}return true})}var b=function(i,g){g=g||{};var j=g.anonymous===undefined?true:g.anonymous,h=g.purgeAllowed||false,f=g.root||((Galaxy&&Galaxy.options)?Galaxy.options.root:"/"),k=c(j,h,f);return new PopupMenu(i,k)};return b}); \ No newline at end of file diff -r 9aabb1c64eed61a0d9afd367eba6160670c9c8d3 -r c6cc1b48564682ac96ef7c5915c6f4982d8184fc templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -126,10 +126,12 @@ }); require([ 'mvc/history/options-menu' ], function( optionsMenu ){ $(function(){ + //##TODO: Galaxy is not reliably available here since index doesn't use app var popupmenu = optionsMenu( $( "#history-options-button" ), { - anonymous : Galaxy.currUser.isAnonymous(), - purgeAllowed : Galaxy.config.allow_user_dataset_purge - }); + anonymous : ${ 'true' if not trans.user else 'false' }, + purgeAllowed : ${ 'true' if trans.app.config.allow_user_dataset_purge else 'false' }, + root : '${ h.url_for( "/" ) }' + }); Galaxy.historyOptionsMenu = popupmenu; }); }); 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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[galaxyproject/usegalaxy-playbook] 958e2d: Update Main.
by GitHub 19 Nov '14

19 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 958e2ddb6a3541e53e40d9ed56c1712a357a07f9 https://github.com/galaxyproject/usegalaxy-playbook/commit/958e2ddb6a3541e5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-11-19 (Wed, 19 Nov 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e131cfefca43/ Changeset: e131cfefca43 Branch: next-stable User: guerler Date: 2014-11-19 15:46:37+00:00 Summary: Fix quotations for option selector Affected #: 6 files diff -r ac2113e38c8843474ceab070643a181caa3b4e20 -r e131cfefca435532efffca4a1ce777216cda1933 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -149,7 +149,7 @@ /** Return the currently selected dataset values */ value : function (dict) { // update current value - if (dict !== undefined) { + if (dict && dict.values) { try { // create list var list = []; diff -r ac2113e38c8843474ceab070643a181caa3b4e20 -r e131cfefca435532efffca4a1ce777216cda1933 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -224,7 +224,7 @@ // update to new selection for (var i in new_val) { - this.$el.find('input[value=' + new_val[i] + ']').prop('checked', true); + this.$el.find('input[value="' + new_val[i] + '"]').prop('checked', true); }; } diff -r ac2113e38c8843474ceab070643a181caa3b4e20 -r e131cfefca435532efffca4a1ce777216cda1933 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -149,7 +149,7 @@ /** Return the currently selected dataset values */ value : function (dict) { // update current value - if (dict !== undefined) { + if (dict && dict.values) { try { // create list var list = []; diff -r ac2113e38c8843474ceab070643a181caa3b4e20 -r e131cfefca435532efffca4a1ce777216cda1933 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -224,7 +224,7 @@ // update to new selection for (var i in new_val) { - this.$el.find('input[value=' + new_val[i] + ']').prop('checked', true); + this.$el.find('input[value="' + new_val[i] + '"]').prop('checked', true); }; } diff -r ac2113e38c8843474ceab070643a181caa3b4e20 -r e131cfefca435532efffca4a1ce777216cda1933 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m!==undefined){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file diff -r ac2113e38c8843474ceab070643a181caa3b4e20 -r e131cfefca435532efffca4a1ce777216cda1933 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement('<div style="display: inline-block;"/>');this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement('<div style="display: inline-block;"/>');this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find('input[value="'+f[g]+'"]').prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/9aabb1c64eed/ Changeset: 9aabb1c64eed User: guerler Date: 2014-11-19 15:47:08+00:00 Summary: Merge Affected #: 6 files diff -r 0ff9945848112c03bfe2ed2429bba9d1faee703e -r 9aabb1c64eed61a0d9afd367eba6160670c9c8d3 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -149,7 +149,7 @@ /** Return the currently selected dataset values */ value : function (dict) { // update current value - if (dict !== undefined) { + if (dict && dict.values) { try { // create list var list = []; diff -r 0ff9945848112c03bfe2ed2429bba9d1faee703e -r 9aabb1c64eed61a0d9afd367eba6160670c9c8d3 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -224,7 +224,7 @@ // update to new selection for (var i in new_val) { - this.$el.find('input[value=' + new_val[i] + ']').prop('checked', true); + this.$el.find('input[value="' + new_val[i] + '"]').prop('checked', true); }; } diff -r 0ff9945848112c03bfe2ed2429bba9d1faee703e -r 9aabb1c64eed61a0d9afd367eba6160670c9c8d3 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -149,7 +149,7 @@ /** Return the currently selected dataset values */ value : function (dict) { // update current value - if (dict !== undefined) { + if (dict && dict.values) { try { // create list var list = []; diff -r 0ff9945848112c03bfe2ed2429bba9d1faee703e -r 9aabb1c64eed61a0d9afd367eba6160670c9c8d3 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -224,7 +224,7 @@ // update to new selection for (var i in new_val) { - this.$el.find('input[value=' + new_val[i] + ']').prop('checked', true); + this.$el.find('input[value="' + new_val[i] + '"]').prop('checked', true); }; } diff -r 0ff9945848112c03bfe2ed2429bba9d1faee703e -r 9aabb1c64eed61a0d9afd367eba6160670c9c8d3 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m!==undefined){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file diff -r 0ff9945848112c03bfe2ed2429bba9d1faee703e -r 9aabb1c64eed61a0d9afd367eba6160670c9c8d3 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement('<div style="display: inline-block;"/>');this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement('<div style="display: inline-block;"/>');this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find('input[value="'+f[g]+'"]').prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file 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: Bugfix: composite uploads broken by upload common assuming bunch's have a UUID field.
by commits-noreply＠bitbucket.org 19 Nov '14

19 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/acc8d1e2bc88/ Changeset: acc8d1e2bc88 Branch: stable User: jmchilton Date: 2014-11-19 15:20:36+00:00 Summary: Bugfix: composite uploads broken by upload common assuming bunch's have a UUID field. Reported by tjkarlsson(a)uma.es here http://dev.list.galaxyproject.org/Problem-to-upload-data-to-Galaxy-when-usi…. Affected #: 1 file diff -r 1af943ca6e39db44bfec74a0debffbf798fc4731 -r acc8d1e2bc88530aa8d8651cf5f88649f6769304 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -403,6 +403,7 @@ dataset.warnings = [] dataset.metadata = {} dataset.composite_files = {} + dataset.uuid = None #load metadata files_metadata = context.get( self.metadata_ref, {} ) metadata_name_substition_default_dict = dict( [ ( composite_file.substitute_name_with_metadata, d_type.metadata_spec[ composite_file.substitute_name_with_metadata ].default ) for composite_file in d_type.composite_files.values() if composite_file.substitute_name_with_metadata ] ) 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.

1 0

[galaxyproject/usegalaxy-playbook] fa1ae6: Update Main with bugfix from Sam.
by GitHub 18 Nov '14

18 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fa1ae6b2c86add7185e1151086f318b4d3f68ea3 https://github.com/galaxyproject/usegalaxy-playbook/commit/fa1ae6b2c86add71… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-11-18 (Tue, 18 Nov 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main with bugfix from Sam.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 18 Nov '14

18 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ac2113e38c88/ Changeset: ac2113e38c88 Branch: next-stable User: guerler Date: 2014-11-18 18:51:18+00:00 Summary: Fix parameter validation, catch errors Affected #: 2 files diff -r c1b54085c3aeb9a7cf97c7277436ab3f7b50d299 -r ac2113e38c8843474ceab070643a181caa3b4e20 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1143,7 +1143,7 @@ """ if self.multiple: #split on newline and , - if value: + if isinstance( value, list ) or isinstance( value, basestring ): column_list = [] if not isinstance( value, list ): value = value.split( '\n' ) diff -r c1b54085c3aeb9a7cf97c7277436ab3f7b50d299 -r ac2113e38c8843474ceab070643a181caa3b4e20 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -626,10 +626,14 @@ group_state['__current_case__'] = current_case group_state[ input.test_param.name ] = value else: - value, error = check_param(trans, input, incoming.get(key, state.get(input.name, None)), context) - if error: - errors[input.name] = error - state[input.name] = value + try: + value, error = check_param(trans, input, incoming.get(key, state.get(input.name, None)), context) + if error: + errors[input.name] = error + state[input.name] = value + except Exception: + log.error('Checking parameter %s failed.', input.name) + pass return errors # builds tool model including all attributes https://bitbucket.org/galaxy/galaxy-central/commits/0ff994584811/ Changeset: 0ff994584811 User: guerler Date: 2014-11-18 18:51:43+00:00 Summary: Merge Affected #: 2 files diff -r 782815ce0a91fb69e82ba73cf811e3487b649d56 -r 0ff9945848112c03bfe2ed2429bba9d1faee703e lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1143,7 +1143,7 @@ """ if self.multiple: #split on newline and , - if value: + if isinstance( value, list ) or isinstance( value, basestring ): column_list = [] if not isinstance( value, list ): value = value.split( '\n' ) diff -r 782815ce0a91fb69e82ba73cf811e3487b649d56 -r 0ff9945848112c03bfe2ed2429bba9d1faee703e lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -626,10 +626,14 @@ group_state['__current_case__'] = current_case group_state[ input.test_param.name ] = value else: - value, error = check_param(trans, input, incoming.get(key, state.get(input.name, None)), context) - if error: - errors[input.name] = error - state[input.name] = value + try: + value, error = check_param(trans, input, incoming.get(key, state.get(input.name, None)), context) + if error: + errors[input.name] = error + state[input.name] = value + except Exception: + log.error('Checking parameter %s failed.', input.name) + pass return errors # builds tool model including all attributes 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: Merged in jmchilton/galaxy-central-fork-1 (pull request #559)
by commits-noreply＠bitbucket.org 18 Nov '14

18 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/782815ce0a91/ Changeset: 782815ce0a91 User: jmchilton Date: 2014-11-18 15:40:21+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #559) Configuration enhancements aim at enabling tool testing of cached data. Affected #: 1 file diff -r e47c67efeda7fa66f9782aae5e2c62ab640310bc -r 782815ce0a91fb69e82ba73cf811e3487b649d56 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -10,6 +10,7 @@ import os import os.path import shutil +import string import tempfile from galaxy import util @@ -71,7 +72,7 @@ tree = util.parse_xml( filename ) root = tree.getroot() for table_elem in root.findall( 'table' ): - table = ToolDataTable.from_elem( table_elem, tool_data_path, from_shed_config ) + table = ToolDataTable.from_elem( table_elem, tool_data_path, from_shed_config, filename=filename ) table_elems.append( table_elem ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table @@ -167,16 +168,17 @@ class ToolDataTable( object ): @classmethod - def from_elem( cls, table_elem, tool_data_path, from_shed_config ): + def from_elem( cls, table_elem, tool_data_path, from_shed_config, filename ): table_type = table_elem.get( 'type', 'tabular' ) assert table_type in tool_data_table_types, "Unknown data table type '%s'" % type - return tool_data_table_types[ table_type ]( table_elem, tool_data_path, from_shed_config=from_shed_config ) + return tool_data_table_types[ table_type ]( table_elem, tool_data_path, from_shed_config=from_shed_config, filename=filename ) - def __init__( self, config_element, tool_data_path, from_shed_config = False): + def __init__( self, config_element, tool_data_path, from_shed_config = False, filename=None ): self.name = config_element.get( 'name' ) self.comment_char = config_element.get( 'comment_char' ) self.empty_field_value = config_element.get( 'empty_field_value', '' ) self.empty_field_values = {} + self.here = filename and os.path.dirname(filename) self.filenames = odict() self.tool_data_path = tool_data_path self.missing_index_file = None @@ -241,8 +243,8 @@ type_key = 'tabular' - def __init__( self, config_element, tool_data_path, from_shed_config = False): - super( TabularToolDataTable, self ).__init__( config_element, tool_data_path, from_shed_config) + def __init__( self, config_element, tool_data_path, from_shed_config = False, filename=None ): + super( TabularToolDataTable, self ).__init__( config_element, tool_data_path, from_shed_config, filename) self.config_element = config_element self.data = [] self.configure_and_load( config_element, tool_data_path, from_shed_config) @@ -265,7 +267,7 @@ repo_info = None # Read every file for file_element in config_element.findall( 'file' ): - filename = file_path = file_element.get( 'path', None ) + filename = file_path = expand_here_template( file_element.get( 'path', None ), here=self.here ) found = False if file_path is None: log.debug( "Encountered a file element (%s) that does not contain a path value when loading tool data table '%s'.", util.xml_to_string( file_element ), self.name ) @@ -300,7 +302,7 @@ errors = [] if found: - self.data.extend( self.parse_file_fields( open( filename ), errors=errors ) ) + self.extend_data_with( filename, errors=errors ) self._update_version() else: self.missing_index_file = filename @@ -326,7 +328,7 @@ def handle_found_index_file( self, filename ): self.missing_index_file = None - self.data.extend( self.parse_file_fields( open( filename ) ) ) + self.extend_data_with( filename ) def get_fields( self ): return self.data @@ -380,7 +382,11 @@ if 'name' not in self.columns: self.columns['name'] = self.columns['value'] - def parse_file_fields( self, reader, errors=None ): + def extend_data_with( self, filename, errors=None ): + here = os.path.dirname(os.path.abspath(filename)) + self.data.extend( self.parse_file_fields( open( filename ), errors=errors, here=here ) ) + + def parse_file_fields( self, reader, errors=None, here="__HERE__" ): """ Parse separated lines from file and return a list of tuples. @@ -394,6 +400,7 @@ continue line = line.rstrip( "\n\r" ) if line: + line = expand_here_template( line, here=here ) fields = line.split( self.separator ) if self.largest_index < len( fields ): rval.append( fields ) @@ -529,5 +536,12 @@ rval['fields'] = self.get_fields() return rval + +def expand_here_template(content, here=None): + if here and content: + content = string.Template(content).safe_substitute( { "__HERE__": here }) + return content + + # Registry of tool data types by type_key tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) 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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