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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 23 Oct '13

23 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/35328380ac82/ Changeset: 35328380ac82 Branch: next-stable User: Dave Bouvier Date: 2013-10-23 16:09:16 Summary: Clean up uninstallation filter. Fix recording of installation errors. Affected #: 1 file diff -r f3c2d456413d9c586c1ac9d861c3c2acca510def -r 35328380ac82c471a942bd6f0b5a4e73413bf272 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -252,10 +252,8 @@ if repository.status in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, app.model.ToolShedRepository.installation_status.DEACTIVATED ]: continue - if repository.status not in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, - app.model.ToolShedRepository.installation_status.ERROR, - app.model.ToolShedRepository.installation_status.INSTALLED, - app.model.ToolShedRepository.installation_status.DEACTIVATED ]: + if repository.status not in [ app.model.ToolShedRepository.installation_status.ERROR, + app.model.ToolShedRepository.installation_status.INSTALLED ]: repository.status = app.model.ToolShedRepository.installation_status.ERROR sa_session.add( repository ) sa_session.flush() @@ -1155,11 +1153,10 @@ repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) except: log.exception( 'Unable to uninstall, no installed repository found.' ) - continue - test_result = dict( tool_shed=repository.tool_shed, - name=repository.name, - owner=repository.owner, - changeset_revision=repository.changeset_revision, + test_result = dict( tool_shed=galaxy_tool_shed_url, + name=repository_info_dict[ 'name' ], + owner=repository_info_dict[ 'owner' ], + changeset_revision=repository_info_dict[ 'changeset_revision' ], error_message=extract_log_data( result, from_tool_test=False ) ) repository_status[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) params[ 'tools_functionally_correct' ] = False @@ -1170,7 +1167,11 @@ repository_status, repository_info_dict, params ) - success = execute_uninstall_method( app, deactivate_only ) + try: + success = execute_uninstall_method( app, deactivate_only ) + except: + log.exception( 'Encountered error attempting to uninstall %s.', repository_info_dict[ 'name' ] ) + success = False if not success: log.error( 'Repository %s failed to uninstall.', repository_info_dict[ 'name' ] ) repositories_failed_install.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) https://bitbucket.org/galaxy/galaxy-central/commits/06d5abc6d407/ Changeset: 06d5abc6d407 User: Dave Bouvier Date: 2013-10-23 16:47:31 Summary: Merge with next-stable. Affected #: 1 file diff -r c5d68c98b9c50b42fdbc2a82f3bd85a1d320ace6 -r 06d5abc6d40748a41493d2beac87fc1cb81f5bf6 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -252,10 +252,8 @@ if repository.status in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, app.model.ToolShedRepository.installation_status.DEACTIVATED ]: continue - if repository.status not in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, - app.model.ToolShedRepository.installation_status.ERROR, - app.model.ToolShedRepository.installation_status.INSTALLED, - app.model.ToolShedRepository.installation_status.DEACTIVATED ]: + if repository.status not in [ app.model.ToolShedRepository.installation_status.ERROR, + app.model.ToolShedRepository.installation_status.INSTALLED ]: repository.status = app.model.ToolShedRepository.installation_status.ERROR sa_session.add( repository ) sa_session.flush() @@ -1155,11 +1153,10 @@ repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) except: log.exception( 'Unable to uninstall, no installed repository found.' ) - continue - test_result = dict( tool_shed=repository.tool_shed, - name=repository.name, - owner=repository.owner, - changeset_revision=repository.changeset_revision, + test_result = dict( tool_shed=galaxy_tool_shed_url, + name=repository_info_dict[ 'name' ], + owner=repository_info_dict[ 'owner' ], + changeset_revision=repository_info_dict[ 'changeset_revision' ], error_message=extract_log_data( result, from_tool_test=False ) ) repository_status[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) params[ 'tools_functionally_correct' ] = False @@ -1170,7 +1167,11 @@ repository_status, repository_info_dict, params ) - success = execute_uninstall_method( app, deactivate_only ) + try: + success = execute_uninstall_method( app, deactivate_only ) + except: + log.exception( 'Encountered error attempting to uninstall %s.', repository_info_dict[ 'name' ] ) + success = False if not success: log.error( 'Repository %s failed to uninstall.', repository_info_dict[ 'name' ] ) repositories_failed_install.append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 22 Oct '13

22 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f3c2d456413d/ Changeset: f3c2d456413d Branch: next-stable User: Dave Bouvier Date: 2013-10-22 22:26:44 Summary: Additional filtering of repositories not to uninstall. Affected #: 1 file diff -r f82ad49f42e16622fd807bb4e8a3b220580dee77 -r f3c2d456413d9c586c1ac9d861c3c2acca510def test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -249,7 +249,8 @@ sa_session = app.model.context.current repositories_to_uninstall = sa_session.query( app.model.ToolShedRepository ).all() for repository in repositories_to_uninstall: - if repository.status == app.model.ToolShedRepository.installation_status.UNINSTALLED: + if repository.status in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, + app.model.ToolShedRepository.installation_status.DEACTIVATED ]: continue if repository.status not in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, app.model.ToolShedRepository.installation_status.ERROR, https://bitbucket.org/galaxy/galaxy-central/commits/c5d68c98b9c5/ Changeset: c5d68c98b9c5 User: Dave Bouvier Date: 2013-10-22 22:27:12 Summary: Merge in next-stable. Affected #: 1 file diff -r 4a035502056b5b19d227a22e4cc7fa6901da3242 -r c5d68c98b9c50b42fdbc2a82f3bd85a1d320ace6 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -249,7 +249,8 @@ sa_session = app.model.context.current repositories_to_uninstall = sa_session.query( app.model.ToolShedRepository ).all() for repository in repositories_to_uninstall: - if repository.status == app.model.ToolShedRepository.installation_status.UNINSTALLED: + if repository.status in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, + app.model.ToolShedRepository.installation_status.DEACTIVATED ]: continue if repository.status not in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, app.model.ToolShedRepository.installation_status.ERROR, 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 22 Oct '13

22 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f82ad49f42e1/ Changeset: f82ad49f42e1 Branch: next-stable User: Dave Bouvier Date: 2013-10-22 21:24:05 Summary: Also exclude deactivated repositories from uninstallation. Affected #: 1 file diff -r b2c6618e150d6397e33ecd6ad4b046b580b35b83 -r f82ad49f42e16622fd807bb4e8a3b220580dee77 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -253,14 +253,15 @@ continue if repository.status not in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, app.model.ToolShedRepository.installation_status.ERROR, - app.model.ToolShedRepository.installation_status.INSTALLED ]: + app.model.ToolShedRepository.installation_status.INSTALLED, + app.model.ToolShedRepository.installation_status.DEACTIVATED ]: repository.status = app.model.ToolShedRepository.installation_status.ERROR sa_session.add( repository ) sa_session.flush() name = str( repository.name ) owner = str( repository.owner ) changeset_revision = str( repository.installed_changeset_revision ) - log.debug( 'Changeset revision %s of repository %s queued for uninstallation.', changeset_revision, name ) + log.debug( 'Changeset revision %s of %s repository %s queued for uninstallation.', changeset_revision, repository.status, name ) repository_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. test_install_repositories.generate_uninstall_method( repository_dict, deactivate_only ) https://bitbucket.org/galaxy/galaxy-central/commits/4a035502056b/ Changeset: 4a035502056b User: Dave Bouvier Date: 2013-10-22 21:24:55 Summary: Merge in fix from next-stable. Affected #: 1 file diff -r 556bf6487abc5a3383a399334d97e93e1a87cb54 -r 4a035502056b5b19d227a22e4cc7fa6901da3242 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -253,14 +253,15 @@ continue if repository.status not in [ app.model.ToolShedRepository.installation_status.UNINSTALLED, app.model.ToolShedRepository.installation_status.ERROR, - app.model.ToolShedRepository.installation_status.INSTALLED ]: + app.model.ToolShedRepository.installation_status.INSTALLED, + app.model.ToolShedRepository.installation_status.DEACTIVATED ]: repository.status = app.model.ToolShedRepository.installation_status.ERROR sa_session.add( repository ) sa_session.flush() name = str( repository.name ) owner = str( repository.owner ) changeset_revision = str( repository.installed_changeset_revision ) - log.debug( 'Changeset revision %s of repository %s queued for uninstallation.', changeset_revision, name ) + log.debug( 'Changeset revision %s of %s repository %s queued for uninstallation.', changeset_revision, repository.status, name ) repository_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. test_install_repositories.generate_uninstall_method( repository_dict, deactivate_only ) 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 22 Oct '13

22 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b2c6618e150d/ Changeset: b2c6618e150d Branch: next-stable User: greg Date: 2013-10-22 20:48:53 Summary: Fix for getting the status from the tool shed for installed repositories. Affected #: 1 file diff -r 2f0053f5952e9b93ded01fcd24ed87783dedc698 -r b2c6618e150d6397e33ecd6ad4b046b580b35b83 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2741,6 +2741,9 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if repository: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) tool_shed_status_dict = {} @@ -2751,21 +2754,24 @@ tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' else: next_installable_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) - if next_installable_revision: - tool_shed_status_dict[ 'latest_installable_revision' ] = 'False' + if repository_metadata is None: + if next_installable_revision: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' + else: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'False' else: - tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' + if next_installable_revision: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'False' + else: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' # Handle revision updates. if changeset_revision == repository.tip( trans.app ): tool_shed_status_dict[ 'revision_update' ] = 'False' else: - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, - trans.security.encode_id( repository.id ), - changeset_revision ) - if repository_metadata: + if repository_metadata is None: + tool_shed_status_dict[ 'revision_update' ] = 'True' + else: tool_shed_status_dict[ 'revision_update' ] = 'False' - else: - tool_shed_status_dict[ 'revision_update' ] = 'True' # Handle revision upgrades. ordered_metadata_changeset_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) num_metadata_revisions = len( ordered_metadata_changeset_revisions ) https://bitbucket.org/galaxy/galaxy-central/commits/556bf6487abc/ Changeset: 556bf6487abc User: greg Date: 2013-10-22 20:49:40 Summary: Merged from next-stable Affected #: 1 file diff -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa -r 556bf6487abc5a3383a399334d97e93e1a87cb54 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2741,6 +2741,9 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if repository: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) tool_shed_status_dict = {} @@ -2751,21 +2754,24 @@ tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' else: next_installable_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) - if next_installable_revision: - tool_shed_status_dict[ 'latest_installable_revision' ] = 'False' + if repository_metadata is None: + if next_installable_revision: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' + else: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'False' else: - tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' + if next_installable_revision: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'False' + else: + tool_shed_status_dict[ 'latest_installable_revision' ] = 'True' # Handle revision updates. if changeset_revision == repository.tip( trans.app ): tool_shed_status_dict[ 'revision_update' ] = 'False' else: - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, - trans.security.encode_id( repository.id ), - changeset_revision ) - if repository_metadata: + if repository_metadata is None: + tool_shed_status_dict[ 'revision_update' ] = 'True' + else: tool_shed_status_dict[ 'revision_update' ] = 'False' - else: - tool_shed_status_dict[ 'revision_update' ] = 'True' # Handle revision upgrades. ordered_metadata_changeset_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) num_metadata_revisions = len( ordered_metadata_changeset_revisions ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History panel: fix empty body on expanded and updating, do not show panel error on double zeros; HDA API: do not attempt set on non-hda; pack scripts
by commits-noreply＠bitbucket.org 22 Oct '13

22 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8bc80aa53e81/ Changeset: 8bc80aa53e81 User: carlfeberhard Date: 2013-10-22 20:13:37 Summary: History panel: fix empty body on expanded and updating, do not show panel error on double zeros; HDA API: do not attempt set on non-hda; pack scripts Affected #: 13 files diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -311,8 +311,9 @@ payload = self._validate_and_parse_update_payload( payload ) hda = self.get_dataset( trans, id, check_ownership=True, check_accessible=True, check_state=True ) - # additional checks here (security, etc.) - changed = self.set_hda_from_dict( trans, hda, payload ) + # get_dataset can return a string during an error + if hda and isinstance( hda, trans.model.HistoryDatasetAssociation ): + changed = self.set_hda_from_dict( trans, hda, payload ) except Exception, exception: log.error( 'Update of history (%s), HDA (%s) failed: %s', diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -46,7 +46,15 @@ _setUpListeners : function(){ // re-rendering on any model changes - this.model.on( 'change', this.render, this ); + this.model.on( 'change', function( model, options ){ + // if the model moved into the ready state and is expanded without details, fetch those details + if( this.model.changedAttributes().state && this.model.inReadyState() + && this.expanded && !this.model.hasDetails() ){ + this.model.fetch(); // will render automatically (due to lines below) + } else { + this.render(); + } + }, this ); //this.on( 'all', function( event ){ // this.log( event ); diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -69,17 +69,19 @@ } this._setUpListeners(); - this._installAjaxErrorHandler( this.ajaxErrorHandler ); // set up update timeout if needed this.checkForUpdates(); }, _setUpListeners : function(){ + this.on( 'error', function( model, xhr, options, msg, details ){ + this.errorHandler( model, xhr, options, msg, details ); + }); + // hda collection listening if( this.hdas ){ this.listenTo( this.hdas, 'error', function(){ - //this.ajaxErrorHandler.apply( this, arguments ); this.trigger.apply( this, [ 'error:hdas' ].concat( jQuery.makeArray( arguments ) ) ); }); } @@ -105,6 +107,11 @@ // } //}, + errorHandler : function( model, xhr, options, msg, details ){ + // clear update timeout on model err + this.clearUpdateTimeout(); + }, + // ........................................................................ common queries hasUser : function(){ var user = this.get( 'user' ); @@ -112,20 +119,6 @@ }, // ........................................................................ ajax - // override to add ajax error event - //TODO: into mixin/base - _installAjaxErrorHandler : function( handler ){ - this.sync = function _sync( method, model, options ){ - return Backbone.Model.prototype.sync.call( model, method, model, options ) - .fail( function( xhr, status, message ){ - handler.call( model, model, xhr, options, method ); - }); - }; - }, - - ajaxErrorHandler : function( model, xhr, options, method ){ - }, - // get the history's state from it's cummulative ds states, delay + update if needed // events: ready checkForUpdates : function( onReadyCallback ){ diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -157,7 +157,9 @@ errorHandler : function( model, xhr, options, msg, details ){ var parsed = this._parseErrorMessage( model, xhr, options, msg, details ); - if( xhr && xhr.status === 502 ){ + if( xhr && xhr.status === 0 && xhr.readyState === 0 ){ + + } else if( xhr && xhr.status === 502 ){ } else { // it's possible to have a triggered error before the message container is rendered - wait for it to show diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/packed/galaxy.upload.js --- a/static/scripts/packed/galaxy.upload.js +++ b/static/scripts/packed/galaxy.upload.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","galaxy.master","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,d,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],state:{init:"fa-icon-trash",queued:"fa-icon-spinner fa-icon-spin",running:"__running__",success:"fa-icon-ok",error:"fa-icon-warning-sign"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}var e=this;this.button_show=new d.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},on_unload:function(){if(e.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.master.prepend(this.button_show);var e=this;c.jsonFromUrl(galaxy_config.root+"api/datatypes",function(f){for(key in f){e.select_extension.push([f[key],f[key]])}});c.jsonFromUrl(galaxy_config.root+"api/genomes",function(f){var g=e.select_genome[0];e.select_genome=[];for(key in f){if(f[key].length>1){if(f[key][1]!==g[1]){e.select_genome.push(f[key])}}}e.select_genome.sort(function(i,h){return i[0]>h[0]?1:i[0]<h[0]?-1:0});e.select_genome.unshift(g)})},event_dragover:function(f){},event_dragleave:function(f){},event_announce:function(i,g,n){var f="#upload-"+i;$(this.el).find("tbody:last").append(this.template_row(f));var h=this.get_upload_item(i);h.fadeIn();h.find("#title").html(g.name);h.find("#size").html(this.size_to_string(g.size));var m=this;h.find("#symbol").on("click",function(){m.event_remove(i)});h.find("#text-content").on("keyup",function(){var o=h.find("#text-content").val().length;h.find("#size").html(m.size_to_string(o))});this.event_progress(i,g,0);this.counter.announce++;this.update_screen();if(g.size==-1){var l=h.find("#text");var j=8;var e=h.width()-2*j;var k=h.height()-j;l.css("width",e+"px");l.css("top",k+"px");h.height(k+l.height()+2*j);l.show()}},event_initialize:function(i,e,n){this.button_show.number(this.counter.announce);var g=this.get_upload_item(i);var k=g.find("#symbol");k.addClass(this.state.running);var j=Galaxy.currHistoryPanel.model.get("id");var f=g.find("#extension").val();var m=g.find("#genome").val();var l=g.find("#text-content").val();var h=g.find("#space_to_tabs").is(":checked");if(!l&&!(e.size>0)){return null}this.uploadbox.configure({url:galaxy_config.root+"api/tools/",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=m;tool_input.file_type=f;tool_input["files_0|NAME"]=e.name;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=l;tool_input.space_to_tabs=h;data={};data.history_id=j;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refresh()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("<strong>Failed: </strong>"+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_start:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#text-content").attr("disabled",true);$(this).find("#genome").attr("disabled",true);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.start()},event_stop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#text-content").attr("disabled",false);$(this).find("#genome").attr("disabled",false);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_create:function(){this.uploadbox.add([{name:"New File",size:-1}])},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Create:function(){f.event_create()},Upload:function(){f.event_start()},Pause:function(){f.event_stop()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()},},height:"400",width:"900"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:function(){f.event_dragover()},dragleave:function(){f.event_dragleave()},announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{if(e>0){e=e*10;f="b"}else{return"<strong>-</strong>"}}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'<div id="'+f+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+e+'" class="upload-info"></h6>'},template_row:function(f){var e='<tr id="'+f.substr(1)+'" class="upload-item"><td><div style="position: relative;"><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You may specify a list of URLs (one per line) or paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';e+='<td><select id="extension" class="extension">';for(key in this.select_extension){e+='<option value="'+this.select_extension[key][1]+'">'+this.select_extension[key][0]+"</option>"}e+="</select></td>";e+='<td><select id="genome" class="genome">';for(key in this.select_genome){e+='<option value="'+this.select_genome[key][1]+'">'+this.select_genome[key][0]+"</option>"}e+="</select></td>";e+='<td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="symbol '+this.state.init+'"></div></td></tr>';return e}});return{GalaxyUpload:a}}); \ No newline at end of file +define(["galaxy.modal","galaxy.master","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,d,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],state:{init:"fa-icon-trash",queued:"fa-icon-spinner fa-icon-spin",running:"__running__",success:"fa-icon-ok",error:"fa-icon-warning-sign"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}var e=this;this.button_show=new d.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},on_unload:function(){if(e.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.master.prepend(this.button_show);var e=this;c.jsonFromUrl(galaxy_config.root+"api/datatypes",function(f){for(key in f){e.select_extension.push([f[key],f[key]])}});c.jsonFromUrl(galaxy_config.root+"api/genomes",function(f){var g=e.select_genome[0];e.select_genome=[];for(key in f){if(f[key].length>1){if(f[key][1]!==g[1]){e.select_genome.push(f[key])}}}e.select_genome.sort(function(i,h){return i[0]>h[0]?1:i[0]<h[0]?-1:0});e.select_genome.unshift(g)})},event_dragover:function(f){},event_dragleave:function(f){},event_announce:function(i,g,n){var f="#upload-"+i;$(this.el).find("tbody:last").append(this.template_row(f));var h=this.get_upload_item(i);h.fadeIn();h.find("#title").html(g.name);h.find("#size").html(this.size_to_string(g.size));var m=this;h.find("#symbol").on("click",function(){m.event_remove(i)});h.find("#text-content").on("keyup",function(){var o=h.find("#text-content").val().length;h.find("#size").html(m.size_to_string(o))});this.event_progress(i,g,0);this.counter.announce++;this.update_screen();if(g.size==-1){var l=h.find("#text");var j=8;var e=h.width()-2*j;var k=h.height()-j;l.css("width",e+"px");l.css("top",k+"px");h.height(k+l.height()+2*j);l.show()}},event_initialize:function(i,e,n){this.button_show.number(this.counter.announce);var g=this.get_upload_item(i);var k=g.find("#symbol");k.addClass(this.state.running);var j=Galaxy.currHistoryPanel.model.get("id");var f=g.find("#extension").val();var m=g.find("#genome").val();var l=g.find("#text-content").val();var h=g.find("#space_to_tabs").is(":checked");if(!l&&!(e.size>0)){return null}this.uploadbox.configure({url:galaxy_config.root+"api/tools/",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=m;tool_input.file_type=f;tool_input["files_0|NAME"]=e.name;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=l;tool_input.space_to_tabs=h;data={};data.history_id=j;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refreshHdas()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("<strong>Failed: </strong>"+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_start:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#text-content").attr("disabled",true);$(this).find("#genome").attr("disabled",true);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.start()},event_stop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#text-content").attr("disabled",false);$(this).find("#genome").attr("disabled",false);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_create:function(){this.uploadbox.add([{name:"New File",size:-1}])},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Create:function(){f.event_create()},Upload:function(){f.event_start()},Pause:function(){f.event_stop()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()},},height:"400",width:"900"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:function(){f.event_dragover()},dragleave:function(){f.event_dragleave()},announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{if(e>0){e=e*10;f="b"}else{return"<strong>-</strong>"}}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'<div id="'+f+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+e+'" class="upload-info"></h6>'},template_row:function(f){var e='<tr id="'+f.substr(1)+'" class="upload-item"><td><div style="position: relative;"><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You may specify a list of URLs (one per line) or paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';e+='<td><select id="extension" class="extension">';for(key in this.select_extension){e+='<option value="'+this.select_extension[key][1]+'">'+this.select_extension[key][0]+"</option>"}e+="</select></td>";e+='<td><select id="genome" class="genome">';for(key in this.select_genome){e+='<option value="'+this.select_genome[key][1]+'">'+this.select_genome[key][0]+"</option>"}e+="</select></td>";e+='<td><input id="space_to_tabs" type="checkbox"></input></td><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="symbol '+this.state.init+'"></div></td></tr>';return e}});return{GalaxyUpload:a}}); \ No newline at end of file diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",this.render,this)},render:function(){var d=this,g=this.model.get("id"),e=this.model.get("state"),c=$("<div/>").attr("id","historyItem-"+g),f=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+g);this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();c.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+e);c.append(this._render_warnings());c.append(this._render_titleBar());this._setUpBehaviors(c);this.body=$(this._render_body());c.append(this.body);this.$el.fadeOut(this.fxSpeed,function(){d.$el.children().remove();d.$el.append(c).fadeIn(d.fxSpeed,function(){d.log(d+" rendered:",d.$el);var h="rendered";if(f){h+=":initial"}else{if(d.model.inReadyState()){h+=":ready"}}d.trigger(h)})});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(a.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var c=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');c.append(this._render_titleButtons());c.append('<span class="state-icon"></span>');c.append(this._render_titleLink());return c},_render_titleButtons:function(){var c=$('<div class="historyItemButtons"></div>');c.append(this._render_displayButton());return c},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var d={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){d.enabled=false;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.enabled=false;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.on_click=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer: "+c.model.get("name"),type:"url",location:"center",content:c.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(d)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(a.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var c=_.extend(this.model.toJSON(),{urls:this.urls});return a.templates.hdaSummary(c)},_render_primaryActionButtons:function(e){var c=this,d=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(e,function(f){d.append(f.call(c))});return d},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var c=a.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(c.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(e){e=e||this.$el;var f=e.find("div.display-apps"),c=this.model.get("display_types"),d=this.model.get("display_apps");if((!this.model.hasData())||(!e||!e.length)||(!f.length)){return}f.html(null);if(!_.isEmpty(c)){f.append(a.templates.displayApps({displayApps:c}))}if(!_.isEmpty(d)){f.append(a.templates.displayApps({displayApps:d}))}},_render_peek:function(){var c=this.model.get("peek");if(!c){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(c))},_render_body:function(){var c=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(c);c.css("display","block")}return c},_render_body_html:function(c){c.html("");switch(this.model.get("state")){case b.HistoryDatasetAssociation.STATES.NEW:this._render_body_new(c);break;case b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(c);break;case b.HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(c);break;case b.HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(c);break;case b.HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(c);break;case b.HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(c);break;case b.HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(c);break;case b.HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(c);break;case b.HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(c);break;case b.HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(c);break;case b.HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(c);break;case b.HistoryDatasetAssociation.STATES.OK:this._render_body_ok(c);break;default:c.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}c.append('<div style="clear: both"></div>');this._setUpBehaviors(c)},_render_body_new:function(d){var c=_l("This is a new dataset and not all of its data are available yet");d.append($("<div>"+_l(c)+"</div>"))},_render_body_not_viewable:function(c){c.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(c){c.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(c){c.append($("<div>"+_l("Job is waiting to run")+"</div>"));c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(c){c.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(c){c.append("<div>"+_l("Job is currently running")+"</div>");c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(c){if(!this.model.get("purged")){c.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}c.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(c){c.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(c){c.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(c){c.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(c){c.append($(a.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(c)},_render_body_ok:function(c){c.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){c.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}c.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));c.append('<div class="clear"/>');c.append(this._render_displayAppArea());this._render_displayApps(c);c.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(e,c){var d=this;c=(c===undefined)?(!this.body.is(":visible")):(c);if(c){if(this.model.inReadyState()&&!this.model.hasDetails()){var f=this.model.fetch();f.done(function(g){d.expandBody()})}else{this.expandBody()}}else{this.collapseBody()}},expandBody:function(){var c=this;c._render_body_html(c.body);this.body.slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})},collapseBody:function(){var c=this;this.body.slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]};return{HDABaseView:a,}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(){var d=this,g=this.model.get("id"),e=this.model.get("state"),c=$("<div/>").attr("id","historyItem-"+g),f=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+g);this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();c.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+e);c.append(this._render_warnings());c.append(this._render_titleBar());this._setUpBehaviors(c);this.body=$(this._render_body());c.append(this.body);this.$el.fadeOut(this.fxSpeed,function(){d.$el.children().remove();d.$el.append(c).fadeIn(d.fxSpeed,function(){d.log(d+" rendered:",d.$el);var h="rendered";if(f){h+=":initial"}else{if(d.model.inReadyState()){h+=":ready"}}d.trigger(h)})});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(a.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var c=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');c.append(this._render_titleButtons());c.append('<span class="state-icon"></span>');c.append(this._render_titleLink());return c},_render_titleButtons:function(){var c=$('<div class="historyItemButtons"></div>');c.append(this._render_displayButton());return c},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var d={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){d.enabled=false;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.enabled=false;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.on_click=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer: "+c.model.get("name"),type:"url",location:"center",content:c.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(d)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(a.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var c=_.extend(this.model.toJSON(),{urls:this.urls});return a.templates.hdaSummary(c)},_render_primaryActionButtons:function(e){var c=this,d=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(e,function(f){d.append(f.call(c))});return d},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var c=a.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(c.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(e){e=e||this.$el;var f=e.find("div.display-apps"),c=this.model.get("display_types"),d=this.model.get("display_apps");if((!this.model.hasData())||(!e||!e.length)||(!f.length)){return}f.html(null);if(!_.isEmpty(c)){f.append(a.templates.displayApps({displayApps:c}))}if(!_.isEmpty(d)){f.append(a.templates.displayApps({displayApps:d}))}},_render_peek:function(){var c=this.model.get("peek");if(!c){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(c))},_render_body:function(){var c=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(c);c.css("display","block")}return c},_render_body_html:function(c){c.html("");switch(this.model.get("state")){case b.HistoryDatasetAssociation.STATES.NEW:this._render_body_new(c);break;case b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(c);break;case b.HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(c);break;case b.HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(c);break;case b.HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(c);break;case b.HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(c);break;case b.HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(c);break;case b.HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(c);break;case b.HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(c);break;case b.HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(c);break;case b.HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(c);break;case b.HistoryDatasetAssociation.STATES.OK:this._render_body_ok(c);break;default:c.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}c.append('<div style="clear: both"></div>');this._setUpBehaviors(c)},_render_body_new:function(d){var c=_l("This is a new dataset and not all of its data are available yet");d.append($("<div>"+_l(c)+"</div>"))},_render_body_not_viewable:function(c){c.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(c){c.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(c){c.append($("<div>"+_l("Job is waiting to run")+"</div>"));c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(c){c.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(c){c.append("<div>"+_l("Job is currently running")+"</div>");c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(c){if(!this.model.get("purged")){c.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}c.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(c){c.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(c){c.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(c){c.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));c.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(c){c.append($(a.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(c)},_render_body_ok:function(c){c.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){c.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}c.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));c.append('<div class="clear"/>');c.append(this._render_displayAppArea());this._render_displayApps(c);c.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(e,c){var d=this;c=(c===undefined)?(!this.body.is(":visible")):(c);if(c){if(this.model.inReadyState()&&!this.model.hasDetails()){var f=this.model.fetch();f.done(function(g){d.expandBody()})}else{this.expandBody()}}else{this.collapseBody()}},expandBody:function(){var c=this;c._render_body_html(c.body);this.body.slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})},collapseBody:function(){var c=this;this.body.slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]};return{HDABaseView:a,}}); \ No newline at end of file diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(a){var c=Backbone.Model.extend(LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories",renameUrl:function(){var e=this.get("id");if(!e){return undefined}return"/history/rename_async?id="+this.get("id")},annotateUrl:function(){var e=this.get("id");if(!e){return undefined}return"/history/annotate_async?id="+this.get("id")},tagUrl:function(){var e=this.get("id");if(!e){return undefined}return"/tag/get_tagging_elt_async?item_id="+this.get("id")+"&item_class=History"},initialize:function(f,g,e){e=e||{};this.logger=e.logger||null;this.log(this+".initialize:",f,g,e);this.hdas=new a.HDACollection(g||[],{historyId:this.get("id")});if(g&&_.isArray(g)){this.hdas.reset(g)}this._setUpListeners();this._installAjaxErrorHandler(this.ajaxErrorHandler);this.checkForUpdates()},_setUpListeners:function(){if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(f,e){if(this.hdas){this.hdas.historyId=e}},this)},hasUser:function(){var e=this.get("user");return !!(e&&e.id)},_installAjaxErrorHandler:function(f){this.sync=function e(i,h,g){return Backbone.Model.prototype.sync.call(h,i,h,g).fail(function(l,j,k){f.call(h,h,l,g,i)})}},ajaxErrorHandler:function(f,g,e,h){},checkForUpdates:function(e){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(e)){e.call(this)}}return this},setUpdateTimeout:function(e){e=e||c.UPDATE_DELAY;var f=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){f.refresh()},e);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(f,e){f=f||[];e=e||{};var g=this;e.data=e.data||{};if(f.length){e.data.details=f.join(",")}var h=this.hdas.fetch(e);h.done(function(i){g.checkForUpdates(function(){this.fetch()})});return h},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});c.UPDATE_DELAY=4000;c.getHistoryData=function d(f,p){p=p||{};var j=p.hdaDetailIds||[];var l=jQuery.Deferred(),k=null;function g(q){return jQuery.ajax("/api/histories/"+f)}function e(q){if(!q||!q.state_ids){return 0}return _.reduce(q.state_ids,function(r,t,s){return r+t.length},0)}function o(r){if(!e(r)){return[]}if(_.isFunction(j)){j=j(r)}var q=(j.length)?({details:j.join(",")}):({});return jQuery.ajax("/api/histories/"+r.id+"/contents",{data:q})}var n=p.historyFn||g,m=p.hdaFn||o;var i=n(f);i.done(function(q){k=q;l.notify({status:"history data retrieved",historyJSON:k})});i.fail(function(s,q,r){l.reject(s,"loading the history")});var h=i.then(m);h.then(function(q){l.notify({status:"dataset data retrieved",historyJSON:k,hdaJSON:q});l.resolve(k,q)});h.fail(function(s,q,r){l.reject(s,"loading the datasets",{history:k})});return l};var b=Backbone.Collection.extend(LoggableMixin).extend({model:c,urlRoot:"api/histories"});return{History:c,HistoryCollection:b}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(a){var c=Backbone.Model.extend(LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories",renameUrl:function(){var e=this.get("id");if(!e){return undefined}return"/history/rename_async?id="+this.get("id")},annotateUrl:function(){var e=this.get("id");if(!e){return undefined}return"/history/annotate_async?id="+this.get("id")},tagUrl:function(){var e=this.get("id");if(!e){return undefined}return"/tag/get_tagging_elt_async?item_id="+this.get("id")+"&item_class=History"},initialize:function(f,g,e){e=e||{};this.logger=e.logger||null;this.log(this+".initialize:",f,g,e);this.hdas=new a.HDACollection(g||[],{historyId:this.get("id")});if(g&&_.isArray(g)){this.hdas.reset(g)}this._setUpListeners();this.checkForUpdates()},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(f,e){if(this.hdas){this.hdas.historyId=e}},this)},errorHandler:function(f,i,e,h,g){this.clearUpdateTimeout()},hasUser:function(){var e=this.get("user");return !!(e&&e.id)},checkForUpdates:function(e){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(e)){e.call(this)}}return this},setUpdateTimeout:function(e){e=e||c.UPDATE_DELAY;var f=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){f.refresh()},e);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(f,e){f=f||[];e=e||{};var g=this;e.data=e.data||{};if(f.length){e.data.details=f.join(",")}var h=this.hdas.fetch(e);h.done(function(i){g.checkForUpdates(function(){this.fetch()})});return h},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});c.UPDATE_DELAY=4000;c.getHistoryData=function d(f,p){p=p||{};var j=p.hdaDetailIds||[];var l=jQuery.Deferred(),k=null;function g(q){return jQuery.ajax("/api/histories/"+f)}function e(q){if(!q||!q.state_ids){return 0}return _.reduce(q.state_ids,function(r,t,s){return r+t.length},0)}function o(r){if(!e(r)){return[]}if(_.isFunction(j)){j=j(r)}var q=(j.length)?({details:j.join(",")}):({});return jQuery.ajax("/api/histories/"+r.id+"/contents",{data:q})}var n=p.historyFn||g,m=p.hdaFn||o;var i=n(f);i.done(function(q){k=q;l.notify({status:"history data retrieved",historyJSON:k})});i.fail(function(s,q,r){l.reject(s,"loading the history")});var h=i.then(m);h.then(function(q){l.notify({status:"dataset data retrieved",historyJSON:k,hdaJSON:q});l.resolve(k,q)});h.fail(function(s,q,r){l.reject(s,"loading the datasets",{history:k})});return l};var b=Backbone.Collection.extend(LoggableMixin).extend({model:c,urlRoot:"api/histories"});return{History:c,HistoryCollection:b}}); \ No newline at end of file diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(d,b,a){var c=Backbone.View.extend(LoggableMixin).extend({HDAView:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:300,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"clearMessages"},initialize:function(e){e=e||{};if(e.logger){this.logger=e.logger}this.log(this+".initialize:",e);this._setUpListeners();this.hdaViews={};this.urls={};this.indicator=new LoadingIndicator(this.$el);if(this.model){this._setUpWebStorage(e.initiallyExpanded,e.show_deleted,e.show_hidden);this._setUpModelEventHandlers()}if(e.onready){e.onready.call(this)}},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});this.on("loading-history",function(){this.showLoadingIndicator()});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(e){this.log(this+"",arguments)},this)}},errorHandler:function(g,j,f,i,h){var e=this._parseErrorMessage(g,j,f,i,h);if(j&&j.status===502){}else{if(!this.$el.find("#message-container").is(":visible")){this.once("rendered",function(){this.displayMessage("error",e.message,e.details)})}else{this.displayMessage("error",e.message,e.details)}}},_parseErrorMessage:function(h,l,g,k,j){var f=Galaxy.currUser,e={message:this._bePolite(k),details:{user:(f instanceof User)?(f.toJSON()):(f+""),source:(h instanceof Backbone.Model)?(h.toJSON()):(h+""),xhr:l,options:(l)?(_.omit(g,"xhr")):(g)}};_.extend(e.details,j||{});if(l&&_.isFunction(l.getAllResponseHeaders)){var i=l.getAllResponseHeaders();i=_.compact(i.split("\n"));i=_.map(i,function(m){return m.split(": ")});e.details.xhr.responseHeaders=_.object(i)}return e},_bePolite:function(e){e=e||_l("An error occurred while getting updates from the server");return e+". "+_l("Please contact a Galaxy administrator if the problem persists.")},_loadHistoryFromXHR:function(g,f){var e=this;g.then(function(h,i){e.setModel(h,i,f)});g.fail(function(i,h){e.render()});return g},setModel:function(g,e,f){f=f||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){g.user=Galaxy.currUser.toJSON()}this.model=new d.History(g,e,f);this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},loadHistory:function(h,g,f,k,i){this.trigger("loading-history",this);g=g||{};var e=this;var j=d.History.getHistoryData(h,{historyFn:f,hdaFn:k,hdaDetailIds:g.initiallyExpanded||i});return this._loadHistoryFromXHR(j,g).fail(function(n,l,m){e.trigger("error",e,n,g,_l("An error was encountered while "+l),{historyId:h,history:m||{}})}).always(function(){e.trigger("loading-done",e)})},loadHistoryWithHDADetails:function(h,g,f,j){var e=this,i=function(k){return e.getExpandedHdaIds(k.id)};return this.loadHistory(h,g,f,j,i)},switchToHistory:function(h,g){var e=this,f=function(){return jQuery.post("/api/histories/"+h+"/set_as_current")};return this.loadHistoryWithHDADetails(h,g,f).then(function(j,i){e.trigger("switched-history",e)})},loadCurrentHistory:function(f){var e=this;return this.loadHistoryWithHDADetails("current",f).then(function(h,g){e.trigger("current-history",e)})},createNewHistory:function(g){var e=this,f=function(){return jQuery.post("/api/histories",{current:true})};return this.loadHistory(undefined,g,f).then(function(i,h){e.trigger("new-history",e)})},refreshHdas:function(f,e){if(this.model){return this.model.refresh(f,e)}return $.when()},_getStorageKey:function(e){if(!e){throw new Error("_getStorageKey needs valid id: "+e)}return("history:"+e)},_setUpWebStorage:function(f,e,g){this.storage=new PersistentStorage(this._getStorageKey(this.model.get("id")),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(f){this.storage.set("exandedHdas",f)}if((e===true)||(e===false)){this.storage.set("show_deleted",e)}if((g===true)||(g===false)){this.storage.set("show_hidden",g)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var e in sessionStorage){if(e.indexOf("HistoryView.")===0){sessionStorage.removeItem(e)}}},getStoredOptions:function(f){if(!f||f==="current"){return(this.storage)?(this.storage.get()):({})}var e=sessionStorage.getItem(this._getStorageKey(f));return(e===null)?({}):(JSON.parse(e))},getExpandedHdaIds:function(e){var f=this.getStoredOptions(e).expandedHdas;return((_.isEmpty(f))?([]):(_.keys(f)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(f,h,e,g){this.errorHandler(f,h,e,g)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this);this.model.hdas.on("state:ready",function(f,g,e){if((!f.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(f.get("id"))}},this)},addHdaView:function(h){this.log("add."+this,h);var f=this;if(!h.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function g(j){var i=f.$el.find("#emptyHistoryMessage");if(i.is(":visible")){i.fadeOut(f.fxSpeed,j)}else{j()}},function e(j){f.scrollToTop();var i=f.$el.find("#"+f.model.get("id")+"-datasets");f.createHdaView(h).$el.hide().prependTo(i).slideDown(f.fxSpeed)}])},createHdaView:function(g){var f=g.get("id"),e=this.storage.get("expandedHdas").get(f),h=new this.HDAView({model:g,expanded:e,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(h);this.hdaViews[f]=h;return h.render()},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(e.get("id"))}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(e.get("id"))}},removeHdaView:function(g){var e=this,f=this.hdaViews[g];if(!f){return}f.$el.fadeOut(e.fxSpeed,function(){f.remove();delete e.hdaViews[g];if(_.isEmpty(e.hdaViews)){e.$el.find("#emptyHistoryMessage").fadeIn(e.fxSpeed)}})},render:function(g){var e=this,f;if(this.model){f=this.renderModel()}else{f=this.renderWithoutModel()}$(e).queue("fx",[function(h){if(e.$el.is(":visible")){e.$el.fadeOut(e.fxSpeed,h)}else{h()}},function(h){e.$el.empty();if(f){e.$el.append(f.children())}e.$el.fadeIn(e.fxSpeed,h)},function(h){e._setUpBehaviours();if(g){g.call(this)}}]);return this},renderModel:function(){var e=$("<div/>");e.append(c.templates.historyPanel(this.model.toJSON()));e.find("[title]").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(e.find("#"+this.model.get("id")+"-datasets"))){e.find("#emptyHistoryMessage").show()}return e},renderWithoutModel:function(){var e=$("<div/>"),f=$("<div/>").attr("id","message-container").css({"margin-left":"4px","margin-right":"4px"});return e.append(f)},renderItems:function(f){this.hdaViews={};var e=this,g=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(g,function(j){var i=j.get("id"),h=e.storage.get("expandedHdas").get(i);e.hdaViews[i]=new e.HDAView({model:j,expanded:h,hasUser:e.model.hasUser(),logger:e.logger});e._setUpHdaListeners(e.hdaViews[i]);f.prepend(e.hdaViews[i].render().$el)});return g.length},_setUpHdaListeners:function(f){var e=this;f.on("body-expanded",function(g){e.storage.get("expandedHdas").set(g,true)});f.on("body-collapsed",function(g){e.storage.get("expandedHdas").deleteKey(g)});f.on("error",function(h,j,g,i){e.errorHandler(h,j,g,i)})},_setUpBehaviours:function(){if(!this.model||!(this.model.get("user")&&this.model.get("user").email)){return}var e=this,f=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(f.is(":hidden")){f.slideDown(e.fxSpeed)}else{f.slideUp(e.fxSpeed)}return false});async_save_text("history-name-container","history-name",this.model.renameUrl(),"new_name",18);async_save_text("history-annotation-container","history-annotation",this.model.annotateUrl(),"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(e){e.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},loadAndDisplayTags:function(g){this.log(this+".loadAndDisplayTags",g);var e=this,h=this.$el.find("#history-tag-area"),f=h.find(".tag-elt");this.log("\t tagArea",h," tagElt",f);if(h.is(":hidden")){if(!jQuery.trim(f.html())){$.ajax({url:e.model.tagUrl(),error:function(k,j,i){e.log("Error loading tag area html",k,j,i);e.trigger("error",e,k,null,_l("Error loading tags"))},success:function(i){f.html(i);f.find("[title]").tooltip();h.slideDown(e.fxSpeed)}})}else{h.slideDown(e.fxSpeed)}}else{h.slideUp(e.fxSpeed)}return false},showLoadingIndicator:function(f,e,g){e=(e!==undefined)?(e):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,g)}else{this.$el.fadeOut(e);this.indicator.show(e,g)}},hideLoadingIndicator:function(e,f){e=(e!==undefined)?(e):(this.fxSpeed);if(this.indicator){this.indicator.hide(e,f)}},displayMessage:function(j,k,i){var g=this;this.scrollToTop();var h=this.$el.find("#message-container"),e=$("<div/>").addClass(j+"message").html(k);if(!_.isEmpty(i)){var f=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(g.messageToModalOptions(j,k,i));return false});e.append(" ",f)}return h.html(e)},messageToModalOptions:function(i,k,h){var e=this,j=$("<div/>"),g={title:"Details"};function f(l){l=_.omit(l,_.functions(l));return["<table>",_.map(l,function(n,m){n=(_.isObject(n))?(f(n)):(n);return'<tr><td style="vertical-align: top; color: grey">'+m+'</td><td style="padding-left: 8px">'+n+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(h)){g.body=j.append(f(h))}else{g.body=j.html(h)}g.buttons={Ok:function(){Galaxy.modal.hide();e.clearMessages()}};return g},clearMessages:function(){var e=this.$el.find("#message-container");e.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(e){this.$el.parent().scrollTop(e)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(f,g){if(!g){this.$el.parent().parent().scrollTop(f);return this}var e=window,h=this.$el.parent().parent(),j=$(e).innerHeight(),i=(j/2)-(g/2);$(h).scrollTop(f-i);return this},scrollToId:function(f){if((!f)||(!this.hdaViews[f])){return this}var e=this.hdaViews[f].$el;this.scrollIntoView(e.offset().top,e.outerHeight());return this},scrollToHid:function(e){var f=this.model.hdas.getByHid(e);if(!f){return this}return this.scrollToId(f.id)},connectToQuotaMeter:function(e){if(!e){return this}this.listenTo(e,"quota:over",this.showQuotaMessage);this.listenTo(e,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(e&&e.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var e=this.$el.find("#quota-message-container");if(e.is(":hidden")){e.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var e=this.$el.find("#quota-message-container");if(!e.is(":hidden")){e.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(e){if(!e){return this}this.on("new-storage",function(g,f){if(e&&g){e.findItemByHtml(_l("Include Deleted Datasets")).checked=g.get("show_deleted");e.findItemByHtml(_l("Include Hidden Datasets")).checked=g.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});c.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]};return{HistoryPanel:c}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(d,b,a){var c=Backbone.View.extend(LoggableMixin).extend({HDAView:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:300,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"clearMessages"},initialize:function(e){e=e||{};if(e.logger){this.logger=e.logger}this.log(this+".initialize:",e);this._setUpListeners();this.hdaViews={};this.urls={};this.indicator=new LoadingIndicator(this.$el);if(this.model){this._setUpWebStorage(e.initiallyExpanded,e.show_deleted,e.show_hidden);this._setUpModelEventHandlers()}if(e.onready){e.onready.call(this)}},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});this.on("loading-history",function(){this.showLoadingIndicator()});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(e){this.log(this+"",arguments)},this)}},errorHandler:function(g,j,f,i,h){var e=this._parseErrorMessage(g,j,f,i,h);if(j&&j.status===0&&j.readyState===0){}else{if(j&&j.status===502){}else{if(!this.$el.find("#message-container").is(":visible")){this.once("rendered",function(){this.displayMessage("error",e.message,e.details)})}else{this.displayMessage("error",e.message,e.details)}}}},_parseErrorMessage:function(h,l,g,k,j){var f=Galaxy.currUser,e={message:this._bePolite(k),details:{user:(f instanceof User)?(f.toJSON()):(f+""),source:(h instanceof Backbone.Model)?(h.toJSON()):(h+""),xhr:l,options:(l)?(_.omit(g,"xhr")):(g)}};_.extend(e.details,j||{});if(l&&_.isFunction(l.getAllResponseHeaders)){var i=l.getAllResponseHeaders();i=_.compact(i.split("\n"));i=_.map(i,function(m){return m.split(": ")});e.details.xhr.responseHeaders=_.object(i)}return e},_bePolite:function(e){e=e||_l("An error occurred while getting updates from the server");return e+". "+_l("Please contact a Galaxy administrator if the problem persists.")},_loadHistoryFromXHR:function(g,f){var e=this;g.then(function(h,i){e.setModel(h,i,f)});g.fail(function(i,h){e.render()});return g},setModel:function(g,e,f){f=f||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){g.user=Galaxy.currUser.toJSON()}this.model=new d.History(g,e,f);this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},loadHistory:function(h,g,f,k,i){this.trigger("loading-history",this);g=g||{};var e=this;var j=d.History.getHistoryData(h,{historyFn:f,hdaFn:k,hdaDetailIds:g.initiallyExpanded||i});return this._loadHistoryFromXHR(j,g).fail(function(n,l,m){e.trigger("error",e,n,g,_l("An error was encountered while "+l),{historyId:h,history:m||{}})}).always(function(){e.trigger("loading-done",e)})},loadHistoryWithHDADetails:function(h,g,f,j){var e=this,i=function(k){return e.getExpandedHdaIds(k.id)};return this.loadHistory(h,g,f,j,i)},switchToHistory:function(h,g){var e=this,f=function(){return jQuery.post("/api/histories/"+h+"/set_as_current")};return this.loadHistoryWithHDADetails(h,g,f).then(function(j,i){e.trigger("switched-history",e)})},loadCurrentHistory:function(f){var e=this;return this.loadHistoryWithHDADetails("current",f).then(function(h,g){e.trigger("current-history",e)})},createNewHistory:function(g){var e=this,f=function(){return jQuery.post("/api/histories",{current:true})};return this.loadHistory(undefined,g,f).then(function(i,h){e.trigger("new-history",e)})},refreshHdas:function(f,e){if(this.model){return this.model.refresh(f,e)}return $.when()},_getStorageKey:function(e){if(!e){throw new Error("_getStorageKey needs valid id: "+e)}return("history:"+e)},_setUpWebStorage:function(f,e,g){this.storage=new PersistentStorage(this._getStorageKey(this.model.get("id")),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(f){this.storage.set("exandedHdas",f)}if((e===true)||(e===false)){this.storage.set("show_deleted",e)}if((g===true)||(g===false)){this.storage.set("show_hidden",g)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var e in sessionStorage){if(e.indexOf("HistoryView.")===0){sessionStorage.removeItem(e)}}},getStoredOptions:function(f){if(!f||f==="current"){return(this.storage)?(this.storage.get()):({})}var e=sessionStorage.getItem(this._getStorageKey(f));return(e===null)?({}):(JSON.parse(e))},getExpandedHdaIds:function(e){var f=this.getStoredOptions(e).expandedHdas;return((_.isEmpty(f))?([]):(_.keys(f)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(f,h,e,g){this.errorHandler(f,h,e,g)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this);this.model.hdas.on("state:ready",function(f,g,e){if((!f.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(f.get("id"))}},this)},addHdaView:function(h){this.log("add."+this,h);var f=this;if(!h.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function g(j){var i=f.$el.find("#emptyHistoryMessage");if(i.is(":visible")){i.fadeOut(f.fxSpeed,j)}else{j()}},function e(j){f.scrollToTop();var i=f.$el.find("#"+f.model.get("id")+"-datasets");f.createHdaView(h).$el.hide().prependTo(i).slideDown(f.fxSpeed)}])},createHdaView:function(g){var f=g.get("id"),e=this.storage.get("expandedHdas").get(f),h=new this.HDAView({model:g,expanded:e,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(h);this.hdaViews[f]=h;return h.render()},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(e.get("id"))}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(e.get("id"))}},removeHdaView:function(g){var e=this,f=this.hdaViews[g];if(!f){return}f.$el.fadeOut(e.fxSpeed,function(){f.remove();delete e.hdaViews[g];if(_.isEmpty(e.hdaViews)){e.$el.find("#emptyHistoryMessage").fadeIn(e.fxSpeed)}})},render:function(g){var e=this,f;if(this.model){f=this.renderModel()}else{f=this.renderWithoutModel()}$(e).queue("fx",[function(h){if(e.$el.is(":visible")){e.$el.fadeOut(e.fxSpeed,h)}else{h()}},function(h){e.$el.empty();if(f){e.$el.append(f.children())}e.$el.fadeIn(e.fxSpeed,h)},function(h){e._setUpBehaviours();if(g){g.call(this)}}]);return this},renderModel:function(){var e=$("<div/>");e.append(c.templates.historyPanel(this.model.toJSON()));e.find("[title]").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(e.find("#"+this.model.get("id")+"-datasets"))){e.find("#emptyHistoryMessage").show()}return e},renderWithoutModel:function(){var e=$("<div/>"),f=$("<div/>").attr("id","message-container").css({"margin-left":"4px","margin-right":"4px"});return e.append(f)},renderItems:function(f){this.hdaViews={};var e=this,g=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(g,function(j){var i=j.get("id"),h=e.storage.get("expandedHdas").get(i);e.hdaViews[i]=new e.HDAView({model:j,expanded:h,hasUser:e.model.hasUser(),logger:e.logger});e._setUpHdaListeners(e.hdaViews[i]);f.prepend(e.hdaViews[i].render().$el)});return g.length},_setUpHdaListeners:function(f){var e=this;f.on("body-expanded",function(g){e.storage.get("expandedHdas").set(g,true)});f.on("body-collapsed",function(g){e.storage.get("expandedHdas").deleteKey(g)});f.on("error",function(h,j,g,i){e.errorHandler(h,j,g,i)})},_setUpBehaviours:function(){if(!this.model||!(this.model.get("user")&&this.model.get("user").email)){return}var e=this,f=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(f.is(":hidden")){f.slideDown(e.fxSpeed)}else{f.slideUp(e.fxSpeed)}return false});async_save_text("history-name-container","history-name",this.model.renameUrl(),"new_name",18);async_save_text("history-annotation-container","history-annotation",this.model.annotateUrl(),"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(e){e.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},loadAndDisplayTags:function(g){this.log(this+".loadAndDisplayTags",g);var e=this,h=this.$el.find("#history-tag-area"),f=h.find(".tag-elt");this.log("\t tagArea",h," tagElt",f);if(h.is(":hidden")){if(!jQuery.trim(f.html())){$.ajax({url:e.model.tagUrl(),error:function(k,j,i){e.log("Error loading tag area html",k,j,i);e.trigger("error",e,k,null,_l("Error loading tags"))},success:function(i){f.html(i);f.find("[title]").tooltip();h.slideDown(e.fxSpeed)}})}else{h.slideDown(e.fxSpeed)}}else{h.slideUp(e.fxSpeed)}return false},showLoadingIndicator:function(f,e,g){e=(e!==undefined)?(e):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,g)}else{this.$el.fadeOut(e);this.indicator.show(e,g)}},hideLoadingIndicator:function(e,f){e=(e!==undefined)?(e):(this.fxSpeed);if(this.indicator){this.indicator.hide(e,f)}},displayMessage:function(j,k,i){var g=this;this.scrollToTop();var h=this.$el.find("#message-container"),e=$("<div/>").addClass(j+"message").html(k);if(!_.isEmpty(i)){var f=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(g.messageToModalOptions(j,k,i));return false});e.append(" ",f)}return h.html(e)},messageToModalOptions:function(i,k,h){var e=this,j=$("<div/>"),g={title:"Details"};function f(l){l=_.omit(l,_.functions(l));return["<table>",_.map(l,function(n,m){n=(_.isObject(n))?(f(n)):(n);return'<tr><td style="vertical-align: top; color: grey">'+m+'</td><td style="padding-left: 8px">'+n+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(h)){g.body=j.append(f(h))}else{g.body=j.html(h)}g.buttons={Ok:function(){Galaxy.modal.hide();e.clearMessages()}};return g},clearMessages:function(){var e=this.$el.find("#message-container");e.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(e){this.$el.parent().scrollTop(e)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(f,g){if(!g){this.$el.parent().parent().scrollTop(f);return this}var e=window,h=this.$el.parent().parent(),j=$(e).innerHeight(),i=(j/2)-(g/2);$(h).scrollTop(f-i);return this},scrollToId:function(f){if((!f)||(!this.hdaViews[f])){return this}var e=this.hdaViews[f].$el;this.scrollIntoView(e.offset().top,e.outerHeight());return this},scrollToHid:function(e){var f=this.model.hdas.getByHid(e);if(!f){return this}return this.scrollToId(f.id)},connectToQuotaMeter:function(e){if(!e){return this}this.listenTo(e,"quota:over",this.showQuotaMessage);this.listenTo(e,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(e&&e.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var e=this.$el.find("#quota-message-container");if(e.is(":hidden")){e.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var e=this.$el.find("#quota-message-container");if(!e.is(":hidden")){e.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(e){if(!e){return this}this.on("new-storage",function(g,f){if(e&&g){e.findItemByHtml(_l("Include Deleted Datasets")).checked=g.get("show_deleted");e.findItemByHtml(_l("Include Hidden Datasets")).checked=g.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});c.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]};return{HistoryPanel:c}}); \ No newline at end of file diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/packed/templates/compiled/history-templates.js --- a/static/scripts/packed/templates/compiled/history-templates.js +++ b/static/scripts/packed/templates/compiled/history-templates.js @@ -1,1 +1,1 @@ -Handlebars.registerPartial("clearFloatDiv",function(a){return'<div class="clear"></div>'});Handlebars.registerHelper("warningmessagesmall",function(a){return'<div class="warningmessagesmall"><strong>'+a.fn(this)+"</strong></div>"});Handlebars.registerHelper("local",function(a){return _l(a.fn(this))});(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-annotationArea"]=b(function(g,m,f,l,k){this.compilerInfo=[4,">= 1.0.0"];f=this.merge(f,g.helpers);k=k||{};var i="",d,p,h="function",j=this.escapeExpression,o=this,n=f.blockHelperMissing;function e(r,q){return"Annotation"}function c(r,q){return"Edit dataset annotation"}i+='\n<div id="';if(d=f.id){d=d.call(m,{hash:{},data:k})}else{d=m.id;d=typeof d===h?d.apply(m):d}i+=j(d)+'-annotation-area" class="annotation-area" style="display: none;">\n <strong>';p={hash:{},inverse:o.noop,fn:o.program(1,e,k),data:k};if(d=f.local){d=d.call(m,p)}else{d=m.local;d=typeof d===h?d.apply(m):d}if(!f.local){d=n.call(m,d,p)}if(d||d===0){i+=d}i+=':</strong>\n <div id="';if(d=f.id){d=d.call(m,{hash:{},data:k})}else{d=m.id;d=typeof d===h?d.apply(m):d}i+=j(d)+'-anotation-elt" class="annotation-elt editable-text"\n style="margin: 1px 0px 1px 0px" title="';p={hash:{},inverse:o.noop,fn:o.program(3,c,k),data:k};if(d=f.local){d=d.call(m,p)}else{d=m.local;d=typeof d===h?d.apply(m):d}if(!f.local){d=n.call(m,d,p)}if(d||d===0){i+=d}i+='">\n </div>\n</div>';return i})})();(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-displayApps"]=b(function(h,m,g,l,k){this.compilerInfo=[4,">= 1.0.0"];g=this.merge(g,h.helpers);k=k||{};var d,i="function",j=this.escapeExpression,o=this,n=g.blockHelperMissing;function f(s,r){var p="",q;p+="\n ";if(q=g.label){q=q.call(s,{hash:{},data:r})}else{q=s.label;q=typeof q===i?q.apply(s):q}p+=j(q)+"\n ";q=g.each.call(s,s.links,{hash:{},inverse:o.noop,fn:o.program(2,e,r),data:r});if(q||q===0){p+=q}p+="\n <br />\n";return p}function e(t,s){var p="",r,q;p+='\n <a target="';if(r=g.target){r=r.call(t,{hash:{},data:s})}else{r=t.target;r=typeof r===i?r.apply(t):r}p+=j(r)+'" href="';if(r=g.href){r=r.call(t,{hash:{},data:s})}else{r=t.href;r=typeof r===i?r.apply(t):r}p+=j(r)+'">';q={hash:{},inverse:o.noop,fn:o.program(3,c,s),data:s};if(r=g.local){r=r.call(t,q)}else{r=t.local;r=typeof r===i?r.apply(t):r}if(!g.local){r=n.call(t,r,q)}if(r||r===0){p+=r}p+="</a>\n ";return p}function c(r,q){var p;if(p=g.text){p=p.call(r,{hash:{},data:q})}else{p=r.text;p=typeof p===i?p.apply(r):p}return j(p)}d=g.each.call(m,m.displayApps,{hash:{},inverse:o.noop,fn:o.program(1,f,k),data:k});if(d||d===0){return d}else{return""}})})();(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-downloadLinks"]=b(function(g,l,f,k,j){this.compilerInfo=[4,">= 1.0.0"];f=this.merge(f,g.helpers);j=j||{};var c,s,h="function",i=this.escapeExpression,q=this,m=f.blockHelperMissing;function e(y,x){var t="",w,v,u;t+='\n<div popupmenu="dataset-';if(w=f.id){w=w.call(y,{hash:{},data:x})}else{w=y.id;w=typeof w===h?w.apply(y):w}t+=i(w)+'-popup">\n <a class="action-button" href="'+i(((w=((w=y.urls),w==null||w===false?w:w.download)),typeof w===h?w.apply(y):w))+'">';u={hash:{},inverse:q.noop,fn:q.program(2,d,x),data:x};if(v=f.local){v=v.call(y,u)}else{v=y.local;v=typeof v===h?v.apply(y):v}if(!f.local){v=m.call(y,v,u)}if(v||v===0){t+=v}t+="</a>\n <a>";u={hash:{},inverse:q.noop,fn:q.program(4,r,x),data:x};if(v=f.local){v=v.call(y,u)}else{v=y.local;v=typeof v===h?v.apply(y):v}if(!f.local){v=m.call(y,v,u)}if(v||v===0){t+=v}t+="</a>\n ";v=f.each.call(y,((w=y.urls),w==null||w===false?w:w.meta_download),{hash:{},inverse:q.noop,fn:q.program(6,p,x),data:x});if(v||v===0){t+=v}t+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';if(v=f.id){v=v.call(y,{hash:{},data:x})}else{v=y.id;v=typeof v===h?v.apply(y):v}t+=i(v)+'-popup">\n <a href="'+i(((w=((w=y.urls),w==null||w===false?w:w.download)),typeof w===h?w.apply(y):w))+'" title="';u={hash:{},inverse:q.noop,fn:q.program(7,o,x),data:x};if(v=f.local){v=v.call(y,u)}else{v=y.local;v=typeof v===h?v.apply(y):v}if(!f.local){v=m.call(y,v,u)}if(v||v===0){t+=v}t+='" class="icon-button disk"></a>\n</div>\n';return t}function d(u,t){return"Download Dataset"}function r(u,t){return"Additional Files"}function p(x,w){var t="",v,u;t+='\n <a class="action-button" href="';if(v=f.url){v=v.call(x,{hash:{},data:w})}else{v=x.url;v=typeof v===h?v.apply(x):v}t+=i(v)+'">';u={hash:{},inverse:q.noop,fn:q.program(7,o,w),data:w};if(v=f.local){v=v.call(x,u)}else{v=x.local;v=typeof v===h?v.apply(x):v}if(!f.local){v=m.call(x,v,u)}if(v||v===0){t+=v}t+=" ";if(v=f.file_type){v=v.call(x,{hash:{},data:w})}else{v=x.file_type;v=typeof v===h?v.apply(x):v}t+=i(v)+"</a>\n ";return t}function o(u,t){return"Download"}function n(y,x){var t="",w,v,u;t+='\n\n<a href="'+i(((w=((w=y.urls),w==null||w===false?w:w.download)),typeof w===h?w.apply(y):w))+'" 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";w={hash:{},inverse:o.noop,fn:o.program(7,i,y),data:y};if(x=p.local){x=x.call(z,w)}else{x=z.local;x=typeof x===e?x.apply(z):x}if(!p.local){x=c.call(z,x,w)}if(x||x===0){v+=x}v+="\n ";x=p["if"].call(z,z.dbkey_unknown_and_editable,{hash:{},inverse:o.program(11,t,y),fn:o.program(9,f,y),data:y});if(x||x===0){v+=x}v+="\n ";return v}function i(w,v){return"database: "}function f(z,y){var v="",x,w;v+='\n <a class="metadata-dbkey" href="'+d(((x=((x=z.urls),x==null||x===false?x:x.edit)),typeof x===e?x.apply(z):x))+'" target="galaxy_main">';if(w=p.metadata_dbkey){w=w.call(z,{hash:{},data:y})}else{w=z.metadata_dbkey;w=typeof w===e?w.apply(z):w}v+=d(w)+"</a>\n ";return v}function t(y,x){var v="",w;v+='\n <span class="metadata-dbkey ';if(w=p.metadata_dbkey){w=w.call(y,{hash:{},data:x})}else{w=y.metadata_dbkey;w=typeof w===e?w.apply(y):w}v+=d(w)+'">';if(w=p.metadata_dbkey){w=w.call(y,{hash:{},data:x})}else{w=y.metadata_dbkey;w=typeof w===e?w.apply(y):w}v+=d(w)+"</span>\n ";return v}function s(y,x){var v="",w;v+='\n<div class="hda-info"> ';if(w=p.misc_info){w=w.call(y,{hash:{},data:x})}else{w=y.misc_info;w=typeof w===e?w.apply(y):w}v+=d(w)+" </div>\n";return v}q+='<div class="hda-summary">\n ';h=p["if"].call(r,r.misc_blurb,{hash:{},inverse:o.noop,fn:o.program(1,n,u),data:u});if(h||h===0){q+=h}q+="\n ";h=p["if"].call(r,r.data_type,{hash:{},inverse:o.noop,fn:o.program(3,m,u),data:u});if(h||h===0){q+=h}q+="\n ";h=p["if"].call(r,r.metadata_dbkey,{hash:{},inverse:o.noop,fn:o.program(6,j,u),data:u});if(h||h===0){q+=h}q+="\n</div>\n";h=p["if"].call(r,r.misc_info,{hash:{},inverse:o.noop,fn:o.program(13,s,u),data:u});if(h||h===0){q+=h}return q})})(); \ No newline at end of file diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/templates/compiled/history-templates.js --- a/static/scripts/templates/compiled/history-templates.js +++ b/static/scripts/templates/compiled/history-templates.js @@ -1,19 +1,268 @@ -/** Hack div to clear re-enclose float'd elements above it in the parent div - */ -Handlebars.registerPartial( 'clearFloatDiv', function( options ){ - return '<div class="clear"></div>'; -}); -/** Renders a warning in a (mostly css) highlighted, iconned warning box - */ -Handlebars.registerHelper( 'warningmessagesmall', function( options ){ - return '<div class="warningmessagesmall"><strong>' + options.fn( this ) + '</strong></div>' -}); -/** Calls _l (from base-mvc.js) to localize strings (if poosible) - * This helper is specifically for localization within templates - */ -Handlebars.registerHelper( 'local', function( options ){ - return _l( options.fn( this ) ); -});(function() { +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { + this.compilerInfo = [4,'>= 1.0.0']; +helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; + var buffer = "", stack1, stack2, options, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; + +function program1(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n <div id=\"history-name\" class=\"editable-text\"\n title=\""; + options = {hash:{},inverse:self.noop,fn:self.program(2, program2, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\">"; + if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</div>\n "; + return buffer; + } +function program2(depth0,data) { + + + return "Click to rename history"; + } + +function program4(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n <div id=\"history-name\"\n title=\""; + options = {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\">"; + if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</div>\n "; + return buffer; + } +function program5(depth0,data) { + + + return "You must be logged in to edit your history name"; + } + +function program7(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n <a id=\"history-tag\" title=\""; + options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button tags\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + options = {hash:{},inverse:self.noop,fn:self.program(10, program10, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button annotate\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n "; + return buffer; + } +function program8(depth0,data) { + + + return "Edit history tags"; + } + +function program10(depth0,data) { + + + return "Edit history annotation"; + } + +function program12(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n <div id=\"history-tag-annotation\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>"; + options = {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ":</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>"; + options = {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ":</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"editable-text\"\n title=\""; + options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\">\n "; + stack1 = helpers['if'].call(depth0, depth0.annotation, {hash:{},inverse:self.program(21, program21, data),fn:self.program(19, program19, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n </div>\n </div>\n </div>\n "; + return buffer; + } +function program13(depth0,data) { + + + return "Tags"; + } + +function program15(depth0,data) { + + + return "Annotation"; + } + +function program17(depth0,data) { + + + return "Click to edit annotation"; + } + +function program19(depth0,data) { + + var buffer = "", stack1; + buffer += "\n "; + if (stack1 = helpers.annotation) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "\n "; + return buffer; + } + +function program21(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n <em>"; + options = {hash:{},inverse:self.noop,fn:self.program(22, program22, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</em>\n "; + return buffer; + } +function program22(depth0,data) { + + + return "Describe or add notes to history"; + } + +function program24(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n "; + options = {hash:{},inverse:self.noop,fn:self.program(25, program25, data),data:data}; + if (stack1 = helpers.warningmessagesmall) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + return buffer; + } +function program25(depth0,data) { + + var stack1, options; + options = {hash:{},inverse:self.noop,fn:self.program(26, program26, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; } + } +function program26(depth0,data) { + + + return "You are currently viewing a deleted history!"; + } + +function program28(depth0,data) { + + var buffer = "", stack1; + buffer += "\n <div class=\""; + if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "message\">"; + if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</div>\n "; + return buffer; + } + +function program30(depth0,data) { + + + return "You are over your disk quota"; + } + +function program32(depth0,data) { + + + return "Tool execution is on hold until your disk usage drops below your allocated quota"; + } + +function program34(depth0,data) { + + + return "Your history is empty. Click 'Get Data' on the left pane to start"; + } + + buffer += "<div id=\"history-controls\">\n\n <div id=\"history-title-area\" class=\"historyLinks\">\n " + + "\n <div id=\"history-name-container\">\n " + + "\n "; + stack2 = helpers['if'].call(depth0, ((stack1 = depth0.user),stack1 == null || stack1 === false ? stack1 : stack1.email), {hash:{},inverse:self.program(4, program4, data),fn:self.program(1, program1, data),data:data}); + if(stack2 || stack2 === 0) { buffer += stack2; } + buffer += "\n </div>\n </div>\n\n <div id=\"history-subtitle-area\">\n <div id=\"history-size\" style=\"float:left;\">"; + if (stack2 = helpers.nice_size) { stack2 = stack2.call(depth0, {hash:{},data:data}); } + else { stack2 = depth0.nice_size; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } + buffer += escapeExpression(stack2) + + "</div>\n\n <div id=\"history-secondary-links\" style=\"float: right;\">\n "; + stack2 = helpers['if'].call(depth0, ((stack1 = depth0.user),stack1 == null || stack1 === false ? stack1 : stack1.email), {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}); + if(stack2 || stack2 === 0) { buffer += stack2; } + buffer += "\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n\n " + + "\n " + + "\n "; + stack2 = helpers['if'].call(depth0, ((stack1 = depth0.user),stack1 == null || stack1 === false ? stack1 : stack1.email), {hash:{},inverse:self.noop,fn:self.program(12, program12, data),data:data}); + if(stack2 || stack2 === 0) { buffer += stack2; } + buffer += "\n\n "; + stack2 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(24, program24, data),data:data}); + if(stack2 || stack2 === 0) { buffer += stack2; } + buffer += "\n\n <div id=\"message-container\">\n "; + stack2 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(28, program28, data),data:data}); + if(stack2 || stack2 === 0) { buffer += stack2; } + buffer += "\n </div>\n\n <div id=\"quota-message-container\" style=\"display: none\">\n <div id=\"quota-message\" class=\"errormessage\">\n "; + options = {hash:{},inverse:self.noop,fn:self.program(30, program30, data),data:data}; + if (stack2 = helpers.local) { stack2 = stack2.call(depth0, options); } + else { stack2 = depth0.local; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } + if (!helpers.local) { stack2 = blockHelperMissing.call(depth0, stack2, options); } + if(stack2 || stack2 === 0) { buffer += stack2; } + buffer += ".\n "; + options = {hash:{},inverse:self.noop,fn:self.program(32, program32, data),data:data}; + if (stack2 = helpers.local) { stack2 = stack2.call(depth0, options); } + else { stack2 = depth0.local; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } + if (!helpers.local) { stack2 = blockHelperMissing.call(depth0, stack2, options); } + if(stack2 || stack2 === 0) { buffer += stack2; } + buffer += ".\n </div>\n </div>\n</div>\n\n<div id=\""; + if (stack2 = helpers.id) { stack2 = stack2.call(depth0, {hash:{},data:data}); } + else { stack2 = depth0.id; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } + buffer += escapeExpression(stack2) + + "-datasets\" class=\"history-datasets-list\"></div>\n\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\" style=\"display: none;\">\n "; + options = {hash:{},inverse:self.noop,fn:self.program(34, program34, data),data:data}; + if (stack2 = helpers.local) { stack2 = stack2.call(depth0, options); } + else { stack2 = depth0.local; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } + if (!helpers.local) { stack2 = blockHelperMissing.call(depth0, stack2, options); } + if(stack2 || stack2 === 0) { buffer += stack2; } + buffer += "\n</div>"; + return buffer; + }); +})();(function() { var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-hda-annotationArea'] = template(function (Handlebars,depth0,helpers,partials,data) { this.compilerInfo = [4,'>= 1.0.0']; @@ -250,65 +499,24 @@ templates['template-hda-hdaSummary'] = template(function (Handlebars,depth0,helpers,partials,data) { this.compilerInfo = [4,'>= 1.0.0']; helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; function program1(depth0,data) { - - return "format: "; + var buffer = "", stack1; + buffer += "\n "; + if (stack1 = helpers.misc_blurb) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "<br />\n "; + return buffer; } function program3(depth0,data) { - - return "database: "; - } - -function program5(depth0,data) { - - var buffer = "", stack1, stack2; - buffer += "\n <a class=\"metadata-dbkey\" href=\"" - + escapeExpression(((stack1 = ((stack1 = depth0.urls),stack1 == null || stack1 === false ? stack1 : stack1.edit)),typeof stack1 === functionType ? stack1.apply(depth0) : stack1)) - + "\" target=\"galaxy_main\">"; - if (stack2 = helpers.metadata_dbkey) { stack2 = stack2.call(depth0, {hash:{},data:data}); } - else { stack2 = depth0.metadata_dbkey; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } - buffer += escapeExpression(stack2) - + "</a>\n "; - return buffer; - } - -function program7(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <span class=\"metadata-dbkey "; - if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\">"; - if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n "; - return buffer; - } - -function program9(depth0,data) { - - var buffer = "", stack1; - buffer += "\n<div class=\"hda-info\"> "; - if (stack1 = helpers.misc_info) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.misc_info; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + " </div>\n"; - return buffer; - } - - buffer += "<div class=\"hda-summary\">\n "; - if (stack1 = helpers.misc_blurb) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "<br />\n "; - options = {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}; + var buffer = "", stack1, options; + buffer += "\n "; + options = {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } @@ -322,16 +530,85 @@ else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } buffer += escapeExpression(stack1) + "</span>,\n "; - options = {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}; + return buffer; + } +function program4(depth0,data) { + + + return "format: "; + } + +function program6(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n "; + options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + stack1 = helpers['if'].call(depth0, depth0.dbkey_unknown_and_editable, {hash:{},inverse:self.program(11, program11, data),fn:self.program(9, program9, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n "; - stack1 = helpers['if'].call(depth0, depth0.dbkey_unknown_and_editable, {hash:{},inverse:self.program(7, program7, data),fn:self.program(5, program5, data),data:data}); + return buffer; + } +function program7(depth0,data) { + + + return "database: "; + } + +function program9(depth0,data) { + + var buffer = "", stack1, stack2; + buffer += "\n <a class=\"metadata-dbkey\" href=\"" + + escapeExpression(((stack1 = ((stack1 = depth0.urls),stack1 == null || stack1 === false ? stack1 : stack1.edit)),typeof stack1 === functionType ? stack1.apply(depth0) : stack1)) + + "\" target=\"galaxy_main\">"; + if (stack2 = helpers.metadata_dbkey) { stack2 = stack2.call(depth0, {hash:{},data:data}); } + else { stack2 = depth0.metadata_dbkey; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } + buffer += escapeExpression(stack2) + + "</a>\n "; + return buffer; + } + +function program11(depth0,data) { + + var buffer = "", stack1; + buffer += "\n <span class=\"metadata-dbkey "; + if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "\">"; + if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</span>\n "; + return buffer; + } + +function program13(depth0,data) { + + var buffer = "", stack1; + buffer += "\n<div class=\"hda-info\"> "; + if (stack1 = helpers.misc_info) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.misc_info; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + " </div>\n"; + return buffer; + } + + buffer += "<div class=\"hda-summary\">\n "; + stack1 = helpers['if'].call(depth0, depth0.misc_blurb, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + stack1 = helpers['if'].call(depth0, depth0.data_type, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + stack1 = helpers['if'].call(depth0, depth0.metadata_dbkey, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>\n"; - stack1 = helpers['if'].call(depth0, depth0.misc_info, {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}); + stack1 = helpers['if'].call(depth0, depth0.misc_info, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } return buffer; }); @@ -569,296 +846,4 @@ if(stack1 || stack1 === 0) { buffer += stack1; } return buffer; }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, stack2, options, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; - -function program1(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div id=\"history-name\" class=\"editable-text\"\n title=\""; - options = {hash:{},inverse:self.noop,fn:self.program(2, program2, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\">"; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } -function program2(depth0,data) { - - - return "Click to rename history"; - } - -function program4(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div id=\"history-name\"\n title=\""; - options = {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\">"; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } -function program5(depth0,data) { - - - return "You must be logged in to edit your history name"; - } - -function program7(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <a id=\"history-tag\" title=\""; - options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button tags\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; - options = {hash:{},inverse:self.noop,fn:self.program(10, program10, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button annotate\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n "; - return buffer; - } -function program8(depth0,data) { - - - return "Edit history tags"; - } - -function program10(depth0,data) { - - - return "Edit history annotation"; - } - -function program12(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div id=\"history-tag-annotation\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>"; - options = {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>"; - options = {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"editable-text\"\n title=\""; - options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\">\n "; - stack1 = helpers['if'].call(depth0, depth0.annotation, {hash:{},inverse:self.program(21, program21, data),fn:self.program(19, program19, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n </div>\n </div>\n </div>\n "; - return buffer; - } -function program13(depth0,data) { - - - return "Tags"; - } - -function program15(depth0,data) { - - - return "Annotation"; - } - -function program17(depth0,data) { - - - return "Click to edit annotation"; - } - -function program19(depth0,data) { - - var buffer = "", stack1; - buffer += "\n "; - if (stack1 = helpers.annotation) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n "; - return buffer; - } - -function program21(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <em>"; - options = {hash:{},inverse:self.noop,fn:self.program(22, program22, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</em>\n "; - return buffer; - } -function program22(depth0,data) { - - - return "Describe or add notes to history"; - } - -function program24(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n "; - options = {hash:{},inverse:self.noop,fn:self.program(25, program25, data),data:data}; - if (stack1 = helpers.warningmessagesmall) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - return buffer; - } -function program25(depth0,data) { - - var stack1, options; - options = {hash:{},inverse:self.noop,fn:self.program(26, program26, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { return stack1; } - else { return ''; } - } -function program26(depth0,data) { - - - return "You are currently viewing a deleted history!"; - } - -function program28(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\""; - if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "message\">"; - if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program30(depth0,data) { - - - return "You are over your disk quota"; - } - -function program32(depth0,data) { - - - return "Tool execution is on hold until your disk usage drops below your allocated quota"; - } - -function program34(depth0,data) { - - - return "Your history is empty. Click 'Get Data' on the left pane to start"; - } - - buffer += "<div id=\"history-controls\">\n\n <div id=\"history-title-area\" class=\"historyLinks\">\n " - + "\n <div id=\"history-name-container\">\n " - + "\n "; - stack2 = helpers['if'].call(depth0, ((stack1 = depth0.user),stack1 == null || stack1 === false ? stack1 : stack1.email), {hash:{},inverse:self.program(4, program4, data),fn:self.program(1, program1, data),data:data}); - if(stack2 || stack2 === 0) { buffer += stack2; } - buffer += "\n </div>\n </div>\n\n <div id=\"history-subtitle-area\">\n <div id=\"history-size\" style=\"float:left;\">"; - if (stack2 = helpers.nice_size) { stack2 = stack2.call(depth0, {hash:{},data:data}); } - else { stack2 = depth0.nice_size; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } - buffer += escapeExpression(stack2) - + "</div>\n\n <div id=\"history-secondary-links\" style=\"float: right;\">\n "; - stack2 = helpers['if'].call(depth0, ((stack1 = depth0.user),stack1 == null || stack1 === false ? stack1 : stack1.email), {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}); - if(stack2 || stack2 === 0) { buffer += stack2; } - buffer += "\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n\n " - + "\n " - + "\n "; - stack2 = helpers['if'].call(depth0, ((stack1 = depth0.user),stack1 == null || stack1 === false ? stack1 : stack1.email), {hash:{},inverse:self.noop,fn:self.program(12, program12, data),data:data}); - if(stack2 || stack2 === 0) { buffer += stack2; } - buffer += "\n\n "; - stack2 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(24, program24, data),data:data}); - if(stack2 || stack2 === 0) { buffer += stack2; } - buffer += "\n\n <div id=\"message-container\">\n "; - stack2 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(28, program28, data),data:data}); - if(stack2 || stack2 === 0) { buffer += stack2; } - buffer += "\n </div>\n\n <div id=\"quota-message-container\" style=\"display: none\">\n <div id=\"quota-message\" class=\"errormessage\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(30, program30, data),data:data}; - if (stack2 = helpers.local) { stack2 = stack2.call(depth0, options); } - else { stack2 = depth0.local; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } - if (!helpers.local) { stack2 = blockHelperMissing.call(depth0, stack2, options); } - if(stack2 || stack2 === 0) { buffer += stack2; } - buffer += ".\n "; - options = {hash:{},inverse:self.noop,fn:self.program(32, program32, data),data:data}; - if (stack2 = helpers.local) { stack2 = stack2.call(depth0, options); } - else { stack2 = depth0.local; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } - if (!helpers.local) { stack2 = blockHelperMissing.call(depth0, stack2, options); } - if(stack2 || stack2 === 0) { buffer += stack2; } - buffer += ".\n </div>\n </div>\n</div>\n\n<div id=\""; - if (stack2 = helpers.id) { stack2 = stack2.call(depth0, {hash:{},data:data}); } - else { stack2 = depth0.id; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } - buffer += escapeExpression(stack2) - + "-datasets\" class=\"history-datasets-list\"></div>\n\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\" style=\"display: none;\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(34, program34, data),data:data}; - if (stack2 = helpers.local) { stack2 = stack2.call(depth0, options); } - else { stack2 = depth0.local; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } - if (!helpers.local) { stack2 = blockHelperMissing.call(depth0, stack2, options); } - if(stack2 || stack2 === 0) { buffer += stack2; } - buffer += "\n</div>"; - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-iconButton'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); partials = this.merge(partials, Handlebars.partials); data = data || {}; - var buffer = "", stack1, self=this; - - - buffer += "\n"; - stack1 = self.invokePartial(partials.iconButton, 'iconButton', depth0, helpers, partials, data); - if(stack1 || stack1 === 0) { buffer += stack1; } - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-warningmessagesmall'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function"; - - - buffer += " \n <div class=\"warningmessagesmall\"><strong>"; - if (stack1 = helpers.warning) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.warning; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</strong></div>"; - return buffer; - }); })(); \ No newline at end of file diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/templates/compiled/template-hda-hdaSummary.js --- a/static/scripts/templates/compiled/template-hda-hdaSummary.js +++ b/static/scripts/templates/compiled/template-hda-hdaSummary.js @@ -3,65 +3,24 @@ templates['template-hda-hdaSummary'] = template(function (Handlebars,depth0,helpers,partials,data) { this.compilerInfo = [4,'>= 1.0.0']; helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; function program1(depth0,data) { - - return "format: "; + var buffer = "", stack1; + buffer += "\n "; + if (stack1 = helpers.misc_blurb) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "<br />\n "; + return buffer; } function program3(depth0,data) { - - return "database: "; - } - -function program5(depth0,data) { - - var buffer = "", stack1, stack2; - buffer += "\n <a class=\"metadata-dbkey\" href=\"" - + escapeExpression(((stack1 = ((stack1 = depth0.urls),stack1 == null || stack1 === false ? stack1 : stack1.edit)),typeof stack1 === functionType ? stack1.apply(depth0) : stack1)) - + "\" target=\"galaxy_main\">"; - if (stack2 = helpers.metadata_dbkey) { stack2 = stack2.call(depth0, {hash:{},data:data}); } - else { stack2 = depth0.metadata_dbkey; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } - buffer += escapeExpression(stack2) - + "</a>\n "; - return buffer; - } - -function program7(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <span class=\"metadata-dbkey "; - if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\">"; - if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n "; - return buffer; - } - -function program9(depth0,data) { - - var buffer = "", stack1; - buffer += "\n<div class=\"hda-info\"> "; - if (stack1 = helpers.misc_info) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.misc_info; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + " </div>\n"; - return buffer; - } - - buffer += "<div class=\"hda-summary\">\n "; - if (stack1 = helpers.misc_blurb) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "<br />\n "; - options = {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}; + var buffer = "", stack1, options; + buffer += "\n "; + options = {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } @@ -75,16 +34,85 @@ else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } buffer += escapeExpression(stack1) + "</span>,\n "; - options = {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}; + return buffer; + } +function program4(depth0,data) { + + + return "format: "; + } + +function program6(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n "; + options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + stack1 = helpers['if'].call(depth0, depth0.dbkey_unknown_and_editable, {hash:{},inverse:self.program(11, program11, data),fn:self.program(9, program9, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n "; - stack1 = helpers['if'].call(depth0, depth0.dbkey_unknown_and_editable, {hash:{},inverse:self.program(7, program7, data),fn:self.program(5, program5, data),data:data}); + return buffer; + } +function program7(depth0,data) { + + + return "database: "; + } + +function program9(depth0,data) { + + var buffer = "", stack1, stack2; + buffer += "\n <a class=\"metadata-dbkey\" href=\"" + + escapeExpression(((stack1 = ((stack1 = depth0.urls),stack1 == null || stack1 === false ? stack1 : stack1.edit)),typeof stack1 === functionType ? stack1.apply(depth0) : stack1)) + + "\" target=\"galaxy_main\">"; + if (stack2 = helpers.metadata_dbkey) { stack2 = stack2.call(depth0, {hash:{},data:data}); } + else { stack2 = depth0.metadata_dbkey; stack2 = typeof stack2 === functionType ? stack2.apply(depth0) : stack2; } + buffer += escapeExpression(stack2) + + "</a>\n "; + return buffer; + } + +function program11(depth0,data) { + + var buffer = "", stack1; + buffer += "\n <span class=\"metadata-dbkey "; + if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "\">"; + if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</span>\n "; + return buffer; + } + +function program13(depth0,data) { + + var buffer = "", stack1; + buffer += "\n<div class=\"hda-info\"> "; + if (stack1 = helpers.misc_info) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.misc_info; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + " </div>\n"; + return buffer; + } + + buffer += "<div class=\"hda-summary\">\n "; + stack1 = helpers['if'].call(depth0, depth0.misc_blurb, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + stack1 = helpers['if'].call(depth0, depth0.data_type, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + stack1 = helpers['if'].call(depth0, depth0.metadata_dbkey, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>\n"; - stack1 = helpers['if'].call(depth0, depth0.misc_info, {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}); + stack1 = helpers['if'].call(depth0, depth0.misc_info, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } return buffer; }); diff -r c0bf145241e7735cd1c7a9dddab44d984425695f -r 8bc80aa53e81d9362e08ead0a0307cd3af0dd8aa static/scripts/templates/hda-templates.html --- a/static/scripts/templates/hda-templates.html +++ b/static/scripts/templates/hda-templates.html @@ -45,13 +45,19 @@ <script type="text/template" class="template-hda" id="template-hda-hdaSummary"><div class="hda-summary"> - {{ misc_blurb }}<br /> - {{#local}}format: {{/local}}<span class="{{ data_type }}">{{ data_type }}</span>, - {{#local}}database: {{/local}} - {{#if dbkey_unknown_and_editable }} - <a class="metadata-dbkey" href="{{ urls.edit }}" target="galaxy_main">{{ metadata_dbkey }}</a> - {{else}} - <span class="metadata-dbkey {{ metadata_dbkey }}">{{ metadata_dbkey }}</span> + {{#if misc_blurb }} + {{ misc_blurb }}<br /> + {{/if}} + {{#if data_type }} + {{#local}}format: {{/local}}<span class="{{ data_type }}">{{ data_type }}</span>, + {{/if}} + {{#if metadata_dbkey }} + {{#local}}database: {{/local}} + {{#if dbkey_unknown_and_editable }} + <a class="metadata-dbkey" href="{{ urls.edit }}" target="galaxy_main">{{ metadata_dbkey }}</a> + {{else}} + <span class="metadata-dbkey {{ metadata_dbkey }}">{{ metadata_dbkey }}</span> + {{/if}} {{/if}} </div> {{#if misc_info}} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 11 new changesets
by commits-noreply＠bitbucket.org 22 Oct '13

22 Oct '13

11 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/320ae026f73a/ Changeset: 320ae026f73a Branch: search User: Kyle Ellrott Date: 2013-06-21 22:31:02 Summary: Adding 'state' field to the jobn search view. Also adding '!=' compatitor to GQL Affected #: 2 files diff -r fd3a82d33bb6896ba6395a5e83add5c6ac7f7fbf -r 320ae026f73a849c77a580410a5a3d6927ef1b91 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -158,8 +158,8 @@ class Job( object, APIItem ): - api_collection_visible_keys = [ 'id' ] - api_element_visible_keys = [ 'id' ] + api_collection_visible_keys = [ 'id', 'state' ] + api_element_visible_keys = [ 'id', 'state' ] """ A job represents a request to run a tool given input datasets, tool diff -r fd3a82d33bb6896ba6395a5e83add5c6ac7f7fbf -r 320ae026f73a849c77a580410a5a3d6927ef1b91 lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -107,6 +107,8 @@ if operator == "=": #print field.sqlalchemy_field == right, field.sqlalchemy_field, right self.query = self.query.filter( field.sqlalchemy_field == right ) + elif operator == "!=": + self.query = self.query.filter( field.sqlalchemy_field != right ) elif operator == "like": self.query = self.query.filter( field.sqlalchemy_field.like(right) ) else: @@ -433,6 +435,7 @@ DOMAIN = "job" FIELDS = { 'tool_name' : ViewField('tool_name', sqlalchemy_field=Job.tool_id), + 'state' : ViewField('state', sqlalchemy_field=Job.state), 'param' : ViewField('param', handler=job_param_filter), 'input_hda' : ViewField('input_hda', handler=job_input_hda_filter, id_decode=True), 'output_hda' : ViewField('output_hda', handler=job_output_hda_filter, id_decode=True) @@ -499,6 +502,7 @@ comparison = ( '=' -> '=' | '>' -> '>' | '<' -> '<' + | '!=' -> '!=' | '>=' -> '>=' | '<=' -> '<=' | 'like' -> 'like' https://bitbucket.org/galaxy/galaxy-central/commits/460c7dc52f92/ Changeset: 460c7dc52f92 Branch: search User: Kyle Ellrott Date: 2013-06-27 20:59:24 Summary: Default merge Affected #: 197 files diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -267,25 +267,25 @@ # bam does not use '#' to indicate comments/headers - we need to strip out those headers from the std. providers #TODO:?? seems like there should be an easier way to do/inherit this - metadata.comment_char? #TODO: incorporate samtools options to control output: regions first, then flags, etc. - @dataproviders.decorators.dataprovider_factory( 'line' ) + @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.line.FilteredLineDataProvider.settings ) def line_dataprovider( self, dataset, **settings ): samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset ) settings[ 'comment_char' ] = '@' return dataproviders.line.FilteredLineDataProvider( samtools_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'regex-line' ) + @dataproviders.decorators.dataprovider_factory( 'regex-line', dataproviders.line.RegexLineDataProvider.settings ) def regex_line_dataprovider( self, dataset, **settings ): samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset ) settings[ 'comment_char' ] = '@' return dataproviders.line.RegexLineDataProvider( samtools_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'column' ) + @dataproviders.decorators.dataprovider_factory( 'column', dataproviders.column.ColumnarDataProvider.settings ) def column_dataprovider( self, dataset, **settings ): samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset ) settings[ 'comment_char' ] = '@' return dataproviders.column.ColumnarDataProvider( samtools_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'map' ) + @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.column.MapDataProvider.settings ) def map_dataprovider( self, dataset, **settings ): samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset ) settings[ 'comment_char' ] = '@' @@ -293,30 +293,30 @@ # these can't be used directly - may need BamColumn, BamMap (Bam metadata -> column/map) # OR - see genomic_region_dataprovider - #(a)dataproviders.decorators.dataprovider_factory( 'dataset-column' ) + #(a)dataproviders.decorators.dataprovider_factory( 'dataset-column', dataproviders.column.ColumnarDataProvider.settings ) #def dataset_column_dataprovider( self, dataset, **settings ): # settings[ 'comment_char' ] = '@' # return super( Sam, self ).dataset_column_dataprovider( dataset, **settings ) - #(a)dataproviders.decorators.dataprovider_factory( 'dataset-map' ) + #(a)dataproviders.decorators.dataprovider_factory( 'dataset-map', dataproviders.column.MapDataProvider.settings ) #def dataset_map_dataprovider( self, dataset, **settings ): # settings[ 'comment_char' ] = '@' # return super( Sam, self ).dataset_map_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'header' ) + @dataproviders.decorators.dataprovider_factory( 'header', dataproviders.line.RegexLineDataProvider.settings ) def header_dataprovider( self, dataset, **settings ): # in this case we can use an option of samtools view to provide just what we need (w/o regex) samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset, '-H' ) return dataproviders.line.RegexLineDataProvider( samtools_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'id-seq-qual' ) + @dataproviders.decorators.dataprovider_factory( 'id-seq-qual', dataproviders.column.MapDataProvider.settings ) def id_seq_qual_dataprovider( self, dataset, **settings ): settings[ 'indeces' ] = [ 0, 9, 10 ] settings[ 'column_types' ] = [ 'str', 'str', 'str' ] settings[ 'column_names' ] = [ 'id', 'seq', 'qual' ] return self.map_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', dataproviders.column.ColumnarDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): # GenomicRegionDataProvider currently requires a dataset as source - may not be necc. #TODO:?? consider (at least) the possible use of a kwarg: metadata_source (def. to source.dataset), @@ -330,7 +330,7 @@ settings[ 'column_types' ] = [ 'str', 'int', 'int' ] return self.column_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', dataproviders.column.MapDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'indeces' ] = [ 2, 3, 3 ] settings[ 'column_types' ] = [ 'str', 'int', 'int' ] diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml @@ -1,5 +1,9 @@ <tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.0" hidden="true"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> bedtools genomecov -bg -split -ibam $input -g $chromInfo diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml @@ -1,5 +1,9 @@ <tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.0" hidden="true"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> ## Remove comments and sort by chromosome. grep -v '^#' $input | sort -k1,1 | diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml @@ -1,6 +1,10 @@ <tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> ## Remove comments and sort by chromosome. diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml @@ -1,4 +1,9 @@ <tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.0" hidden="true"> + <requirements> + <requirement type="package">ucsc_tools</requirement> + <requirement type="package">samtools</requirement> + <requirement type="package">bedtools</requirement> + </requirements><command> samtools view -bh $input | bedtools genomecov -bg -split -ibam stdin -g $chromInfo diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -593,7 +593,6 @@ Base dataprovider factory for all datatypes that returns the proper provider for the given `data_format` or raises a `NoProviderAvailable`. """ - #TODO:?? is this handling super class providers? if self.has_dataprovider( data_format ): return self.dataproviders[ data_format ]( self, dataset, **settings ) raise dataproviders.exceptions.NoProviderAvailable( self, data_format ) @@ -603,12 +602,12 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.base.DataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'chunk' ) + @dataproviders.decorators.dataprovider_factory( 'chunk', dataproviders.chunk.ChunkDataProvider.settings ) def chunk_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.chunk.ChunkDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'chunk64' ) + @dataproviders.decorators.dataprovider_factory( 'chunk64', dataproviders.chunk.Base64ChunkDataProvider.settings ) def chunk64_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.chunk.Base64ChunkDataProvider( dataset_source, **settings ) @@ -785,7 +784,7 @@ split = classmethod(split) # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'line' ) + @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.line.FilteredLineDataProvider.settings ) def line_dataprovider( self, dataset, **settings ): """ Returns an iterator over the dataset's lines (that have been `strip`ed) @@ -794,7 +793,7 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.line.FilteredLineDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'regex-line' ) + @dataproviders.decorators.dataprovider_factory( 'regex-line', dataproviders.line.RegexLineDataProvider.settings ) def regex_line_dataprovider( self, dataset, **settings ): """ Returns an iterator over the dataset's lines diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/dataproviders/base.py --- a/lib/galaxy/datatypes/dataproviders/base.py +++ b/lib/galaxy/datatypes/dataproviders/base.py @@ -22,8 +22,13 @@ icorporate existing visualization/dataproviders some of the sources (esp. in datasets) don't need to be re-created +YAGNI: InterleavingMultiSourceDataProvider, CombiningMultiSourceDataProvider -YAGNI: InterleavingMultiSourceDataProvider, CombiningMultiSourceDataProvider +datasets API entry point: + kwargs should be parsed from strings 2 layers up (in the DatasetsAPI) - that's the 'proper' place for that. + but how would it know how/what to parse if it doesn't have access to the classes used in the provider? + Building a giant list by sweeping all possible dprov classes doesn't make sense + For now - I'm burying them in the class __init__s - but I don't like that """ import logging @@ -31,6 +36,31 @@ # ----------------------------------------------------------------------------- base classes +class HasSettings( type ): + """ + Metaclass for data providers that allows defining and inheriting + a dictionary named 'settings'. + + Useful for allowing class level access to expected variable types + passed to class `__init__` functions so they can be parsed from a query string. + """ + # yeah - this is all too acrobatic + def __new__( cls, name, base_classes, attributes ): + settings = {} + # get settings defined in base classes + for base_class in base_classes: + base_settings = getattr( base_class, 'settings', None ) + if base_settings: + settings.update( base_settings ) + # get settings defined in this class + new_settings = attributes.pop( 'settings', None ) + if new_settings: + settings.update( new_settings ) + attributes[ 'settings' ] = settings + return type.__new__( cls, name, base_classes, attributes ) + + +# ----------------------------------------------------------------------------- base classes class DataProvider( object ): """ Base class for all data providers. Data providers: @@ -39,6 +69,12 @@ (c) do not allow write methods (but otherwise implement the other file object interface methods) """ + # a definition of expected types for keyword arguments sent to __init__ + # useful for controlling how query string dictionaries can be parsed into correct types for __init__ + # empty in this base class + __metaclass__ = HasSettings + settings = {} + def __init__( self, source, **kwargs ): """ :param source: the source that this iterator will loop over. @@ -130,13 +166,16 @@ - `num_valid_data_read`: how many data have been returned from `filter`. - `num_data_returned`: how many data has this provider yielded. """ + # not useful here - we don't want functions over the query string + #settings.update({ 'filter_fn': 'function' }) + def __init__( self, source, filter_fn=None, **kwargs ): """ :param filter_fn: a lambda or function that will be passed a datum and return either the (optionally modified) datum or None. """ super( FilteredDataProvider, self ).__init__( source, **kwargs ) - self.filter_fn = filter_fn + self.filter_fn = filter_fn if hasattr( filter_fn, '__call__' ) else None # count how many data we got from the source self.num_data_read = 0 # how many valid data have we gotten from the source @@ -179,6 +218,12 @@ Useful for grabbing sections from a source (e.g. pagination). """ + # define the expected types of these __init__ arguments so they can be parsed out from query strings + settings = { + 'limit' : 'int', + 'offset': 'int' + } + #TODO: may want to squash this into DataProvider def __init__( self, source, offset=0, limit=None, **kwargs ): """ diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/dataproviders/chunk.py --- a/lib/galaxy/datatypes/dataproviders/chunk.py +++ b/lib/galaxy/datatypes/dataproviders/chunk.py @@ -26,6 +26,10 @@ """ MAX_CHUNK_SIZE = 2**16 DEFAULT_CHUNK_SIZE = MAX_CHUNK_SIZE + settings = { + 'chunk_index' : 'int', + 'chunk_size' : 'int' + } #TODO: subclass from LimitedOffsetDataProvider? # see web/framework/base.iterate_file, util/__init__.file_reader, and datatypes.tabular @@ -38,8 +42,8 @@ (gen. in bytes). """ super( ChunkDataProvider, self ).__init__( source, **kwargs ) - self.chunk_size = chunk_size - self.chunk_pos = chunk_index * self.chunk_size + self.chunk_size = int( chunk_size ) + self.chunk_pos = int( chunk_index ) * self.chunk_size def validate_source( self, source ): """ diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/dataproviders/column.py --- a/lib/galaxy/datatypes/dataproviders/column.py +++ b/lib/galaxy/datatypes/dataproviders/column.py @@ -29,6 +29,14 @@ the same number of columns as the number of indeces asked for (even if they are filled with None). """ + settings = { + 'indeces' : 'list:int', + 'column_count' : 'int', + 'column_types' : 'list:str', + 'parse_columns' : 'bool', + 'deliminator' : 'str' + } + def __init__( self, source, indeces=None, column_count=None, column_types=None, parsers=None, parse_columns=True, deliminator='\t', **kwargs ): @@ -91,11 +99,11 @@ # how/whether to parse each column value self.parsers = {} if parse_columns: - self.parsers = self._get_default_parsers() + self.parsers = self.get_default_parsers() # overwrite with user desired parsers self.parsers.update( parsers or {} ) - def _get_default_parsers( self ): + def get_default_parsers( self ): """ Return parser dictionary keyed for each columnar type (as defined in datatypes). @@ -132,7 +140,7 @@ #'gffstrand': # -, +, ?, or '.' for None, etc. } - def _parse_value( self, val, type ): + def parse_value( self, val, type ): """ Attempt to parse and return the given value based on the given type. @@ -153,7 +161,7 @@ return None return val - def _get_column_type( self, index ): + def get_column_type( self, index ): """ Get the column type for the parser from `self.column_types` or `None` if the type is unavailable. @@ -165,18 +173,18 @@ except IndexError, ind_err: return None - def _parse_column_at_index( self, columns, parser_index, index ): + def parse_column_at_index( self, columns, parser_index, index ): """ Get the column type for the parser from `self.column_types` or `None` if the type is unavailable. """ try: - return self._parse_value( columns[ index ], self._get_column_type( parser_index ) ) + return self.parse_value( columns[ index ], self.get_column_type( parser_index ) ) # if a selected index is not within columns, return None except IndexError, index_err: return None - def _parse_columns_from_line( self, line ): + def parse_columns_from_line( self, line ): """ Returns a list of the desired, parsed columns. :param line: the line to parse @@ -188,13 +196,13 @@ selected_indeces = self.selected_column_indeces or list( xrange( len( all_columns ) ) ) parsed_columns = [] for parser_index, column_index in enumerate( selected_indeces ): - parsed_columns.append( self._parse_column_at_index( all_columns, parser_index, column_index ) ) + parsed_columns.append( self.parse_column_at_index( all_columns, parser_index, column_index ) ) return parsed_columns def __iter__( self ): parent_gen = super( ColumnarDataProvider, self ).__iter__() for line in parent_gen: - columns = self._parse_columns_from_line( line ) + columns = self.parse_columns_from_line( line ) yield columns #TODO: implement column filters here and not below - flatten hierarchy @@ -223,6 +231,10 @@ .. note: that the subclass constructors are passed kwargs - so they're params (limit, offset, etc.) are also applicable here. """ + settings = { + 'column_names' : 'list:str', + } + def __init__( self, source, column_names=None, **kwargs ): """ :param column_names: an ordered list of strings that will be used as the keys diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -141,7 +141,7 @@ """ # metadata columns are 1-based indeces column = getattr( self.dataset.metadata, name ) - return ( column - 1 ) if isinstance( column, int ) else None + return ( column - 1 ) if ( isinstance( column, int ) and column > 0 ) else None def get_genomic_region_indeces( self, check=False ): """ @@ -271,6 +271,12 @@ """ # dictionary keys when named_columns=True COLUMN_NAMES = [ 'chrom', 'start', 'end' ] + settings = { + 'chrom_column' : 'int', + 'start_column' : 'int', + 'end_column' : 'int', + 'named_columns' : 'bool', + } def __init__( self, dataset, chrom_column=None, start_column=None, end_column=None, named_columns=False, **kwargs ): """ @@ -333,6 +339,14 @@ 'chrom', 'start', 'end' (and 'strand' and 'name' if available). """ COLUMN_NAMES = [ 'chrom', 'start', 'end', 'strand', 'name' ] + settings = { + 'chrom_column' : 'int', + 'start_column' : 'int', + 'end_column' : 'int', + 'strand_column' : 'int', + 'name_column' : 'int', + 'named_columns' : 'bool', + } def __init__( self, dataset, chrom_column=None, start_column=None, end_column=None, strand_column=None, name_column=None, named_columns=False, **kwargs ): @@ -349,25 +363,40 @@ dataset_source = DatasetDataProvider( dataset ) # get genomic indeces and add strand and name + self.column_names = [] + indeces = [] + #TODO: this is sort of involved and oogly if chrom_column == None: chrom_column = dataset_source.get_metadata_column_index_by_name( 'chromCol' ) + if chrom_column != None: + self.column_names.append( 'chrom' ) + indeces.append( chrom_column ) if start_column == None: start_column = dataset_source.get_metadata_column_index_by_name( 'startCol' ) + if start_column != None: + self.column_names.append( 'start' ) + indeces.append( start_column ) if end_column == None: end_column = dataset_source.get_metadata_column_index_by_name( 'endCol' ) + if end_column != None: + self.column_names.append( 'end' ) + indeces.append( end_column ) if strand_column == None: strand_column = dataset_source.get_metadata_column_index_by_name( 'strandCol' ) + if strand_column != None: + self.column_names.append( 'strand' ) + indeces.append( strand_column ) if name_column == None: name_column = dataset_source.get_metadata_column_index_by_name( 'nameCol' ) - indeces = [ chrom_column, start_column, end_column, strand_column, name_column ] + if name_column != None: + self.column_names.append( 'name' ) + indeces.append( name_column ) + kwargs.update({ 'indeces' : indeces }) - if not kwargs.get( 'column_types', None ): kwargs.update({ 'column_types' : dataset_source.get_metadata_column_types( indeces=indeces ) }) self.named_columns = named_columns - if self.named_columns: - self.column_names = self.COLUMN_NAMES super( IntervalDataProvider, self ).__init__( dataset_source, **kwargs ) @@ -390,6 +419,10 @@ sequence: <joined lines of nucleotide/amino data> } """ + settings = { + 'ids' : 'list:str', + } + def __init__( self, source, ids=None, **kwargs ): """ :param ids: optionally return only ids (and sequences) that are in this list. @@ -419,6 +452,10 @@ sequence: <joined lines of nucleotide/amino data> } """ + settings = { + 'ids' : 'list:str', + } + def __init__( self, source, ids=None, **kwargs ): """ :param ids: optionally return only ids (and sequences) that are in this list. @@ -445,6 +482,10 @@ Class that returns chrom, pos, data from a wiggle source. """ COLUMN_NAMES = [ 'chrom', 'pos', 'value' ] + settings = { + 'named_columns' : 'bool', + 'column_names' : 'list:str', + } def __init__( self, source, named_columns=False, column_names=None, **kwargs ): """ @@ -483,6 +524,10 @@ Class that returns chrom, pos, data from a wiggle source. """ COLUMN_NAMES = [ 'chrom', 'pos', 'value' ] + settings = { + 'named_columns' : 'bool', + 'column_names' : 'list:str', + } def __init__( self, source, chrom, start, end, named_columns=False, column_names=None, **kwargs ): """ diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/dataproviders/decorators.py --- a/lib/galaxy/datatypes/dataproviders/decorators.py +++ b/lib/galaxy/datatypes/dataproviders/decorators.py @@ -87,17 +87,40 @@ # log.debug( '\t\t ', fn.__doc__ ) return cls -def dataprovider_factory( name ): +def dataprovider_factory( name, settings=None ): """ - Wraps a class method and marks it as a dataprovider factory. + Wraps a class method and marks it as a dataprovider factory and creates a + function to parse query strings to __init__ arguments as the + `parse_query_string_settings` attribute of the factory function. + + An example use of the `parse_query_string_settings`: + ..example:: + kwargs = dataset.datatype.dataproviders[ provider ].parse_query_string_settings( query_kwargs ) + return list( dataset.datatype.dataprovider( dataset, provider, **kwargs ) ) :param name: what name/key to register the factory under in `cls.dataproviders` - :param type: any hashable var + :type name: any hashable var + :param settings: dictionary containing key/type pairs for parsing query strings + to __init__ arguments + :type settings: dictionary """ + #TODO:?? use *args for settings allowing mulitple dictionaries + # make a function available through the name->provider dispatch to parse query strings + # callable like: + # settings_dict = dataproviders[ provider_name ].parse_query_string_settings( query_kwargs ) + #TODO: ugh - overly complicated but the best I could think of + def parse_query_string_settings( query_kwargs ): + return _parse_query_string_settings( query_kwargs, settings ) + #log.debug( 'dataprovider:', name ) def named_dataprovider_factory( func ): #log.debug( 'named_dataprovider_factory:', name, '->', func.__name__ ) setattr( func, _DATAPROVIDER_METHOD_NAME_KEY, name ) + + setattr( func, 'parse_query_string_settings', parse_query_string_settings ) + setattr( func, 'settings', settings ) + #TODO: I want a way to inherit settings from the previous provider( this_name ) instead of defining over and over + #log.debug( '\t setting:', getattr( func, _DATAPROVIDER_METHOD_NAME_KEY ) ) @wraps( func ) def wrapped_dataprovider_factory( self, *args, **kwargs ): @@ -105,3 +128,38 @@ return func( self, *args, **kwargs ) return wrapped_dataprovider_factory return named_dataprovider_factory + +def _parse_query_string_settings( query_kwargs, settings=None ): + """ + Parse the values in `query_kwargs` from strings to the proper types + listed in the same key in `settings`. + """ + def list_from_query_string( s ): + # assume csv + return s.split( ',' ) + + parsers = { + 'int' : int, + 'float' : float, + 'bool' : bool, + 'list:str' : lambda s: list_from_query_string( s ), + 'list:int' : lambda s: [ int( i ) for i in list_from_query_string( s ) ], + } + settings = settings or {} + # yay! yet another set of query string parsers! <-- sarcasm + # work through the keys in settings finding matching keys in query_kwargs + # if found in both, get the expected/needed type from settings and store the new parsed value + # if we can't parse it (no parser, bad value), delete the key from query_kwargs so the provider will use the defaults + for key in settings: + if key in query_kwargs: + #TODO: this would be the place to sanitize any strings + query_value = query_kwargs[ key ] + needed_type = settings[ key ] + try: + query_kwargs[ key ] = parsers[ needed_type ]( query_value ) + except ( KeyError, ValueError ): + del query_kwargs[ key ] + + #TODO:?? do we want to remove query_kwarg entries NOT in settings? + return query_kwargs + diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/dataproviders/line.py --- a/lib/galaxy/datatypes/dataproviders/line.py +++ b/lib/galaxy/datatypes/dataproviders/line.py @@ -27,6 +27,12 @@ to return. """ DEFAULT_COMMENT_CHAR = '#' + settings = { + 'string_lines' : 'bool', + 'provide_blank' : 'bool', + 'comment_char' : 'str', + } + def __init__( self, source, strip_lines=True, provide_blank=False, comment_char=DEFAULT_COMMENT_CHAR, **kwargs ): """ :param strip_lines: remove whitespace from the beginning an ending @@ -78,6 +84,11 @@ .. note:: the regex matches are effectively OR'd (if **any** regex matches the line it is considered valid and will be provided). """ + settings = { + 'regex_list' : 'list:str', + 'invert' : 'bool', + } + def __init__( self, source, regex_list=None, invert=False, **kwargs ): """ :param regex_list: list of strings or regular expression strings that will diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -334,20 +334,24 @@ return None # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'interval' ) + @dataproviders.decorators.dataprovider_factory( 'interval', + dataproviders.dataset.IntervalDataProvider.settings ) def interval_dataprovider( self, dataset, **settings ): return dataproviders.dataset.IntervalDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'interval-map' ) + @dataproviders.decorators.dataprovider_factory( 'interval-map', + dataproviders.dataset.IntervalDataProvider.settings ) def interval_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.interval_dataprovider( dataset, **settings ) @@ -809,20 +813,24 @@ # ------------- Dataproviders # redefine bc super is Tabular - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, 0, 3, 4, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'interval' ) + @dataproviders.decorators.dataprovider_factory( 'interval', + dataproviders.dataset.IntervalDataProvider.settings ) def interval_dataprovider( self, dataset, **settings ): return dataproviders.dataset.IntervalDataProvider( dataset, 0, 3, 4, 6, 2, **settings ) - @dataproviders.decorators.dataprovider_factory( 'interval-map' ) + @dataproviders.decorators.dataprovider_factory( 'interval-map', + dataproviders.dataset.IntervalDataProvider.settings ) def interval_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.interval_dataprovider( dataset, **settings ) @@ -1193,12 +1201,12 @@ return resolution # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'wiggle' ) + @dataproviders.decorators.dataprovider_factory( 'wiggle', dataproviders.dataset.WiggleDataProvider.settings ) def wiggle_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.dataset.WiggleDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'wiggle-map' ) + @dataproviders.decorators.dataprovider_factory( 'wiggle-map', dataproviders.dataset.WiggleDataProvider.settings ) def wiggle_map_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) settings[ 'named_columns' ] = True diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -15,8 +15,6 @@ from galaxy import util from sniff import * -from galaxy.datatypes import dataproviders - import pkg_resources pkg_resources.require("simplejson") import simplejson @@ -399,15 +397,6 @@ f.close() _count_split = classmethod(_count_split) - def provider( self, dataset, data_format, **settings ): - from galaxy.dataproviders import dataset as dataset_providers - - if data_format == 'id_seq': - source = dataset_providers.DatasetDataProvider( dataset ) - return dataset_providers.FastaDataProvider( source, **settings ) - - return super( Fasta, self ).provider( dataset, data_format, **settings ) - class csFasta( Sequence ): """ Class representing the SOLID Color-Space sequence ( csfasta ) """ diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -6,6 +6,7 @@ from galaxy import util from galaxy.datatypes.checkers import * from encodings import search_function as encodings_search_function +from binary import Binary log = logging.getLogger(__name__) diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -345,26 +345,25 @@ return vizs # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'column' ) + @dataproviders.decorators.dataprovider_factory( 'column', dataproviders.column.ColumnarDataProvider.settings ) def column_dataprovider( self, dataset, **settings ): """Uses column settings that are passed in""" - print 'Tabular.comment_char:', settings.get( 'comment_char', None ) - dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.column.ColumnarDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'dataset-column' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-column', + dataproviders.column.ColumnarDataProvider.settings ) def dataset_column_dataprovider( self, dataset, **settings ): """Attempts to get column settings from dataset.metadata""" return dataproviders.dataset.DatasetColumnarDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'map' ) + @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.column.MapDataProvider.settings ) def map_dataprovider( self, dataset, **settings ): """Uses column settings that are passed in""" dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.column.MapDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'dataset-map' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-map', dataproviders.column.MapDataProvider.settings ) def dataset_map_dataprovider( self, dataset, **settings ): """Attempts to get column settings from dataset.metadata""" return dataproviders.dataset.DatasetMapDataProvider( dataset, **settings ) @@ -502,55 +501,58 @@ # ------------- Dataproviders # sam does not use '#' to indicate comments/headers - we need to strip out those headers from the std. providers #TODO:?? seems like there should be an easier way to do this - metadata.comment_char? - @dataproviders.decorators.dataprovider_factory( 'line' ) + @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.line.FilteredLineDataProvider.settings ) def line_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).line_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'regex-line' ) + @dataproviders.decorators.dataprovider_factory( 'regex-line', dataproviders.line.RegexLineDataProvider.settings ) def regex_line_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).regex_line_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'column' ) + @dataproviders.decorators.dataprovider_factory( 'column', dataproviders.column.ColumnarDataProvider.settings ) def column_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).column_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'dataset-column' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-column', + dataproviders.column.ColumnarDataProvider.settings ) def dataset_column_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).dataset_column_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'map' ) + @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.column.MapDataProvider.settings ) def map_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).map_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'dataset-map' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-map', dataproviders.column.MapDataProvider.settings ) def dataset_map_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return super( Sam, self ).dataset_map_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'header' ) + @dataproviders.decorators.dataprovider_factory( 'header', dataproviders.line.RegexLineDataProvider.settings ) def header_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) headers_source = dataproviders.line.RegexLineDataProvider( dataset_source, regex_list=[ '^@' ] ) return dataproviders.line.RegexLineDataProvider( headers_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'id-seq-qual' ) + @dataproviders.decorators.dataprovider_factory( 'id-seq-qual', map_dataprovider.settings ) def id_seq_qual_dataprovider( self, dataset, **settings ): # provided as an example of a specified column map (w/o metadata) settings[ 'indeces' ] = [ 0, 9, 10 ] settings[ 'column_names' ] = [ 'id', 'seq', 'qual' ] return self.map_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return dataproviders.dataset.GenomicRegionDataProvider( dataset, 2, 3, 3, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return dataproviders.dataset.GenomicRegionDataProvider( dataset, 2, 3, 3, True, **settings ) @@ -621,11 +623,13 @@ return False # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) @@ -668,11 +672,13 @@ dataset.metadata.sample_names = line.split()[ 9: ] # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, 0, 1, 1, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -692,7 +692,10 @@ incoming['__user_email__'] = incoming['userEmail'] = user_email incoming['__user_name__'] = user_name # Build params, done before hook so hook can use - param_dict = self.tool.build_param_dict( incoming, inp_data, out_data, self.get_output_fnames(), self.working_directory ) + param_dict = self.tool.build_param_dict( incoming, + inp_data, out_data, + self.get_output_fnames(), + self.working_directory ) # Certain tools require tasks to be completed prior to job execution # ( this used to be performed in the "exec_before_job" hook, but hooks are deprecated ). self.tool.exec_before_job( self.queue.app, inp_data, out_data, param_dict ) @@ -919,8 +922,6 @@ return self.fail( "Job %s's output dataset(s) could not be read" % job.id ) job_context = ExpressionContext( dict( stdout = job.stdout, stderr = job.stderr ) ) - #DBTODO unused - #job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) for dataset_assoc in job.output_datasets + job.output_library_datasets: context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset ) #should this also be checking library associations? - can a library item be added from a history before the job has ended? - lets not allow this to occur diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -10,7 +10,7 @@ from sqlalchemy.sql.expression import and_, or_, select, func -from galaxy import util, model +from galaxy import model from galaxy.jobs import Sleeper, JobWrapper, TaskWrapper, JobDestination log = logging.getLogger( __name__ ) diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3569,7 +3569,7 @@ def repository_dependencies_being_installed( self ): required_repositories_being_installed = [] for required_repository in self.repository_dependencies: - if tool_dependency.status == ToolDependency.installation_status.INSTALLING: + if required_repository.status == self.installation_status.INSTALLING: required_repositories_being_installed.append( required_repository ) return required_repositories_being_installed @property diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -16,6 +16,7 @@ from sqlalchemy.orm.collections import attribute_mapped_collection from galaxy import model +from galaxy.model.orm import dialect_to_egg from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType from galaxy.security import GalaxyRBACAgent from galaxy.util.bunch import Bunch @@ -29,11 +30,6 @@ # For backward compatibility with "context.current" context.current = Session -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "mysql" : "MySQL_python" -} # NOTE REGARDING TIMESTAMPS: # It is currently difficult to have the timestamps calculated by the @@ -1616,17 +1612,27 @@ primaryjoin=( model.LibraryDatasetDatasetInfoAssociation.table.c.form_values_id == model.FormValues.table.c.id ) ) ) ) -mapper( model.JobToInputDatasetAssociation, model.JobToInputDatasetAssociation.table, - properties=dict( job=relation( model.Job ), dataset=relation( model.HistoryDatasetAssociation, lazy=False, backref="dependent_jobs" ) ) ) +mapper( model.JobToInputDatasetAssociation, + model.JobToInputDatasetAssociation.table, properties=dict( + job=relation( model.Job ), dataset=relation( + model.HistoryDatasetAssociation, lazy=False, + backref="dependent_jobs" ) ) ) -mapper( model.JobToOutputDatasetAssociation, model.JobToOutputDatasetAssociation.table, - properties=dict( job=relation( model.Job ), dataset=relation( model.HistoryDatasetAssociation, lazy=False ) ) ) +mapper( model.JobToOutputDatasetAssociation, + model.JobToOutputDatasetAssociation.table, properties=dict( + job=relation( model.Job ), dataset=relation( + model.HistoryDatasetAssociation, lazy=False ) ) ) -mapper( model.JobToInputLibraryDatasetAssociation, model.JobToInputLibraryDatasetAssociation.table, - properties=dict( job=relation( model.Job ), dataset=relation( model.LibraryDatasetDatasetAssociation, lazy=False, backref="dependent_jobs" ) ) ) +mapper( model.JobToInputLibraryDatasetAssociation, + model.JobToInputLibraryDatasetAssociation.table, properties=dict( + job=relation( model.Job ), dataset=relation( + model.LibraryDatasetDatasetAssociation, lazy=False, + backref="dependent_jobs" ) ) ) -mapper( model.JobToOutputLibraryDatasetAssociation, model.JobToOutputLibraryDatasetAssociation.table, - properties=dict( job=relation( model.Job ), dataset=relation( model.LibraryDatasetDatasetAssociation, lazy=False ) ) ) +mapper( model.JobToOutputLibraryDatasetAssociation, + model.JobToOutputLibraryDatasetAssociation.table, properties=dict( + job=relation( model.Job ), dataset=relation( + model.LibraryDatasetDatasetAssociation, lazy=False ) ) ) mapper( model.JobParameter, model.JobParameter.table ) diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py +++ b/lib/galaxy/model/migrate/check.py @@ -12,16 +12,13 @@ from sqlalchemy.exc import NoSuchTableError from migrate.versioning import repository, schema +from galaxy.model.orm import dialect_to_egg + log = logging.getLogger( __name__ ) # path relative to galaxy migrate_repository_directory = os.path.dirname( __file__ ).replace( os.getcwd() + os.path.sep, '', 1 ) migrate_repository = repository.Repository( migrate_repository_directory ) -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "mysql" : "MySQL_python" -} def create_or_verify_database( url, galaxy_config_file, engine_options={}, app=None ): """ @@ -47,6 +44,7 @@ # Let this go, it could possibly work with db's we don't support log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) # Create engine and metadata + print url, engine_options engine = create_engine( url, **engine_options ) meta = MetaData( bind=engine ) # Try to load dataset table diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/model/orm/__init__.py --- a/lib/galaxy/model/orm/__init__.py +++ b/lib/galaxy/model/orm/__init__.py @@ -7,3 +7,10 @@ import sqlalchemy.exc from sqlalchemy.ext.orderinglist import ordering_list + +dialect_to_egg = { + "sqlite" : "pysqlite>=2", + "postgres" : "psycopg2", + "postgresql" : "psycopg2", + "mysql" : "MySQL_python" +} diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -816,6 +816,7 @@ """ def __init__( self ): self.page = 0 + self.rerun_remap_job_id = None self.inputs = None def encode( self, tool, app, secure=True ): """ @@ -825,6 +826,7 @@ # page in that dict value = params_to_strings( tool.inputs, self.inputs, app ) value["__page__"] = self.page + value["__rerun_remap_job_id__"] = self.rerun_remap_job_id value = simplejson.dumps( value ) # Make it secure if secure: @@ -846,6 +848,10 @@ # Restore from string values = json_fix( simplejson.loads( value ) ) self.page = values.pop( "__page__" ) + if '__rerun_remap_job_id__' in values: + self.rerun_remap_job_id = values.pop( "__rerun_remap_job_id__" ) + else: + self.rerun_remap_job_id = None self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True ) class ToolOutput( object ): @@ -933,6 +939,7 @@ self.input_required = False self.display_interface = True self.require_login = False + self.rerun = False # Define a place to keep track of all input These # differ from the inputs dictionary in that inputs can be page # elements like conditionals, but input_params are basic form @@ -1521,7 +1528,8 @@ elif ( re.search( "fatal", err_level, re.IGNORECASE ) ): return_level = StdioErrorLevel.FATAL else: - log.debug( "Error level %s did not match warning/fatal" % err_level ) + log.debug( "Tool %s: error level %s did not match log/warning/fatal" % + ( self.id, err_level ) ) except Exception: log.error( "Exception in parse_error_level " + str(sys.exc_info() ) ) @@ -1933,7 +1941,10 @@ # If we've completed the last page we can execute the tool elif state.page == self.last_page: try: - _, out_data = self.execute( trans, incoming=params, history=history ) + rerun_remap_job_id = None + if 'rerun_remap_job_id' in incoming: + rerun_remap_job_id = trans.app.security.decode_id(incoming['rerun_remap_job_id']) + _, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) except httpexceptions.HTTPFound, e: #if it's a paste redirect exception, pass it up the stack raise e @@ -2502,7 +2513,6 @@ datatypes_registry = self.app.datatypes_registry, tool = self, name = name ) - if data: for child in data.children: param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child ) diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -1,15 +1,16 @@ +import os +import galaxy.tools + +from galaxy.exceptions import ObjectInvalid from galaxy.model import LibraryDatasetDatasetAssociation -from galaxy.util.bunch import Bunch +from galaxy.tools.parameters import DataToolParameter, SelectToolParameter +from galaxy.tools.parameters.grouping import Conditional, Repeat +from galaxy.util.json import from_json_string +from galaxy.util.json import to_json_string +from galaxy.util.none_like import NoneDataset from galaxy.util.odict import odict -from galaxy.util.json import to_json_string -from galaxy.tools.parameters import * -from galaxy.tools.parameters.grouping import * from galaxy.util.template import fill_template -from galaxy.util.none_like import NoneDataset from galaxy.web import url_for -from galaxy.exceptions import ObjectInvalid -import galaxy.tools -from types import * import logging log = logging.getLogger( __name__ ) @@ -107,7 +108,7 @@ tool.visit_inputs( param_values, visitor ) return input_datasets - def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, set_output_history=True, history=None, job_params=None ): + def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True, set_output_history=True, history=None, job_params=None, rerun_remap_job_id=None): """ Executes a tool, creating job and tool outputs, associating them, and submitting the job to the job queue. If history is not specified, use @@ -409,6 +410,40 @@ job.params = to_json_string( job_params ) job.set_handler(tool.get_job_handler(job_params)) trans.sa_session.add( job ) + # Now that we have a job id, we can remap any outputs if this is a rerun and the user chose to continue dependent jobs + # This functionality requires tracking jobs in the database. + if trans.app.config.track_jobs_in_database and rerun_remap_job_id is not None: + try: + old_job = trans.sa_session.query( trans.app.model.Job ).get(rerun_remap_job_id) + assert old_job is not None, '(%s/%s): Old job id is invalid' % (rerun_remap_job_id, job.id) + assert old_job.tool_id == job.tool_id, '(%s/%s): Old tool id (%s) does not match rerun tool id (%s)' % (old_job.id, job.id, old_job.tool_id, job.tool_id) + if trans.user is not None: + assert old_job.user_id == trans.user.id, '(%s/%s): Old user id (%s) does not match rerun user id (%s)' % (old_job.id, job.id, old_job.user_id, trans.user.id) + elif trans.user is None and type( galaxy_session ) == trans.model.GalaxySession: + assert old_job.session_id == galaxy_session.id, '(%s/%s): Old session id (%s) does not match rerun session id (%s)' % (old_job.id, job.id, old_job.session_id, galaxy_session.id) + else: + raise Exception('(%s/%s): Remapping via the API is not (yet) supported' % (old_job.id, job.id)) + for jtod in old_job.output_datasets: + for (job_to_remap, jtid) in [(jtid.job, jtid) for jtid in jtod.dataset.dependent_jobs]: + if (trans.user is not None and job_to_remap.user_id == trans.user.id) or (trans.user is None and job_to_remap.session_id == galaxy_session.id): + if job_to_remap.state == job_to_remap.states.PAUSED: + job_to_remap.state = job_to_remap.states.NEW + for hda in [ dep_jtod.dataset for dep_jtod in job_to_remap.output_datasets ]: + if hda.state == hda.states.PAUSED: + hda.state = hda.states.NEW + hda.info = None + for p in job_to_remap.parameters: + if p.name == jtid.name and p.value == str(jtod.dataset.id): + p.value = str(out_data[jtod.name].id) + jtid.dataset = out_data[jtod.name] + jtid.dataset.hid = jtod.dataset.hid + log.info('Job %s input HDA %s remapped to new HDA %s' % (job_to_remap.id, jtod.dataset.id, jtid.dataset.id)) + trans.sa_session.add(job_to_remap) + trans.sa_session.add(jtid) + jtod.dataset.visible = False + trans.sa_session.add(jtod) + except Exception, e: + log.exception('Cannot remap rerun dependencies.') trans.sa_session.flush() # Some tools are not really executable, but jobs are still created for them ( for record keeping ). # Examples include tools that redirect to other applications ( epigraph ). These special tools must diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/tools/actions/history_imp_exp.py --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -9,7 +9,7 @@ class ImportHistoryToolAction( ToolAction ): """Tool action used for importing a history to an archive. """ - def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None ): + def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None, **kwargs ): # # Create job. # @@ -57,7 +57,7 @@ class ExportHistoryToolAction( ToolAction ): """Tool action used for exporting a history to an archive. """ - def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None ): + def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None, **kwargs ): # # Get history to export. # diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py +++ b/lib/galaxy/tools/actions/metadata.py @@ -9,7 +9,7 @@ class SetMetadataToolAction( ToolAction ): """Tool action used for setting external metadata on an existing dataset""" - def execute( self, tool, trans, incoming={}, set_output_hid=False, overwrite=True, history=None, job_params=None ): + def execute( self, tool, trans, incoming={}, set_output_hid=False, overwrite=True, history=None, job_params=None, **kwargs ): """ Execute using a web transaction. """ diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py +++ b/lib/galaxy/tools/actions/upload.py @@ -5,7 +5,7 @@ log = logging.getLogger( __name__ ) class UploadToolAction( ToolAction ): - def execute( self, tool, trans, incoming={}, set_output_hid = True, history=None ): + def execute( self, tool, trans, incoming={}, set_output_hid = True, history=None, **kwargs ): dataset_upload_inputs = [] for input_name, input in tool.inputs.iteritems(): if input.type == "upload_dataset": diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/visualization/data_providers/registry.py --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -32,7 +32,7 @@ "bigwig": genome.BigWigDataProvider, "bigbed": genome.BigBedDataProvider, - "column": ColumnDataProvider + "column_with_stats": ColumnDataProvider } def get_data_provider( self, trans, name=None, source='data', raw=False, original_dataset=None ): diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -15,22 +15,27 @@ log = logging.getLogger( __name__ ) __TODO__ = """ - BUGS: - anon users clicking a viz link gets 'must be' msg in galaxy_main (w/ masthead) - should not show visualizations (no icon)? - newick files aren't being sniffed prop? - datatype is txt +BUGS: + anon users clicking a viz link gets 'must be' msg in galaxy_main (w/ masthead) + should not show visualizations (no icon)? + newick files aren't being sniffed prop? - datatype is txt - have parsers create objects instead of dicts - allow data_sources with no model_class but have tests (isAdmin, etc.) - maybe that's an instance of User model_class? - some confused vocabulary in docs, var names - tests: - anding, grouping, not - data_sources: - lists of - add description element to visualization. +have parsers create objects instead of dicts +allow data_sources with no model_class but have tests (isAdmin, etc.) + maybe that's an instance of User model_class? +some confused vocabulary in docs, var names +tests: + anding, grouping, not +data_sources: + lists of +add description element to visualization. + +TESTS to add: + has dataprovider + user is admin """ +# ------------------------------------------------------------------- the registry class VisualizationsRegistry( object ): """ Main responsibilities are: @@ -93,6 +98,45 @@ """ self.listings = VisualizationsConfigParser.parse( self.configuration_filepath ) + def get_visualization( self, trans, visualization_name, target_object ): + """ + Return data to build a url to the visualization with the given + `visualization_name` if it's applicable to `target_object` or + `None` if it's not. + """ + # a little weird to pass trans because this registry is part of the trans.app + listing_data = self.listings.get( visualization_name, None ) + if not listing_data: + return None + + data_sources = listing_data[ 'data_sources' ] + for data_source in data_sources: + # currently a model class is required + model_class = data_source[ 'model_class' ] + if not isinstance( target_object, model_class ): + continue + + # tests are optional - default is the above class test + tests = data_source[ 'tests' ] + if tests and not self.is_object_applicable( trans, target_object, tests ): + continue + + param_data = data_source[ 'to_params' ] + url = self.get_visualization_url( trans, target_object, visualization_name, param_data ) + link_text = listing_data.get( 'link_text', None ) + if not link_text: + # default to visualization name, titlecase, and replace underscores + link_text = visualization_name.title().replace( '_', ' ' ) + render_location = listing_data.get( 'render_location' ) + # remap some of these vars for direct use in ui.js, PopupMenu (e.g. text->html) + return { + 'href' : url, + 'html' : link_text, + 'target': render_location + } + + return None + # -- building links to visualizations from objects -- def get_visualizations( self, trans, target_object ): """ @@ -100,36 +144,11 @@ the urls to call in order to render the visualizations. """ #TODO:?? a list of objects? YAGNI? - # a little weird to pass trans because this registry is part of the trans.app applicable_visualizations = [] - for vis_name, listing_data in self.listings.items(): - - data_sources = listing_data[ 'data_sources' ] - for data_source in data_sources: - # currently a model class is required - model_class = data_source[ 'model_class' ] - if not isinstance( target_object, model_class ): - continue - - # tests are optional - default is the above class test - tests = data_source[ 'tests' ] - if tests and not self.is_object_applicable( trans, target_object, tests ): - continue - - param_data = data_source[ 'to_params' ] - url = self.get_visualization_url( trans, target_object, vis_name, param_data ) - link_text = listing_data.get( 'link_text', None ) - if not link_text: - # default to visualization name, titlecase, and replace underscores - link_text = vis_name.title().replace( '_', ' ' ) - render_location = listing_data.get( 'render_location' ) - # remap some of these vars for direct use in ui.js, PopupMenu (e.g. text->html) - applicable_visualizations.append({ - 'href' : url, - 'html' : link_text, - 'target': render_location - }) - + for vis_name in self.listings: + url_data = self.get_visualization( trans, vis_name, target_object ) + if url_data: + applicable_visualizations.append( url_data ) return applicable_visualizations def is_object_applicable( self, trans, target_object, data_source_tests ): @@ -151,10 +170,11 @@ # convert datatypes to their actual classes (for use with isinstance) test_result = trans.app.datatypes_registry.get_datatype_class_by_name( test_result ) if not test_result: - # warn if can't find class, but continue + # warn if can't find class, but continue (with other tests) log.warn( 'visualizations_registry cannot find class (%s) for applicability test', test_result ) continue + #NOTE: tests are OR'd, if any test passes - the visualization can be applied if test_fn( target_object, test_result ): #log.debug( 'test passed' ) return True diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -6,6 +6,7 @@ from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin from galaxy.web.base.controller import UsesHistoryMixin from galaxy.web.framework.helpers import is_true +from galaxy.datatypes import dataproviders import logging log = logging.getLogger( __name__ ) @@ -217,10 +218,24 @@ return msg registry = trans.app.data_provider_registry + # allow the caller to specifiy which provider is used - if provider and provider in registry.dataset_type_name_to_data_provider: - data_provider = registry.dataset_type_name_to_data_provider[ provider ]( dataset ) - # or have it look up by datatype + # pulling from the original providers if possible, then the new providers + if provider: + if provider in registry.dataset_type_name_to_data_provider: + data_provider = registry.dataset_type_name_to_data_provider[ provider ]( dataset ) + + elif dataset.datatype.has_dataprovider( provider ): + kwargs = dataset.datatype.dataproviders[ provider ].parse_query_string_settings( kwargs ) + # use dictionary to allow more than the data itself to be returned (data totals, other meta, etc.) + return { + 'data': list( dataset.datatype.dataprovider( dataset, provider, **kwargs ) ) + } + + else: + raise dataproviders.exceptions.NoProviderAvailable( dataset.datatype, provider ) + + # no provider name: look up by datatype else: data_provider = registry.get_data_provider( trans, raw=True, original_dataset=dataset ) diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -220,7 +220,8 @@ return { 'error' : 'user has no permission to add to library folder (%s)' %( folder_id ) } ldda = self.copy_hda_to_library_folder( trans, hda, folder, ldda_message=ldda_message ) - rval = ldda.get_api_value() + ldda_dict = ldda.get_api_value() + rval = trans.security.encode_dict_ids( ldda_dict ) except Exception, exc: #TODO: grrr... @@ -234,7 +235,6 @@ return rval - @web.expose_api def update( self, trans, id, library_id, payload, **kwd ): """ diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -3,13 +3,13 @@ """ import logging from galaxy import web -from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin from paste.httpexceptions import HTTPNotImplemented, HTTPBadRequest log = logging.getLogger( __name__ ) -class BaseProvenanceController( BaseAPIController ): +class BaseProvenanceController( BaseAPIController, UsesHistoryMixin ): """ """ @web.expose_api @@ -43,7 +43,7 @@ item = item.copied_from_library_dataset_dataset_association return { "id" : trans.security.encode_id(item.id), - "uuid" : item.dataset.uuid, + "uuid" : ( lambda uuid: str( uuid ) if uuid else None )( item.dataset.uuid), "tool_id" : item.creating_job.tool_id, "parameters" : self._get_job_record(trans, item.creating_job, follow) } @@ -59,7 +59,7 @@ else: out[in_d.name] = { "id" : trans.security.encode_id(in_d.dataset.id), - "uuid" : in_d.dataset.dataset.uuid + "uuid" : ( lambda uuid: str( uuid ) if uuid else None )( in_d.dataset.dataset.uuid ) } return out diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -9,6 +9,7 @@ from tool_shed.galaxy_install import repository_util from tool_shed.util import common_util +from tool_shed.util import encoding_util import tool_shed.util.shed_util_common as suc log = logging.getLogger( __name__ ) @@ -179,6 +180,11 @@ # Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain the repository information. install_repository_dependencies = payload.get( 'install_repository_dependencies', False ) install_tool_dependencies = payload.get( 'install_tool_dependencies', False ) + if install_tool_dependencies: + if trans.app.config.tool_dependency_dir is None: + no_tool_dependency_dir_message = "Tool dependencies can be automatically installed only if you set the value of your 'tool_dependency_dir' " + no_tool_dependency_dir_message += "setting in your Galaxy configuration file (universe_wsgi.ini) and restart your Galaxy server." + raise HTTPBadRequest( detail=no_tool_dependency_dir_message ) new_tool_panel_section = payload.get( 'new_tool_panel_section_label', '' ) shed_tool_conf = payload.get( 'shed_tool_conf', None ) if shed_tool_conf: @@ -211,13 +217,8 @@ tool_path=tool_path, tool_shed_url=tool_shed_url ) # Create the tool_shed_repository database records and gather additional information for repository installation. - created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ repository_util.handle_tool_shed_repositories( trans, installation_dict, using_api=True ) - if message and len( repo_info_dicts ) == 1: - # We're attempting to install a single repository that has already been installed into this Galaxy instance. - log.error( message, exc_info=True ) - trans.response.status = 500 - return dict( status='error', error=message ) if created_or_updated_tool_shed_repositories: # Build the dictionary of information necessary for installing the repositories. installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories, @@ -244,7 +245,7 @@ # order the list of tsr_ids to ensure all repositories install in the required order. tsr_ids = [ trans.security.encode_id( tool_shed_repository.id ) for tool_shed_repository in tool_shed_repositories ] ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ - repository_util.order_components_for_installation( trans, tsr_ids, repo_info_dicts, tool_panel_section_keys ) + repository_util.order_components_for_installation( trans, tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys ) # Install the repositories, keeping track of each one for later display. for index, tsr_id in enumerate( ordered_tsr_ids ): tool_shed_repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) @@ -266,11 +267,7 @@ action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) installed_tool_shed_repositories.append( tool_shed_repository_dict ) - elif message: - log.error( message, exc_info=True ) - trans.response.status = 500 - return dict( status='error', error=message ) - elif not created_or_updated_tool_shed_repositories and not message: + else: # We're attempting to install more than 1 repository, and all of them have already been installed. return dict( status='error', error='All repositories that you are attempting to install have been previously installed.' ) # Display the list of installed repositories. @@ -362,3 +359,56 @@ elif isinstance( installed_tool_shed_repositories, list ): all_installed_tool_shed_repositories.extend( installed_tool_shed_repositories ) return all_installed_tool_shed_repositories + + @web.expose_api + def repair_repository_revision( self, trans, payload, **kwd ): + """ + POST /api/tool_shed_repositories/repair_repository_revision + Repair a specified repository revision previously installed into Galaxy. + + :param key: the current Galaxy admin user's API key + + The following parameters are included in the payload. + :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed + :param name (required): the name of the Repository + :param owner (required): the owner of the Repository + :param changset_revision (required): the changset_revision of the RepositoryMetadata object associated with the Repository + """ + api_key = kwd.get( 'key', None ) + # Get the information about the repository to be installed from the payload. + tool_shed_url = payload.get( 'tool_shed_url', '' ) + if not tool_shed_url: + raise HTTPBadRequest( detail="Missing required parameter 'tool_shed_url'." ) + name = payload.get( 'name', '' ) + if not name: + raise HTTPBadRequest( detail="Missing required parameter 'name'." ) + owner = payload.get( 'owner', '' ) + if not owner: + raise HTTPBadRequest( detail="Missing required parameter 'owner'." ) + changeset_revision = payload.get( 'changeset_revision', '' ) + if not changeset_revision: + raise HTTPBadRequest( detail="Missing required parameter 'changeset_revision'." ) + tool_shed_repositories = [] + tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision ) + repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) + ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) + ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) + if ordered_tsr_ids and ordered_repo_info_dicts: + repositories_for_repair = [] + for index, tsr_id in enumerate( ordered_tsr_ids ): + repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) + repo_info_dict = ordered_repo_info_dicts[ index ] + # TODO: handle errors in repair_dict. + repair_dict = repository_util.repair_tool_shed_repository( trans, + repository, + encoding_util.tool_shed_encode( repo_info_dict ) ) + repository_dict = repository.get_api_value( value_mapper=default_tool_shed_repository_value_mapper( trans, repository ) ) + repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', + action='show', + id=trans.security.encode_id( repository.id ) ) + if repair_dict: + errors = repair_dict.get( repository.name, [] ) + repository_dict[ 'errors_attempting_repair' ] = ' '.join( errors ) + tool_shed_repositories.append( repository_dict ) + # Display the list of repaired repositories. + return tool_shed_repositories diff -r 320ae026f73a849c77a580410a5a3d6927ef1b91 -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -163,12 +163,13 @@ webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', - 'tool_shed_repositories', - controller='tool_shed_repositories', - name_prefix='tool_shed_repository_', - path_prefix='/api', - new={ 'install_repository_revision' : 'POST' }, - parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) ) + 'tool_shed_repositories', + member={ 'repair_repository_revision' : 'POST' }, + controller='tool_shed_repositories', + name_prefix='tool_shed_repository_', + path_prefix='/api', + new={ 'install_repository_revision' : 'POST' }, + parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) ) # Connect logger from app if app.trace_logger: webapp.trace_logger = app.trace_logger This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/5f24b2c4f38b/ Changeset: 5f24b2c4f38b Branch: search User: Kyle Ellrott Date: 2013-06-27 21:00:27 Summary: Fixing the job input/output values to format that is consistant with format used in other areas of galaxy. Affected #: 1 file diff -r 460c7dc52f92abac4d9ea9e5700dc8238b2a7fc4 -r 5f24b2c4f38bd65453cccad0b9bf526eff315918 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -372,10 +372,10 @@ input_dict = {} for i in self.input_datasets: if i.dataset is not None: - input_dict[i.name] = {"hda_id" : i.dataset.id} + input_dict[i.name] = {"id" : i.dataset.id, "src" : "hda"} for i in self.input_library_datasets: if i.dataset is not None: - input_dict[i.name] = {"ldda_id" : i.dataset.id} + input_dict[i.name] = {"id" : i.dataset.id, "src" : "ldda"} for k in input_dict: if k in param_dict: del param_dict[k] @@ -384,10 +384,10 @@ output_dict = {} for i in self.output_datasets: if i.dataset is not None: - output_dict[i.name] = {"hda_id" : i.dataset.id} + output_dict[i.name] = {"id" : i.dataset.id, "src" : "hda"} for i in self.output_library_datasets: if i.dataset is not None: - output_dict[i.name] = {"ldda_id" : i.dataset.id} + output_dict[i.name] = {"id" : i.dataset.id, "src" : "ldda"} rval['outputs'] = output_dict return rval https://bitbucket.org/galaxy/galaxy-central/commits/f4272212f722/ Changeset: f4272212f722 Branch: search User: Kyle Ellrott Date: 2013-06-27 21:01:43 Summary: Removing stray print statement Affected #: 1 file diff -r 5f24b2c4f38bd65453cccad0b9bf526eff315918 -r f4272212f72244f5fb045b8d978dc140e7cfa7ca lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py +++ b/lib/galaxy/model/migrate/check.py @@ -44,7 +44,6 @@ # Let this go, it could possibly work with db's we don't support log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) # Create engine and metadata - print url, engine_options engine = create_engine( url, **engine_options ) meta = MetaData( bind=engine ) # Try to load dataset table https://bitbucket.org/galaxy/galaxy-central/commits/c2fb95ef8617/ Changeset: c2fb95ef8617 Branch: search User: Kyle Ellrott Date: 2013-06-27 22:37:14 Summary: Allowing zero length strings to be compared in the search conditions Affected #: 1 file diff -r f4272212f72244f5fb045b8d978dc140e7cfa7ca -r c2fb95ef8617cc8156ba936ee6d064ed098a8b9a lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -507,7 +507,7 @@ | '<=' -> '<=' | 'like' -> 'like' ) -quote_word = "'" not_quote+:x "'" -> "".join(x) +quote_word = "'" not_quote*:x "'" -> "".join(x) not_quote = anything:x ?(x != "'") -> x not_dquote = anything:x ?(x != '"') -> x """ https://bitbucket.org/galaxy/galaxy-central/commits/0b7b71c9d296/ Changeset: 0b7b71c9d296 Branch: search User: Kyle Ellrott Date: 2013-07-03 01:39:01 Summary: Adding in input_ldda field to job search Affected #: 1 file diff -r c2fb95ef8617cc8156ba936ee6d064ed098a8b9a -r 0b7b71c9d296c8ce92a41905f489d1a109e85f02 lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -418,6 +418,20 @@ ) ) +def job_input_ldda_filter(view, left, operator, right): + view.do_query = True + alias = aliased( JobToInputLibraryDatasetAssociation ) + param_name = re.sub(r'^input_ldda.', '', left) + view.query = view.query.filter( + and_( + Job.id == alias.job_id, + alias.name == param_name, + alias.dataset_id == right + ) + ) + + + def job_output_hda_filter(view, left, operator, right): view.do_query = True alias = aliased( JobToOutputDatasetAssociation ) @@ -437,6 +451,7 @@ 'tool_name' : ViewField('tool_name', sqlalchemy_field=Job.tool_id), 'state' : ViewField('state', sqlalchemy_field=Job.state), 'param' : ViewField('param', handler=job_param_filter), + 'input_ldda' : ViewField('input_ldda', handler=job_input_ldda_filter, id_decode=True), 'input_hda' : ViewField('input_hda', handler=job_input_hda_filter, id_decode=True), 'output_hda' : ViewField('output_hda', handler=job_output_hda_filter, id_decode=True) } https://bitbucket.org/galaxy/galaxy-central/commits/3b419687739b/ Changeset: 3b419687739b Branch: search User: Kyle Ellrott Date: 2013-07-03 01:44:41 Summary: Adding missing import to search Affected #: 1 file diff -r 0b7b71c9d296c8ce92a41905f489d1a109e85f02 -r 3b419687739b3d4a759e73e99ff91633096bbbec lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -35,7 +35,7 @@ History, Library, LibraryFolder, LibraryDataset,StoredWorkflowTagAssociation, StoredWorkflow, HistoryTagAssociation,HistoryDatasetAssociationTagAssociation, ExtendedMetadata, ExtendedMetadataIndex, HistoryAnnotationAssociation, Job, JobParameter, -JobToInputDatasetAssociation, JobToOutputDatasetAssociation, ToolVersion) +JobToInputDatasetAssociation, JobToInputLibraryDatasetAssociation, JobToOutputDatasetAssociation, ToolVersion) from galaxy.util.json import to_json_string from sqlalchemy import and_ https://bitbucket.org/galaxy/galaxy-central/commits/df1b861724c2/ Changeset: df1b861724c2 Branch: search User: Kyle Ellrott Date: 2013-07-03 01:49:50 Summary: Fixing field name in selection statement Affected #: 1 file diff -r 3b419687739b3d4a759e73e99ff91633096bbbec -r df1b861724c205412a786cce00434dc39db391b1 lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -426,7 +426,7 @@ and_( Job.id == alias.job_id, alias.name == param_name, - alias.dataset_id == right + alias.ldda_id == right ) ) https://bitbucket.org/galaxy/galaxy-central/commits/74ad9ec46632/ Changeset: 74ad9ec46632 Branch: search User: Kyle Ellrott Date: 2013-07-18 23:46:32 Summary: Adding code to allow for search selection by 'copied_from_ldda_id' field Affected #: 2 files diff -r df1b861724c205412a786cce00434dc39db391b1 -r 74ad9ec46632d97d43f207098b80a824170bea58 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1715,6 +1715,9 @@ misc_info = hda.info, misc_blurb = hda.blurb ) + if hda.copied_from_library_dataset_dataset_association is not None: + rval['copied_from_ldda_id'] = hda.copied_from_library_dataset_dataset_association.id + if hda.history is not None: rval['history_id'] = hda.history.id diff -r df1b861724c205412a786cce00434dc39db391b1 -r 74ad9ec46632d97d43f207098b80a824170bea58 lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -296,8 +296,11 @@ FIELDS = { 'name' : ViewField('name', sqlalchemy_field=HistoryDatasetAssociation.name), 'id' : ViewField('id',sqlalchemy_field=HistoryDatasetAssociation.id, id_decode=True), - 'tag' : ViewField("tag", handler=history_dataset_handle_tag) - + 'tag' : ViewField("tag", handler=history_dataset_handle_tag), + 'copied_from_ldda_id' : ViewField("copied_from_ldda_id", + sqlalchemy_field=HistoryDatasetAssociation.copied_from_library_dataset_dataset_association_id, + id_decode=True), + 'deleted' : ViewField('deleted', sqlalchemy_field=HistoryDatasetAssociation.deleted) } def search(self, trans): https://bitbucket.org/galaxy/galaxy-central/commits/0e2c8d03786a/ Changeset: 0e2c8d03786a Branch: search User: kellrott Date: 2013-08-05 01:59:14 Summary: Merging Affected #: 1 file diff -r 74ad9ec46632d97d43f207098b80a824170bea58 -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -173,6 +173,7 @@ 'id' : ViewField('id', sqlalchemy_field=LibraryDatasetDatasetAssociation.id, id_decode=True), 'deleted' : ViewField('deleted', sqlalchemy_field=LibraryDatasetDatasetAssociation.deleted), 'parent_library_id' : ViewField('parent_library_id', id_decode=True, post_filter=ldda_parent_library_filter), + 'data_type' : ViewField('data_type', sqlalchemy_field=LibraryDatasetDatasetAssociation.extension) } def search(self, trans): https://bitbucket.org/galaxy/galaxy-central/commits/506d00954a3e/ Changeset: 506d00954a3e Branch: search User: Kyle Ellrott Date: 2013-08-23 21:05:41 Summary: galaxy-central default merge and resolve Affected #: 417 files diff -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b -r 506d00954a3eec4808ed8c0104b5e0404841b6af .coveragerc --- /dev/null +++ b/.coveragerc @@ -0,0 +1,3 @@ +[run] +branch = True +include = lib/galaxy/* diff -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b -r 506d00954a3eec4808ed8c0104b5e0404841b6af .hgignore --- a/.hgignore +++ b/.hgignore @@ -60,7 +60,7 @@ job_conf.xml data_manager_conf.xml shed_data_manager_conf.xml -visualizations_conf.xml +config/* static/welcome.html.* static/welcome.html @@ -82,6 +82,10 @@ # Test output run_functional_tests.html test/tool_shed/tmp/* +.coverage +htmlcov +run_unit_tests.html +test/unit/**.log # Project files *.kpf diff -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b -r 506d00954a3eec4808ed8c0104b5e0404841b6af .hgtags --- a/.hgtags +++ b/.hgtags @@ -3,3 +3,4 @@ 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 +1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 diff -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b -r 506d00954a3eec4808ed8c0104b5e0404841b6af README.txt --- a/README.txt +++ b/README.txt @@ -7,7 +7,7 @@ HOW TO START ============ -Galaxy requires Python 2.5, 2.6 or 2.7. To check your python version, run: +Galaxy requires Python 2.6 or 2.7. To check your python version, run: % python -V Python 2.7.3 diff -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b -r 506d00954a3eec4808ed8c0104b5e0404841b6af buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -65,6 +65,7 @@ " SAMPLES=" +tool_conf.xml.sample datatypes_conf.xml.sample universe_wsgi.ini.sample tool_data_table_conf.xml.sample diff -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b -r 506d00954a3eec4808ed8c0104b5e0404841b6af config/plugins/visualizations/README.txt --- /dev/null +++ b/config/plugins/visualizations/README.txt @@ -0,0 +1,34 @@ +Custom visualization plugins +---------------------------- + +Visualizations can be added to your Galaxy instance by creating +sub-directories, templates, and static files here. + +Properly configured and written visualizations will be accessible to +the user when they click the 'visualizations' icon for a dataset +in their history panel. + +The framework must be enabled in your 'universe_wsgi.ini' file by +uncommenting (and having a valid path for) the +'visualizations_plugin_directory' entry. + +For more information, see http://wiki.galaxyproject.org/VisualizationsRegistry + + +Sub-directory structure +----------------------- + +In general, sub-directories should follow the pattern: + + my_visualization/ + config/ + my_visualization.xml + static/ + ... any static files the visualization needs (if any) + templates/ + ... any Mako templates the visualization needs + +The XML config file for a visualization plugin can be validated on the command +line using (from your plugin directory): + + xmllint my_visualization/config/my_visualization.xml --valid --noout diff -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b -r 506d00954a3eec4808ed8c0104b5e0404841b6af config/plugins/visualizations/circster/config/circster.xml --- /dev/null +++ b/config/plugins/visualizations/circster/config/circster.xml @@ -0,0 +1,28 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "../../visualization.dtd"> +<visualization name="circster"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="hda">hda_ldda</to_param> + </data_source> + <data_source> + <model_class>LibraryDatasetDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="ldda">hda_ldda</to_param> + </data_source> + </data_sources> + <params> + <param type="visualization">id</param> + <param type="hda_or_ldda">dataset_id</param> + <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier> + <param type="dbkey">dbkey</param> + </params> +  + <template_root>webapps/galaxy/visualization</template_root> + <template>circster.mako</template> + <render_location>_top</render_location> +</visualization> diff -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b -r 506d00954a3eec4808ed8c0104b5e0404841b6af config/plugins/visualizations/graphview/config/graphview.xml --- /dev/null +++ b/config/plugins/visualizations/graphview/config/graphview.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "../../visualization.dtd"> +<visualization name="Graphview"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="has_dataprovider" test_attr="datatype">node-edge</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">graph.Rdf</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + </params> + <template>graphview/templates/graphview.mako</template> +</visualization> diff -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b -r 506d00954a3eec4808ed8c0104b5e0404841b6af config/plugins/visualizations/graphview/static/graphview.css --- /dev/null +++ b/config/plugins/visualizations/graphview/static/graphview.css @@ -0,0 +1,70 @@ +svg { + border: 1px solid lightgrey; + background-color: #FFF; + cursor: default; + -webkit-user-select: none; + -moz-user-select: none; + -ms-user-select: none; + -o-user-select: none; + user-select: none; +} + +svg:not(.active):not(.ctrl) { + cursor: crosshair; +} + +path.link { + fill: none; + stroke: #000; + stroke-width: 4px; + cursor: default; +} + +svg:not(.active):not(.ctrl) path.link { + cursor: pointer; +} + +path.link.selected { + stroke-dasharray: 10,2; +} + +path.link.dragline { + pointer-events: none; +} + +path.link.hidden { + stroke-width: 0; +} + +circle.node { + stroke-width: 1.0px; + cursor: pointer; +} + +circle.node.reflexive { + stroke: #000 !important; + stroke-width: 2.5px; +} + +text { + font: 12px sans-serif; + pointer-events: none; +} + +text.id { + text-anchor: middle; + font-weight: bold; +} + +div.tooltip { + position: absolute; + text-align: center; + width: 60px; + height: 28px; + padding: 2px; + font: 12px sans-serif; + background: lightsteelblue; + border: 0px; + border-radius: 8px; + pointer-events: none; +} diff -r 0e2c8d03786a9bf22cde5f14da3e868dd4607e0b -r 506d00954a3eec4808ed8c0104b5e0404841b6af config/plugins/visualizations/graphview/static/graphview.js --- /dev/null +++ b/config/plugins/visualizations/graphview/static/graphview.js @@ -0,0 +1,175 @@ +function get_firstChild(n) { + y=n.firstChild; + while (y && y.nodeType!=1) { + y=y.nextSibling; + } + return y; +} + +function get_nextSibling(n) { + y=n.nextSibling; + while (y) { + if (y.nodeType==1) { + return y; + } + y=y.nextSibling; + } + return y; +} + +function parse_xgmml_attr(elm) { + out = {}; + var c = get_firstChild(elm); + while (c) { + if (c.nodeName == "att") { + if (c.attributes['type'].value == "string") { + out[c.attributes['name'].value] = c.attributes['value'].value; + } + } + c = get_nextSibling(c); + } + return out +} + +function parse_xgmml(root, add_node, add_edge) { + graph=root.getElementsByTagName("graph")[0]; + elm = get_firstChild(graph); + while (elm) { + if (elm.nodeName == "node") { + var attr = parse_xgmml_attr(elm); + add_node( elm.attributes['id'].value, elm.attributes['label'].value, attr ); + } + if (elm.nodeName == "edge") { + var attr = parse_xgmml_attr(elm); + add_edge( elm.attributes['source'].value, elm.attributes['target'].value, attr ); + } + + elm = get_nextSibling(elm); + } +} + +function parse_sif(data, add_node, add_edge) { + var lines = data.split("\n") + for (var i in lines) { + var tmp = lines[i].split("\t"); + if (tmp.length == 3) { + add_edge(tmp[0], tmp[2], {type:tmp[1]}); + } + } + +} + +jQuery.fn.graphViewer = function(config) { + + var svg, colors; + var nodes = [], + links = []; + + var height = config.height; + var width = config.width; + + + colors = d3.scale.category10(); + + this.each(function() { + svg = d3.select(this) + .append('svg') + .attr('width', width) + .attr('height', height); + } + ); + + var tooltip_div = d3.select("#tooltip").attr("class", "tooltip").style("opacity", 0);; + + this.add_node = function(node_id, node_label, attr) { + nodes.push( {id: node_id, label:node_label, attr:attr} ); + } + + this.add_edge = function(src_id, dst_id, attr) { + var src, target; + for (var i in nodes) { + if (nodes[i].id == src_id) { + src = nodes[i]; + } + if (nodes[i].id == dst_id) { + target = nodes[i]; + } + } + if (typeof src==="undefined") { + i = nodes.length + nodes.push( {id:src_id, label:src_id, attr:{}} ) + src = nodes[i] + } + if (typeof target==="undefined") { + i = nodes.length + nodes.push( {id:dst_id, label:dst_id, attr:{}} ) + target = nodes[i] + } + if (src && target) { + links.push( {source: src, target: target, left: false, right: true } ); + } + } + + this.render = function() { + var path = svg.append('svg:g').selectAll('path'), + circle = svg.append('svg:g').selectAll('g'); + + + circle = circle.data(nodes, function(d) { return d.id; }); + var g = circle.enter().append('svg:g'); + + circle.on('mouseover', function(d) { + tooltip_div.transition() + .duration(200) + .style("opacity", .9); + tooltip_div.html( "<div>" + d.label + "</div><div>" + d.attr.type + "</div>" ).style("left", (d3.event.pageX + 40) + "px") + .style("top", (d3.event.pageY - 35) + "px"); + }) + .on("mouseout", function(d) { + tooltip_div.transition() + .duration(500) + .style("opacity", 0); + }); + + path = path.data(links); + + + function tick() { + path.attr('d', function(d) { + return 'M' + d.source.x + ',' + d.source.y + 'L' + d.target.x + ',' + d.target.y; + }); + circle.attr('transform', function(d) { + return 'translate(' + d.x + ',' + d.y + ')'; + }); + } + + + g.append('svg:circle') + .attr('class', 'node') + .attr('r', 8) + .style('stroke', 'black') + .attr('fill', function(d) { + return colors(d['attr']['type']) + }); + + path.enter().append('svg:path') + .attr('class', 'link') + + + // init D3 force layout + var force = d3.layout.force() + .nodes(nodes) + .links(links) + .size([width, height]) + .linkDistance(25) + .charge(-50) + .on('tick', tick) + circle.call(force.drag) + force.start() + + } + + return this + +} + This diff is so big that we needed to truncate the remainder. 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

commit/galaxy-central: guerler: Use refreshHdas to refresh history during upload
by commits-noreply＠bitbucket.org 22 Oct '13

22 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82cd70ba007c/ Changeset: 82cd70ba007c User: guerler Date: 2013-10-22 04:00:42 Summary: Use refreshHdas to refresh history during upload Affected #: 1 file diff -r 8ae19975dd333c6b4b4c15f93a0350a24f3c10db -r 82cd70ba007ced10ee3f4e32486569641b83dc0a static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -278,7 +278,7 @@ sy.addClass(this.state.success); // update galaxy history - Galaxy.currHistoryPanel.refresh(); + Galaxy.currHistoryPanel.refreshHdas(); }, // error 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

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 22 Oct '13

22 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f0053f5952e/ Changeset: 2f0053f5952e Branch: next-stable User: jgoecks Date: 2013-10-22 02:58:20 Summary: Fix track height calculation. Affected #: 2 files diff -r 3d138ced1f26c810a24bead0aa8fa6d8a65a7812 -r 2f0053f5952e9b93ded01fcd24ed87783dedc698 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();var ar=n[ai.attr("id")];if(ap.offsetY<aq){$(this).insertBefore(ai);ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){if(ac.tool_state!==undefined){this.set("hidden",ac.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=aj.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:this.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=ae.default_value});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input />").attr("id",am).attr("name",am).val(ax).css("float","left").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:X.Dataset.findOrCreate(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}this.max_height_px=Math.max(this.max_height_px,$(ae.canvas).height());ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color",default_value:l.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();var ar=n[ai.attr("id")];if(ap.offsetY<aq){$(this).insertBefore(ai);ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){if(ac.tool_state!==undefined){this.set("hidden",ac.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=aj.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:this.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=ae.default_value});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input />").attr("id",am).attr("name",am).val(ax).css("float","left").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:X.Dataset.findOrCreate(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height());ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color",default_value:l.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff -r 3d138ced1f26c810a24bead0aa8fa6d8a65a7812 -r 2f0053f5952e9b93ded01fcd24ed87783dedc698 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3384,9 +3384,11 @@ } // -- Update track, tile heights based on new tile. -- + + tile_element.css('height', 'auto'); - // Update max height based on current tile's canvas. - this.max_height_px = Math.max(this.max_height_px, $(tile.canvas).height()); + // Update max height based on current tile's height. + this.max_height_px = Math.max(this.max_height_px, tile_element.height()); // Update height for all tiles based on max height. tile_element.parent().children().css("height", this.max_height_px + "px"); https://bitbucket.org/galaxy/galaxy-central/commits/8ae19975dd33/ Changeset: 8ae19975dd33 User: jgoecks Date: 2013-10-22 02:59:36 Summary: Automated merge of next-stable Affected #: 2 files diff -r 100a64a1d85cbb582bd83ab9bbdd6cbd73a566f2 -r 8ae19975dd333c6b4b4c15f93a0350a24f3c10db static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();var ar=n[ai.attr("id")];if(ap.offsetY<aq){$(this).insertBefore(ai);ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){if(ac.tool_state!==undefined){this.set("hidden",ac.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=aj.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:this.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=ae.default_value});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input />").attr("id",am).attr("name",am).val(ax).css("float","left").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:X.Dataset.findOrCreate(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}this.max_height_px=Math.max(this.max_height_px,$(ae.canvas).height());ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color",default_value:l.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();var ar=n[ai.attr("id")];if(ap.offsetY<aq){$(this).insertBefore(ai);ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){if(ac.tool_state!==undefined){this.set("hidden",ac.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=aj.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:this.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=ae.default_value});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input />").attr("id",am).attr("name",am).val(ax).css("float","left").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:X.Dataset.findOrCreate(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height());ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color",default_value:l.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff -r 100a64a1d85cbb582bd83ab9bbdd6cbd73a566f2 -r 8ae19975dd333c6b4b4c15f93a0350a24f3c10db static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3384,9 +3384,11 @@ } // -- Update track, tile heights based on new tile. -- + + tile_element.css('height', 'auto'); - // Update max height based on current tile's canvas. - this.max_height_px = Math.max(this.max_height_px, $(tile.canvas).height()); + // Update max height based on current tile's height. + this.max_height_px = Math.max(this.max_height_px, tile_element.height()); // Update height for all tiles based on max height. tile_element.parent().children().css("height", this.max_height_px + "px"); 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 21 Oct '13

21 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/17b09bab9eea/ Changeset: 17b09bab9eea User: remy_d1 Date: 2013-03-05 17:22:20 Summary: add userskeys feature/controller which is usefull to manage user's API key through admin panel Affected #: 4 files diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 17b09bab9eead7e90f0981cdeee033dd860df72a lib/galaxy/webapps/galaxy/controllers/userskeys.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/controllers/userskeys.py @@ -0,0 +1,108 @@ +""" +Contains the user interface in the Universe class +""" + +import glob +import logging +import os +import socket +import string +import random +import pprint + +from galaxy import web +from galaxy import util, model +from galaxy.model.orm import and_ +from galaxy.security.validate_user_input import validate_email, validate_publicname, validate_password, transform_publicname +from galaxy.util.json import from_json_string, to_json_string +from galaxy.web import url_for +from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin +from galaxy.web.form_builder import CheckboxField, build_select_field +from galaxy.web.framework.helpers import time_ago, grids + +from inspect import getmembers + +log = logging.getLogger( __name__ ) + +require_login_template = """ +<p> + This %s has been configured such that only users who are logged in may use it.%s +</p> +<p/> +""" + +class UserOpenIDGrid( grids.Grid ): + use_panels = False + title = "OpenIDs linked to your account" + model_class = model.UserOpenID + template = '/user/openid_manage.mako' + default_filter = { "openid" : "All" } + default_sort_key = "-create_time" + columns = [ + grids.TextColumn( "OpenID URL", key="openid", link=( lambda x: dict( action='openid_auth', login_button="Login", openid_url=x.openid if not x.provider else '', openid_provider=x.provider, auto_associate=True ) ) ), + grids.GridColumn( "Created", key="create_time", format=time_ago ), + ] + operations = [ + grids.GridOperation( "Delete", async_compatible=True ), + ] + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( self.model_class ).filter( self.model_class.user_id == trans.user.id ) + +class User( BaseUIController, UsesFormDefinitionsMixin ): + user_openid_grid = UserOpenIDGrid() + installed_len_files = None + + + @web.expose + @web.require_login() + @web.require_admin + def index( self, trans, cntrller, **kwd ): + return trans.fill_template( 'webapps/galaxy/user/list_users.mako', action='all_users', cntrller=cntrller ) + + + + @web.expose + @web.require_login() + @web.require_admin + def api_keys( self, trans, cntrller, uid, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + uid = params.get('uid', uid) + pprint.pprint(uid) + if params.get( 'new_api_key_button', False ): + new_key = trans.app.model.APIKeys() + new_key.user_id = uid + new_key.key = trans.app.security.get_new_guid() + trans.sa_session.add( new_key ) + trans.sa_session.flush() + message = "Generated a new web API key" + status = "done" + return trans.fill_template( 'webapps/galaxy/user/ok_admin_api_keys.mako', + cntrller=cntrller, + message=message, + status=status ) + + + @web.expose + @web.require_login() + @web.require_admin + def all_users( self, trans, cntrller="userskeys", **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + users = [] + for user in trans.sa_session.query( trans.app.model.User ) \ + .filter( trans.app.model.User.table.c.deleted==False ) \ + .order_by( trans.app.model.User.table.c.email ): + uid = int(user.id) + userkey = "" + for api_user in trans.sa_session.query(trans.app.model.APIKeys) \ + .filter( trans.app.model.APIKeys.user_id == uid): + userkey = api_user.key + users.append({'uid':uid, 'email':user.email, 'key':userkey}) + return trans.fill_template( 'webapps/galaxy/user/list_users.mako', + cntrller=cntrller, + users=users, + message=message, + status=status ) diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 17b09bab9eead7e90f0981cdeee033dd860df72a templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -45,6 +45,7 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users' )}" target="galaxy_main">Manage users</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups' )}" target="galaxy_main">Manage groups</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles' )}" target="galaxy_main">Manage roles</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='userskeys', action='all_users' )}" target="galaxy_main">Manage users API keys</a></div> %if trans.app.config.allow_user_impersonation: <div class="toolTitle"><a href="${h.url_for( controller='admin', action='impersonate' )}" target="galaxy_main">Impersonate a user</a></div> %endif diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 17b09bab9eead7e90f0981cdeee033dd860df72a templates/webapps/galaxy/user/list_users.mako --- /dev/null +++ b/templates/webapps/galaxy/user/list_users.mako @@ -0,0 +1,37 @@ +<%inherit file="/base.mako"/> + +%if message: + ${render_msg( message, status )} +%endif + + +%if users: + <div class="toolForm"> + <div class="toolFormTitle">Users informations</div> + <table> + <thead><th>UID</th><th>email</th></thead> + <tbody> + %for user in users: + <tr> + <td>${user['uid']}</td> + <td>${user['email']}</td> + <td>${user['key']}</td> + <td> + <form action="${h.url_for( controller='userskeys', action='api_keys', cntrller=cntrller )}" method="POST"> + <input type="hidden" name="uid" value=${user['uid']} /> + <input type="submit" name="new_api_key_button" value="Generate a new key now" /> + </form> + </td> + </tr> + %endfor + </tbody> + </table> + <div style="clear: both"></div> + </div> +%else: + <div>No informations available</div> +%endif + + +<p/> + diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 17b09bab9eead7e90f0981cdeee033dd860df72a templates/webapps/galaxy/user/ok_admin_api_keys.mako --- /dev/null +++ b/templates/webapps/galaxy/user/ok_admin_api_keys.mako @@ -0,0 +1,28 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<br/><br/> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='userskeys', action='all_users', cntrller=cntrller )}">List users API keys</a> + </li> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + + <div> + <div style="clear: both;"> + SUCCESS. A new API key has been generated. + </div> + + + <div style="clear: both;"> + An API key will allow you to access Galaxy via its web + API (documentation forthcoming). Please note that + <strong>this key acts as an alternate means to access + your account, and should be treated with the same care + as your login password</strong>. + </div> + </div> https://bitbucket.org/galaxy/galaxy-central/commits/a1a06f6deb41/ Changeset: a1a06f6deb41 User: remy_d1 Date: 2013-03-05 17:50:40 Summary: modified method name 'api_keys' to 'admin_api_keys' for user vs userskeys controller Affected #: 2 files diff -r 17b09bab9eead7e90f0981cdeee033dd860df72a -r a1a06f6deb410e1c50b4cb86c28e97a75df4f91b lib/galaxy/webapps/galaxy/controllers/userskeys.py --- a/lib/galaxy/webapps/galaxy/controllers/userskeys.py +++ b/lib/galaxy/webapps/galaxy/controllers/userskeys.py @@ -64,7 +64,7 @@ @web.expose @web.require_login() @web.require_admin - def api_keys( self, trans, cntrller, uid, **kwd ): + def admin_api_keys( self, trans, cntrller, uid, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) diff -r 17b09bab9eead7e90f0981cdeee033dd860df72a -r a1a06f6deb410e1c50b4cb86c28e97a75df4f91b templates/webapps/galaxy/user/list_users.mako --- a/templates/webapps/galaxy/user/list_users.mako +++ b/templates/webapps/galaxy/user/list_users.mako @@ -17,7 +17,7 @@ <td>${user['email']}</td><td>${user['key']}</td><td> - <form action="${h.url_for( controller='userskeys', action='api_keys', cntrller=cntrller )}" method="POST"> + <form action="${h.url_for( controller='userskeys', action='admin_api_keys', cntrller=cntrller )}" method="POST"><input type="hidden" name="uid" value=${user['uid']} /><input type="submit" name="new_api_key_button" value="Generate a new key now" /></form> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 Oct '13

21 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3d138ced1f26/ Changeset: 3d138ced1f26 Branch: next-stable User: jgoecks Date: 2013-10-22 00:41:45 Summary: Pack script. Affected #: 1 file diff -r 14fbaad2645bd7b8a0a2f9a4a682b38ecf18c7d0 -r 3d138ced1f26c810a24bead0aa8fa6d8a65a7812 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();var ar=n[ai.attr("id")];if(ap.offsetY<aq){$(this).insertBefore(ai);ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new 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content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){if(ac.tool_state!==undefined){this.set("hidden",ac.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=aj.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:this.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=ae.default_value});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input />").attr("id",am).attr("name",am).val(ax).css("float","left").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:X.Dataset.findOrCreate(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}this.max_height_px=Math.max(this.max_height_px,$(ae.canvas).height());ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color",default_value:l.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();var ar=n[ai.attr("id")];if(ap.offsetY<aq){$(this).insertBefore(ai);ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){if(ac.tool_state!==undefined){this.set("hidden",ac.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=aj.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:this.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=ae.default_value});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input />").attr("id",am).attr("name",am).val(ax).css("float","left").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:X.Dataset.findOrCreate(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}this.max_height_px=Math.max(this.max_height_px,$(ae.canvas).height());ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color",default_value:l.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/04225eb28389/ Changeset: 04225eb28389 User: jgoecks Date: 2013-10-22 00:42:04 Summary: Automated merge of next-stable Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 9 new changesets
by commits-noreply＠bitbucket.org 21 Oct '13

21 Oct '13

9 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0eafcb644470/ Changeset: 0eafcb644470 Branch: next-stable User: dannon Date: 2013-10-21 22:23:43 Summary: Strip unused data_provider_registry Affected #: 1 file diff -r 81880a04e6e79d944a6d9c225b36417114cd38ec -r 0eafcb6444701fb40339ee6918a3d33fdf4a0479 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -101,7 +101,6 @@ # If there is a chrom, check for data on the chrom. if chrom: - data_provider_registry = trans.app.data_provider_registry data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) if not data_provider.has_data( chrom ): https://bitbucket.org/galaxy/galaxy-central/commits/86912262ab6f/ Changeset: 86912262ab6f Branch: next-stable User: dannon Date: 2013-10-21 22:40:30 Summary: Expose dataset api anonymously -- this reflects the behavior one expects in the web interface, delegating permission enforcement to the backend Affected #: 1 file diff -r 0eafcb6444701fb40339ee6918a3d33fdf4a0479 -r 86912262ab6f47a9019556731940d0cde19f7b99 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -23,7 +23,7 @@ trans.response.status = 501 return 'not implemented' - @web.expose_api + @web.expose_api_anonymous def show( self, trans, id, hda_ldda='hda', data_type=None, provider=None, **kwd ): """ GET /api/datasets/{encoded_dataset_id} @@ -243,7 +243,7 @@ return data - @web.expose_api_raw + @web.expose_api_raw_anonymous def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): """ https://bitbucket.org/galaxy/galaxy-central/commits/bf169fb107cc/ Changeset: bf169fb107cc Branch: next-stable User: dannon Date: 2013-10-21 22:41:04 Summary: Add decorator for exposing via the api both anonymously and raw -- to be refactored later Affected #: 1 file diff -r 86912262ab6f47a9019556731940d0cde19f7b99 -r bf169fb107cc441fbefbf01544764d87fa6e2af1 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -110,6 +110,14 @@ """ return expose_api( func, to_json=False ) +#DBTODO refactor these post-dist. +def expose_api_raw_anonymous( func ): + """ + Expose this function via the API but don't dump the results + to JSON. + """ + return expose_api( func, to_json=False, user_required=False ) + def expose_api_anonymous( func, to_json=True ): """ Expose this function via the API but don't require a set user. https://bitbucket.org/galaxy/galaxy-central/commits/e9a6c1738ffc/ Changeset: e9a6c1738ffc Branch: next-stable User: dannon Date: 2013-10-21 23:31:09 Summary: Add expose_api_raw_anonymous to galaxy/web package Affected #: 1 file diff -r bf169fb107cc441fbefbf01544764d87fa6e2af1 -r e9a6c1738ffc3dab035f5c2eb01b99c57fe77aa5 lib/galaxy/web/__init__.py --- a/lib/galaxy/web/__init__.py +++ b/lib/galaxy/web/__init__.py @@ -13,4 +13,5 @@ from framework import expose_api from framework import expose_api_anonymous from framework import expose_api_raw +from framework import expose_api_raw_anonymous from framework.base import httpexceptions https://bitbucket.org/galaxy/galaxy-central/commits/902bf096a4aa/ Changeset: 902bf096a4aa User: dannon Date: 2013-10-21 23:31:50 Summary: Merge next-stable to default Affected #: 3 files diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 902bf096a4aa1be446676d178ac5f6db4e5b558f lib/galaxy/web/__init__.py --- a/lib/galaxy/web/__init__.py +++ b/lib/galaxy/web/__init__.py @@ -13,4 +13,5 @@ from framework import expose_api from framework import expose_api_anonymous from framework import expose_api_raw +from framework import expose_api_raw_anonymous from framework.base import httpexceptions diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 902bf096a4aa1be446676d178ac5f6db4e5b558f lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -110,6 +110,14 @@ """ return expose_api( func, to_json=False ) +#DBTODO refactor these post-dist. +def expose_api_raw_anonymous( func ): + """ + Expose this function via the API but don't dump the results + to JSON. + """ + return expose_api( func, to_json=False, user_required=False ) + def expose_api_anonymous( func, to_json=True ): """ Expose this function via the API but don't require a set user. diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 902bf096a4aa1be446676d178ac5f6db4e5b558f lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -23,7 +23,7 @@ trans.response.status = 501 return 'not implemented' - @web.expose_api + @web.expose_api_anonymous def show( self, trans, id, hda_ldda='hda', data_type=None, provider=None, **kwd ): """ GET /api/datasets/{encoded_dataset_id} @@ -101,7 +101,6 @@ # If there is a chrom, check for data on the chrom. if chrom: - data_provider_registry = trans.app.data_provider_registry data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) if not data_provider.has_data( chrom ): @@ -244,7 +243,7 @@ return data - @web.expose_api_raw + @web.expose_api_raw_anonymous def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): """ https://bitbucket.org/galaxy/galaxy-central/commits/bb8975aafcd9/ Changeset: bb8975aafcd9 User: dannon Date: 2013-10-21 23:32:06 Summary: Merge with central Affected #: 29 files diff -r 902bf096a4aa1be446676d178ac5f6db4e5b558f -r bb8975aafcd91ca055ab5aa64a7b8e6a866f8cce lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -633,11 +633,11 @@ # if a tool declares 'force_history_refresh' in its xml, when the hda -> ready, reload the history panel # expensive - if( ( hda.state in [ 'running', 'queued' ] ) - and ( hda.creating_job and hda.creating_job.tool_id ) ): - tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) - if tool_used and tool_used.force_history_refresh: - hda_dict[ 'force_history_refresh' ] = True + #if( ( hda.state in [ 'running', 'queued' ] ) + #and ( hda.creating_job and hda.creating_job.tool_id ) ): + # tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) + # if tool_used and tool_used.force_history_refresh: + # hda_dict[ 'force_history_refresh' ] = True return trans.security.encode_dict_ids( hda_dict ) @@ -653,13 +653,14 @@ 'accessible': False }) - def get_hda_dict_with_error( self, trans, hda, error_msg='' ): + def get_hda_dict_with_error( self, trans, hda=None, history_id=None, id=None, error_msg='Error' ): return trans.security.encode_dict_ids({ - 'id' : hda.id, - 'history_id': hda.history.id, - 'hid' : hda.hid, - 'name' : hda.name, - 'error' : error_msg + 'id' : hda.id if hda else id, + 'history_id': hda.history.id if hda else history_id, + 'hid' : hda.hid if hda else '(unknown)', + 'name' : hda.name if hda else '(unknown)', + 'error' : error_msg, + 'state' : trans.model.Dataset.states.NEW }) def get_display_apps( self, trans, hda ): diff -r 902bf096a4aa1be446676d178ac5f6db4e5b558f -r bb8975aafcd91ca055ab5aa64a7b8e6a866f8cce lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -97,6 +97,9 @@ # Most recent active history for user sessions, not deleted history = trans.user.galaxy_sessions[0].histories[-1].history + elif history_id == "current": + history = trans.get_history( create=True ) + else: history = self.get_history( trans, history_id, check_ownership=False, check_accessible=True, deleted=deleted ) @@ -110,7 +113,7 @@ except Exception, e: msg = "Error in history API at showing history detail: %s" % ( str( e ) ) - log.exception( msg, exc_info=True ) + log.exception( e ) trans.response.status = 500 return msg @@ -174,7 +177,8 @@ trans.sa_session.add( new_history ) trans.sa_session.flush() - item = new_history.to_dict(view='element', value_mapper={'id':trans.security.encode_id}) + #item = new_history.to_dict(view='element', value_mapper={'id':trans.security.encode_id}) + item = self.get_history_dict( trans, new_history ) item['url'] = url_for( 'history', id=item['id'] ) #TODO: possibly default to True here - but favor explicit for now (and backwards compat) diff -r 902bf096a4aa1be446676d178ac5f6db4e5b558f -r bb8975aafcd91ca055ab5aa64a7b8e6a866f8cce lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -59,22 +59,21 @@ encoded_hda_id = trans.security.encode_id( hda.id ) if encoded_hda_id in ids: #TODO: share code with show - try: - hda_dict = self.get_hda_dict( trans, hda ) - hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) - hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) - rval.append( hda_dict ) - - except Exception, exc: - # don't fail entire list if hda err's, record and move on - log.error( "Error in history API at listing contents with history %s, hda %s: (%s) %s", - history_id, encoded_hda_id, type( exc ), str( exc ), exc_info=True ) - rval.append( self.get_hda_dict_with_error( trans, hda, str( exc ) ) ) + rval.append( self._detailed_hda_dict( trans, hda ) ) # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history else: + details = kwd.get( 'details', None ) or [] + if details and details != 'all': + details = util.listify( details ) + for hda in history.datasets: - rval.append( self._summary_hda_dict( trans, history_id, hda ) ) + encoded_hda_id = trans.security.encode_id( hda.id ) + if( ( encoded_hda_id in details ) + or ( details == 'all' ) ): + rval.append( self._detailed_hda_dict( trans, hda ) ) + else: + rval.append( self._summary_hda_dict( trans, history_id, hda ) ) except Exception, e: # for errors that are not specific to one hda (history lookup or summary list) @@ -85,7 +84,7 @@ return rval #TODO: move to model or Mixin - def _summary_hda_dict( self, trans, history_id, hda ): + def _summary_hda_dict( self, trans, encoded_history_id, hda ): """ Returns a dictionary based on the HDA in summary form:: { @@ -99,11 +98,32 @@ encoded_id = trans.security.encode_id( hda.id ) return { 'id' : encoded_id, + 'history_id' : encoded_history_id, 'name' : hda.name, 'type' : api_type, - 'url' : url_for( 'history_content', history_id=history_id, id=encoded_id, ), + 'state' : hda.state, + 'deleted': hda.deleted, + 'visible': hda.visible, + 'hid' : hda.hid, + 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, ), } + def _detailed_hda_dict( self, trans, hda ): + """ + Detailed dictionary of hda values. + """ + try: + hda_dict = self.get_hda_dict( trans, hda ) + hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) + hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) + return hda_dict + + except Exception, exc: + # catch error here - returning a briefer hda_dict with an error attribute + log.exception( "Error in history API at listing contents with history %s, hda %s: (%s) %s", + hda.history_id, hda.id, type( exc ), str( exc ) ) + return self.get_hda_dict_with_error( trans, hda=hda, error_msg=str( exc ) ) + @web.expose_api_anonymous def show( self, trans, id, history_id, **kwd ): """ @@ -244,7 +264,7 @@ trans.response.status = 501 return - @web.expose_api + @web.expose_api_anonymous def update( self, trans, history_id, id, payload, **kwd ): """ update( self, trans, history_id, id, payload, **kwd ) @@ -269,10 +289,28 @@ #TODO: PUT /api/histories/{encoded_history_id} payload = { rating: rating } (w/ no security checks) changed = {} try: - hda = self.get_dataset( trans, id, - check_ownership=True, check_accessible=True, check_state=True ) - # validation handled here and some parsing, processing, and conversion - payload = self._validate_and_parse_update_payload( payload ) + # anon user + if trans.user == None: + if history_id != trans.security.encode_id( trans.history.id ): + trans.response.status = 401 + return { 'error': 'Anonymous users cannot edit histories other than their current history' } + + anon_allowed_payload = {} + if 'deleted' in payload: + anon_allowed_payload[ 'deleted' ] = payload[ 'deleted' ] + if 'visible' in payload: + anon_allowed_payload[ 'visible' ] = payload[ 'visible' ] + + payload = self._validate_and_parse_update_payload( anon_allowed_payload ) + hda = self.get_dataset( trans, id, check_ownership=False, check_accessible=False, check_state=True ) + if hda.history != trans.history: + trans.response.status = 401 + return { 'error': 'Anonymous users cannot edit datasets outside their current history' } + + else: + payload = self._validate_and_parse_update_payload( payload ) + hda = self.get_dataset( trans, id, check_ownership=True, check_accessible=True, check_state=True ) + # additional checks here (security, etc.) changed = self.set_hda_from_dict( trans, hda, payload ) diff -r 902bf096a4aa1be446676d178ac5f6db4e5b558f -r bb8975aafcd91ca055ab5aa64a7b8e6a866f8cce lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -5,7 +5,7 @@ import os import urllib -from paste.httpexceptions import HTTPNotFound +from paste.httpexceptions import HTTPNotFound, HTTPBadGateway from galaxy import web from galaxy.web import url_for @@ -30,7 +30,8 @@ @web.expose def index(self, trans, id=None, tool_id=None, mode=None, workflow_id=None, m_c=None, m_a=None, **kwd): - """Called on the root url to display the main Galaxy page. + """ + Called on the root url to display the main Galaxy page. """ return trans.fill_template( "root/index.mako", tool_id=tool_id, @@ -99,63 +100,75 @@ show_deleted=string_as_bool( show_deleted ), show_hidden=string_as_bool( show_hidden ) ) - @web.expose - def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, hda_id=None, **kwd ): - """Display the current history, creating a new history if necessary. - - NOTE: No longer accepts "id" or "template" options for security reasons. - """ - if as_xml: - return self.history_as_xml( trans, - show_deleted=string_as_bool( show_deleted ), show_hidden=string_as_bool( show_hidden ) ) - - # get all datasets server-side, client-side will get flags and render appropriately - show_deleted = string_as_bool_or_none( show_deleted ) - show_purged = show_deleted - show_hidden = string_as_bool_or_none( show_hidden ) - params = Params( kwd ) - message = params.get( 'message', '' ) - #TODO: ugh... - message = message if message != 'None' else '' - status = params.get( 'status', 'done' ) - - if trans.app.config.require_login and not trans.user: - return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' ) - - def err_msg( where=None ): - where = where if where else 'getting the history data from the server' - err_msg = ( 'An error occurred %s. ' - + 'Please contact a Galaxy administrator if the problem persists.' ) %( where ) - return err_msg, 'error' - + def _get_current_history_data( self, trans ): history_dictionary = {} hda_dictionaries = [] + try: history = trans.get_history( create=True ) hdas = self.get_history_datasets( trans, history, show_deleted=True, show_hidden=True, show_purged=True ) for hda in hdas: + hda_dict = {} try: - hda_dictionaries.append( self.get_hda_dict( trans, hda ) ) + hda_dict = self.get_hda_dict( trans, hda ) except Exception, exc: # don't fail entire list if hda err's, record and move on log.error( 'Error bootstrapping hda %d: %s', hda.id, str( exc ), exc_info=True ) - hda_dictionaries.append( self.get_hda_dict_with_error( trans, hda, str( exc ) ) ) + hda_dict = self.get_hda_dict_with_error( trans, hda, str( exc ) ) + + hda_dictionaries.append( hda_dict ) # re-use the hdas above to get the history data... history_dictionary = self.get_history_dict( trans, history, hda_dictionaries=hda_dictionaries ) except Exception, exc: user_id = str( trans.user.id ) if trans.user else '(anonymous)' - log.error( 'Error bootstrapping history for user %s: %s', user_id, str( exc ), exc_info=True ) - message, status = err_msg() + log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) ) + message = ( 'An error occurred getting the history data from the server. ' + + 'Please contact a Galaxy administrator if the problem persists.' ) history_dictionary[ 'error' ] = message - return trans.stream_template_mako( "root/history.mako", - history_json = to_json_string( history_dictionary ), hda_json = to_json_string( hda_dictionaries ), - show_deleted=show_deleted, show_hidden=show_hidden, hda_id=hda_id, log=log, message=message, status=status ) + return { + 'history' : history_dictionary, + 'hdas' : hda_dictionaries + } + + @web.expose + def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, **kwd ): + """ + Display the current history in it's own page or as xml. + """ + if as_xml: + return self.history_as_xml( trans, + show_deleted=string_as_bool( show_deleted ), show_hidden=string_as_bool( show_hidden ) ) + + if trans.app.config.require_login and not trans.user: + return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' ) + + # get all datasets server-side, client-side will get flags and render appropriately + show_deleted = string_as_bool_or_none( show_deleted ) + show_purged = show_deleted + show_hidden = string_as_bool_or_none( show_hidden ) + + history_dictionary = {} + hda_dictionaries = [] + try: + history_data = self._get_current_history_data( trans ) + history_dictionary = history_data[ 'history' ] + hda_dictionaries = history_data[ 'hdas' ] + + except Exception, exc: + user_id = str( trans.user.id ) if trans.user else '(anonymous)' + log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) ) + history_dictionary[ 'error' ] = ( 'An error occurred getting the history data from the server. ' + + 'Please contact a Galaxy administrator if the problem persists.' ) + + return trans.fill_template_mako( "root/history.mako", + history = history_dictionary, hdas = hda_dictionaries, + show_deleted=show_deleted, show_hidden=show_hidden ) ## ---- Dataset display / editing ---------------------------------------- @web.expose @@ -503,7 +516,22 @@ return rval @web.expose - def generate_error( self, trans ): + def generate_error( self, trans, code=500 ): """Raises an exception (debugging). """ + trans.response.status = code raise Exception( "Fake error!" ) + + @web.json + def generate_json_error( self, trans, code=500 ): + """Raises an exception (debugging). + """ + try: + code = int( code ) + except Exception, exc: + code = 500 + + if code == 502: + raise HTTPBadGateway() + trans.response.status = code + return { 'error': 'Fake error!' } diff -r 902bf096a4aa1be446676d178ac5f6db4e5b558f -r bb8975aafcd91ca055ab5aa64a7b8e6a866f8cce lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -325,4 +325,5 @@ <p><b>Please do not use your browser\'s "stop" or "reload" buttons until the upload is complete, or it may be interrupted.</b></p><p>You may safely continue to use Galaxy while the upload is in progress. Using "stop" and "reload" on pages other than Galaxy is also safe.</p> """ + #return trans.show_message( msg, refresh_frames=[ 'history' ] ) return trans.show_message( msg ) diff -r 902bf096a4aa1be446676d178ac5f6db4e5b558f -r bb8975aafcd91ca055ab5aa64a7b8e6a866f8cce static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -7,31 +7,30 @@ name: null, hidden: false }, - + show: function() { this.set("hidden", false); }, - + hide: function() { this.set("hidden", true); }, - + is_visible: function() { return !this.attributes.hidden; } }); - /** * Base view that handles visibility based on model's hidden attribute. */ var BaseView = Backbone.View.extend({ - + initialize: function() { this.model.on("change:hidden", this.update_visible, this); this.update_visible(); }, - + update_visible: function() { if( this.model.attributes.hidden ){ this.$el.hide(); @@ -120,7 +119,8 @@ // ~constants for the current engine var STORAGE_ENGINE = sessionStorage, STORAGE_ENGINE_GETTER = function sessionStorageGet( key ){ - return JSON.parse( this.getItem( key ) ); + var item = this.getItem( key ); + return ( item !== null )?( JSON.parse( this.getItem( key ) ) ):( null ); }, STORAGE_ENGINE_SETTER = function sessionStorageSet( key, val ){ return this.setItem( key, JSON.stringify( val ) ); @@ -182,7 +182,7 @@ } //??: more readable to make another class? - var returnedStorage = {}; + var returnedStorage = {}, // attempt to get starting data from engine... data = STORAGE_ENGINE_GETTER.call( STORAGE_ENGINE, storageKey ); @@ -216,3 +216,63 @@ return returnedStorage; }; + + +//============================================================================== +function LoadingIndicator( $where ){ + var self = this, + $indicator; + + function setPosition(){ + // even tho pos is 'fixed' - give illusion of width 100% and margin by manually setting width, offset + var padding = 4, + width = $indicator.parent().width() || $where.width(), + offset = $indicator.parent().offset() || $where.offset(); + + $indicator.outerWidth( width - ( padding * 2 ) ); + // have to use css top, left and not offset (wont work when indicator is hidden) + $indicator.css({ top: offset.top + padding + 'px' , left: offset.left + padding + 'px' }); + } + + function render(){ + var $spinner = $( '<span class="fa-icon-spinner fa-icon-spin fa-icon-large"></span>') + .css({ 'color' : 'grey', 'font-size' : '16px' }); + var $message = $( '<i>loading...</i>' ) + .css({ 'color' : 'grey', 'margin-left' : '8px' }); + $indicator = $( '<div/>' ).addClass( 'loading-indicator' ) + .css({ + 'position' : 'fixed', + 'padding' : '4px', + 'text-align' : 'center', + 'background-color' : 'white', + 'opacity' : '0.85', + 'border-radius' : '3px' + }) + .append( $spinner, $message ) + //NOTE: insert as sibling to $where + .insertBefore( $where ); + setPosition(); + return $indicator.hide(); + } + + self.show = function( speed, callback ){ + speed = speed || 'fast'; + setPosition(); + $indicator.fadeIn( speed, callback ); + // not using full fadeOut allows using scroll to still work + //$whatIsLoading.fadeTo( speed, 0.0001, callback ); + return self; + }; + + self.hide = function( speed, callback ){ + speed = speed || 'fast'; + //$whatIsLoading.fadeTo( speed, 1.0, function(){ + // if( callback ){ callback(); } + //}); + $indicator.fadeOut( speed, callback ); + return self; + }; + $indicator = render(); + return self; +} + diff -r 902bf096a4aa1be446676d178ac5f6db4e5b558f -r bb8975aafcd91ca055ab5aa64a7b8e6a866f8cce static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -1,7 +1,6 @@ -//define([ -// "../mvc/base-mvc" -//], function(){ - +define([ + "mvc/dataset/hda-model" +], function( hdaModel ){ /* global Backbone, LoggableMixin, HistoryDatasetAssociation, HDABaseView */ //============================================================================== /** @class Read only view for HistoryDatasetAssociation. @@ -22,6 +21,8 @@ tagName : "div", className : "historyItemContainer", + fxSpeed : 'fast', + // ......................................................................... SET UP /** Set up the view, cache url templates, bind listeners * @param {Object} attributes @@ -38,33 +39,20 @@ this._render_showParamsButton ]; - // cache urlTemplates (gen. provided by GalaxyPaths) to urls - if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } - this.urlTemplates = attributes.urlTemplates; - /** is the body of this hda view expanded/not. */ this.expanded = attributes.expanded || false; + this._setUpListeners(); + }, + _setUpListeners : function(){ // re-rendering on any model changes - this.model.bind( 'change', function( model, options ){ - // if more than the display apps have changed: render everything - var nonDisplayAppChanges = _.omit( this.model.changedAttributes(), 'display_apps', 'display_types' ); - if( _.keys( nonDisplayAppChanges ).length ){ - this.render(); + this.model.on( 'change', this.render, this ); - // if just the display links, and it's already expanded: render the links only - } else { - if( this.expanded ){ - this._render_displayApps(); - } - } - }, this ); - - //this.bind( 'all', function( event ){ + //this.on( 'all', function( event ){ // this.log( event ); //}, this ); }, - + // ......................................................................... RENDER MAIN /** Render this HDA, set up ui. * @fires rendered:ready when rendered and NO running HDAs @@ -86,9 +74,8 @@ // handle that here by removing previous view's tooltips this.$el.find("[title]").tooltip( "destroy" ); - /** web controller urls for functions relating to this hda. - * These are rendered from urlTemplates using the model data. */ - this.urls = this._renderUrls( this.urlTemplates, this.model.toJSON() ); + /** web controller urls for functions relating to this hda. */ + this.urls = this.model.urls(); itemWrapper .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) @@ -104,9 +91,9 @@ itemWrapper.append( this.body ); // transition... - this.$el.fadeOut( 'fast', function(){ + this.$el.fadeOut( this.fxSpeed, function(){ view.$el.children().remove(); - view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ + view.$el.append( itemWrapper ).fadeIn( view.fxSpeed, function(){ view.log( view + ' rendered:', view.$el ); var renderedEventName = 'rendered'; @@ -121,55 +108,6 @@ return this; }, - /** render the urls for this hda using the model data and the url templates from initialize. - * @param {Object} urlTemplates a map (or nested map) of underscore templates (currently, anyhoo) - * @param {Object} modelJson data from the model - * @returns {Object} the templated urls - */ - _renderUrls : function( urlTemplates, modelJson ){ - var hdaView = this, - urls = {}; - _.each( urlTemplates, function( urlTemplateOrObj, urlKey ){ - // object == nested templates: recurse - if( _.isObject( urlTemplateOrObj ) ){ - urls[ urlKey ] = hdaView._renderUrls( urlTemplateOrObj, modelJson ); - - // string == template: - } else { - // meta_down load is a special case (see renderMetaDownloadUrls) - //TODO: should be a better (gen.) way to handle this case - if( urlKey === 'meta_download' ){ - urls[ urlKey ] = hdaView._renderMetaDownloadUrls( urlTemplateOrObj, modelJson ); - - } else { - try { - urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); - } catch( Error ){ - throw( hdaView + '._renderUrls error: ' + Error + - '\n rendering:' + urlTemplateOrObj + - '\n with ' + JSON.stringify( modelJson ) ); - } - } - } - }); - return urls; - }, - - /** there can be more than one meta_file (e.g. bam index) to download, - * so return a list of url and file_type for each - * @param {Object} urlTemplate underscore templates for meta download urls - * @param {Object} modelJson data from the model - * @returns {Object} url and filetype for each meta file - */ - _renderMetaDownloadUrls : function( urlTemplate, modelJson ){ - return _.map( modelJson.meta_files, function( meta_file ){ - return { - url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), - file_type : meta_file.file_type - }; - }); - }, - /** set up js behaviors, event handlers for elements within the given container * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) */ @@ -218,8 +156,8 @@ _render_displayButton : function(){ // don't show display if not viewable or not accessible // (do show if in error, running) - if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NEW ) + if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) || ( !this.model.get( 'accessible' ) ) ){ this.displayButton = null; return null; @@ -237,7 +175,7 @@ displayBtnData.title = _l( 'Cannot display datasets removed from disk' ); // disable if still uploading - } else if( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ){ + } else if( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.UPLOAD ){ displayBtnData.enabled = false; displayBtnData.title = _l( 'This dataset must finish uploading before it can be viewed' ); @@ -406,40 +344,40 @@ body.html( '' ); //TODO: not a fan of this dispatch switch( this.model.get( 'state' ) ){ - case HistoryDatasetAssociation.STATES.NEW : + case hdaModel.HistoryDatasetAssociation.STATES.NEW : this._render_body_new( body ); break; - case HistoryDatasetAssociation.STATES.NOT_VIEWABLE : + case hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE : this._render_body_not_viewable( body ); break; - case HistoryDatasetAssociation.STATES.UPLOAD : + case hdaModel.HistoryDatasetAssociation.STATES.UPLOAD : this._render_body_uploading( body ); break; - case HistoryDatasetAssociation.STATES.PAUSED: + case hdaModel.HistoryDatasetAssociation.STATES.PAUSED: this._render_body_paused( body ); break; - case HistoryDatasetAssociation.STATES.QUEUED : + case hdaModel.HistoryDatasetAssociation.STATES.QUEUED : this._render_body_queued( body ); break; - case HistoryDatasetAssociation.STATES.RUNNING : + case hdaModel.HistoryDatasetAssociation.STATES.RUNNING : this._render_body_running( body ); break; - case HistoryDatasetAssociation.STATES.ERROR : + case hdaModel.HistoryDatasetAssociation.STATES.ERROR : this._render_body_error( body ); break; - case HistoryDatasetAssociation.STATES.DISCARDED : + case hdaModel.HistoryDatasetAssociation.STATES.DISCARDED : this._render_body_discarded( body ); break; - case HistoryDatasetAssociation.STATES.SETTING_METADATA : + case hdaModel.HistoryDatasetAssociation.STATES.SETTING_METADATA : this._render_body_setting_metadata( body ); break; - case HistoryDatasetAssociation.STATES.EMPTY : + case hdaModel.HistoryDatasetAssociation.STATES.EMPTY : this._render_body_empty( body ); break; - case HistoryDatasetAssociation.STATES.FAILED_METADATA : + case hdaModel.HistoryDatasetAssociation.STATES.FAILED_METADATA : this._render_body_failed_metadata( body ); break; - case HistoryDatasetAssociation.STATES.OK : + case hdaModel.HistoryDatasetAssociation.STATES.OK : this._render_body_ok( body ); break; default: @@ -591,27 +529,44 @@ * @fires body-expanded when a body has been expanded * @fires body-collapsed when a body has been collapsed */ - toggleBodyVisibility : function( event, expanded ){ + toggleBodyVisibility : function( event, expand ){ var hdaView = this; - this.expanded = ( expanded === undefined )?( !this.body.is( ':visible' ) ):( expanded ); - //this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body ); + expand = ( expand === undefined )?( !this.body.is( ':visible' ) ):( expand ); + if( expand ){ + if( this.model.inReadyState() && !this.model.hasDetails() ){ + var xhr = this.model.fetch(); + xhr.done( function( model ){ + hdaView.expandBody(); + }); + } else { + this.expandBody(); + } + } else { + this.collapseBody(); + } + }, - if( this.expanded ){ - hdaView._render_body_html( hdaView.body ); - this.body.slideDown( 'fast', function(){ - hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) ); - }); - } else { - this.body.slideUp( 'fast', function(){ - hdaView.trigger( 'body-collapsed', hdaView.model.get( 'id' ) ); - }); - } + expandBody : function(){ + var hdaView = this; + hdaView._render_body_html( hdaView.body ); + this.body.slideDown( hdaView.fxSpeed, function(){ + hdaView.expanded = true; + hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) ); + }); + }, + + collapseBody : function(){ + var hdaView = this; + this.body.slideUp( hdaView.fxSpeed, function(){ + hdaView.expanded = false; + hdaView.trigger( 'body-collapsed', hdaView.model.get( 'id' ) ); + }); }, // ......................................................................... DELETION remove : function( callback ){ var hdaView = this; - this.$el.fadeOut( 'fast', function(){ + this.$el.fadeOut( hdaView.fxSpeed, function(){ hdaView.$el.remove(); hdaView.off(); if( callback ){ callback(); } @@ -638,6 +593,6 @@ }; //============================================================================== -//return { -// HDABaseView : HDABaseView, -//};}); +return { + HDABaseView : HDABaseView, +};}); diff -r 902bf096a4aa1be446676d178ac5f6db4e5b558f -r bb8975aafcd91ca055ab5aa64a7b8e6a866f8cce static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -1,6 +1,7 @@ -//define([ -// "../mvc/base-mvc" -//], function(){ +define([ + "mvc/dataset/hda-model", + "mvc/dataset/hda-base" +], function( hdaModel, hdaBase ){ //============================================================================== /** @class Editing view for HistoryDatasetAssociation. * @name HDAEditView @@ -10,7 +11,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var HDAEditView = HDABaseView.extend( LoggableMixin ).extend( +var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( /** @lends HDAEditView.prototype */{ // ......................................................................... SET UP @@ -22,7 +23,8 @@ * @see HDABaseView#initialize */ initialize : function( attributes ){ - HDABaseView.prototype.initialize.call( this, attributes ); + hdaBase.HDABaseView.prototype.initialize.call( this, attributes ); + this.hasUser = attributes.hasUser; /** list of rendering functions for the default, primary icon-buttons. */ this.defaultPrimaryActionButtonRenderers = [ @@ -37,33 +39,8 @@ * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) */ _setUpBehaviors : function( $container ){ - //TODO: ideally this would be a DELETE call to the api - // using purge async for now - HDABaseView.prototype._setUpBehaviors.call( this, $container ); - - // use purge_async with an ajax call - var hdaView = this, - purge_url = this.urls.purge, - purge_link = $container.find( '#historyItemPurger-' + this.model.get( 'id' ) ); - if( purge_link ){ - //TODO: remove href from template - purge_link.attr( 'href', [ "javascript", "void(0)" ].join( ':' ) ); - purge_link.click( function( event ){ - //TODO??: confirm? - var xhr = jQuery.ajax( purge_url ); - xhr.success( function( message, status, responseObj ){ - hdaView.model.set( 'purged', true ); - hdaView.trigger( 'purged', hdaView ); - }); - xhr.error( function( error, status, message ){ - //TODO: Exception messages are hidden within error page - //!NOTE: that includes the 'Removal of datasets by users is not allowed in this Galaxy instance.' - view.trigger( 'error', - hdaView, xhr, { url: purge_url }, _l( "Unable to purge this dataset" ) ); - }); - }); - } - //TODO: same with undelete_async + hdaBase.HDABaseView.prototype._setUpBehaviors.call( this, $container ); + //var hdaView = this; }, // ......................................................................... RENDER WARNINGS @@ -74,7 +51,7 @@ */ _render_warnings : function(){ // jQ errs on building dom with whitespace - if there are no messages, trim -> '' - return $( jQuery.trim( HDABaseView.templates.messages( + return $( jQuery.trim( hdaBase.HDABaseView.templates.messages( _.extend( this.model.toJSON(), { urls: this.urls } ) ))); }, @@ -101,9 +78,9 @@ // don't show edit while uploading, in-accessible // DO show if in error (ala previous history panel) //TODO??: not viewable/accessible are essentially the same (not viewable set from accessible) - if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NEW ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) + || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.UPLOAD ) + || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ this.editButton = null; return null; @@ -138,44 +115,26 @@ _render_deleteButton : function(){ // don't show delete if... //TODO??: not viewable/accessible are essentially the same (not viewable set from accessible) - if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NEW ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) + || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ this.deleteButton = null; return null; } var self = this, + id = 'historyItemDeleter-' + self.model.get( 'id' ), delete_url = self.urls[ 'delete' ], deleteBtnData = { - title : _l( 'Delete' ), - href : delete_url, - id : 'historyItemDeleter-' + this.model.get( 'id' ), - icon_class : 'delete', - on_click : function() { - // Delete the dataset on the server and update HDA + view depending on success/failure. - // FIXME: when HDA-delete is implemented in the API, can call set(), then save directly - // on the model. - $.ajax({ - url: delete_url, - type: 'POST', - error: function() { - // Something went wrong, so show HDA again. - // TODO: an error notification would be good. - self.trigger( 'error', self, null, null, { url: delete_url }, _l( 'deletion failed' ) ); - self.$el.show(); - }, - success: function() { - // FIXME: setting model attribute causes re-rendering, which is unnecessary. - //self.$el.remove(); - - self.model.set({ deleted: true }); - } - }); - - // Return false so that anchor action (page reload) does not happen. - //return false; - } + title : _l( 'Delete' ), + href : delete_url, + id : id, + icon_class : 'delete', + on_click : function() { + // ...bler... tooltips being left behind in DOM (hover out never called on deletion) + self.$el.find( '.menu-button.delete' ).trigger( 'mouseout' ); + self.model[ 'delete' ](); + } }; if( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ){ deleteBtnData = { @@ -202,7 +161,7 @@ //TODO: use HDABaseView and select/replace base on this switch _.extend( modelData, { dbkey_unknown_and_editable : true }); } - return HDABaseView.templates.hdaSummary( modelData ); + return hdaBase.HDABaseView.templates.hdaSummary( modelData ); }, // ......................................................................... primary actions @@ -210,7 +169,7 @@ * @returns {jQuery} rendered DOM */ _render_errButton : function(){ - if( this.model.get( 'state' ) !== HistoryDatasetAssociation.STATES.ERROR ){ + if( this.model.get( 'state' ) !== hdaModel.HistoryDatasetAssociation.STATES.ERROR ){ this.errButton = null; return null; } @@ -378,8 +337,7 @@ //TODO: these should be a sub-MV _render_tagButton : function(){ //TODO: check for User - if( !( this.model.hasData() ) - || ( !this.urls.tags.get ) ){ + if( !this.hasUser || !this.urls.tags.get ){ this.tagButton = null; return null; } @@ -399,8 +357,7 @@ //TODO: these should be a sub-MV _render_annotateButton : function(){ //TODO: check for User - if( !( this.model.hasData() ) - || ( !this.urls.annotation.get ) ){ + if( !this.hasUser || !this.urls.annotation.get ){ this.annotateButton = null; return null; } @@ -417,8 +374,8 @@ /** Render area to display tags. * @returns {jQuery} rendered DOM */ - //TODO: into sub-MV - //TODO: check for User +//TODO: into sub-MV +//TODO: check for User _render_tagArea : function(){ if( !this.urls.tags.set ){ return null; } //TODO: move to mvc/tags.js @@ -430,8 +387,8 @@ /** Render area to display annotation. * @returns {jQuery} rendered DOM */ - //TODO: into sub-MV - //TODO: check for User +//TODO: into sub-MV +//TODO: check for User _render_annotationArea : function(){ if( !this.urls.annotation.get ){ return null; } //TODO: move to mvc/annotations.js @@ -447,7 +404,7 @@ * @see HDABaseView#_render_body_error */ _render_body_error : function( parent ){ - HDABaseView.prototype._render_body_error.call( this, parent ); + hdaBase.HDABaseView.prototype._render_body_error.call( this, parent ); var primaryActions = parent.find( '#primary-actions-' + this.model.get( 'id' ) ); primaryActions.prepend( this._render_errButton() ); }, @@ -498,11 +455,21 @@ /** event map */ events : { 'click .historyItemTitle' : 'toggleBodyVisibility', + 'click .historyItemUndelete' : function( ev ){ this.model.undelete(); return false; }, + 'click .historyItemUnhide' : function( ev ){ this.model.unhide(); return false; }, + 'click .historyItemPurge' : 'confirmPurge', + 'click a.icon-button.tags' : 'loadAndDisplayTags', 'click a.icon-button.annotate' : 'loadAndDisplayAnnotation' }, // ......................................................................... STATE CHANGES / MANIPULATION + confirmPurge : function _confirmPurge( ev ){ + //TODO: confirm dialog + this.model.purge({ url: this.urls.purge }); + return false; + }, + /** Find the tag area and, if initial: load the html (via ajax) for displaying them; otherwise, unhide/hide */ //TODO: into sub-MV @@ -523,30 +490,29 @@ url: this.urls.tags.get, error: function( xhr, status, error ){ view.log( "Tagging failed", xhr, status, error ); - view.trigger( 'error', view, xhr, { url: view.urls.tags.get }, _l( "Tagging failed" ) ); + view.trigger( 'error', view, xhr, {}, _l( "Tagging failed" ) ); }, success: function(tag_elt_html) { tagElt.html(tag_elt_html); tagElt.find("[title]").tooltip(); - tagArea.slideDown("fast"); + tagArea.slideDown( view.fxSpeed ); } }); } else { // Tag element is filled; show. - tagArea.slideDown("fast"); + tagArea.slideDown( view.fxSpeed ); } } else { // Hide. - tagArea.slideUp("fast"); + tagArea.slideUp( view.fxSpeed ); } return false; }, /** Find the annotation area and, if initial: load the html (via ajax) for displaying them; otherwise, unhide/hide */ - //TODO: into sub-MV loadAndDisplayAnnotation : function( event ){ - //TODO: this is a drop in from history.mako - should use MV as well +//TODO: this is a drop in from history.mako - should use MV as well this.log( this + '.loadAndDisplayAnnotation', event ); var view = this, annotationArea = this.$el.find( '.annotation-area' ), @@ -559,10 +525,9 @@ // Need to fill annotation element. $.ajax({ url: this.urls.annotation.get, - error: function( xhr, status, message ){ - view.log( "Annotation failed", xhr, status, message ); - view.trigger( 'error', - view, xhr, { url: view.urls.annotation.get }, _l( "Annotation failed" ) ); + error: function(){ + view.log( "Annotation failed", xhr, status, error ); + view.trigger( 'error', view, xhr, {}, _l( "Annotation failed" ) ); }, success: function( htmlFromAjax ){ if( htmlFromAjax === "" ){ @@ -576,16 +541,16 @@ setAnnotationUrl, "new_annotation", 18, true, 4 ); - annotationArea.slideDown("fast"); + annotationArea.slideDown( view.fxSpeed ); } }); } else { - annotationArea.slideDown("fast"); + annotationArea.slideDown( view.fxSpeed ); } } else { // Hide. - annotationArea.slideUp("fast"); + annotationArea.slideUp( view.fxSpeed ); } return false; }, @@ -712,6 +677,6 @@ //============================================================================== -//return { -// HDAView : HDAView, -//};}); +return { + HDAEditView : HDAEditView, +};}); diff -r 902bf096a4aa1be446676d178ac5f6db4e5b558f -r bb8975aafcd91ca055ab5aa64a7b8e6a866f8cce static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -1,6 +1,5 @@ -//define([ -// "../mvc/base-mvc" -//], function(){ +define([ +], function(){ //============================================================================== /** @class (HDA) model for a Galaxy dataset * related to a history. @@ -34,6 +33,13 @@ name : '(unnamed dataset)', // one of HistoryDatasetAssociation.STATES state : 'new', + + deleted : false, + visible : true, + + accessible : true, + purged : false, + // sniffed datatype (sam, tabular, bed, etc.) data_type : null, // size in bytes @@ -44,37 +50,67 @@ meta_files : [], misc_blurb : '', - misc_info : '', - - deleted : false, - purged : false, - visible : true, - accessible : true + misc_info : '' }, /** fetch location of this history in the api */ urlRoot: 'api/histories/', url : function(){ - //TODO: get this via url router return this.urlRoot + this.get( 'history_id' ) + '/contents/' + this.get( 'id' ); - //TODO: this breaks on save() }, + urls : function(){ + var id = this.get( 'id' ); + if( !id ){ return {}; } + var urls = { + 'delete' : '/datasets/' + id + '/delete_async', + 'purge' : '/datasets/' + id + '/purge_async', + 'unhide' : '/datasets/' + id + '/unhide', + 'undelete' : '/datasets/' + id + '/undelete', + + 'display' : '/datasets/' + id + '/display/?preview=True', + 'download' : '/datasets/' + id + '/display?to_ext=' + this.get( 'file_ext' ), + 'edit' : '/datasets/' + id + '/edit', + 'report_error': '/dataset/errors?id=' + id, + 'rerun' : '/tool_runner/rerun?id=' + id, + 'show_params': '/datasets/' + id + '/show_params', + 'visualization': '/visualization', + + 'annotation': { 'get': '/dataset/get_annotation_async?id=' + id, + 'set': '/dataset/annotate_async?id=' + id }, + 'tags' : { 'get': '/tag/get_tagging_elt_async?item_id=' + id + '&item_class=HistoryDatasetAssociation', + 'set': '/tag/retag?item_id=' + id + '&item_class=HistoryDatasetAssociation' } + }; + //'meta_download': '/dataset/get_metadata_file?hda_id=%3C%25%3D+id+%25%3E&metadata_name=%3C%25%3D+file_type+%25%3E', + var meta_files = this.get( 'meta_files' ); + if( meta_files ){ + urls.meta_download = _.map( meta_files, function( meta_file ){ + return { + //url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), + url : '/dataset/get_metadata_file?hda_id=' + id + '&metadata_name=' + meta_file.file_type, + file_type : meta_file.file_type + }; + }); + } + return urls; + }, + /** Set up the model, determine if accessible, bind listeners * @see Backbone.Model#initialize */ - //TODO:? use initialize (or validate) to check purged AND deleted -> purged XOR deleted - initialize : function(){ + initialize : function( data ){ this.log( this + '.initialize', this.attributes ); this.log( '\tparent history_id: ' + this.get( 'history_id' ) ); - // (curr) only handles changing state of non-accessible hdas to STATES.NOT_VIEWABLE //!! this state is not in trans.app.model.Dataset.states - set it here - - //TODO: change to server side. if( !this.get( 'accessible' ) ){ this.set( 'state', HistoryDatasetAssociation.STATES.NOT_VIEWABLE ); } + this._setUpListeners(); + }, + + _setUpListeners : function(){ // if the state has changed and the new state is a ready state, fire an event this.on( 'change:state', function( currModel, newState ){ this.log( this + ' has changed state:', currModel, newState ); @@ -82,16 +118,9 @@ this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); } }); - - // debug on change events - //this.on( 'change', function( currModel, changedList ){ - // this.log( this + ' has changed:', currModel, changedList ); - //}); - //this.bind( 'all', function( event ){ - // this.log( this + '', arguments ); - //}); }, + // ........................................................................ common queries /** Is this hda deleted or purged? */ isDeletedOrPurged : function(){ @@ -117,24 +146,21 @@ return isVisible; }, + hidden : function(){ + return !this.get( 'visible' ); + }, + /** Is this HDA in a 'ready' state; where 'Ready' states are states where no * processing (for the ds) is left to do on the server. - * Currently: NEW, OK, EMPTY, FAILED_METADATA, NOT_VIEWABLE, DISCARDED, - * and ERROR */ inReadyState : function(){ - var state = this.get( 'state' ); - //TODO: to list inclusion test - //TODO: class level readyStates list - return ( - this.isDeletedOrPurged() - || ( state === HistoryDatasetAssociation.STATES.OK ) - || ( state === HistoryDatasetAssociation.STATES.EMPTY ) - || ( state === HistoryDatasetAssociation.STATES.FAILED_METADATA ) - || ( state === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( state === HistoryDatasetAssociation.STATES.DISCARDED ) - || ( state === HistoryDatasetAssociation.STATES.ERROR ) - ); + var ready = _.contains( HistoryDatasetAssociation.READY_STATES, this.get( 'state' ) ); + return ( this.isDeletedOrPurged() || ready ); + }, + + hasDetails : function(){ + //?? this may not be reliable + return _.has( this.attributes, 'genome_build' ); }, /** Convenience function to match hda.has_data. @@ -144,6 +170,64 @@ return ( this.get( 'file_size' ) > 0 ); }, + // ........................................................................ ajax + 'delete' : function _delete( options ){ + return this.save( { deleted: true }, options ); + }, + undelete : function _undelete( options ){ + return this.save( { deleted: false }, options ); + }, + + hide : function _hide( options ){ + return this.save( { visible: false }, options ); + }, + unhide : function _uhide( options ){ + return this.save( { visible: true }, options ); + }, + + purge : function _purge( options ){ + //TODO: ideally this would be a DELETE call to the api + // using purge async for now + var hda = this, + xhr = jQuery.ajax( options ); + xhr.done( function( message, status, responseObj ){ + hda.set( 'purged', true ); + }); + xhr.fail( function( xhr, status, message ){ + // Exception messages are hidden within error page including: '...not allowed in this Galaxy instance.' + // unbury and re-add to xhr + var error = _l( "Unable to purge this dataset" ); + var messageBuriedInUnfortunatelyFormattedError = ( 'Removal of datasets by users ' + + 'is not allowed in this Galaxy instance' ); + if( xhr.responseJSON && xhr.responseJSON.error ){ + error = xhr.responseJSON.error; + } else if( xhr.responseText.indexOf( messageBuriedInUnfortunatelyFormattedError ) !== -1 ){ + error = messageBuriedInUnfortunatelyFormattedError; + } + xhr.responseText = error; + hda.trigger( 'error', hda, xhr, options, _l( error ), { error: error } ); + }); + }, + + // ........................................................................ sorting/filtering + searchKeys : [ + 'name', 'file_ext', 'genome_build', 'misc_blurb', 'misc_info', 'annotation', 'tags' + ], + + search : function( searchFor ){ + var model = this; + searchFor = searchFor.toLowerCase(); + return _.filter( this.searchKeys, function( key ){ + var attr = model.get( key ); + return ( _.isString( attr ) && attr.toLowerCase().indexOf( searchFor ) !== -1 ); + }); + }, + + matches : function( matchesWhat ){ + return !!this.search( matchesWhat ).length; + }, + + // ........................................................................ misc /** String representation */ toString : function(){ @@ -165,8 +249,6 @@ UPLOAD : 'upload', /** the job that will produce the dataset queued in the runner */ QUEUED : 'queued', - /** the job that will produce the dataset paused */ - PAUSED : 'paused', /** the job that will produce the dataset is running */ RUNNING : 'running', /** metadata for the dataset is being discovered/set */ @@ -180,6 +262,8 @@ /** has successfully completed running */ OK : 'ok', + /** the job that will produce the dataset paused */ + PAUSED : 'paused', /** metadata discovery/setting failed or errored (but otherwise ok) */ FAILED_METADATA : 'failed_metadata', /** not accessible to the current user (i.e. due to permissions) */ @@ -190,6 +274,24 @@ ERROR : 'error' }; +HistoryDatasetAssociation.READY_STATES = [ + HistoryDatasetAssociation.STATES.NEW, + HistoryDatasetAssociation.STATES.OK, + HistoryDatasetAssociation.STATES.EMPTY, + HistoryDatasetAssociation.STATES.PAUSED, + HistoryDatasetAssociation.STATES.FAILED_METADATA, + HistoryDatasetAssociation.STATES.NOT_VIEWABLE, + HistoryDatasetAssociation.STATES.DISCARDED, + HistoryDatasetAssociation.STATES.ERROR +]; + +HistoryDatasetAssociation.NOT_READY_STATES = [ + HistoryDatasetAssociation.STATES.UPLOAD, + HistoryDatasetAssociation.STATES.QUEUED, + HistoryDatasetAssociation.STATES.RUNNING, + HistoryDatasetAssociation.STATES.SETTING_METADATA +]; + //============================================================================== /** @class Backbone collection of (HDA) models * @@ -204,83 +306,35 @@ ///** logger used to record this.log messages, commonly set to console */ //// comment this out to suppress log output //logger : console, + urlRoot : '/api/histories', + url : function(){ + return this.urlRoot + '/' + this.historyId + '/contents'; + }, /** Set up. * @see Backbone.Collection#initialize */ - initialize : function(){ - //this.bind( 'all', function( event ){ - // this.log( this + '', arguments ); - //}); + initialize : function( models, options ){ + options = options || {}; + this.historyId = options.historyId; + this._setUpListeners(); }, + _setUpListeners : function(){ + }, + + // ........................................................................ common queries /** Get the ids of every hda in this collection - * @returns array of encoded ids + * @returns array of encoded ids */ ids : function(){ return this.map( function( hda ){ return hda.id; }); }, - /** Get the hda with the given hid - * @param {Int} hid the hid to search for - * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found - */ - getByHid : function( hid ){ - return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) ); - }, - - /** If the given hid is in the collection, return it's index. If not, return the insertion point it would need. - * NOTE: assumes hids are unique and valid - * @param {Int} hid the hid to find or create. If hid is 0, null, undefined: return the last hid + 1 - * @returns the collection index of the existing hda or an insertion point if it doesn't exist - */ - hidToCollectionIndex : function( hid ){ - // if the hid is 0, null, undefined: assume a request for a new hid (return the last index) - if( !hid ){ - return this.models.length; - } - - var endingIndex = this.models.length - 1; - //TODO: prob. more efficient to cycle backwards through these (assuming ordered by hid) - for( var i=endingIndex; i>=0; i-- ){ - var hdaHid = this.at( i ).get( 'hid' ); - //this.log( i, 'hdaHid:', hdaHid ); - if( hdaHid === hid ){ - //this.log( '\t match:', hdaHid, hid, ' returning:', i ); - return i; - } - if( hdaHid < hid ){ - //this.log( '\t past it, returning:', ( i + 1 ) ); - return i + 1; - } - } - return null; - }, - - /** Get every 'shown' hda in this collection based on show_deleted/hidden - * @param {Boolean} show_deleted are we showing deleted hdas? - * @param {Boolean} show_hidden are we showing hidden hdas? - * @returns array of hda models - * @see HistoryDatasetAssociation#isVisible - */ - getVisible : function( show_deleted, show_hidden ){ - return this.filter( function( item ){ return item.isVisible( show_deleted, show_hidden ); }); - }, - - /** For each possible hda state, get an array of all hda ids in that state - * @returns a map of states -> hda ids - * @see HistoryDatasetAssociation#STATES - */ - getStateLists : function(){ - var stateLists = {}; - _.each( _.values( HistoryDatasetAssociation.STATES ), function( state ){ - stateLists[ state ] = []; + notReady : function(){ + return this.filter( function( hda ){ + return !hda.inReadyState(); }); - //NOTE: will err on unknown state - this.each( function( item ){ - stateLists[ item.get( 'state' ) ].push( item.get( 'id' ) ); - }); - return stateLists; }, /** Get the id of every hda in this collection not in a 'ready' state (running). @@ -297,26 +351,55 @@ return idList; }, - /** Update (fetch) the data of the hdas with the given ids. - * @param {String[]} ids an array of hda ids to update - * @returns {HistoryDatasetAssociation[]} hda models that were updated - * @see HistoryDatasetAssociation#fetch + /** Get the hda with the given hid + * @param {Int} hid the hid to search for + * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found */ - update : function( ids ){ - this.log( this + 'update:', ids ); + getByHid : function( hid ){ + return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) ); + }, - if( !( ids && ids.length ) ){ return []; } + /** Get every 'shown' hda in this collection based on show_deleted/hidden + * @param {Boolean} show_deleted are we showing deleted hdas? + * @param {Boolean} show_hidden are we showing hidden hdas? + * @returns array of hda models + * @see HistoryDatasetAssociation#isVisible + */ + getVisible : function( show_deleted, show_hidden ){ + return this.filter( function( item ){ return item.isVisible( show_deleted, show_hidden ); }); + }, - var collection = this, - updatedHdas = null; - _.each( ids, function( id, index ){ - var hda = collection.get( id ); - if( hda ){ - hda.fetch(); - updatedHdas.push( hda ); - } + // ........................................................................ ajax + fetchAllDetails : function(){ + return this.fetch({ data : { details : 'all' } }); + }, + + // ........................................................................ sorting/filtering + matches : function( matchesWhat ){ + return this.filter( function( hda ){ + return hda.matches( matchesWhat ); }); - return updatedHdas; + }, + + // ........................................................................ misc + set : function( models, options ){ + // arrrrrrrrrrrrrrrrrg... + // override to get a correct/smarter merge when incoming data is partial (e.g. stupid backbone) + // w/o this partial models from the server will fill in missing data with model defaults + // and overwrite existing data on the client + // see Backbone.Collection.set and _prepareModel + var collection = this; + models = _.map( models, function( model ){ + var existing = collection.get( model.id ); + if( !existing ){ return model; } + + // merge the models _BEFORE_ calling the superclass version + var merged = existing.toJSON(); + _.extend( merged, model ); + return merged; + }); + // now call superclass when the data is filled + Backbone.Collection.prototype.set.call( this, models, options ); }, /** String representation. */ @@ -326,7 +409,7 @@ }); //============================================================================== -//return { -// HistoryDatasetAssociation : HistoryDatasetAssociation, -// HDACollection : HDACollection, -//};}); +return { + HistoryDatasetAssociation : HistoryDatasetAssociation, + HDACollection : HDACollection +};}); This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/14fbaad2645b/ Changeset: 14fbaad2645b Branch: next-stable User: dannon Date: 2013-10-21 23:32:34 Summary: Merge next-stable Affected #: 3 files diff -r 3b4cbba69871ab36384f1f8b28cb5555ba3dd20b -r 14fbaad2645bd7b8a0a2f9a4a682b38ecf18c7d0 lib/galaxy/web/__init__.py --- a/lib/galaxy/web/__init__.py +++ b/lib/galaxy/web/__init__.py @@ -13,4 +13,5 @@ from framework import expose_api from framework import expose_api_anonymous from framework import expose_api_raw +from framework import expose_api_raw_anonymous from framework.base import httpexceptions diff -r 3b4cbba69871ab36384f1f8b28cb5555ba3dd20b -r 14fbaad2645bd7b8a0a2f9a4a682b38ecf18c7d0 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -110,6 +110,14 @@ """ return expose_api( func, to_json=False ) +#DBTODO refactor these post-dist. +def expose_api_raw_anonymous( func ): + """ + Expose this function via the API but don't dump the results + to JSON. + """ + return expose_api( func, to_json=False, user_required=False ) + def expose_api_anonymous( func, to_json=True ): """ Expose this function via the API but don't require a set user. diff -r 3b4cbba69871ab36384f1f8b28cb5555ba3dd20b -r 14fbaad2645bd7b8a0a2f9a4a682b38ecf18c7d0 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -23,7 +23,7 @@ trans.response.status = 501 return 'not implemented' - @web.expose_api + @web.expose_api_anonymous def show( self, trans, id, hda_ldda='hda', data_type=None, provider=None, **kwd ): """ GET /api/datasets/{encoded_dataset_id} @@ -101,7 +101,6 @@ # If there is a chrom, check for data on the chrom. if chrom: - data_provider_registry = trans.app.data_provider_registry data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) if not data_provider.has_data( chrom ): @@ -244,7 +243,7 @@ return data - @web.expose_api_raw + @web.expose_api_raw_anonymous def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): """ https://bitbucket.org/galaxy/galaxy-central/commits/361f581d1e51/ Changeset: 361f581d1e51 User: dannon Date: 2013-10-21 23:33:47 Summary: Merge Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/315018626d87/ Changeset: 315018626d87 User: dannon Date: 2013-10-21 23:34:09 Summary: Merge. Affected #: 1 file diff -r 361f581d1e5188b01476f6da5ca22af7d5c6ba5e -r 315018626d873654e822ef97984c0f3288360fb2 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -113,7 +113,7 @@ except Exception, e: msg = "Error in history API at showing history detail: %s" % ( str( e ) ) - log.exception( e ) + log.exception( msg ) trans.response.status = 500 return msg @@ -148,7 +148,7 @@ except Exception, e: msg = "Error in history API when switching current history: %s" % ( str( e ) ) - log.exception( e ) + log.exception( msg ) trans.response.status = 500 return msg 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: carlfeberhard: Histories API: use proper logging technique for exceptions
by commits-noreply＠bitbucket.org 21 Oct '13

21 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/80db2712720c/ Changeset: 80db2712720c User: carlfeberhard Date: 2013-10-21 23:32:12 Summary: Histories API: use proper logging technique for exceptions Affected #: 1 file diff -r fbf1898d7dea43a46a0f8ec80fd41540ac6fc204 -r 80db2712720c4ea153e51bbc72e981cc9886e73c lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -113,7 +113,7 @@ except Exception, e: msg = "Error in history API at showing history detail: %s" % ( str( e ) ) - log.exception( e ) + log.exception( msg ) trans.response.status = 500 return msg @@ -148,7 +148,7 @@ except Exception, e: msg = "Error in history API when switching current history: %s" % ( str( e ) ) - log.exception( e ) + log.exception( msg ) trans.response.status = 500 return msg 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 21 Oct '13

21 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b4cbba69871/ Changeset: 3b4cbba69871 Branch: next-stable User: jgoecks Date: 2013-10-21 23:11:17 Summary: Use progressive approach to integrate tabular chunked data display into collaboration framework. This fixes a bug that prevented chunkable datasets from being viewable in pages. Affected #: 1 file diff -r 81880a04e6e79d944a6d9c225b36417114cd38ec -r 3b4cbba69871ab36384f1f8b28cb5555ba3dd20b templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -18,6 +18,12 @@ }); require(['mvc/data'], function(data) { + // + // Use tabular data display progressively by deleting data from page body + // and then showing dataset view. + // + $('.page-body').children().remove(); + data.createTabularDatasetChunkedView( // Dataset config. TODO: encode id. _.extend( ${h.to_json_string( item.to_dict() )}, @@ -59,10 +65,10 @@ title="Import dataset"></a></%def> +## Renders dataset content. Function is used to render data in stand-along page and to provide content for embedded datasets as well. <%def name="render_item( data, data_to_render )"> - ## Chunkable data is rendered in JavaScript above; render unchunkable data below. ${ render_deleted_data_message( data ) } - %if not data.datatype.CHUNKABLE and data_to_render: + %if data_to_render: %if truncated: <div class="warningmessagelarge"> This dataset is large and only the first megabyte is shown below. | https://bitbucket.org/galaxy/galaxy-central/commits/fbf1898d7dea/ Changeset: fbf1898d7dea User: jgoecks Date: 2013-10-21 23:11:48 Summary: Automated merge of next-stable branch into default Affected #: 1 file diff -r 4f1c25230dd009efd1f04f8d7a74d83733f8b75a -r fbf1898d7dea43a46a0f8ec80fd41540ac6fc204 templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -18,6 +18,12 @@ }); require(['mvc/data'], function(data) { + // + // Use tabular data display progressively by deleting data from page body + // and then showing dataset view. + // + $('.page-body').children().remove(); + data.createTabularDatasetChunkedView( // Dataset config. TODO: encode id. _.extend( ${h.to_json_string( item.to_dict() )}, @@ -59,10 +65,10 @@ title="Import dataset"></a></%def> +## Renders dataset content. Function is used to render data in stand-along page and to provide content for embedded datasets as well. <%def name="render_item( data, data_to_render )"> - ## Chunkable data is rendered in JavaScript above; render unchunkable data below. ${ render_deleted_data_message( data ) } - %if not data.datatype.CHUNKABLE and data_to_render: + %if data_to_render: %if truncated: <div class="warningmessagelarge"> This dataset is large and only the first megabyte is shown below. | 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: carlfeberhard: History panel: remove from iframe, general improvements; pack scripts
by commits-noreply＠bitbucket.org 21 Oct '13

21 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4f1c25230dd0/ Changeset: 4f1c25230dd0 User: carlfeberhard Date: 2013-10-21 22:26:47 Summary: History panel: remove from iframe, general improvements; pack scripts Affected #: 28 files diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 4f1c25230dd009efd1f04f8d7a74d83733f8b75a lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -633,11 +633,11 @@ # if a tool declares 'force_history_refresh' in its xml, when the hda -> ready, reload the history panel # expensive - if( ( hda.state in [ 'running', 'queued' ] ) - and ( hda.creating_job and hda.creating_job.tool_id ) ): - tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) - if tool_used and tool_used.force_history_refresh: - hda_dict[ 'force_history_refresh' ] = True + #if( ( hda.state in [ 'running', 'queued' ] ) + #and ( hda.creating_job and hda.creating_job.tool_id ) ): + # tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) + # if tool_used and tool_used.force_history_refresh: + # hda_dict[ 'force_history_refresh' ] = True return trans.security.encode_dict_ids( hda_dict ) @@ -653,13 +653,14 @@ 'accessible': False }) - def get_hda_dict_with_error( self, trans, hda, error_msg='' ): + def get_hda_dict_with_error( self, trans, hda=None, history_id=None, id=None, error_msg='Error' ): return trans.security.encode_dict_ids({ - 'id' : hda.id, - 'history_id': hda.history.id, - 'hid' : hda.hid, - 'name' : hda.name, - 'error' : error_msg + 'id' : hda.id if hda else id, + 'history_id': hda.history.id if hda else history_id, + 'hid' : hda.hid if hda else '(unknown)', + 'name' : hda.name if hda else '(unknown)', + 'error' : error_msg, + 'state' : trans.model.Dataset.states.NEW }) def get_display_apps( self, trans, hda ): diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 4f1c25230dd009efd1f04f8d7a74d83733f8b75a lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -97,6 +97,9 @@ # Most recent active history for user sessions, not deleted history = trans.user.galaxy_sessions[0].histories[-1].history + elif history_id == "current": + history = trans.get_history( create=True ) + else: history = self.get_history( trans, history_id, check_ownership=False, check_accessible=True, deleted=deleted ) @@ -110,7 +113,7 @@ except Exception, e: msg = "Error in history API at showing history detail: %s" % ( str( e ) ) - log.exception( msg, exc_info=True ) + log.exception( e ) trans.response.status = 500 return msg @@ -174,7 +177,8 @@ trans.sa_session.add( new_history ) trans.sa_session.flush() - item = new_history.to_dict(view='element', value_mapper={'id':trans.security.encode_id}) + #item = new_history.to_dict(view='element', value_mapper={'id':trans.security.encode_id}) + item = self.get_history_dict( trans, new_history ) item['url'] = url_for( 'history', id=item['id'] ) #TODO: possibly default to True here - but favor explicit for now (and backwards compat) diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 4f1c25230dd009efd1f04f8d7a74d83733f8b75a lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -59,22 +59,21 @@ encoded_hda_id = trans.security.encode_id( hda.id ) if encoded_hda_id in ids: #TODO: share code with show - try: - hda_dict = self.get_hda_dict( trans, hda ) - hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) - hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) - rval.append( hda_dict ) - - except Exception, exc: - # don't fail entire list if hda err's, record and move on - log.error( "Error in history API at listing contents with history %s, hda %s: (%s) %s", - history_id, encoded_hda_id, type( exc ), str( exc ), exc_info=True ) - rval.append( self.get_hda_dict_with_error( trans, hda, str( exc ) ) ) + rval.append( self._detailed_hda_dict( trans, hda ) ) # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history else: + details = kwd.get( 'details', None ) or [] + if details and details != 'all': + details = util.listify( details ) + for hda in history.datasets: - rval.append( self._summary_hda_dict( trans, history_id, hda ) ) + encoded_hda_id = trans.security.encode_id( hda.id ) + if( ( encoded_hda_id in details ) + or ( details == 'all' ) ): + rval.append( self._detailed_hda_dict( trans, hda ) ) + else: + rval.append( self._summary_hda_dict( trans, history_id, hda ) ) except Exception, e: # for errors that are not specific to one hda (history lookup or summary list) @@ -85,7 +84,7 @@ return rval #TODO: move to model or Mixin - def _summary_hda_dict( self, trans, history_id, hda ): + def _summary_hda_dict( self, trans, encoded_history_id, hda ): """ Returns a dictionary based on the HDA in summary form:: { @@ -99,11 +98,32 @@ encoded_id = trans.security.encode_id( hda.id ) return { 'id' : encoded_id, + 'history_id' : encoded_history_id, 'name' : hda.name, 'type' : api_type, - 'url' : url_for( 'history_content', history_id=history_id, id=encoded_id, ), + 'state' : hda.state, + 'deleted': hda.deleted, + 'visible': hda.visible, + 'hid' : hda.hid, + 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, ), } + def _detailed_hda_dict( self, trans, hda ): + """ + Detailed dictionary of hda values. + """ + try: + hda_dict = self.get_hda_dict( trans, hda ) + hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) + hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) + return hda_dict + + except Exception, exc: + # catch error here - returning a briefer hda_dict with an error attribute + log.exception( "Error in history API at listing contents with history %s, hda %s: (%s) %s", + hda.history_id, hda.id, type( exc ), str( exc ) ) + return self.get_hda_dict_with_error( trans, hda=hda, error_msg=str( exc ) ) + @web.expose_api_anonymous def show( self, trans, id, history_id, **kwd ): """ @@ -244,7 +264,7 @@ trans.response.status = 501 return - @web.expose_api + @web.expose_api_anonymous def update( self, trans, history_id, id, payload, **kwd ): """ update( self, trans, history_id, id, payload, **kwd ) @@ -269,10 +289,28 @@ #TODO: PUT /api/histories/{encoded_history_id} payload = { rating: rating } (w/ no security checks) changed = {} try: - hda = self.get_dataset( trans, id, - check_ownership=True, check_accessible=True, check_state=True ) - # validation handled here and some parsing, processing, and conversion - payload = self._validate_and_parse_update_payload( payload ) + # anon user + if trans.user == None: + if history_id != trans.security.encode_id( trans.history.id ): + trans.response.status = 401 + return { 'error': 'Anonymous users cannot edit histories other than their current history' } + + anon_allowed_payload = {} + if 'deleted' in payload: + anon_allowed_payload[ 'deleted' ] = payload[ 'deleted' ] + if 'visible' in payload: + anon_allowed_payload[ 'visible' ] = payload[ 'visible' ] + + payload = self._validate_and_parse_update_payload( anon_allowed_payload ) + hda = self.get_dataset( trans, id, check_ownership=False, check_accessible=False, check_state=True ) + if hda.history != trans.history: + trans.response.status = 401 + return { 'error': 'Anonymous users cannot edit datasets outside their current history' } + + else: + payload = self._validate_and_parse_update_payload( payload ) + hda = self.get_dataset( trans, id, check_ownership=True, check_accessible=True, check_state=True ) + # additional checks here (security, etc.) changed = self.set_hda_from_dict( trans, hda, payload ) diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 4f1c25230dd009efd1f04f8d7a74d83733f8b75a lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -5,7 +5,7 @@ import os import urllib -from paste.httpexceptions import HTTPNotFound +from paste.httpexceptions import HTTPNotFound, HTTPBadGateway from galaxy import web from galaxy.web import url_for @@ -30,7 +30,8 @@ @web.expose def index(self, trans, id=None, tool_id=None, mode=None, workflow_id=None, m_c=None, m_a=None, **kwd): - """Called on the root url to display the main Galaxy page. + """ + Called on the root url to display the main Galaxy page. """ return trans.fill_template( "root/index.mako", tool_id=tool_id, @@ -99,63 +100,75 @@ show_deleted=string_as_bool( show_deleted ), show_hidden=string_as_bool( show_hidden ) ) - @web.expose - def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, hda_id=None, **kwd ): - """Display the current history, creating a new history if necessary. - - NOTE: No longer accepts "id" or "template" options for security reasons. - """ - if as_xml: - return self.history_as_xml( trans, - show_deleted=string_as_bool( show_deleted ), show_hidden=string_as_bool( show_hidden ) ) - - # get all datasets server-side, client-side will get flags and render appropriately - show_deleted = string_as_bool_or_none( show_deleted ) - show_purged = show_deleted - show_hidden = string_as_bool_or_none( show_hidden ) - params = Params( kwd ) - message = params.get( 'message', '' ) - #TODO: ugh... - message = message if message != 'None' else '' - status = params.get( 'status', 'done' ) - - if trans.app.config.require_login and not trans.user: - return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' ) - - def err_msg( where=None ): - where = where if where else 'getting the history data from the server' - err_msg = ( 'An error occurred %s. ' - + 'Please contact a Galaxy administrator if the problem persists.' ) %( where ) - return err_msg, 'error' - + def _get_current_history_data( self, trans ): history_dictionary = {} hda_dictionaries = [] + try: history = trans.get_history( create=True ) hdas = self.get_history_datasets( trans, history, show_deleted=True, show_hidden=True, show_purged=True ) for hda in hdas: + hda_dict = {} try: - hda_dictionaries.append( self.get_hda_dict( trans, hda ) ) + hda_dict = self.get_hda_dict( trans, hda ) except Exception, exc: # don't fail entire list if hda err's, record and move on log.error( 'Error bootstrapping hda %d: %s', hda.id, str( exc ), exc_info=True ) - hda_dictionaries.append( self.get_hda_dict_with_error( trans, hda, str( exc ) ) ) + hda_dict = self.get_hda_dict_with_error( trans, hda, str( exc ) ) + + hda_dictionaries.append( hda_dict ) # re-use the hdas above to get the history data... history_dictionary = self.get_history_dict( trans, history, hda_dictionaries=hda_dictionaries ) except Exception, exc: user_id = str( trans.user.id ) if trans.user else '(anonymous)' - log.error( 'Error bootstrapping history for user %s: %s', user_id, str( exc ), exc_info=True ) - message, status = err_msg() + log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) ) + message = ( 'An error occurred getting the history data from the server. ' + + 'Please contact a Galaxy administrator if the problem persists.' ) history_dictionary[ 'error' ] = message - return trans.stream_template_mako( "root/history.mako", - history_json = to_json_string( history_dictionary ), hda_json = to_json_string( hda_dictionaries ), - show_deleted=show_deleted, show_hidden=show_hidden, hda_id=hda_id, log=log, message=message, status=status ) + return { + 'history' : history_dictionary, + 'hdas' : hda_dictionaries + } + + @web.expose + def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, **kwd ): + """ + Display the current history in it's own page or as xml. + """ + if as_xml: + return self.history_as_xml( trans, + show_deleted=string_as_bool( show_deleted ), show_hidden=string_as_bool( show_hidden ) ) + + if trans.app.config.require_login and not trans.user: + return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' ) + + # get all datasets server-side, client-side will get flags and render appropriately + show_deleted = string_as_bool_or_none( show_deleted ) + show_purged = show_deleted + show_hidden = string_as_bool_or_none( show_hidden ) + + history_dictionary = {} + hda_dictionaries = [] + try: + history_data = self._get_current_history_data( trans ) + history_dictionary = history_data[ 'history' ] + hda_dictionaries = history_data[ 'hdas' ] + + except Exception, exc: + user_id = str( trans.user.id ) if trans.user else '(anonymous)' + log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) ) + history_dictionary[ 'error' ] = ( 'An error occurred getting the history data from the server. ' + + 'Please contact a Galaxy administrator if the problem persists.' ) + + return trans.fill_template_mako( "root/history.mako", + history = history_dictionary, hdas = hda_dictionaries, + show_deleted=show_deleted, show_hidden=show_hidden ) ## ---- Dataset display / editing ---------------------------------------- @web.expose @@ -503,7 +516,22 @@ return rval @web.expose - def generate_error( self, trans ): + def generate_error( self, trans, code=500 ): """Raises an exception (debugging). """ + trans.response.status = code raise Exception( "Fake error!" ) + + @web.json + def generate_json_error( self, trans, code=500 ): + """Raises an exception (debugging). + """ + try: + code = int( code ) + except Exception, exc: + code = 500 + + if code == 502: + raise HTTPBadGateway() + trans.response.status = code + return { 'error': 'Fake error!' } diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 4f1c25230dd009efd1f04f8d7a74d83733f8b75a lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -325,4 +325,5 @@ <p><b>Please do not use your browser\'s "stop" or "reload" buttons until the upload is complete, or it may be interrupted.</b></p><p>You may safely continue to use Galaxy while the upload is in progress. Using "stop" and "reload" on pages other than Galaxy is also safe.</p> """ + #return trans.show_message( msg, refresh_frames=[ 'history' ] ) return trans.show_message( msg ) diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 4f1c25230dd009efd1f04f8d7a74d83733f8b75a static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -7,31 +7,30 @@ name: null, hidden: false }, - + show: function() { this.set("hidden", false); }, - + hide: function() { this.set("hidden", true); }, - + is_visible: function() { return !this.attributes.hidden; } }); - /** * Base view that handles visibility based on model's hidden attribute. */ var BaseView = Backbone.View.extend({ - + initialize: function() { this.model.on("change:hidden", this.update_visible, this); this.update_visible(); }, - + update_visible: function() { if( this.model.attributes.hidden ){ this.$el.hide(); @@ -120,7 +119,8 @@ // ~constants for the current engine var STORAGE_ENGINE = sessionStorage, STORAGE_ENGINE_GETTER = function sessionStorageGet( key ){ - return JSON.parse( this.getItem( key ) ); + var item = this.getItem( key ); + return ( item !== null )?( JSON.parse( this.getItem( key ) ) ):( null ); }, STORAGE_ENGINE_SETTER = function sessionStorageSet( key, val ){ return this.setItem( key, JSON.stringify( val ) ); @@ -182,7 +182,7 @@ } //??: more readable to make another class? - var returnedStorage = {}; + var returnedStorage = {}, // attempt to get starting data from engine... data = STORAGE_ENGINE_GETTER.call( STORAGE_ENGINE, storageKey ); @@ -216,3 +216,63 @@ return returnedStorage; }; + + +//============================================================================== +function LoadingIndicator( $where ){ + var self = this, + $indicator; + + function setPosition(){ + // even tho pos is 'fixed' - give illusion of width 100% and margin by manually setting width, offset + var padding = 4, + width = $indicator.parent().width() || $where.width(), + offset = $indicator.parent().offset() || $where.offset(); + + $indicator.outerWidth( width - ( padding * 2 ) ); + // have to use css top, left and not offset (wont work when indicator is hidden) + $indicator.css({ top: offset.top + padding + 'px' , left: offset.left + padding + 'px' }); + } + + function render(){ + var $spinner = $( '<span class="fa-icon-spinner fa-icon-spin fa-icon-large"></span>') + .css({ 'color' : 'grey', 'font-size' : '16px' }); + var $message = $( '<i>loading...</i>' ) + .css({ 'color' : 'grey', 'margin-left' : '8px' }); + $indicator = $( '<div/>' ).addClass( 'loading-indicator' ) + .css({ + 'position' : 'fixed', + 'padding' : '4px', + 'text-align' : 'center', + 'background-color' : 'white', + 'opacity' : '0.85', + 'border-radius' : '3px' + }) + .append( $spinner, $message ) + //NOTE: insert as sibling to $where + .insertBefore( $where ); + setPosition(); + return $indicator.hide(); + } + + self.show = function( speed, callback ){ + speed = speed || 'fast'; + setPosition(); + $indicator.fadeIn( speed, callback ); + // not using full fadeOut allows using scroll to still work + //$whatIsLoading.fadeTo( speed, 0.0001, callback ); + return self; + }; + + self.hide = function( speed, callback ){ + speed = speed || 'fast'; + //$whatIsLoading.fadeTo( speed, 1.0, function(){ + // if( callback ){ callback(); } + //}); + $indicator.fadeOut( speed, callback ); + return self; + }; + $indicator = render(); + return self; +} + diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 4f1c25230dd009efd1f04f8d7a74d83733f8b75a static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -1,7 +1,6 @@ -//define([ -// "../mvc/base-mvc" -//], function(){ - +define([ + "mvc/dataset/hda-model" +], function( hdaModel ){ /* global Backbone, LoggableMixin, HistoryDatasetAssociation, HDABaseView */ //============================================================================== /** @class Read only view for HistoryDatasetAssociation. @@ -22,6 +21,8 @@ tagName : "div", className : "historyItemContainer", + fxSpeed : 'fast', + // ......................................................................... SET UP /** Set up the view, cache url templates, bind listeners * @param {Object} attributes @@ -38,33 +39,20 @@ this._render_showParamsButton ]; - // cache urlTemplates (gen. provided by GalaxyPaths) to urls - if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } - this.urlTemplates = attributes.urlTemplates; - /** is the body of this hda view expanded/not. */ this.expanded = attributes.expanded || false; + this._setUpListeners(); + }, + _setUpListeners : function(){ // re-rendering on any model changes - this.model.bind( 'change', function( model, options ){ - // if more than the display apps have changed: render everything - var nonDisplayAppChanges = _.omit( this.model.changedAttributes(), 'display_apps', 'display_types' ); - if( _.keys( nonDisplayAppChanges ).length ){ - this.render(); + this.model.on( 'change', this.render, this ); - // if just the display links, and it's already expanded: render the links only - } else { - if( this.expanded ){ - this._render_displayApps(); - } - } - }, this ); - - //this.bind( 'all', function( event ){ + //this.on( 'all', function( event ){ // this.log( event ); //}, this ); }, - + // ......................................................................... RENDER MAIN /** Render this HDA, set up ui. * @fires rendered:ready when rendered and NO running HDAs @@ -86,9 +74,8 @@ // handle that here by removing previous view's tooltips this.$el.find("[title]").tooltip( "destroy" ); - /** web controller urls for functions relating to this hda. - * These are rendered from urlTemplates using the model data. */ - this.urls = this._renderUrls( this.urlTemplates, this.model.toJSON() ); + /** web controller urls for functions relating to this hda. */ + this.urls = this.model.urls(); itemWrapper .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) @@ -104,9 +91,9 @@ itemWrapper.append( this.body ); // transition... - this.$el.fadeOut( 'fast', function(){ + this.$el.fadeOut( this.fxSpeed, function(){ view.$el.children().remove(); - view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ + view.$el.append( itemWrapper ).fadeIn( view.fxSpeed, function(){ view.log( view + ' rendered:', view.$el ); var renderedEventName = 'rendered'; @@ -121,55 +108,6 @@ return this; }, - /** render the urls for this hda using the model data and the url templates from initialize. - * @param {Object} urlTemplates a map (or nested map) of underscore templates (currently, anyhoo) - * @param {Object} modelJson data from the model - * @returns {Object} the templated urls - */ - _renderUrls : function( urlTemplates, modelJson ){ - var hdaView = this, - urls = {}; - _.each( urlTemplates, function( urlTemplateOrObj, urlKey ){ - // object == nested templates: recurse - if( _.isObject( urlTemplateOrObj ) ){ - urls[ urlKey ] = hdaView._renderUrls( urlTemplateOrObj, modelJson ); - - // string == template: - } else { - // meta_down load is a special case (see renderMetaDownloadUrls) - //TODO: should be a better (gen.) way to handle this case - if( urlKey === 'meta_download' ){ - urls[ urlKey ] = hdaView._renderMetaDownloadUrls( urlTemplateOrObj, modelJson ); - - } else { - try { - urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); - } catch( Error ){ - throw( hdaView + '._renderUrls error: ' + Error + - '\n rendering:' + urlTemplateOrObj + - '\n with ' + JSON.stringify( modelJson ) ); - } - } - } - }); - return urls; - }, - - /** there can be more than one meta_file (e.g. bam index) to download, - * so return a list of url and file_type for each - * @param {Object} urlTemplate underscore templates for meta download urls - * @param {Object} modelJson data from the model - * @returns {Object} url and filetype for each meta file - */ - _renderMetaDownloadUrls : function( urlTemplate, modelJson ){ - return _.map( modelJson.meta_files, function( meta_file ){ - return { - url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), - file_type : meta_file.file_type - }; - }); - }, - /** set up js behaviors, event handlers for elements within the given container * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) */ @@ -218,8 +156,8 @@ _render_displayButton : function(){ // don't show display if not viewable or not accessible // (do show if in error, running) - if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NEW ) + if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) || ( !this.model.get( 'accessible' ) ) ){ this.displayButton = null; return null; @@ -237,7 +175,7 @@ displayBtnData.title = _l( 'Cannot display datasets removed from disk' ); // disable if still uploading - } else if( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ){ + } else if( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.UPLOAD ){ displayBtnData.enabled = false; displayBtnData.title = _l( 'This dataset must finish uploading before it can be viewed' ); @@ -406,40 +344,40 @@ body.html( '' ); //TODO: not a fan of this dispatch switch( this.model.get( 'state' ) ){ - case HistoryDatasetAssociation.STATES.NEW : + case hdaModel.HistoryDatasetAssociation.STATES.NEW : this._render_body_new( body ); break; - case HistoryDatasetAssociation.STATES.NOT_VIEWABLE : + case hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE : this._render_body_not_viewable( body ); break; - case HistoryDatasetAssociation.STATES.UPLOAD : + case hdaModel.HistoryDatasetAssociation.STATES.UPLOAD : this._render_body_uploading( body ); break; - case HistoryDatasetAssociation.STATES.PAUSED: + case hdaModel.HistoryDatasetAssociation.STATES.PAUSED: this._render_body_paused( body ); break; - case HistoryDatasetAssociation.STATES.QUEUED : + case hdaModel.HistoryDatasetAssociation.STATES.QUEUED : this._render_body_queued( body ); break; - case HistoryDatasetAssociation.STATES.RUNNING : + case hdaModel.HistoryDatasetAssociation.STATES.RUNNING : this._render_body_running( body ); break; - case HistoryDatasetAssociation.STATES.ERROR : + case hdaModel.HistoryDatasetAssociation.STATES.ERROR : this._render_body_error( body ); break; - case HistoryDatasetAssociation.STATES.DISCARDED : + case hdaModel.HistoryDatasetAssociation.STATES.DISCARDED : this._render_body_discarded( body ); break; - case HistoryDatasetAssociation.STATES.SETTING_METADATA : + case hdaModel.HistoryDatasetAssociation.STATES.SETTING_METADATA : this._render_body_setting_metadata( body ); break; - case HistoryDatasetAssociation.STATES.EMPTY : + case hdaModel.HistoryDatasetAssociation.STATES.EMPTY : this._render_body_empty( body ); break; - case HistoryDatasetAssociation.STATES.FAILED_METADATA : + case hdaModel.HistoryDatasetAssociation.STATES.FAILED_METADATA : this._render_body_failed_metadata( body ); break; - case HistoryDatasetAssociation.STATES.OK : + case hdaModel.HistoryDatasetAssociation.STATES.OK : this._render_body_ok( body ); break; default: @@ -591,27 +529,44 @@ * @fires body-expanded when a body has been expanded * @fires body-collapsed when a body has been collapsed */ - toggleBodyVisibility : function( event, expanded ){ + toggleBodyVisibility : function( event, expand ){ var hdaView = this; - this.expanded = ( expanded === undefined )?( !this.body.is( ':visible' ) ):( expanded ); - //this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body ); + expand = ( expand === undefined )?( !this.body.is( ':visible' ) ):( expand ); + if( expand ){ + if( this.model.inReadyState() && !this.model.hasDetails() ){ + var xhr = this.model.fetch(); + xhr.done( function( model ){ + hdaView.expandBody(); + }); + } else { + this.expandBody(); + } + } else { + this.collapseBody(); + } + }, - if( this.expanded ){ - hdaView._render_body_html( hdaView.body ); - this.body.slideDown( 'fast', function(){ - hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) ); - }); - } else { - this.body.slideUp( 'fast', function(){ - hdaView.trigger( 'body-collapsed', hdaView.model.get( 'id' ) ); - }); - } + expandBody : function(){ + var hdaView = this; + hdaView._render_body_html( hdaView.body ); + this.body.slideDown( hdaView.fxSpeed, function(){ + hdaView.expanded = true; + hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) ); + }); + }, + + collapseBody : function(){ + var hdaView = this; + this.body.slideUp( hdaView.fxSpeed, function(){ + hdaView.expanded = false; + hdaView.trigger( 'body-collapsed', hdaView.model.get( 'id' ) ); + }); }, // ......................................................................... DELETION remove : function( callback ){ var hdaView = this; - this.$el.fadeOut( 'fast', function(){ + this.$el.fadeOut( hdaView.fxSpeed, function(){ hdaView.$el.remove(); hdaView.off(); if( callback ){ callback(); } @@ -638,6 +593,6 @@ }; //============================================================================== -//return { -// HDABaseView : HDABaseView, -//};}); +return { + HDABaseView : HDABaseView, +};}); diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 4f1c25230dd009efd1f04f8d7a74d83733f8b75a static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -1,6 +1,7 @@ -//define([ -// "../mvc/base-mvc" -//], function(){ +define([ + "mvc/dataset/hda-model", + "mvc/dataset/hda-base" +], function( hdaModel, hdaBase ){ //============================================================================== /** @class Editing view for HistoryDatasetAssociation. * @name HDAEditView @@ -10,7 +11,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var HDAEditView = HDABaseView.extend( LoggableMixin ).extend( +var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( /** @lends HDAEditView.prototype */{ // ......................................................................... SET UP @@ -22,7 +23,8 @@ * @see HDABaseView#initialize */ initialize : function( attributes ){ - HDABaseView.prototype.initialize.call( this, attributes ); + hdaBase.HDABaseView.prototype.initialize.call( this, attributes ); + this.hasUser = attributes.hasUser; /** list of rendering functions for the default, primary icon-buttons. */ this.defaultPrimaryActionButtonRenderers = [ @@ -37,33 +39,8 @@ * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) */ _setUpBehaviors : function( $container ){ - //TODO: ideally this would be a DELETE call to the api - // using purge async for now - HDABaseView.prototype._setUpBehaviors.call( this, $container ); - - // use purge_async with an ajax call - var hdaView = this, - purge_url = this.urls.purge, - purge_link = $container.find( '#historyItemPurger-' + this.model.get( 'id' ) ); - if( purge_link ){ - //TODO: remove href from template - purge_link.attr( 'href', [ "javascript", "void(0)" ].join( ':' ) ); - purge_link.click( function( event ){ - //TODO??: confirm? - var xhr = jQuery.ajax( purge_url ); - xhr.success( function( message, status, responseObj ){ - hdaView.model.set( 'purged', true ); - hdaView.trigger( 'purged', hdaView ); - }); - xhr.error( function( error, status, message ){ - //TODO: Exception messages are hidden within error page - //!NOTE: that includes the 'Removal of datasets by users is not allowed in this Galaxy instance.' - view.trigger( 'error', - hdaView, xhr, { url: purge_url }, _l( "Unable to purge this dataset" ) ); - }); - }); - } - //TODO: same with undelete_async + hdaBase.HDABaseView.prototype._setUpBehaviors.call( this, $container ); + //var hdaView = this; }, // ......................................................................... RENDER WARNINGS @@ -74,7 +51,7 @@ */ _render_warnings : function(){ // jQ errs on building dom with whitespace - if there are no messages, trim -> '' - return $( jQuery.trim( HDABaseView.templates.messages( + return $( jQuery.trim( hdaBase.HDABaseView.templates.messages( _.extend( this.model.toJSON(), { urls: this.urls } ) ))); }, @@ -101,9 +78,9 @@ // don't show edit while uploading, in-accessible // DO show if in error (ala previous history panel) //TODO??: not viewable/accessible are essentially the same (not viewable set from accessible) - if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NEW ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) + || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.UPLOAD ) + || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ this.editButton = null; return null; @@ -138,44 +115,26 @@ _render_deleteButton : function(){ // don't show delete if... //TODO??: not viewable/accessible are essentially the same (not viewable set from accessible) - if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NEW ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) + || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ this.deleteButton = null; return null; } var self = this, + id = 'historyItemDeleter-' + self.model.get( 'id' ), delete_url = self.urls[ 'delete' ], deleteBtnData = { - title : _l( 'Delete' ), - href : delete_url, - id : 'historyItemDeleter-' + this.model.get( 'id' ), - icon_class : 'delete', - on_click : function() { - // Delete the dataset on the server and update HDA + view depending on success/failure. - // FIXME: when HDA-delete is implemented in the API, can call set(), then save directly - // on the model. - $.ajax({ - url: delete_url, - type: 'POST', - error: function() { - // Something went wrong, so show HDA again. - // TODO: an error notification would be good. - self.trigger( 'error', self, null, null, { url: delete_url }, _l( 'deletion failed' ) ); - self.$el.show(); - }, - success: function() { - // FIXME: setting model attribute causes re-rendering, which is unnecessary. - //self.$el.remove(); - - self.model.set({ deleted: true }); - } - }); - - // Return false so that anchor action (page reload) does not happen. - //return false; - } + title : _l( 'Delete' ), + href : delete_url, + id : id, + icon_class : 'delete', + on_click : function() { + // ...bler... tooltips being left behind in DOM (hover out never called on deletion) + self.$el.find( '.menu-button.delete' ).trigger( 'mouseout' ); + self.model[ 'delete' ](); + } }; if( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ){ deleteBtnData = { @@ -202,7 +161,7 @@ //TODO: use HDABaseView and select/replace base on this switch _.extend( modelData, { dbkey_unknown_and_editable : true }); } - return HDABaseView.templates.hdaSummary( modelData ); + return hdaBase.HDABaseView.templates.hdaSummary( modelData ); }, // ......................................................................... primary actions @@ -210,7 +169,7 @@ * @returns {jQuery} rendered DOM */ _render_errButton : function(){ - if( this.model.get( 'state' ) !== HistoryDatasetAssociation.STATES.ERROR ){ + if( this.model.get( 'state' ) !== hdaModel.HistoryDatasetAssociation.STATES.ERROR ){ this.errButton = null; return null; } @@ -378,8 +337,7 @@ //TODO: these should be a sub-MV _render_tagButton : function(){ //TODO: check for User - if( !( this.model.hasData() ) - || ( !this.urls.tags.get ) ){ + if( !this.hasUser || !this.urls.tags.get ){ this.tagButton = null; return null; } @@ -399,8 +357,7 @@ //TODO: these should be a sub-MV _render_annotateButton : function(){ //TODO: check for User - if( !( this.model.hasData() ) - || ( !this.urls.annotation.get ) ){ + if( !this.hasUser || !this.urls.annotation.get ){ this.annotateButton = null; return null; } @@ -417,8 +374,8 @@ /** Render area to display tags. * @returns {jQuery} rendered DOM */ - //TODO: into sub-MV - //TODO: check for User +//TODO: into sub-MV +//TODO: check for User _render_tagArea : function(){ if( !this.urls.tags.set ){ return null; } //TODO: move to mvc/tags.js @@ -430,8 +387,8 @@ /** Render area to display annotation. * @returns {jQuery} rendered DOM */ - //TODO: into sub-MV - //TODO: check for User +//TODO: into sub-MV +//TODO: check for User _render_annotationArea : function(){ if( !this.urls.annotation.get ){ return null; } //TODO: move to mvc/annotations.js @@ -447,7 +404,7 @@ * @see HDABaseView#_render_body_error */ _render_body_error : function( parent ){ - HDABaseView.prototype._render_body_error.call( this, parent ); + hdaBase.HDABaseView.prototype._render_body_error.call( this, parent ); var primaryActions = parent.find( '#primary-actions-' + this.model.get( 'id' ) ); primaryActions.prepend( this._render_errButton() ); }, @@ -498,11 +455,21 @@ /** event map */ events : { 'click .historyItemTitle' : 'toggleBodyVisibility', + 'click .historyItemUndelete' : function( ev ){ this.model.undelete(); return false; }, + 'click .historyItemUnhide' : function( ev ){ this.model.unhide(); return false; }, + 'click .historyItemPurge' : 'confirmPurge', + 'click a.icon-button.tags' : 'loadAndDisplayTags', 'click a.icon-button.annotate' : 'loadAndDisplayAnnotation' }, // ......................................................................... STATE CHANGES / MANIPULATION + confirmPurge : function _confirmPurge( ev ){ + //TODO: confirm dialog + this.model.purge({ url: this.urls.purge }); + return false; + }, + /** Find the tag area and, if initial: load the html (via ajax) for displaying them; otherwise, unhide/hide */ //TODO: into sub-MV @@ -523,30 +490,29 @@ url: this.urls.tags.get, error: function( xhr, status, error ){ view.log( "Tagging failed", xhr, status, error ); - view.trigger( 'error', view, xhr, { url: view.urls.tags.get }, _l( "Tagging failed" ) ); + view.trigger( 'error', view, xhr, {}, _l( "Tagging failed" ) ); }, success: function(tag_elt_html) { tagElt.html(tag_elt_html); tagElt.find("[title]").tooltip(); - tagArea.slideDown("fast"); + tagArea.slideDown( view.fxSpeed ); } }); } else { // Tag element is filled; show. - tagArea.slideDown("fast"); + tagArea.slideDown( view.fxSpeed ); } } else { // Hide. - tagArea.slideUp("fast"); + tagArea.slideUp( view.fxSpeed ); } return false; }, /** Find the annotation area and, if initial: load the html (via ajax) for displaying them; otherwise, unhide/hide */ - //TODO: into sub-MV loadAndDisplayAnnotation : function( event ){ - //TODO: this is a drop in from history.mako - should use MV as well +//TODO: this is a drop in from history.mako - should use MV as well this.log( this + '.loadAndDisplayAnnotation', event ); var view = this, annotationArea = this.$el.find( '.annotation-area' ), @@ -559,10 +525,9 @@ // Need to fill annotation element. $.ajax({ url: this.urls.annotation.get, - error: function( xhr, status, message ){ - view.log( "Annotation failed", xhr, status, message ); - view.trigger( 'error', - view, xhr, { url: view.urls.annotation.get }, _l( "Annotation failed" ) ); + error: function(){ + view.log( "Annotation failed", xhr, status, error ); + view.trigger( 'error', view, xhr, {}, _l( "Annotation failed" ) ); }, success: function( htmlFromAjax ){ if( htmlFromAjax === "" ){ @@ -576,16 +541,16 @@ setAnnotationUrl, "new_annotation", 18, true, 4 ); - annotationArea.slideDown("fast"); + annotationArea.slideDown( view.fxSpeed ); } }); } else { - annotationArea.slideDown("fast"); + annotationArea.slideDown( view.fxSpeed ); } } else { // Hide. - annotationArea.slideUp("fast"); + annotationArea.slideUp( view.fxSpeed ); } return false; }, @@ -712,6 +677,6 @@ //============================================================================== -//return { -// HDAView : HDAView, -//};}); +return { + HDAEditView : HDAEditView, +};}); diff -r 6882fa888d10b469524669325a547a2c0f6c7e41 -r 4f1c25230dd009efd1f04f8d7a74d83733f8b75a static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -1,6 +1,5 @@ -//define([ -// "../mvc/base-mvc" -//], function(){ +define([ +], function(){ //============================================================================== /** @class (HDA) model for a Galaxy dataset * related to a history. @@ -34,6 +33,13 @@ name : '(unnamed dataset)', // one of HistoryDatasetAssociation.STATES state : 'new', + + deleted : false, + visible : true, + + accessible : true, + purged : false, + // sniffed datatype (sam, tabular, bed, etc.) data_type : null, // size in bytes @@ -44,37 +50,67 @@ meta_files : [], misc_blurb : '', - misc_info : '', - - deleted : false, - purged : false, - visible : true, - accessible : true + misc_info : '' }, /** fetch location of this history in the api */ urlRoot: 'api/histories/', url : function(){ - //TODO: get this via url router return this.urlRoot + this.get( 'history_id' ) + '/contents/' + this.get( 'id' ); - //TODO: this breaks on save() }, + urls : function(){ + var id = this.get( 'id' ); + if( !id ){ return {}; } + var urls = { + 'delete' : '/datasets/' + id + '/delete_async', + 'purge' : '/datasets/' + id + '/purge_async', + 'unhide' : '/datasets/' + id + '/unhide', + 'undelete' : '/datasets/' + id + '/undelete', + + 'display' : '/datasets/' + id + '/display/?preview=True', + 'download' : '/datasets/' + id + '/display?to_ext=' + this.get( 'file_ext' ), + 'edit' : '/datasets/' + id + '/edit', + 'report_error': '/dataset/errors?id=' + id, + 'rerun' : '/tool_runner/rerun?id=' + id, + 'show_params': '/datasets/' + id + '/show_params', + 'visualization': '/visualization', + + 'annotation': { 'get': '/dataset/get_annotation_async?id=' + id, + 'set': '/dataset/annotate_async?id=' + id }, + 'tags' : { 'get': '/tag/get_tagging_elt_async?item_id=' + id + '&item_class=HistoryDatasetAssociation', + 'set': '/tag/retag?item_id=' + id + '&item_class=HistoryDatasetAssociation' } + }; + //'meta_download': '/dataset/get_metadata_file?hda_id=%3C%25%3D+id+%25%3E&metadata_name=%3C%25%3D+file_type+%25%3E', + var meta_files = this.get( 'meta_files' ); + if( meta_files ){ + urls.meta_download = _.map( meta_files, function( meta_file ){ + return { + //url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), + url : '/dataset/get_metadata_file?hda_id=' + id + '&metadata_name=' + meta_file.file_type, + file_type : meta_file.file_type + }; + }); + } + return urls; + }, + /** Set up the model, determine if accessible, bind listeners * @see Backbone.Model#initialize */ - //TODO:? use initialize (or validate) to check purged AND deleted -> purged XOR deleted - initialize : function(){ + initialize : function( data ){ this.log( this + '.initialize', this.attributes ); this.log( '\tparent history_id: ' + this.get( 'history_id' ) ); - // (curr) only handles changing state of non-accessible hdas to STATES.NOT_VIEWABLE //!! this state is not in trans.app.model.Dataset.states - set it here - - //TODO: change to server side. if( !this.get( 'accessible' ) ){ this.set( 'state', HistoryDatasetAssociation.STATES.NOT_VIEWABLE ); } + this._setUpListeners(); + }, + + _setUpListeners : function(){ // if the state has changed and the new state is a ready state, fire an event this.on( 'change:state', function( currModel, newState ){ this.log( this + ' has changed state:', currModel, newState ); @@ -82,16 +118,9 @@ this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); } }); - - // debug on change events - //this.on( 'change', function( currModel, changedList ){ - // this.log( this + ' has changed:', currModel, changedList ); - //}); - //this.bind( 'all', function( event ){ - // this.log( this + '', arguments ); - //}); }, + // ........................................................................ common queries /** Is this hda deleted or purged? */ isDeletedOrPurged : function(){ @@ -117,24 +146,21 @@ return isVisible; }, + hidden : function(){ + return !this.get( 'visible' ); + }, + /** Is this HDA in a 'ready' state; where 'Ready' states are states where no * processing (for the ds) is left to do on the server. - * Currently: NEW, OK, EMPTY, FAILED_METADATA, NOT_VIEWABLE, DISCARDED, - * and ERROR */ inReadyState : function(){ - var state = this.get( 'state' ); - //TODO: to list inclusion test - //TODO: class level readyStates list - return ( - this.isDeletedOrPurged() - || ( state === HistoryDatasetAssociation.STATES.OK ) - || ( state === HistoryDatasetAssociation.STATES.EMPTY ) - || ( state === HistoryDatasetAssociation.STATES.FAILED_METADATA ) - || ( state === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( state === HistoryDatasetAssociation.STATES.DISCARDED ) - || ( state === HistoryDatasetAssociation.STATES.ERROR ) - ); + var ready = _.contains( HistoryDatasetAssociation.READY_STATES, this.get( 'state' ) ); + return ( this.isDeletedOrPurged() || ready ); + }, + + hasDetails : function(){ + //?? this may not be reliable + return _.has( this.attributes, 'genome_build' ); }, /** Convenience function to match hda.has_data. @@ -144,6 +170,64 @@ return ( this.get( 'file_size' ) > 0 ); }, + // ........................................................................ ajax + 'delete' : function _delete( options ){ + return this.save( { deleted: true }, options ); + }, + undelete : function _undelete( options ){ + return this.save( { deleted: false }, options ); + }, + + hide : function _hide( options ){ + return this.save( { visible: false }, options ); + }, + unhide : function _uhide( options ){ + return this.save( { visible: true }, options ); + }, + + purge : function _purge( options ){ + //TODO: ideally this would be a DELETE call to the api + // using purge async for now + var hda = this, + xhr = jQuery.ajax( options ); + xhr.done( function( message, status, responseObj ){ + hda.set( 'purged', true ); + }); + xhr.fail( function( xhr, status, message ){ + // Exception messages are hidden within error page including: '...not allowed in this Galaxy instance.' + // unbury and re-add to xhr + var error = _l( "Unable to purge this dataset" ); + var messageBuriedInUnfortunatelyFormattedError = ( 'Removal of datasets by users ' + + 'is not allowed in this Galaxy instance' ); + if( xhr.responseJSON && xhr.responseJSON.error ){ + error = xhr.responseJSON.error; + } else if( xhr.responseText.indexOf( messageBuriedInUnfortunatelyFormattedError ) !== -1 ){ + error = messageBuriedInUnfortunatelyFormattedError; + } + xhr.responseText = error; + hda.trigger( 'error', hda, xhr, options, _l( error ), { error: error } ); + }); + }, + + // ........................................................................ sorting/filtering + searchKeys : [ + 'name', 'file_ext', 'genome_build', 'misc_blurb', 'misc_info', 'annotation', 'tags' + ], + + search : function( searchFor ){ + var model = this; + searchFor = searchFor.toLowerCase(); + return _.filter( this.searchKeys, function( key ){ + var attr = model.get( key ); + return ( _.isString( attr ) && attr.toLowerCase().indexOf( searchFor ) !== -1 ); + }); + }, + + matches : function( matchesWhat ){ + return !!this.search( matchesWhat ).length; + }, + + // ........................................................................ misc /** String representation */ toString : function(){ @@ -165,8 +249,6 @@ UPLOAD : 'upload', /** the job that will produce the dataset queued in the runner */ QUEUED : 'queued', - /** the job that will produce the dataset paused */ - PAUSED : 'paused', /** the job that will produce the dataset is running */ RUNNING : 'running', /** metadata for the dataset is being discovered/set */ @@ -180,6 +262,8 @@ /** has successfully completed running */ OK : 'ok', + /** the job that will produce the dataset paused */ + PAUSED : 'paused', /** metadata discovery/setting failed or errored (but otherwise ok) */ FAILED_METADATA : 'failed_metadata', /** not accessible to the current user (i.e. due to permissions) */ @@ -190,6 +274,24 @@ ERROR : 'error' }; +HistoryDatasetAssociation.READY_STATES = [ + HistoryDatasetAssociation.STATES.NEW, + HistoryDatasetAssociation.STATES.OK, + HistoryDatasetAssociation.STATES.EMPTY, + HistoryDatasetAssociation.STATES.PAUSED, + HistoryDatasetAssociation.STATES.FAILED_METADATA, + HistoryDatasetAssociation.STATES.NOT_VIEWABLE, + HistoryDatasetAssociation.STATES.DISCARDED, + HistoryDatasetAssociation.STATES.ERROR +]; + +HistoryDatasetAssociation.NOT_READY_STATES = [ + HistoryDatasetAssociation.STATES.UPLOAD, + HistoryDatasetAssociation.STATES.QUEUED, + HistoryDatasetAssociation.STATES.RUNNING, + HistoryDatasetAssociation.STATES.SETTING_METADATA +]; + //============================================================================== /** @class Backbone collection of (HDA) models * @@ -204,83 +306,35 @@ ///** logger used to record this.log messages, commonly set to console */ //// comment this out to suppress log output //logger : console, + urlRoot : '/api/histories', + url : function(){ + return this.urlRoot + '/' + this.historyId + '/contents'; + }, /** Set up. * @see Backbone.Collection#initialize */ - initialize : function(){ - //this.bind( 'all', function( event ){ - // this.log( this + '', arguments ); - //}); + initialize : function( models, options ){ + options = options || {}; + this.historyId = options.historyId; + this._setUpListeners(); }, + _setUpListeners : function(){ + }, + + // ........................................................................ common queries /** Get the ids of every hda in this collection - * @returns array of encoded ids + * @returns array of encoded ids */ ids : function(){ return this.map( function( hda ){ return hda.id; }); }, - /** Get the hda with the given hid - * @param {Int} hid the hid to search for - * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found - */ - getByHid : function( hid ){ - return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) ); - }, - - /** If the given hid is in the collection, return it's index. If not, return the insertion point it would need. - * NOTE: assumes hids are unique and valid - * @param {Int} hid the hid to find or create. If hid is 0, null, undefined: return the last hid + 1 - * @returns the collection index of the existing hda or an insertion point if it doesn't exist - */ - hidToCollectionIndex : function( hid ){ - // if the hid is 0, null, undefined: assume a request for a new hid (return the last index) - if( !hid ){ - return this.models.length; - } - - var endingIndex = this.models.length - 1; - //TODO: prob. more efficient to cycle backwards through these (assuming ordered by hid) - for( var i=endingIndex; i>=0; i-- ){ - var hdaHid = this.at( i ).get( 'hid' ); - //this.log( i, 'hdaHid:', hdaHid ); - if( hdaHid === hid ){ - //this.log( '\t match:', hdaHid, hid, ' returning:', i ); - return i; - } - if( hdaHid < hid ){ - //this.log( '\t past it, returning:', ( i + 1 ) ); - return i + 1; - } - } - return null; - }, - - /** Get every 'shown' hda in this collection based on show_deleted/hidden - * @param {Boolean} show_deleted are we showing deleted hdas? - * @param {Boolean} show_hidden are we showing hidden hdas? - * @returns array of hda models - * @see HistoryDatasetAssociation#isVisible - */ - getVisible : function( show_deleted, show_hidden ){ - return this.filter( function( item ){ return item.isVisible( show_deleted, show_hidden ); }); - }, - - /** For each possible hda state, get an array of all hda ids in that state - * @returns a map of states -> hda ids - * @see HistoryDatasetAssociation#STATES - */ - getStateLists : function(){ - var stateLists = {}; - _.each( _.values( HistoryDatasetAssociation.STATES ), function( state ){ - stateLists[ state ] = []; + notReady : function(){ + return this.filter( function( hda ){ + return !hda.inReadyState(); }); - //NOTE: will err on unknown state - this.each( function( item ){ - stateLists[ item.get( 'state' ) ].push( item.get( 'id' ) ); - }); - return stateLists; }, /** Get the id of every hda in this collection not in a 'ready' state (running). @@ -297,26 +351,55 @@ return idList; }, - /** Update (fetch) the data of the hdas with the given ids. - * @param {String[]} ids an array of hda ids to update - * @returns {HistoryDatasetAssociation[]} hda models that were updated - * @see HistoryDatasetAssociation#fetch + /** Get the hda with the given hid + * @param {Int} hid the hid to search for + * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found */ - update : function( ids ){ - this.log( this + 'update:', ids ); + getByHid : function( hid ){ + return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) ); + }, - if( !( ids && ids.length ) ){ return []; } + /** Get every 'shown' hda in this collection based on show_deleted/hidden + * @param {Boolean} show_deleted are we showing deleted hdas? + * @param {Boolean} show_hidden are we showing hidden hdas? + * @returns array of hda models + * @see HistoryDatasetAssociation#isVisible + */ + getVisible : function( show_deleted, show_hidden ){ + return this.filter( function( item ){ return item.isVisible( show_deleted, show_hidden ); }); + }, - var collection = this, - updatedHdas = null; - _.each( ids, function( id, index ){ - var hda = collection.get( id ); - if( hda ){ - hda.fetch(); - updatedHdas.push( hda ); - } + // ........................................................................ ajax + fetchAllDetails : function(){ + return this.fetch({ data : { details : 'all' } }); + }, + + // ........................................................................ sorting/filtering + matches : function( matchesWhat ){ + return this.filter( function( hda ){ + return hda.matches( matchesWhat ); }); - return updatedHdas; + }, + + // ........................................................................ misc + set : function( models, options ){ + // arrrrrrrrrrrrrrrrrg... + // override to get a correct/smarter merge when incoming data is partial (e.g. stupid backbone) + // w/o this partial models from the server will fill in missing data with model defaults + // and overwrite existing data on the client + // see Backbone.Collection.set and _prepareModel + var collection = this; + models = _.map( models, function( model ){ + var existing = collection.get( model.id ); + if( !existing ){ return model; } + + // merge the models _BEFORE_ calling the superclass version + var merged = existing.toJSON(); + _.extend( merged, model ); + return merged; + }); + // now call superclass when the data is filled + Backbone.Collection.prototype.set.call( this, models, options ); }, /** String representation. */ @@ -326,7 +409,7 @@ }); //============================================================================== -//return { -// HistoryDatasetAssociation : HistoryDatasetAssociation, -// HDACollection : HDACollection, -//};}); +return { + HistoryDatasetAssociation : HistoryDatasetAssociation, + HDACollection : HDACollection +};}); This diff is so big that we needed to truncate the remainder. 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

commit/galaxy-central: dannon: Datatypes controller should allow anonymous access.
by commits-noreply＠bitbucket.org 21 Oct '13

21 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/81880a04e6e7/ Changeset: 81880a04e6e7 Branch: next-stable User: dannon Date: 2013-10-21 22:16:01 Summary: Datatypes controller should allow anonymous access. Affected #: 1 file diff -r 000d11c7ce7e6125998d7095a247774a150c120e -r 81880a04e6e79d944a6d9c225b36417114cd38ec lib/galaxy/webapps/galaxy/api/datatypes.py --- a/lib/galaxy/webapps/galaxy/api/datatypes.py +++ b/lib/galaxy/webapps/galaxy/api/datatypes.py @@ -4,13 +4,12 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController -from galaxy.datatypes.registry import Registry import logging log = logging.getLogger( __name__ ) class DatatypesController( BaseAPIController ): - @web.expose_api + @web.expose_api_anonymous def index( self, trans, **kwd ): """ GET /api/datatypes @@ -18,8 +17,7 @@ """ try: return trans.app.datatypes_registry.upload_file_formats - except Exception, exception: log.error( 'could not get datatypes: %s', str( exception ), exc_info=True ) trans.response.status = 500 - return { 'error': str( exception ) } \ No newline at end of file + return { 'error': str( exception ) } 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

commit/galaxy-central: dannon: Datatypes controller should allow anonymous access.
by commits-noreply＠bitbucket.org 21 Oct '13

21 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6882fa888d10/ Changeset: 6882fa888d10 User: dannon Date: 2013-10-21 22:16:01 Summary: Datatypes controller should allow anonymous access. Affected #: 1 file diff -r d1fb4c641a79eb5451320397d4e22068d1c95bcf -r 6882fa888d10b469524669325a547a2c0f6c7e41 lib/galaxy/webapps/galaxy/api/datatypes.py --- a/lib/galaxy/webapps/galaxy/api/datatypes.py +++ b/lib/galaxy/webapps/galaxy/api/datatypes.py @@ -4,13 +4,12 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController -from galaxy.datatypes.registry import Registry import logging log = logging.getLogger( __name__ ) class DatatypesController( BaseAPIController ): - @web.expose_api + @web.expose_api_anonymous def index( self, trans, **kwd ): """ GET /api/datatypes @@ -18,8 +17,7 @@ """ try: return trans.app.datatypes_registry.upload_file_formats - except Exception, exception: log.error( 'could not get datatypes: %s', str( exception ), exc_info=True ) trans.response.status = 500 - return { 'error': str( exception ) } \ No newline at end of file + return { 'error': str( exception ) } 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: Merge stable branch.
by commits-noreply＠bitbucket.org 21 Oct '13

21 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1fb4c641a79/ Changeset: d1fb4c641a79 User: natefoo Date: 2013-10-21 16:10:54 Summary: Merge stable branch. Affected #: 1 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.

1 0

commit/galaxy-central: jgoecks: Trackster: add needed height config preference.
by commits-noreply＠bitbucket.org 19 Oct '13

19 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2778e2829d28/ Changeset: 2778e2829d28 User: jgoecks Date: 2013-10-19 21:59:43 Summary: Trackster: add needed height config preference. Affected #: 1 file diff -r 95815478f355009d925ea91e95e4db0a9d887ded -r 2778e2829d28bb053b12d47c6615c98052134a83 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -4220,7 +4220,8 @@ { key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true }, { key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true }, { key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 }, - { key: 'mode', type: 'string', default_value: this.mode, hidden: true } + { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, + { key: 'height', type: 'int', default_value: 0, hidden: true } ] ), config_onchange: function() { 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

commit/galaxy-central: greg: Enhance the Repair repository feature for tool shed repositories installed into Galaxy to handle repository and tool dependencies that are not only in an error status, but may also have one of the "installing" status values. This feature will now properly handle dependencies that are stuck in one of these installing states foe some reason. Existing system processes are not automatically killed (if they happen to exist), but warning messages are displayed.
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/95815478f355/ Changeset: 95815478f355 User: greg Date: 2013-10-18 22:43:29 Summary: Enhance the Repair repository feature for tool shed repositories installed into Galaxy to handle repository and tool dependencies that are not only in an error status, but may also have one of the "installing" status values. This feature will now properly handle dependencies that are stuck in one of these installing states foe some reason. Existing system processes are not automatically killed (if they happen to exist), but warning messages are displayed. Affected #: 7 files diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3679,7 +3679,11 @@ """Return the repository's repository dependencies that are currently being installed.""" required_repositories_being_installed = [] for required_repository in self.repository_dependencies: - if required_repository.status == self.installation_status.INSTALLING: + if required_repository.status in [ self.installation_status.CLONING, + self.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES, + self.installation_status.INSTALLING_TOOL_DEPENDENCIES, + self.installation_status.LOADING_PROPRIETARY_DATATYPES, + self.installation_status.SETTING_TOOL_VERSIONS ]: required_repositories_being_installed.append( required_repository ) return required_repositories_being_installed diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded 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 @@ -1185,6 +1185,21 @@ message=message, status=status ) + @web.expose + @web.require_admin + def repair_tool_shed_repositories( self, trans, tool_shed_repositories, repo_info_dicts, **kwd ): + """Repair specified tool shed repositories.""" + # The received lists of tool_shed_repositories and repo_info_dicts are ordered. + for index, tool_shed_repository in enumerate( tool_shed_repositories ): + repo_info_dict = repo_info_dicts[ index ] + repair_dict = repository_util.repair_tool_shed_repository( trans, + tool_shed_repository, + encoding_util.tool_shed_encode( repo_info_dict ) ) + tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ] + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='monitor_repository_installation', + tool_shed_repository_ids=tsr_ids_for_monitoring ) ) + @web.json def repository_installation_status_updates( self, trans, ids=None, status_list=None ): # Avoid caching @@ -1208,21 +1223,6 @@ @web.expose @web.require_admin - def repair_tool_shed_repositories( self, trans, tool_shed_repositories, repo_info_dicts, **kwd ): - """Repair specified tool shed repositories.""" - # The received lists of tool_shed_repositories and repo_info_dicts are ordered. - for index, tool_shed_repository in enumerate( tool_shed_repositories ): - repo_info_dict = repo_info_dicts[ index ] - repair_dict = repository_util.repair_tool_shed_repository( trans, - tool_shed_repository, - encoding_util.tool_shed_encode( repo_info_dict ) ) - tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ] - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='monitor_repository_installation', - tool_shed_repository_ids=tsr_ids_for_monitoring ) ) - - @web.expose - @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): """ Select or change the tool panel section to contain the tools included in the tool shed repository being reinstalled. If there are updates diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -101,33 +101,7 @@ class StatusColumn( grids.TextColumn ): def get_value( self, trans, grid, tool_shed_repository ): - status_label = tool_shed_repository.status - if tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING, - trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS, - trans.model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES, - trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES, - trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]: - bgcolor = trans.model.ToolShedRepository.states.INSTALLING - elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, - trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: - bgcolor = trans.model.ToolShedRepository.states.UNINSTALLED - elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR ]: - bgcolor = trans.model.ToolShedRepository.states.ERROR - elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.DEACTIVATED ]: - bgcolor = trans.model.ToolShedRepository.states.WARNING - elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.INSTALLED ]: - if tool_shed_repository.missing_repository_dependencies: - bgcolor = trans.model.ToolShedRepository.states.WARNING - status_label = '%s, missing repository dependencies' % status_label - elif tool_shed_repository.missing_tool_dependencies: - bgcolor = trans.model.ToolShedRepository.states.WARNING - status_label = '%s, missing tool dependencies' % status_label - else: - bgcolor = trans.model.ToolShedRepository.states.OK - else: - bgcolor = trans.model.ToolShedRepository.states.ERROR - rval = '<div class="count-box state-color-%s">%s</div>' % ( bgcolor, status_label ) - return rval + return suc.get_tool_shed_repository_status_label( trans, tool_shed_repository ) class ToolShedColumn( grids.TextColumn ): diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -758,7 +758,6 @@ log.debug( error_message ) repair_dict [ repository.name ] = error_message elif repository.status not in [ trans.model.ToolShedRepository.installation_status.INSTALLED ]: - # TODO: this may cause problems if the repository is currently being installed. shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) # Reset the repository attributes to the New state for installation. if metadata: @@ -793,7 +792,8 @@ work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-itdep" ) # Reset missing tool dependencies. for tool_dependency in repository.missing_tool_dependencies: - if tool_dependency.status in [ trans.model.ToolDependency.installation_status.ERROR ]: + if tool_dependency.status in [ trans.model.ToolDependency.installation_status.ERROR, + trans.model.ToolDependency.installation_status.INSTALLING ]: tool_dependency_util.set_tool_dependency_attributes( trans, tool_dependency, trans.model.ToolDependency.installation_status.UNINSTALLED, diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1282,6 +1282,53 @@ log.exception( "Error attempting to get tool shed status for installed repository %s: %s" % ( str( repository.name ), str( e ) ) ) return {} +def get_tool_shed_repository_status_label( trans, tool_shed_repository=None, name=None, owner=None, changeset_revision=None, repository_clone_url=None ): + """Return a color-coded label for the status of the received tool-shed_repository installed into Galaxy.""" + if tool_shed_repository is None: + if name is not None and owner is not None and repository_clone_url is not None: + tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) + tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( trans.app, + tool_shed, + name, + owner, + changeset_revision ) + if tool_shed_repository: + status_label = tool_shed_repository.status + if tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING, + trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS, + trans.model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES, + trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES, + trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]: + bgcolor = trans.model.ToolShedRepository.states.INSTALLING + elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, + trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: + bgcolor = trans.model.ToolShedRepository.states.UNINSTALLED + elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR ]: + bgcolor = trans.model.ToolShedRepository.states.ERROR + elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.DEACTIVATED ]: + bgcolor = trans.model.ToolShedRepository.states.WARNING + elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.INSTALLED ]: + if tool_shed_repository.repository_dependencies_being_installed: + bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, %s' % ( status_label, trans.model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES ) + elif tool_shed_repository.missing_repository_dependencies: + bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, missing repository dependencies' % status_label + elif tool_shed_repository.tool_dependencies_being_installed: + bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, %s' % (status_label, trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + elif tool_shed_repository.missing_tool_dependencies: + bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, missing tool dependencies' % status_label + else: + bgcolor = trans.model.ToolShedRepository.states.OK + else: + bgcolor = trans.model.ToolShedRepository.states.ERROR + else: + bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, unknown status' % status_label + return '<div class="count-box state-color-%s">%s</div>' % ( bgcolor, status_label ) + def get_updated_changeset_revisions( trans, name, owner, changeset_revision ): """ Return a string of comma-separated changeset revision hashes for all available updates to the received changeset revision for the repository diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded templates/admin/tool_shed_repository/repair_repository.mako --- a/templates/admin/tool_shed_repository/repair_repository.mako +++ b/templates/admin/tool_shed_repository/repair_repository.mako @@ -18,27 +18,56 @@ %endif <div class="warningmessage"> - The following repositories will be inspected and repaired in the order listed to ensure each repository and all of it's tool dependencies are correctly - installed. Click <b>Repair</b> to inspect and repair these repositories. + <p> + The following repositories will be inspected and repaired in the order listed to ensure each repository and all of it's tool dependencies are + correctly installed. + </p> + <p> + Existing system processes associated with repositories or tool dependencies that are currently being installed will not be automatically + terminated. If possible, make sure no installation processes are still running for repositories whose status is or includes <b>cloning</b>, + <b>setting tool versions</b>, <b>installing repository dependencies</b>, or <b>installing tool dependencies</b> before clicking the <b>Repair</b> + button. + </p> + <p> + All repositories that do not display an <b>Installed</b> status will be removed from disk and reinstalled. + </p> + <p> + Click <b>Repair</b> to inspect and repair these repositories. + </p></div><div class="toolForm"> - <div class="toolFormTitle">Repair tool shed repository '${repository.name}'</div> - <br/><br/> - <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ), repair_dict=encoded_repair_dict )}" method="post" > - <% ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) %> + <div class="toolFormTitle">Repair tool shed repository <b>${repository.name}</b></div> + <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <input type="hidden" name="repair_dict" value="${encoded_repair_dict}"/> + <% + from tool_shed.util.shed_util_common import get_tool_shed_repository_status_label + ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) + %><table class="grid"> - <tr><th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Owner</th><th bgcolor="#D8D8D8">Changeset revision</th></tr> + <tr> + <th bgcolor="#D8D8D8">Name</th> + <th bgcolor="#D8D8D8">Owner</th> + <th bgcolor="#D8D8D8">Changeset revision</th> + <th bgcolor="#D8D8D8">Status</th> + </tr> %for repo_info_dict in ordered_repo_info_dicts: <% for name, repo_info_tuple in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple break + status_label = get_tool_shed_repository_status_label( trans, + tool_shed_repository=None, + name=name, + owner=repository_owner, + changeset_revision=changeset_revision, + repository_clone_url=repository_clone_url ) %><tr><td>${name | h}</td><td>${repository_owner | h}</td><td>${changeset_revision | h}</td> + <td>${status_label}</td></tr> %endfor </table> diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -969,7 +969,7 @@ self.check_for_strings( [ 'Metadata has been reset' ] ) def reset_metadata_on_selected_repositories( self, repository_ids ): - self.visit_url( '/admin/reset_metadata_on_selected_repositories' ) + self.visit_url( '/admin/reset_metadata_on_selected_repositories_in_tool_shed' ) kwd = dict( repository_ids=repository_ids ) self.submit_form( form_no=1, button="reset_metadata_on_selected_repositories_button", **kwd ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Tools API, show: remove unused flag, show io_details/link_details where possible; ToolParameters: improve polymorphism in to_dict
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/068afb09a7ba/ Changeset: 068afb09a7ba User: carlfeberhard Date: 2013-10-18 21:37:59 Summary: Tools API, show: remove unused flag, show io_details/link_details where possible; ToolParameters: improve polymorphism in to_dict Affected #: 2 files diff -r 799dca8ebe2375f962603382380dfc1da720764f -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -17,6 +17,7 @@ log = logging.getLogger(__name__) + class ToolParameter( object, Dictifiable ): """ Describes a parameter accepted by a tool. This is just a simple stub at the @@ -172,9 +173,10 @@ def to_dict( self, trans, view='collection', value_mapper=None ): """ to_dict tool parameter. This can be overridden by subclasses. """ - tool_dict = super( ToolParameter, self ).to_dict() - tool_dict[ 'html' ] = urllib.quote( self.get_html( trans ) ) + #TODO: removing html as it causes a lot of errors on subclasses - needs histories, etc. + #tool_dict[ 'html' ] = urllib.quote( self.get_html( trans ) ) + tool_dict[ 'model_class' ] = self.__class__.__name__ if hasattr( self, 'value' ): tool_dict[ 'value' ] = self.value return tool_dict @@ -193,6 +195,7 @@ else: return parameter_types[param_type]( tool, param ) + class TextToolParameter( ToolParameter ): """ Parameter that can take on any text value. @@ -210,12 +213,14 @@ self.size = elem.get( 'size' ) self.value = elem.get( 'value' ) self.area = string_as_bool( elem.get( 'area', False ) ) + def get_html_field( self, trans=None, value=None, other_values={} ): if value is None: value = self.value if self.area: return form_builder.TextArea( self.name, self.size, value ) else: return form_builder.TextField( self.name, self.size, value ) + def get_initial_value( self, trans, context, history=None ): return self.value @@ -266,6 +271,7 @@ if isinstance( value, int ): value = str( value ) return super( IntegerToolParameter, self ).get_html_field( trans=trans, value=value, other_values=other_values ) + def from_html( self, value, trans=None, other_values={} ): try: return int( value ) @@ -273,12 +279,14 @@ if not value and self.optional: return "" raise ValueError( "An integer is required" ) + def to_string( self, value, app ): """Convert a value to a string representation suitable for persisting""" if value is None: return "" else: return str( value ) + def to_python( self, value, app ): try: return int( value ) @@ -286,12 +294,14 @@ if not value and self.optional: return None raise err + def get_initial_value( self, trans, context, history=None ): if self.value: return int( self.value ) else: return None + class FloatToolParameter( TextToolParameter ): """ Parameter that takes a real number value. @@ -334,10 +344,12 @@ raise ValueError( "A real number is required" ) if self.min and self.max: self.validators.append( validation.InRangeValidator( None, self.min, self.max ) ) + def get_html_field( self, trans=None, value=None, other_values={} ): if isinstance( value, float ): value = str( value ) return super( FloatToolParameter, self ).get_html_field( trans=trans, value=value, other_values=other_values ) + def from_html( self, value, trans=None, other_values={} ): try: return float( value ) @@ -345,12 +357,14 @@ if not value and self.optional: return "" raise ValueError( "A real number is required" ) + def to_string( self, value, app ): """Convert a value to a string representation suitable for persisting""" if value is None: return "" else: return str( value ) + def to_python( self, value, app ): try: return float( value ) @@ -358,12 +372,14 @@ if not value and self.optional: return None raise err + def get_initial_value( self, trans, context, history=None ): try: return float( self.value ) except: return None + class BooleanToolParameter( ToolParameter ): """ Parameter that takes one of two values. @@ -387,31 +403,39 @@ self.truevalue = elem.get( 'truevalue', 'true' ) self.falsevalue = elem.get( 'falsevalue', 'false' ) self.checked = string_as_bool( elem.get( 'checked' ) ) + def get_html_field( self, trans=None, value=None, other_values={} ): checked = self.checked if value is not None: checked = form_builder.CheckboxField.is_checked( value ) return form_builder.CheckboxField( self.name, checked, refresh_on_change = self.refresh_on_change ) + def from_html( self, value, trans=None, other_values={} ): return form_builder.CheckboxField.is_checked( value ) + def to_html_value( self, value, app ): if value: return [ 'true', 'true' ] else: return [ 'true' ] + def to_python( self, value, app ): return ( value == 'True' ) + def get_initial_value( self, trans, context, history=None ): return self.checked + def to_param_dict_string( self, value, other_values={} ): if value: return self.truevalue else: return self.falsevalue + @property def legal_values( self ): return [ self.truevalue, self.falsevalue ] + class FileToolParameter( ToolParameter ): """ Parameter that takes an uploaded file as a value. @@ -431,8 +455,10 @@ """ ToolParameter.__init__( self, tool, elem ) self.ajax = string_as_bool( elem.get( 'ajax-upload' ) ) + def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.FileField( self.name, ajax = self.ajax, value = value ) + def from_html( self, value, trans=None, other_values={} ): # Middleware or proxies may encode files in special ways (TODO: this # should be pluggable) @@ -450,11 +476,13 @@ local_filename = local_filename ) return value + def get_required_enctype( self ): """ File upload elements require the multipart/form-data encoding """ return "multipart/form-data" + def to_string( self, value, app ): if value in [ None, '' ]: return None @@ -467,6 +495,7 @@ except: return None raise Exception( "FileToolParameter cannot be persisted" ) + def to_python( self, value, app ): if value is None: return None @@ -474,9 +503,11 @@ return value else: raise Exception( "FileToolParameter cannot be persisted" ) + def get_initial_value( self, trans, context, history=None ): return None + class FTPFileToolParameter( ToolParameter ): """ Parameter that takes a file uploaded via FTP as a value. @@ -486,36 +517,43 @@ Example: C{<param name="bins" type="file" />} """ ToolParameter.__init__( self, tool, elem ) + @property def visible( self ): if self.tool.app.config.ftp_upload_dir is None or self.tool.app.config.ftp_upload_site is None: return False return True + def get_html_field( self, trans=None, value=None, other_values={} ): if trans is None or trans.user is None: user_ftp_dir = None else: user_ftp_dir = trans.user_ftp_dir return form_builder.FTPFileField( self.name, user_ftp_dir, trans.app.config.ftp_upload_site, value = value ) + def from_html( self, value, trans=None, other_values={} ): try: assert type( value ) is list except: value = [ value ] return value + def to_string( self, value, app ): if value in [ None, '' ]: return None elif isinstance( value, unicode ) or isinstance( value, str ) or isinstance( value, list ): return value + def to_python( self, value, app ): if value is None: return None elif isinstance( value, unicode ) or isinstance( value, str ) or isinstance( value, list ): return value + def get_initial_value( self, trans, context, history=None ): return None + class HiddenToolParameter( ToolParameter ): """ Parameter that takes one of two values. @@ -532,10 +570,13 @@ def __init__( self, tool, elem ): ToolParameter.__init__( self, tool, elem ) self.value = elem.get( 'value' ) + def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.HiddenField( self.name, self.value ) + def get_initial_value( self, trans, context, history=None ): return self.value + def get_label( self ): return None @@ -543,26 +584,33 @@ ## can change, there needs to be a different way to specify this. I'm leaving ## it for now to avoid breaking any tools. + class BaseURLToolParameter( ToolParameter ): """ Returns a parameter the contains its value prepended by the current server base url. Used in all redirects. """ + def __init__( self, tool, elem ): ToolParameter.__init__( self, tool, elem ) self.value = elem.get( 'value', '' ) + def get_value( self, trans ): # url = trans.request.base + self.value url = url_for( self.value, qualified=True ) return url + def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.HiddenField( self.name, self.get_value( trans ) ) + def get_initial_value( self, trans, context, history=None ): return self.value + def get_label( self ): # BaseURLToolParameters are ultimately "hidden" parameters return None + class SelectToolParameter( ToolParameter ): """ Parameter that takes on one (or many) or a specific set of values. @@ -665,6 +713,7 @@ selected = string_as_bool( option.get( "selected", False ) ) self.static_options.append( ( option.text or value, value, selected ) ) self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.options is not None ) ) + def get_options( self, trans, other_values ): if self.options: return self.options.get_options( trans, other_values ) @@ -672,6 +721,7 @@ return eval( self.dynamic_options, self.tool.code_namespace, other_values ) else: return self.static_options + def get_legal_values( self, trans, other_values ): def _get_UnvalidatedValue_value( value ): if isinstance( value, UnvalidatedValue ): @@ -683,6 +733,7 @@ return set( v for _, v, _ in eval( self.dynamic_options, self.tool.code_namespace, other_values ) ) else: return self.legal_values + def get_html_field( self, trans=None, value=None, context={} ): # Dynamic options are not yet supported in workflow, allow # specifying the value as text for now. @@ -710,6 +761,7 @@ selected = ( optval in value ) field.add_option( text, optval, selected ) return field + def from_html( self, value, trans=None, context={} ): if self.need_late_validation( trans, context ): if self.multiple: @@ -747,11 +799,13 @@ if value not in legal_values: raise ValueError( "An invalid option was selected, please verify" ) return value + def to_html_value( self, value, app ): if isinstance( value, list ): return value else: return str( value ) + def to_param_dict_string( self, value, other_values={} ): if value is None: return "None" @@ -769,6 +823,7 @@ if isinstance( value, list ): value = self.separator.join( value ) return value + def value_to_basic( self, value, app ): if isinstance( value, UnvalidatedValue ): return { "__class__": "UnvalidatedValue", "value": value.value } @@ -778,10 +833,12 @@ # breaks multiple selection return { "__class__": "RuntimeValue" } return value + def value_from_basic( self, value, app, ignore_errors=False ): if isinstance( value, dict ) and value.get( "__class__", None ) == "UnvalidatedValue": return UnvalidatedValue( value["value"] ) return super( SelectToolParameter, self ).value_from_basic( value, app, ignore_errors=ignore_errors ) + def need_late_validation( self, trans, context ): """ Determine whether we need to wait to validate this parameters value @@ -826,6 +883,7 @@ return True # Dynamic, but all dependenceis are known and have values return False + def get_initial_value( self, trans, context, history=None ): # More working around dynamic options for workflow if self.need_late_validation( trans, context ): @@ -844,6 +902,7 @@ elif len( value ) == 1: value = value[0] return value + def value_to_display_text( self, value, app ): if isinstance( value, UnvalidatedValue ): suffix = "\n(value not yet validated)" @@ -863,6 +922,7 @@ if v in value: rval.append( t ) return "\n".join( rval ) + suffix + def get_dependencies( self ): """ Get the *names* of the other params this param depends on. @@ -876,17 +936,24 @@ d = super( SelectToolParameter, self ).to_dict( trans ) # Get options, value. - options = self.get_options( trans, [] ) - value = options[0][1] - for option in options: - if option[2]: - # Found selected option. - value = option[1] + options = [] + try: + options = self.get_options( trans, {} ) + except AssertionError, assertion: + # we dont/cant set other_values (the {} above), so params that require other params to be filled will error: + # required dependency in filter_options + # associated DataToolParam in get_column_list + pass - d.update( { - 'options': options, - 'value': value - } ) + d[ 'options' ] = options + if options: + value = options[0][1] + for option in options: + if option[2]: + # Found selected option. + value = option[1] + d[ 'value' ] = options + return d @@ -933,6 +1000,7 @@ def __init__( self, *args, **kwds ): super( GenomeBuildParameter, self ).__init__( *args, **kwds ) self.static_options = [ ( value, key, False ) for key, value in util.dbnames ] + def get_options( self, trans, other_values ): if not trans.history: yield 'unspecified', '?', False @@ -940,11 +1008,31 @@ last_used_build = trans.history.genome_build for dbkey, build_name in trans.db_builds: yield build_name, dbkey, ( dbkey == last_used_build ) + def get_legal_values( self, trans, other_values ): if not trans.history: return set( '?' ) return set( dbkey for dbkey, _ in trans.db_builds ) + def to_dict( self, trans, view='collection', value_mapper=None ): + # skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here + d = ToolParameter.to_dict( self, trans ) + + # Get options, value - options is a generator here, so compile to list + options = list( self.get_options( trans, {} ) ) + value = options[0][1] + for option in options: + if option[2]: + # Found selected option. + value = option[1] + + d.update({ + 'options': options, + 'value': value + }) + return d + + class ColumnListParameter( SelectToolParameter ): """ Select list that consists of either the total number of columns or only @@ -1081,10 +1169,13 @@ return UnvalidatedValue( self.default_value ) return self.default_value return SelectToolParameter.get_initial_value( self, trans, context ) + def get_legal_values( self, trans, other_values ): return set( self.get_column_list( trans, other_values ) ) + def get_dependencies( self ): return [ self.data_ref ] + def need_late_validation( self, trans, context ): if super( ColumnListParameter, self ).need_late_validation( trans, context ): return True @@ -1245,7 +1336,6 @@ call_other_values.update( other_values.dict ) return eval( self.dynamic_options, self.tool.code_namespace, call_other_values ) - def get_options( self, trans=None, value=None, other_values={} ): if self.is_dynamic: if self.dynamic_options: @@ -1353,6 +1443,7 @@ else: rval = sanitize_param( rval ) return rval + def get_initial_value( self, trans, context, history=None ): def recurse_options( initial_values, options ): for option in options: @@ -1407,9 +1498,26 @@ """ return self.filtered.keys() + def to_dict( self, trans, view='collection', value_mapper=None ): + # skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here + d = ToolParameter.to_dict( self, trans ) + + options = [] + try: + options = self.get_options( trans, {} ) + except KeyError, key_err: + # will sometimes error if self.is_dynamic and self.filtered + # bc we dont/cant fill out other_values above ({}) + pass + + d[ 'options' ] = options; + return d + + class DummyDataset( object ): pass + class DataToolParameter( ToolParameter ): # TODO, Nate: Make sure the following unit tests appropriately test the dataset security # components. Add as many additional tests as necessary. @@ -1720,6 +1828,7 @@ ref = ref() return ref + class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ): """ Hidden parameter that behaves as a DataToolParameter. As with all hidden @@ -1845,9 +1954,11 @@ """ def __init__( self, value ): self.value = value + def __str__( self ): return str( self.value ) + class RuntimeValue( object ): """ Wrapper to note a value that is not yet set, but will be required at diff -r 799dca8ebe2375f962603382380dfc1da720764f -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,3 +1,5 @@ +import urllib + from galaxy import web, util from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin from galaxy.visualization.genomes import GenomeRegion @@ -44,8 +46,16 @@ GET /api/tools/{tool_id} Returns tool information, including parameters and inputs. """ + io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) + link_details = util.string_as_bool( kwd.get( 'link_details', False ) ) try: - return self.app.toolbox.tools_by_id[ id ].to_dict( trans, for_display=True ) + id = urllib.unquote_plus( id ) + tool = self.app.toolbox.tools_by_id.get( id, None ) + if not tool: + trans.response.status = 404 + return { 'error': 'tool not found', 'id': id } + return tool.to_dict( trans, io_details=io_details, link_details=link_details ) + except Exception, exc: log.error( 'could not convert tool (%s) to dictionary: %s', id, str( exc ), exc_info=True ) trans.response.status = 500 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: carlfeberhard: HDA API, delete: fix namespacing on exceptions
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/799dca8ebe23/ Changeset: 799dca8ebe23 User: carlfeberhard Date: 2013-10-18 21:28:09 Summary: HDA API, delete: fix namespacing on exceptions Affected #: 1 file diff -r 99161bb83a3ec96fcc58ff14af9958fd8a19e0ce -r 799dca8ebe2375f962603382380dfc1da720764f lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -325,7 +325,8 @@ if purge: if not trans.app.config.allow_user_dataset_purge: - raise HTTPForbidden( detail='This instance does not allow user dataset purging' ) + raise exceptions.httpexceptions.HTTPForbidden( + detail='This instance does not allow user dataset purging' ) hda.purged = True trans.sa_session.add( hda ) @@ -345,11 +346,11 @@ trans.sa_session.flush() rval[ 'deleted' ] = True - except HTTPInternalServerError, http_server_err: + except exceptions.httpexceptions.HTTPInternalServerError, http_server_err: log.exception( 'HDA API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', id, str( kwd ), str( http_server_err ) ) raise - except HTTPException, http_exc: + except exceptions.httpexceptions.HTTPException, http_exc: raise except Exception, exc: log.exception( 'HDA API, delete: uncaught exception: %s, %s\n%s', 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: aswarren: API enable copying from one history to another
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0f8890ee9be5/ Changeset: 0f8890ee9be5 Branch: api_copy_history User: aswarren Date: 2013-08-02 00:02:54 Summary: API enable copying from one history to another Affected #: 1 file diff -r fe5867b89ec01bfde18591df8809526d85fb821e -r 0f8890ee9be56218a50dea5505a500e3fb9b3762 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -174,6 +174,7 @@ #TODO: copy existing, accessible hda - dataset controller, copy_datasets #TODO: convert existing, accessible hda - model.DatasetInstance(or hda.datatype).get_converter_types from_ld_id = payload.get( 'from_ld_id', None ) + from_hda_id= payload.get( 'from_hda_id', None ) try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False ) except Exception, e: @@ -197,7 +198,19 @@ hda = ld.library_dataset_dataset_association.to_history_dataset_association( history, add_to_history=True ) trans.sa_session.flush() return hda.get_api_value() - + elif from_hda_id: + try: + hda = self.get_dataset(trans, from_hda_id) + assert trans.user.id == hda.history.user_id, "HistoryDatasetAssocation does not belong to current user" + except AssertionError, e: + trans.response.status=400 + return "HistoryDatasetAssocation does not belong to current user" + except Exception, e: + return str(e) + data_copy=hda.copy(copy_children = True) + result=history.add_dataset(data_copy) + trans.sa_session.flush() + return result.get_api_value() else: # TODO: implement other "upload" methods here. trans.response.status = 501 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: greg: Restrict diff file size to something reasonable when browsing changesets in the Tool shed, and add some additional logging and error handling when setting metadata on repositories in the tool shed and Galaxy.
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/148a93733033/ Changeset: 148a93733033 User: greg Date: 2013-10-18 19:07:37 Summary: Restrict diff file size to something reasonable when browsing changesets in the Tool shed, and add some additional logging and error handling when setting metadata on repositories in the tool shed and Galaxy. Affected #: 7 files diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -517,10 +517,10 @@ message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) results[ 'unsuccessful_count' ] += 1 else: - message = "Successfully reset metadata on repository %s" % str( repository.name ) + message = "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), str( repository.owner ) ) results[ 'successful_count' ] += 1 except Exception, e: - message = "Error resetting metadata on repository %s: %s" % ( str( repository.name ), str( e ) ) + message = "Error resetting metadata on repository %s owned by %s: %s" % ( str( repository.name ), str( repository.owner ), str( e ) ) results[ 'unsuccessful_count' ] += 1 results[ 'repository_status' ].append( message ) stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -231,8 +231,11 @@ in addition to those repositories of type tool_dependency_definition. This param is ignored if the current user is not an admin user, in which case this same restriction is automatic. :param encoded_ids_to_skip (optional): a list of encoded repository ids for repositories that should not be processed. + :param skip_file (optional): A local file name that contains the encoded repository ids associated with repositories to skip. + This param can be used as an alternative to the above encoded_ids_to_skip. """ def handle_repository( trans, repository, results ): + log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) repository_id = trans.security.encode_id( repository.id ) try: invalid_file_tups, metadata_dict = metadata_util.reset_all_metadata_on_repository_in_tool_shed( trans, repository_id ) @@ -240,12 +243,13 @@ message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) results[ 'unsuccessful_count' ] += 1 else: - message = "Successfully reset metadata on repository %s" % str( repository.name ) + message = "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), str( repository.user.username ) ) results[ 'successful_count' ] += 1 except Exception, e: - message = "Error resetting metadata on repository %s: %s" % ( str( repository.name ), str( e ) ) + message = "Error resetting metadata on repository %s owned by %s: %s" % ( str( repository.name ), str( repository.user.username ), str( e ) ) results[ 'unsuccessful_count' ] += 1 - results[ 'repository_status' ].append( message ) + status = '%s : %s' % ( str( repository.name ), message ) + results[ 'repository_status' ].append( status ) return results try: start_time = strftime( "%Y-%m-%d %H:%M:%S" ) @@ -255,6 +259,16 @@ unsuccessful_count=0 ) handled_repository_ids = [] encoded_ids_to_skip = payload.get( 'encoded_ids_to_skip', [] ) + skip_file = payload.get( 'skip_file', None ) + if skip_file and os.path.exists( skip_file ) and not encoded_ids_to_skip: + # Load the list of encoded_ids_to_skip from the skip_file. + # Contents of file must be 1 encoded repository id per line. + lines = open( skip_file, 'rb' ).readlines() + for line in lines: + if line.startswith( '#' ): + # Skip comments. + continue + encoded_ids_to_skip.append( line.rstrip( '\n' ) ) if trans.user_is_admin(): my_writable = util.asbool( payload.get( 'my_writable', False ) ) else: @@ -306,17 +320,18 @@ if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) else: - message = "Successfully reset metadata on repository %s" % str( repository.name ) + message = "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), str( repository.user.username ) ) except Exception, e: - message = "Error resetting metadata on repository %s: %s" % ( str( repository.name ), str( e ) ) - - results[ 'repository_status' ].append( message ) + message = "Error resetting metadata on repository %s owned by %s: %s" % ( str( repository.name ), str( repository.user.username ), str( e ) ) + status = '%s : %s' % ( str( repository.name ), message ) + results[ 'repository_status' ].append( status ) return results try: repository_id = payload.get( 'repository_id', None ) if repository_id is not None: repository = suc.get_repository_in_tool_shed( trans, repository_id ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) + log.debug( "%s...resetting metadata on repository %s" % ( start_time, str( repository.name ) ) ) results = handle_repository( trans, start_time, repository ) stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) results[ 'stop_time' ] = stop_time diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -39,7 +39,9 @@ # Set metadata using the repository files on disk. error_message, status = set_repository_metadata( trans, repository ) if status == 'ok' and error_message: - log.debug( "Successfully reset metadata on repository %s, but encountered problem: %s" % ( repository.name, error_message ) ) + log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ + ( str( repository.name ), str( repository.user.username ), error_message ) ) elif status != 'ok' and error_message: - log.debug( "Error resetting metadata on repository %s: %s" % ( repository.name, error_message ) ) + log.debug( "Error resetting metadata on repository %s owned by %s: %s" % \ + ( str( repository.name ), str( repository.user.username ), error_message ) ) return wsgi_app diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -42,6 +42,7 @@ from mercurial import commands from mercurial import hg +from mercurial import mdiff from mercurial import patch from mercurial import ui @@ -2856,11 +2857,19 @@ ctx_child = ctx.children()[ 0 ] else: ctx_child = None + diffs = [] + options_dict = suc.get_mercurial_default_options_dict( 'diff' ) + # Not quite sure if the following settings make any difference, but with a combination of them and the size check on each + # diff, we don't run out of memory when viewing the changelog of the cisortho2 repository on the test tool shed. + options_dict[ 'maxfile' ] = suc.MAXDIFFSIZE + options_dict[ 'maxtotal' ] = suc.MAXDIFFSIZE + diffopts = mdiff.diffopts( **options_dict ) + for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node(), opts=diffopts ): + if len( diff ) > suc.MAXDIFFSIZE: + diff = util.shrink_string_by_size( diff, suc.MAXDIFFSIZE ) + diffs.append( suc.to_html_string( diff ) ) modified, added, removed, deleted, unknown, ignored, clean = repo.status( node1=ctx_parent.node(), node2=ctx.node() ) anchors = modified + added + removed + deleted + unknown + ignored + clean - diffs = [] - for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): - diffs.append( suc.to_html_string( diff ) ) metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True ) # For rendering the prev button. if ctx_parent: diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/tool_shed/scripts/api/reset_metadata_on_repositories.py --- a/lib/tool_shed/scripts/api/reset_metadata_on_repositories.py +++ b/lib/tool_shed/scripts/api/reset_metadata_on_repositories.py @@ -25,33 +25,55 @@ else: return False +def read_skip_file( skip_file ): + encoded_ids_to_skip = [] + if os.path.exists( skip_file ): + # Contents of file must be 1 encoded repository id per line. + lines = open( skip_file, 'rb' ).readlines() + for line in lines: + if line.startswith( '#' ): + # Skip comments. + continue + encoded_ids_to_skip.append( line.rstrip( '\n' ) ) + return encoded_ids_to_skip + def main( options ): api_key = options.api base_tool_shed_url = options.tool_shed_url.rstrip( '/' ) my_writable = options.my_writable one_per_request = options.one_per_request skip_file = options.skip_file - encoded_ids_to_skip = [] - if skip_file and os.path.exists( skip_file ): - # Contents of file must be 1 encoded repository id per line. - contents = open( skip_file, 'rb' ).read() - if contents: - encoded_ids_to_skip = contents.split( '\n' ) + if skip_file: + encoded_ids_to_skip = read_skip_file( skip_file ) + else: + encoded_ids_to_skip = [] if string_as_bool( one_per_request ): url = '%s/api/repositories/repository_ids_for_setting_metadata?key=%s&my_writable=%s' % ( base_tool_shed_url, api_key, str( my_writable ) ) repository_ids = get( url, api_key ) for repository_id in repository_ids: if repository_id in encoded_ids_to_skip: + print "--------" print "Skipping repository with id %s because it is in skip file %s" % ( str( repository_id ), str( skip_file ) ) + print "--------" else: data = dict( repository_id=repository_id ) url = '%s/api/repositories/reset_metadata_on_repository' % base_tool_shed_url - submit( url, data, options.api ) + try: + submit( url, data, options.api ) + except Exception, e: + log.exception( ">>>>>>>>>>>>>>>Blew up on data: %s, exception: %s" % ( str( data ), str( e ) ) ) + # An nginx timeout undoubtedly occurred. + sys.exit( 1 ) else: data = dict( encoded_ids_to_skip=encoded_ids_to_skip, my_writable=my_writable ) url = '%s/api/repositories/reset_metadata_on_repositories' % base_tool_shed_url - submit( url, data, options.api ) + try: + submit( url, data, options.api ) + except Exception, e: + log.exception( str( e ) ) + # An nginx timeout undoubtedly occurred. + sys.exit( 1 ) if __name__ == '__main__': parser = argparse.ArgumentParser( description='Reset metadata on certain repositories in the Tool Shed via the Tool Shed API.' ) diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1772,17 +1772,19 @@ if trans.webapp.name == 'tool_shed': # We're in the tool shed. repository = suc.get_repository_in_tool_shed( trans, repository_id ) + owner = str( repository.user.username ) invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, repository_id ) else: # We're in Galaxy. repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + owner = str( repository.owner ) invalid_file_tups, metadata_dict = reset_all_metadata_on_installed_repository( trans, repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) log.debug( message ) unsuccessful_count += 1 else: - log.debug( "Successfully reset metadata on repository %s" % str( repository.name ) ) + log.debug( "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), owner ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) ) diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -40,6 +40,7 @@ CHUNK_SIZE = 2**20 # 1Mb INITIAL_CHANGELOG_HASH = '000000000000' MAX_CONTENT_SIZE = 1048576 +MAXDIFFSIZE = 8000 MAX_DISPLAY_SIZE = 32768 DATATYPES_CONFIG_FILENAME = 'datatypes_conf.xml' REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = 'data_manager_conf.xml' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History Panel: match arg order with Backbone when handling errors; pack scripts
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a5d98e64b173/ Changeset: a5d98e64b173 User: carlfeberhard Date: 2013-10-18 18:53:31 Summary: History Panel: match arg order with Backbone when handling errors; pack scripts Affected #: 8 files diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -50,15 +50,16 @@ purge_link.attr( 'href', [ "javascript", "void(0)" ].join( ':' ) ); purge_link.click( function( event ){ //TODO??: confirm? - var ajaxPromise = jQuery.ajax( purge_url ); - ajaxPromise.success( function( message, status, responseObj ){ + var xhr = jQuery.ajax( purge_url ); + xhr.success( function( message, status, responseObj ){ hdaView.model.set( 'purged', true ); hdaView.trigger( 'purged', hdaView ); }); - ajaxPromise.error( function( error, status, message ){ + xhr.error( function( error, status, message ){ //TODO: Exception messages are hidden within error page //!NOTE: that includes the 'Removal of datasets by users is not allowed in this Galaxy instance.' - hdaView.trigger( 'error', _l( "Unable to purge this dataset" ), error, status, message ); + view.trigger( 'error', + hdaView, xhr, { url: purge_url }, _l( "Unable to purge this dataset" ) ); }); }); } @@ -161,6 +162,7 @@ error: function() { // Something went wrong, so show HDA again. // TODO: an error notification would be good. + self.trigger( 'error', self, null, null, { url: delete_url }, _l( 'deletion failed' ) ); self.$el.show(); }, success: function() { @@ -521,7 +523,7 @@ url: this.urls.tags.get, error: function( xhr, status, error ){ view.log( "Tagging failed", xhr, status, error ); - view.trigger( 'error', _l( "Tagging failed" ), xhr, status, error ); + view.trigger( 'error', view, xhr, { url: view.urls.tags.get }, _l( "Tagging failed" ) ); }, success: function(tag_elt_html) { tagElt.html(tag_elt_html); @@ -546,7 +548,8 @@ loadAndDisplayAnnotation : function( event ){ //TODO: this is a drop in from history.mako - should use MV as well this.log( this + '.loadAndDisplayAnnotation', event ); - var annotationArea = this.$el.find( '.annotation-area' ), + var view = this, + annotationArea = this.$el.find( '.annotation-area' ), annotationElem = annotationArea.find( '.annotation-elt' ), setAnnotationUrl = this.urls.annotation.set; @@ -556,9 +559,10 @@ // Need to fill annotation element. $.ajax({ url: this.urls.annotation.get, - error: function(){ - view.log( "Annotation failed", xhr, status, error ); - view.trigger( 'error', _l( "Annotation failed" ), xhr, status, error ); + error: function( xhr, status, message ){ + view.log( "Annotation failed", xhr, status, message ); + view.trigger( 'error', + view, xhr, { url: view.urls.annotation.get }, _l( "Annotation failed" ) ); }, success: function( htmlFromAjax ){ if( htmlFromAjax === "" ){ diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -72,6 +72,10 @@ this.updateAfterDelay(); } }, this ); + + this.hdas.bind( 'error', function( model, xhr, options, msg ){ + this.trigger( 'error', model, xhr, options, msg ); + }, this ); }, setOwnEventHandlers : function(){ @@ -176,20 +180,26 @@ historyXhr.fail( function( xhr, status, error ){ //TODO: use ajax.status handlers here // keep rolling on a bad gateway - server restart - if( xhr.status === 502 ){ + + //if( xhr.status === 0 && xhr.readyState === 0 ){ + + if( ( xhr.status === 0 && xhr.readyState === 0 ) + || ( xhr.status === 502 ) ){ + + //if( xhr.status === 502 ){ + history.log( 'Bad Gateway error. Retrying...' ); setTimeout( function(){ - history.log( 'Bad Gateway error. Retrying...' ); //TODO: someway to throw error on X tries history.stateUpdater(); }, History.UPDATE_DELAY ); // if not interruption by iframe reload //TODO: remove when iframes are removed - } else if( !( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ) ){ + } else { history.log( 'stateUpdater error:', error, 'responseText:', xhr.responseText ); var msg = _l( 'An error occurred while getting updates from the server.' ) + ' ' + _l( 'Please contact a Galaxy administrator if the problem persists.' ); - history.trigger( 'error', msg, xhr, status, error ); + history.trigger( 'error', history, xhr, {}, msg ); } }); }, @@ -228,7 +238,7 @@ hdaIds, xhr, status, error, errorJson ); var msg = _l( 'An error occurred while getting dataset details from the server.' ) + ' ' + _l( 'Please contact a Galaxy administrator if the problem persists.' ); - history.trigger( 'error', msg, xhr, status, error ); + history.trigger( 'error', history, xhr, {}, msg ); } }, @@ -295,12 +305,13 @@ fetchDisplayApplications : function( ids ){ this.log( this + '.fetchDisplayApplications:', ids ); var history = this, + display_app_url = 'history/get_display_application_links', // if any ids passed place them in the query string data data = ( ids && _.isArray( ids ) )?({ hda_ids : ids.join( ',' ) }):({}); //TODO: hardcoded history.log( this + ': fetching display application data' ); - jQuery.ajax( 'history/get_display_application_links', { + jQuery.ajax( display_app_url, { data : data, success : function( displayAppList, status, xhr ){ //history.hdas.set( data, { merge: true } ); // doesn't work - clears all other attributes @@ -314,7 +325,7 @@ history.log( 'Error fetching display applications:', ids, xhr, status, error ); var msg = _l( 'An error occurred while getting display applications from the server.' ) + ' ' + _l( 'Please contact a Galaxy administrator if the problem persists.' ); - history.trigger( 'error', msg, xhr, status, error ); + history.trigger( 'error', history, xhr, { url: display_app_url }, msg ); } } }); @@ -322,7 +333,7 @@ toString : function(){ var nameString = ( this.get( 'name' ) )? - ( ',' + this.get( 'name' ) ) : ( '' ); + ( ', ' + this.get( 'name' ) ) : ( '' ); return 'History(' + this.get( 'id' ) + nameString + ')'; } }); diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -114,9 +114,21 @@ this.urls = {}; }, - // refresh function + errorHandler : function( model, xhr, options, msg ){ + // let 'lost contact' errors fail silently + if( xhr && ( ( xhr.status === 0 && xhr.readyState === 0 ) + || ( xhr.status === 502 ) ) ){ + this.log( 'lost contact with server', model, xhr, options, msg ); + return; + } + + // otherwise display a message + msg = msg || _l( 'An error occurred while getting updates from the server.' ) + ' ' + + _l( 'Please contact a Galaxy administrator if the problem persists.' ); + this.displayMessage( 'error', msg ); + }, + refresh : function() { - // refresh // TODO: refresh content without reloading frame window.location = window.location; }, @@ -128,8 +140,8 @@ this.model.bind( 'change:nice_size', this.updateHistoryDiskSize, this ); // don't need to re-render entire model on all changes, just render disk size when it changes - this.model.bind( 'error', function( msg, xhr, error, status ){ - this.displayMessage( 'error', msg ); + this.model.bind( 'error', function( model, xhr, options, msg ){ + this.errorHandler( model, xhr, options, msg ); this.model.attributes.error = undefined; }, this ); @@ -157,8 +169,8 @@ }, this ); // ---- self - this.bind( 'error', function( msg, xhr, error, status ){ - this.displayMessage( 'error', msg ); + this.bind( 'error', function( model, xhr, options, msg ){ + this.errorHandler( model, xhr, options, msg ); }); if( this.logger ){ @@ -380,8 +392,8 @@ hdaView.bind( 'body-collapsed', function( id ){ historyView.storage.get( 'expandedHdas' ).deleteKey( id ); }); - hdaView.bind( 'error', function( msg, xhr, status, error ){ - historyView.displayMessage( 'error', msg ); + hdaView.bind( 'error', function( model, xhr, options, msg ){ + historyView.errorHandler( model, xhr, options, msg ); }); }, @@ -488,7 +500,7 @@ url: view.urls.tag, error: function( xhr, error, status ) { panel.log( 'Error loading tag area html', xhr, error, status ); - panel.trigger( 'error', _l( "Tagging failed" ), xhr, error, status ); + panel.trigger( 'error', panel, {}, {}, _l( "Tagging failed" ) ); }, success: function(tag_elt_html) { //view.log( view + ' tag elt html (ajax)', tag_elt_html ); diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:f+"/"+h+"?"+$.param(g)})}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find("[title]").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find("[title]").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:a+"/scatterplot?"+$.param(b),location:"center"});$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){f.Galaxy.modal.hide()},"View in saved visualization":function(){f.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e,buttons:{Cancel:function(){f.Galaxy.modal.hide()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){f.Galaxy.modal.hide();var g=$(this).val();c.id=g;f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})})}}})},"View in new visualization":function(){f.Galaxy.modal.hide();var g=a+"/trackster?"+$.param(c);f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:g})}}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){view.trigger("error",a,f,{url:b},_l("Unable to purge this dataset"))})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.trigger("error",a,null,null,{url:b},_l("deletion failed"));a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:f+"/"+h+"?"+$.param(g)})}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",a,g,{url:a.urls.tags.get},_l("Tagging failed"))},success:function(e){b.html(e);b.find("[title]").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(c){this.log(this+".loadAndDisplayAnnotation",c);var a=this,e=this.$el.find(".annotation-area"),d=e.find(".annotation-elt"),b=this.urls.annotation.set;if(e.is(":hidden")){if(!jQuery.trim(d.html())){$.ajax({url:this.urls.annotation.get,error:function(h,f,g){a.log("Annotation failed",h,f,g);a.trigger("error",a,h,{url:a.urls.annotation.get},_l("Annotation failed"))},success:function(f){if(f===""){f="<em>"+_l("Describe or add notes to dataset")+"</em>"}d.html(f);e.find("[title]").tooltip();async_save_text(d.attr("id"),d.attr("id"),b,"new_annotation",18,true,4);e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:a+"/scatterplot?"+$.param(b),location:"center"});$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){f.Galaxy.modal.hide()},"View in saved visualization":function(){f.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e,buttons:{Cancel:function(){f.Galaxy.modal.hide()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){f.Galaxy.modal.hide();var g=$(this).val();c.id=g;f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})})}}})},"View in new visualization":function(){f.Galaxy.modal.hide();var g=a+"/trackster?"+$.param(c);f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:g})}}})}});return false}}; \ No newline at end of file diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.fetchDisplayApplications()}}this.setHdaEventHandlers();this.setOwnEventHandlers()},setHdaEventHandlers:function(){this.hdas.bind("state:ready",function(b,c,a){if(b.get("force_history_refresh")){this.updateAfterDelay()}},this)},setOwnEventHandlers:function(){if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.updateTimeoutId=null;a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},isRunning:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.RUNNING)||(a===HistoryDatasetAssociation.STATES.QUEUED))},isReady:function(){return !this.isRunning()},checkForUpdates:function(){if(this.isRunning()){this.updateAfterDelay()}else{this.trigger("ready")}return this},findHdasToUpdate:function(){var c=this,a=c.get("state_ids"),b=[];_.each(a,function(d,e){_.each(d,function(g){var f=c.hdas.get(g);if(!f||f.get("state")!==e){b.push(g)}})});return b},stateUpdater:function(){var c=this,a=this.get("state"),b=this.fetch();b.done(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=c.findHdasToUpdate();if(e.length){c.fetchHdaUpdates(e).done(function(f){c.checkForUpdates()})}else{c.checkForUpdates()}});b.fail(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},fetchDisplayApplications:function(a){this.log(this+".fetchDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.fetchDisplayApplications()}}this.setHdaEventHandlers();this.setOwnEventHandlers()},setHdaEventHandlers:function(){this.hdas.bind("state:ready",function(b,c,a){if(b.get("force_history_refresh")){this.updateAfterDelay()}},this);this.hdas.bind("error",function(b,d,a,c){this.trigger("error",b,d,a,c)},this)},setOwnEventHandlers:function(){if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.updateTimeoutId=null;a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},isRunning:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.RUNNING)||(a===HistoryDatasetAssociation.STATES.QUEUED))},isReady:function(){return !this.isRunning()},checkForUpdates:function(){if(this.isRunning()){this.updateAfterDelay()}else{this.trigger("ready")}return this},findHdasToUpdate:function(){var c=this,a=c.get("state_ids"),b=[];_.each(a,function(d,e){_.each(d,function(g){var f=c.hdas.get(g);if(!f||f.get("state")!==e){b.push(g)}})});return b},stateUpdater:function(){var c=this,a=this.get("state"),b=this.fetch();b.done(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=c.findHdasToUpdate();if(e.length){c.fetchHdaUpdates(e).done(function(f){c.checkForUpdates()})}else{c.checkForUpdates()}});b.fail(function(g,d,e){if((g.status===0&&g.readyState===0)||(g.status===502)){c.log("Bad Gateway error. Retrying...");setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",c,g,{},f)}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",a,i,{},h)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},fetchDisplayApplications:function(a){this.log(this+".fetchDisplayApplications:",a);var d=this,c="history/get_display_application_links",b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});d.log(this+": fetching display application data");jQuery.ajax(c,{data:b,success:function(g,e,f){_.each(g,function(i){var h=d.hdas.get(i.id);if(h){h.set(i)}})},error:function(h,e,f){if(!((h.readyState===0)&&(h.status===0))){d.log("Error fetching display applications:",a,h,e,f);var g=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");d.trigger("error",d,h,{url:c},g)}}})},toString:function(){var a=(this.get("name"))?(", "+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -var HistoryPanel=Backbone.View.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"removeMessage"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this._setUpEventHandlers();this.hdaViews={};this.urls={}},refresh:function(){window.location=window.location},_setUpEventHandlers:function(){this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.bind("error",function(d,c,b,a){this.displayMessage("error",d);this.model.attributes.error=undefined},this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:purged",function(a){this.model.fetch()},this);this.model.hdas.bind("state:ready",function(b,c,a){if((!b.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(b.get("id"))}},this);this.bind("error",function(d,c,b,a){this.displayMessage("error",d)});if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},_setUpWebStorage:function(b,a,c){this.storage=new PersistentStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var a in sessionStorage){if(a.indexOf("HistoryView.")===0){sessionStorage.removeItem(a)}}},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find("[title]").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)});b.bind("error",function(f,e,c,d){a.displayMessage("error",f)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(d){this.log(this+".loadAndDisplayTags",d);var b=this,e=this.$el.find("#history-tag-area"),c=e.find(".tag-elt");this.log("\t tagArea",e," tagElt",c);if(e.is(":hidden")){if(!jQuery.trim(c.html())){var a=this;$.ajax({url:a.urls.tag,error:function(h,g,f){b.log("Error loading tag area html",h,g,f);b.trigger("error",_l("Tagging failed"),h,g,f)},success:function(f){c.html(f);c.find("[title]").tooltip();e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},displayMessage:function(c,d){var b=this.$el.find("#message-container"),a=$("<div/>").addClass(c+"message").text(d);b.html(a)},removeMessage:function(){var a=this.$el.find("#message-container");a.html(null)},scrollToTop:function(){$(document).scrollTop(0);return this},scrollIntoView:function(b,c){if(!c){$(document).scrollTop(b);return this}var a=window,d=this.$el.parent(),f=$(a).innerHeight(),e=(f/2)-(c/2);$(d).scrollTop(b-e);return this},scrollToId:function(b){if((!b)||(!this.hdaViews[b])){return this}var a=this.hdaViews[b].$el;this.scrollIntoView(a.offset().top,a.outerHeight());return this},scrollToHid:function(a){var b=this.model.hdas.getByHid(a);if(!b){return this}return this.scrollToId(b.id)},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=Backbone.View.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"removeMessage"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this._setUpEventHandlers();this.hdaViews={};this.urls={}},errorHandler:function(b,d,a,c){if(d&&((d.status===0&&d.readyState===0)||(d.status===502))){this.log("lost contact with server",b,d,a,c);return}c=c||_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");this.displayMessage("error",c)},refresh:function(){window.location=window.location},_setUpEventHandlers:function(){this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.bind("error",function(b,d,a,c){this.errorHandler(b,d,a,c);this.model.attributes.error=undefined},this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:purged",function(a){this.model.fetch()},this);this.model.hdas.bind("state:ready",function(b,c,a){if((!b.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(b.get("id"))}},this);this.bind("error",function(b,d,a,c){this.errorHandler(b,d,a,c)});if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},_setUpWebStorage:function(b,a,c){this.storage=new PersistentStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var a in sessionStorage){if(a.indexOf("HistoryView.")===0){sessionStorage.removeItem(a)}}},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find("[title]").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)});b.bind("error",function(d,f,c,e){a.errorHandler(d,f,c,e)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(d){this.log(this+".loadAndDisplayTags",d);var b=this,e=this.$el.find("#history-tag-area"),c=e.find(".tag-elt");this.log("\t tagArea",e," tagElt",c);if(e.is(":hidden")){if(!jQuery.trim(c.html())){var a=this;$.ajax({url:a.urls.tag,error:function(h,g,f){b.log("Error loading tag area html",h,g,f);b.trigger("error",b,{},{},_l("Tagging failed"))},success:function(f){c.html(f);c.find("[title]").tooltip();e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},displayMessage:function(c,d){var b=this.$el.find("#message-container"),a=$("<div/>").addClass(c+"message").text(d);b.html(a)},removeMessage:function(){var a=this.$el.find("#message-container");a.html(null)},scrollToTop:function(){$(document).scrollTop(0);return this},scrollIntoView:function(b,c){if(!c){$(document).scrollTop(b);return this}var a=window,d=this.$el.parent(),f=$(a).innerHeight(),e=(f/2)-(c/2);$(d).scrollTop(b-e);return this},scrollToId:function(b){if((!b)||(!this.hdaViews[b])){return this}var a=this.hdaViews[b].$el;this.scrollIntoView(a.offset().top,a.outerHeight());return this},scrollToHid:function(a){var b=this.model.hdas.getByHid(a);if(!b){return this}return this.scrollToId(b.id)},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/packed/viz/trackster.js --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1,1 +1,1 @@ -var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file +var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.prefs.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.prefs.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.prefs.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].prefs.name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ 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: natefoo: Log failures when setting peek.
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/febd76229248/ Changeset: febd76229248 User: natefoo Date: 2013-10-18 17:43:01 Summary: Log failures when setting peek. Affected #: 1 file diff -r 503d939099fcd8913202300b83221a8d3269b9f9 -r febd7622924885dd0729ce00924289cc1f0eb741 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -227,6 +227,7 @@ out.append( '</th>' ) out.append( '</tr>' ) except Exception, exc: + log.exception( 'make_html_peek_header failed on HDA %s' % dataset.id ) raise Exception, "Can't create peek header %s" % str( exc ) return "".join( out ) @@ -254,6 +255,7 @@ out.append( '<td>%s</td>' % escape( elem ) ) out.append( '</tr>' ) except Exception, exc: + log.exception( 'make_html_peek_rows failed on HDA %s' % dataset.id ) raise Exception, "Can't create peek rows %s" % str( exc ) return "".join( out ) 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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