From 296105ee395194c48d962671a8c367469ea74907 Mon Sep 17 00:00:00 2001 From: Brad Langhorst Date: Sun, 26 Aug 2018 12:20:47 -0400 Subject: [PATCH 1/2] row ids that are all numeric become ints... Since the "F" prefix is checked with substring, row_id must always be a string --- .../scripts/mvc/library/library-foldertoolbar-view.js | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js index 2164fcabaf8..5c124cacca5 100644 --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -1072,7 +1072,8 @@ var FolderToolbarView = Backbone.View.extend({ $checkedValues.each(function() { var row_id = $(this) .closest("tr") - .data("id"); + .data("id") + .toString(); if (row_id !== undefined) { if (row_id.substring(0, 1) == "F") { folder_ids.push(row_id); @@ -1201,7 +1202,8 @@ var FolderToolbarView = Backbone.View.extend({ this.findCheckedRows().each(function() { var row_id = $(this) .closest("tr") - .data("id"); + .data("id") + .toString(); if (row_id.substring(0, 1) == "F") { folder_ids.push(row_id); } else { From 55d350d015f20afc1c350130caaa0aa9858b7aa0 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 26 Aug 2018 20:36:51 +0200 Subject: [PATCH 2/2] Add static for 2a148ff1ec37c68e280c431fceee88ee0510e017 --- static/scripts/admin.toolshed.js | 3 ++- static/scripts/bundled/admin.bundled.js | 3 ++- static/scripts/bundled/analysis.bundled.js | 3 ++- static/scripts/bundled/chart.bundled.js | 3 ++- static/scripts/bundled/extended.bundled.js | 3 ++- static/scripts/bundled/libs.bundled.js | 3 ++- static/scripts/bundled/login.bundled.js | 3 ++- static/scripts/galaxy.interactive_environments.js | 3 ++- static/scripts/galaxy.js | 3 ++- static/scripts/galaxy.library.js | 3 ++- static/scripts/galaxy.pages.js | 3 ++- static/scripts/i18n.js | 3 ++- static/scripts/layout/communication-server-view.js | 3 ++- static/scripts/layout/masthead.js | 3 ++- static/scripts/layout/menu.js | 3 ++- static/scripts/layout/modal.js | 3 ++- static/scripts/layout/page.js | 3 ++- static/scripts/layout/panel.js | 3 ++- static/scripts/layout/router.js | 3 ++- static/scripts/layout/scratchbook.js | 3 ++- static/scripts/legacy/grid/grid-model.js | 3 ++- static/scripts/legacy/grid/grid-template.js | 3 ++- static/scripts/legacy/grid/grid-view.js | 3 ++- static/scripts/mocha/test.js | 3 ++- static/scripts/mocha/tests/rules_tests.js | 3 ++- static/scripts/mvc/annotation.js | 3 ++- static/scripts/mvc/base-mvc.js | 3 ++- static/scripts/mvc/base/controlled-fetch-collection.js | 3 ++- static/scripts/mvc/collection/base-creator.js | 3 ++- static/scripts/mvc/collection/collection-li-edit.js | 3 ++- static/scripts/mvc/collection/collection-li.js | 3 ++- static/scripts/mvc/collection/collection-model.js | 3 ++- static/scripts/mvc/collection/collection-view-edit.js | 3 ++- static/scripts/mvc/collection/collection-view.js | 3 ++- static/scripts/mvc/collection/list-collection-creator.js | 3 ++- .../scripts/mvc/collection/list-of-pairs-collection-creator.js | 3 ++- static/scripts/mvc/collection/pair-collection-creator.js | 3 ++- static/scripts/mvc/dataset/data.js | 3 ++- static/scripts/mvc/dataset/dataset-choice.js | 3 ++- static/scripts/mvc/dataset/dataset-edit-attributes.js | 3 ++- static/scripts/mvc/dataset/dataset-error.js | 3 ++- static/scripts/mvc/dataset/dataset-li-edit.js | 3 ++- static/scripts/mvc/dataset/dataset-li.js | 3 ++- static/scripts/mvc/dataset/dataset-list.js | 3 ++- static/scripts/mvc/dataset/dataset-model.js | 3 ++- static/scripts/mvc/dataset/states.js | 3 ++- static/scripts/mvc/form/form-data.js | 3 ++- static/scripts/mvc/form/form-input.js | 3 ++- static/scripts/mvc/form/form-parameters.js | 3 ++- static/scripts/mvc/form/form-repeat.js | 3 ++- static/scripts/mvc/form/form-section.js | 3 ++- static/scripts/mvc/form/form-view.js | 3 ++- static/scripts/mvc/form/form-wrapper.js | 3 ++- static/scripts/mvc/grid/grid-model.js | 3 ++- static/scripts/mvc/grid/grid-shared.js | 3 ++- static/scripts/mvc/grid/grid-template.js | 3 ++- static/scripts/mvc/grid/grid-view.js | 3 ++- static/scripts/mvc/history/copy-dialog.js | 3 ++- static/scripts/mvc/history/hda-li-edit.js | 3 ++- static/scripts/mvc/history/hda-li.js | 3 ++- static/scripts/mvc/history/hda-model.js | 3 ++- static/scripts/mvc/history/hdca-li-edit.js | 3 ++- static/scripts/mvc/history/hdca-li.js | 3 ++- static/scripts/mvc/history/hdca-model.js | 3 ++- static/scripts/mvc/history/history-content-model.js | 3 ++- static/scripts/mvc/history/history-contents.js | 3 ++- static/scripts/mvc/history/history-item-li.js | 3 ++- static/scripts/mvc/history/history-list.js | 3 ++- static/scripts/mvc/history/history-model.js | 3 ++- static/scripts/mvc/history/history-preferences.js | 3 ++- static/scripts/mvc/history/history-structure-view.js | 3 ++- static/scripts/mvc/history/history-view-annotated.js | 3 ++- static/scripts/mvc/history/history-view-edit-current.js | 3 ++- static/scripts/mvc/history/history-view-edit.js | 3 ++- static/scripts/mvc/history/history-view.js | 3 ++- static/scripts/mvc/history/job-dag.js | 3 ++- static/scripts/mvc/history/job-states-model.js | 3 ++- static/scripts/mvc/history/multi-panel.js | 3 ++- static/scripts/mvc/history/options-menu.js | 3 ++- static/scripts/mvc/job/job-li.js | 3 ++- static/scripts/mvc/job/job-model.js | 3 ++- static/scripts/mvc/job/job-params.js | 3 ++- static/scripts/mvc/lazy/lazy-limited.js | 3 ++- static/scripts/mvc/library/library-dataset-view.js | 3 ++- static/scripts/mvc/library/library-folder-view.js | 3 ++- static/scripts/mvc/library/library-folderlist-view.js | 3 ++- static/scripts/mvc/library/library-folderrow-view.js | 3 ++- static/scripts/mvc/library/library-foldertoolbar-view.js | 3 ++- static/scripts/mvc/library/library-library-view.js | 3 ++- static/scripts/mvc/library/library-librarylist-view.js | 3 ++- static/scripts/mvc/library/library-libraryrow-view.js | 3 ++- static/scripts/mvc/library/library-librarytoolbar-view.js | 3 ++- static/scripts/mvc/library/library-model.js | 3 ++- static/scripts/mvc/library/library-util.js | 3 ++- static/scripts/mvc/list/list-item.js | 3 ++- static/scripts/mvc/list/list-view.js | 3 ++- static/scripts/mvc/rules/rule-definitions.js | 3 ++- static/scripts/mvc/tag.js | 3 ++- static/scripts/mvc/tool/tool-form-base.js | 3 ++- static/scripts/mvc/tool/tool-form-composite.js | 3 ++- static/scripts/mvc/tool/tool-form.js | 3 ++- static/scripts/mvc/tool/tool-genomespace.js | 3 ++- static/scripts/mvc/tool/tools.js | 3 ++- static/scripts/mvc/toolshed/categories-view.js | 3 ++- static/scripts/mvc/toolshed/repo-queue-view.js | 3 ++- static/scripts/mvc/toolshed/repo-status-view.js | 3 ++- static/scripts/mvc/toolshed/repositories-view.js | 3 ++- static/scripts/mvc/toolshed/repository-queue-view.js | 3 ++- static/scripts/mvc/toolshed/repository-view.js | 3 ++- static/scripts/mvc/toolshed/shed-list-view.js | 3 ++- static/scripts/mvc/toolshed/toolshed-model.js | 3 ++- static/scripts/mvc/toolshed/util.js | 3 ++- static/scripts/mvc/toolshed/workflows-view.js | 3 ++- static/scripts/mvc/tours.js | 3 ++- static/scripts/mvc/ui/error-modal.js | 3 ++- static/scripts/mvc/ui/icon-button.js | 3 ++- static/scripts/mvc/ui/popup-menu.js | 3 ++- static/scripts/mvc/ui/ui-buttons.js | 3 ++- static/scripts/mvc/ui/ui-color-picker.js | 3 ++- static/scripts/mvc/ui/ui-drilldown.js | 3 ++- static/scripts/mvc/ui/ui-frames.js | 3 ++- static/scripts/mvc/ui/ui-list.js | 3 ++- static/scripts/mvc/ui/ui-misc.js | 3 ++- static/scripts/mvc/ui/ui-modal.js | 3 ++- static/scripts/mvc/ui/ui-options.js | 3 ++- static/scripts/mvc/ui/ui-popover.js | 3 ++- static/scripts/mvc/ui/ui-portlet.js | 3 ++- static/scripts/mvc/ui/ui-rules-edit.js | 3 ++- static/scripts/mvc/ui/ui-select-content.js | 3 ++- static/scripts/mvc/ui/ui-select-default.js | 3 ++- static/scripts/mvc/ui/ui-select-ftp.js | 3 ++- static/scripts/mvc/ui/ui-select-genomespace.js | 3 ++- static/scripts/mvc/ui/ui-select-library.js | 3 ++- static/scripts/mvc/ui/ui-select.js | 3 ++- static/scripts/mvc/ui/ui-slider.js | 3 ++- static/scripts/mvc/ui/ui-table.js | 3 ++- static/scripts/mvc/ui/ui-tabs.js | 3 ++- static/scripts/mvc/ui/ui-thumbnails.js | 3 ++- static/scripts/mvc/upload/collection/collection-row.js | 3 ++- static/scripts/mvc/upload/collection/collection-view.js | 3 ++- static/scripts/mvc/upload/collection/rules-input-view.js | 3 ++- static/scripts/mvc/upload/composite/composite-row.js | 3 ++- static/scripts/mvc/upload/composite/composite-view.js | 3 ++- static/scripts/mvc/upload/default/default-row.js | 3 ++- static/scripts/mvc/upload/default/default-view.js | 3 ++- static/scripts/mvc/upload/upload-button.js | 3 ++- static/scripts/mvc/upload/upload-extension.js | 3 ++- static/scripts/mvc/upload/upload-ftp.js | 3 ++- static/scripts/mvc/upload/upload-model.js | 3 ++- static/scripts/mvc/upload/upload-settings.js | 3 ++- static/scripts/mvc/upload/upload-utils.js | 3 ++- static/scripts/mvc/upload/upload-view.js | 3 ++- static/scripts/mvc/user/user-custom-builds.js | 3 ++- static/scripts/mvc/user/user-model.js | 3 ++- static/scripts/mvc/user/user-preferences.js | 3 ++- static/scripts/mvc/user/user-quotameter.js | 3 ++- static/scripts/mvc/visualization/chart/chart-client.js | 3 ++- static/scripts/mvc/visualization/chart/components/model.js | 3 ++- .../scripts/mvc/visualization/chart/components/screenshot.js | 3 ++- static/scripts/mvc/visualization/chart/utilities/datasets.js | 3 ++- static/scripts/mvc/visualization/chart/utilities/jobs.js | 3 ++- static/scripts/mvc/visualization/chart/utilities/series.js | 3 ++- static/scripts/mvc/visualization/chart/views/description.js | 3 ++- static/scripts/mvc/visualization/chart/views/editor.js | 3 ++- static/scripts/mvc/visualization/chart/views/groups.js | 3 ++- static/scripts/mvc/visualization/chart/views/menu.js | 3 ++- static/scripts/mvc/visualization/chart/views/settings.js | 3 ++- static/scripts/mvc/visualization/chart/views/viewer.js | 3 ++- static/scripts/mvc/visualization/visualization-model.js | 3 ++- static/scripts/mvc/webhooks.js | 3 ++- static/scripts/mvc/workflow/workflow-canvas.js | 3 ++- static/scripts/mvc/workflow/workflow-connector.js | 3 ++- static/scripts/mvc/workflow/workflow-forms.js | 3 ++- static/scripts/mvc/workflow/workflow-icons.js | 3 ++- static/scripts/mvc/workflow/workflow-manager.js | 3 ++- static/scripts/mvc/workflow/workflow-model.js | 3 ++- static/scripts/mvc/workflow/workflow-node.js | 3 ++- static/scripts/mvc/workflow/workflow-terminals.js | 3 ++- static/scripts/mvc/workflow/workflow-view-data.js | 3 ++- static/scripts/mvc/workflow/workflow-view-node.js | 3 ++- static/scripts/mvc/workflow/workflow-view-terminals.js | 3 ++- static/scripts/mvc/workflow/workflow-view.js | 3 ++- static/scripts/mvc/workflow/workflow.js | 3 ++- static/scripts/nls/de/locale.js | 3 ++- static/scripts/nls/es/locale.js | 3 ++- static/scripts/nls/fr/locale.js | 3 ++- static/scripts/nls/ja/locale.js | 3 ++- static/scripts/nls/locale.js | 3 ++- static/scripts/nls/zh/locale.js | 3 ++- static/scripts/onload.js | 3 ++- static/scripts/polyfills.js | 3 ++- static/scripts/reports/run_stats.js | 3 ++- static/scripts/toolshed/groups/group-detail-view.js | 3 ++- static/scripts/toolshed/groups/group-list-view.js | 3 ++- static/scripts/toolshed/groups/group-listrow-view.js | 3 ++- static/scripts/toolshed/groups/group-model.js | 3 ++- static/scripts/toolshed/toolshed.groups.js | 3 ++- static/scripts/ui/autocom_tagging.js | 3 ++- static/scripts/ui/editable-text.js | 3 ++- static/scripts/ui/fa-icon-button.js | 3 ++- static/scripts/ui/filter-control.js | 3 ++- static/scripts/ui/hoverhighlight.js | 3 ++- static/scripts/ui/loading-indicator.js | 3 ++- static/scripts/ui/mode-button.js | 3 ++- static/scripts/ui/pagination.js | 3 ++- static/scripts/ui/peek-column-selector.js | 3 ++- static/scripts/ui/popupmenu.js | 3 ++- static/scripts/ui/scroll-panel.js | 3 ++- static/scripts/ui/search-input.js | 3 ++- static/scripts/utils/add-logging.js | 3 ++- static/scripts/utils/ajax-queue.js | 3 ++- static/scripts/utils/async-save-text.js | 3 ++- static/scripts/utils/config.js | 3 ++- static/scripts/utils/deferred.js | 3 ++- static/scripts/utils/graph.js | 3 ++- static/scripts/utils/levenshtein.js | 3 ++- static/scripts/utils/localization.js | 3 ++- static/scripts/utils/metrics-logger.js | 3 ++- static/scripts/utils/natural-sort.js | 3 ++- static/scripts/utils/query-string-parsing.js | 3 ++- static/scripts/utils/uploadbox.js | 3 ++- static/scripts/utils/utils.js | 3 ++- static/scripts/viz/bbi-data-manager.js | 3 ++- static/scripts/viz/circster.js | 3 ++- static/scripts/viz/phyloviz.js | 3 ++- static/scripts/viz/sweepster.js | 3 ++- static/scripts/viz/trackster.js | 3 ++- static/scripts/viz/trackster/filters.js | 3 ++- static/scripts/viz/trackster/painters.js | 3 ++- static/scripts/viz/trackster/slotting.js | 3 ++- static/scripts/viz/trackster/tracks.js | 3 ++- static/scripts/viz/trackster/util.js | 3 ++- static/scripts/viz/visualization.js | 3 ++- static/scripts/viz/viz_views.js | 3 ++- 234 files changed, 468 insertions(+), 234 deletions(-) diff --git a/static/scripts/admin.toolshed.js b/static/scripts/admin.toolshed.js index b673be740c2..a2fadfea25f 100644 --- a/static/scripts/admin.toolshed.js +++ b/static/scripts/admin.toolshed.js @@ -1 +1,2 @@ -define("admin.toolshed",["exports","mvc/toolshed/shed-list-view","mvc/toolshed/categories-view","mvc/toolshed/repositories-view","mvc/toolshed/repository-view","mvc/toolshed/repository-queue-view","mvc/toolshed/repo-status-view","mvc/toolshed/workflows-view"],function(e,o,t,a,i,s,d,r){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var l=n(o),p=n(t),h=n(a),u=n(i),w=n(s),m=n(d),y=n(r),c=Backbone.Router.extend({initialize:function(){this.routesHit=0,Backbone.history.on("route",function(){this.routesHit++},this),this.bind("route",this.trackPageview)},routes:{"":"toolsheds",sheds:"toolsheds",queue:"queue",workflows:"workflows","status/r/:repositories":"status",status:"status","categories/s/:tool_shed":"categories","category/s/:tool_shed/c/:cateory_id":"repositories","repository/s/:tool_shed/r/:repository_id":"repository"},back:function(){this.routesHit>1?window.history.back():this.navigate("#",{trigger:!0,replace:!0})}}),f=Backbone.View.extend({app_config:{known_views:["toolsheds","queue","status","categories","repositories","repoository"]},initialize:function(){Galaxy.admintoolshedapp=this,this.admin_toolshed_router=new c,this.admin_toolshed_router.on("route:queue",function(){Galaxy.admintoolshedapp.adminRepoQueueView?Galaxy.admintoolshedapp.adminRepoQueueView.reDraw():Galaxy.admintoolshedapp.adminRepoQueueView=new w.default.RepoQueueView}),this.admin_toolshed_router.on("route:toolsheds",function(){Galaxy.admintoolshedapp.adminShedListView?Galaxy.admintoolshedapp.adminShedListView.reDraw():Galaxy.admintoolshedapp.adminShedListView=new l.default.ShedListView}),this.admin_toolshed_router.on("route:categories",function(e){Galaxy.admintoolshedapp.adminShedCategoriesView?Galaxy.admintoolshedapp.adminShedCategoriesView.reDraw({tool_shed:e.replace(/\//g,"%2f")}):Galaxy.admintoolshedapp.adminShedCategoriesView=new p.default.CategoryView({tool_shed:e.replace(/\//g,"%2f")})}),this.admin_toolshed_router.on("route:repositories",function(e,o){Galaxy.admintoolshedapp.adminShedCategoryView?Galaxy.admintoolshedapp.adminShedCategoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),category_id:o}):Galaxy.admintoolshedapp.adminShedCategoryView=new h.default.Category({tool_shed:e.replace(/\//g,"%2f"),category_id:o})}),this.admin_toolshed_router.on("route:repository",function(e,o){Galaxy.admintoolshedapp.adminRepositoryView?Galaxy.admintoolshedapp.adminRepositoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),repository_id:o}):Galaxy.admintoolshedapp.adminRepositoryView=new u.default.RepoDetails({tool_shed:e.replace(/\//g,"%2f"),repository_id:o})}),this.admin_toolshed_router.on("route:status",function(e){Galaxy.admintoolshedapp.adminRepoStatusView?Galaxy.admintoolshedapp.adminRepoStatusView.reDraw({repositories:e.split("|")}):Galaxy.admintoolshedapp.adminRepoStatusView=new m.default.RepoStatus({repositories:e.split("|")})}),this.admin_toolshed_router.on("route:workflows",function(){Galaxy.admintoolshedapp.adminWorkflowsView?Galaxy.admintoolshedapp.adminWorkflowsView.reDraw():Galaxy.admintoolshedapp.adminWorkflowsView=new y.default.Workflows}),Backbone.history.start({pushState:!1})}});e.default={GalaxyApp:f}}); \ No newline at end of file +define("admin.toolshed",["exports","mvc/toolshed/shed-list-view","mvc/toolshed/categories-view","mvc/toolshed/repositories-view","mvc/toolshed/repository-view","mvc/toolshed/repository-queue-view","mvc/toolshed/repo-status-view","mvc/toolshed/workflows-view"],function(e,o,t,a,i,s,d,r){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var l=n(o),p=n(t),h=n(a),u=n(i),w=n(s),m=n(d),y=n(r),c=Backbone.Router.extend({initialize:function(){this.routesHit=0,Backbone.history.on("route",function(){this.routesHit++},this),this.bind("route",this.trackPageview)},routes:{"":"toolsheds",sheds:"toolsheds",queue:"queue",workflows:"workflows","status/r/:repositories":"status",status:"status","categories/s/:tool_shed":"categories","category/s/:tool_shed/c/:cateory_id":"repositories","repository/s/:tool_shed/r/:repository_id":"repository"},back:function(){this.routesHit>1?window.history.back():this.navigate("#",{trigger:!0,replace:!0})}}),f=Backbone.View.extend({app_config:{known_views:["toolsheds","queue","status","categories","repositories","repoository"]},initialize:function(){Galaxy.admintoolshedapp=this,this.admin_toolshed_router=new c,this.admin_toolshed_router.on("route:queue",function(){Galaxy.admintoolshedapp.adminRepoQueueView?Galaxy.admintoolshedapp.adminRepoQueueView.reDraw():Galaxy.admintoolshedapp.adminRepoQueueView=new w.default.RepoQueueView}),this.admin_toolshed_router.on("route:toolsheds",function(){Galaxy.admintoolshedapp.adminShedListView?Galaxy.admintoolshedapp.adminShedListView.reDraw():Galaxy.admintoolshedapp.adminShedListView=new l.default.ShedListView}),this.admin_toolshed_router.on("route:categories",function(e){Galaxy.admintoolshedapp.adminShedCategoriesView?Galaxy.admintoolshedapp.adminShedCategoriesView.reDraw({tool_shed:e.replace(/\//g,"%2f")}):Galaxy.admintoolshedapp.adminShedCategoriesView=new p.default.CategoryView({tool_shed:e.replace(/\//g,"%2f")})}),this.admin_toolshed_router.on("route:repositories",function(e,o){Galaxy.admintoolshedapp.adminShedCategoryView?Galaxy.admintoolshedapp.adminShedCategoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),category_id:o}):Galaxy.admintoolshedapp.adminShedCategoryView=new h.default.Category({tool_shed:e.replace(/\//g,"%2f"),category_id:o})}),this.admin_toolshed_router.on("route:repository",function(e,o){Galaxy.admintoolshedapp.adminRepositoryView?Galaxy.admintoolshedapp.adminRepositoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),repository_id:o}):Galaxy.admintoolshedapp.adminRepositoryView=new u.default.RepoDetails({tool_shed:e.replace(/\//g,"%2f"),repository_id:o})}),this.admin_toolshed_router.on("route:status",function(e){Galaxy.admintoolshedapp.adminRepoStatusView?Galaxy.admintoolshedapp.adminRepoStatusView.reDraw({repositories:e.split("|")}):Galaxy.admintoolshedapp.adminRepoStatusView=new m.default.RepoStatus({repositories:e.split("|")})}),this.admin_toolshed_router.on("route:workflows",function(){Galaxy.admintoolshedapp.adminWorkflowsView?Galaxy.admintoolshedapp.adminWorkflowsView.reDraw():Galaxy.admintoolshedapp.adminWorkflowsView=new y.default.Workflows}),Backbone.history.start({pushState:!1})}});e.default={GalaxyApp:f}}); +//# 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'},_templateWorkflowTable:function(){return'
"+e.join("")+""+r+"").text(t),r=this.model.get_metadata("column_types");return void 0!==i?n.attr("colspan",i).addClass("stringalign"):r&&e"),r=this.model.get_metadata("columns");return this.row_count%2!=0&&i.addClass("dark_row"),e.length===r?n.each(e,function(t,e){i.append(this._renderCell(t,e))},this):e.length>r?(n.each(e.slice(0,r-1),function(t,e){i.append(this._renderCell(t,e))},this),i.append(this._renderCell(e.slice(r-1).join("\t"),r-1))):1===e.length?i.append(this._renderCell(t,0,r)):(n.each(e,function(t,e){i.append(this._renderCell(t,e))},this),n.each(n.range(r-e.length),function(){i.append(a(""))})),this.row_count++,i},_renderChunk:function(t){var e=this.$el.find("table");n.each(t.ck_data.split("\n"),function(t,i){""!==t&&e.append(this._renderRow(t))},this)}}),p=_.extend({initialize:function(t){_.prototype.initialize.call(this,t);var e=n.find(this.$el.parents(),function(t){return"auto"===a(t).css("overflow")});e||(e=window),this.scroll_elt=a(e)},scrolled_to_bottom:function(){return this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),m=_.extend({initialize:function(t){_.prototype.initialize.call(this,t),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:t.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),v=t.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(t){var e=parent.Galaxy;if(e&&e.modal&&(this.modal=e.modal),e&&e.frame&&(this.frame=e.frame),this.modal&&this.frame){var i=t.model,n=i.get("metadata");if(i.get("file_ext")){if(this.file_ext=i.get("file_ext"),"bed"==this.file_ext){if(!(n.get("chromCol")&&n.get("startCol")&&n.get("endCol")))return void console.log("TabularButtonTrackster : Bed-file metadata incomplete.");this.col.chrom=n.get("chromCol")-1,this.col.start=n.get("startCol")-1,this.col.end=n.get("endCol")-1}if("vcf"==this.file_ext){var a=function(t,e){for(var i=0;i100?l(new Uint8Array(t.buffer,t.byteOffset+e,a),i,n):s(t,e,i,n,a)}}function s(t,e,i,n,a){for(var r=0;r15?(this.inflateEnd(t),-2):(this.wbits=e,t.istate.blocks=new i(t,0!=t.istate.nowrap?null:this,1<>4)>t.istate.wbits){t.istate.mode=13,t.msg="invalid window size",t.istate.marker=5;break}t.istate.mode=1;case 1:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,n=255&t.next_in[t.next_in_index++],((t.istate.method<<8)+n)%31!=0){t.istate.mode=13,t.msg="incorrect header check",t.istate.marker=5;break}if(0==(32&n)){t.istate.mode=7;break}t.istate.mode=2;case 2:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=3;case 3:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=4;case 4:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=5;case 5:return 0==t.avail_in?i:(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.adler=t.istate.need,t.istate.mode=6,2);case 6:return t.istate.mode=13,t.msg="need dictionary",t.istate.marker=0,-2;case 7:if(-3==(i=t.istate.blocks.proc(t,i))){t.istate.mode=13,t.istate.marker=0;break}if(i==f&&(i=e),i!=_)return i;if(i=e,t.istate.blocks.reset(t,t.istate.was),0!=t.istate.nowrap){t.istate.mode=12;break}t.istate.mode=8;case 8:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need=(255&t.next_in[t.next_in_index++])<<24&4278190080,t.istate.mode=9;case 9:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<16&16711680,t.istate.mode=10;case 10:if(0==t.avail_in)return i;i=e,t.avail_in--,t.total_in++,t.istate.need+=(255&t.next_in[t.next_in_index++])<<8&65280,t.istate.mode=11;case 11:if(0==t.avail_in)return i;if(i=e,t.avail_in--,t.total_in++,t.istate.need+=255&t.next_in[t.next_in_index++],t.istate.was[0]!=t.istate.need){t.istate.mode=13,t.msg="incorrect data check",t.istate.marker=5;break}t.istate.mode=12;case 12:return _;case 13:return-3;default:return-2}},e.prototype.inflateSetDictionary=function(t,e,i){var n=0,a=i;return null==t||null==t.istate||6!=t.istate.mode?-2:t._adler.adler32(1,e,0,i)!=t.adler?-3:(t.adler=t._adler.adler32(0,null,0,0),a>=1<>>1){case 0:n>>>=3,a-=3,i=7&a,n>>>=i,a-=i,this.mode=1;break;case 1:var d=new Int32Array(1),h=new Int32Array(1),p=[],g=[];r(d,h,p,g,t),this.codes.init(d[0],h[0],p[0],0,g[0],0,t),n>>>=3,a-=3,this.mode=6;break;case 2:n>>>=3,a-=3,this.mode=3;break;case 3:return n>>>=3,a-=3,this.mode=13,t.msg="invalid block type",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e)}break;case 1:for(;a<32;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<>>16&65535)!=(65535&n))return this.mode=13,t.msg="invalid stored block lengths",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);this.left=65535&n,n=a=0,this.mode=0!=this.left?2:0!=this.last?7:v;break;case 2:if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=u,this.inflate_flush(t,e);if(0==c&&(u==end&&0!=read&&(u=0,c=ul&&(i=l),i>c&&(i=c),o(t.next_in,s,this.window,u,i),s+=i,l-=i,u+=i,c-=i,0!=(this.left-=i))break;this.mode=0!=this.last?7:v;break;case 3:for(;a<14;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<29||(i>>5&31)>29)return this.mode=9,t.msg="too many length or distance symbols",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);if(i=258+(31&i)+(i>>5&31),null==this.blens||this.blens.length>>=14,a-=14,this.index=0,mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;a<3;){if(0==l)return this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);e=f,l--,n|=(255&t.next_in[s++])<>>=3,a-=3}for(;this.index<19;)this.blens[S[this.index++]]=0;if(this.bb[0]=7,(i=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,t))!=f)return e=i,-3==e&&(this.blens=null,this.mode=9),this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,write=u,this.inflate_flush(t,e);this.index=0,this.mode=5;case 5:for(;;){if(i=this.table,!(this.index<258+(31&i)+(i>>5&31)))break;var w,b,y;for(i=this.bb[0];a>>=i,a-=i,this.blens[this.index++]=y;else{for(w=18==y?7:y-14,b=18==y?11:3;a>>=i,a-=i,b+=n&m[w],n>>>=w,a-=w,w=this.index,i=this.table,w+b>258+(31&i)+(i>>5&31)||16==y&&w<1)return this.blens=null,this.mode=9,t.msg="invalid bit length repeat",e=-3,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);y=16==y?this.blens[w-1]:0;do{this.blens[w++]=y}while(0!=--b);this.index=w}}this.tb[0]=-1;var d=new Int32Array(1),h=new Int32Array(1),p=new Int32Array(1),g=new Int32Array(1);if(d[0]=9,h[0]=6,i=this.table,(i=this.inftree.inflate_trees_dynamic(257+(31&i),1+(i>>5&31),this.blens,d,h,p,g,this.hufts,t))!=f)return-3==i&&(this.blens=null,this.mode=13),e=i,this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,this.inflate_flush(t,e);this.codes.init(d[0],h[0],this.hufts,p[0],this.hufts,g[0],t),this.mode=6;case 6:if(this.bitb=n,this.bitk=a,t.avail_in=l,t.total_in+=s-t.next_in_index,t.next_in_index=s,this.write=u,(e=this.codes.proc(this,t,e))!=_)return this.inflate_flush(t,e);if(e=f,this.codes.free(t),s=t.next_in_index,l=t.avail_in,n=this.bitb,a=this.bitk,u=this.write,c=ut.avail_out&&(i=t.avail_out),0!=i&&e==p&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i,a==this.end&&(a=0,this.write==this.end&&(this.write=0),i=this.write-a,i>t.avail_out&&(i=t.avail_out),0!=i&&e==p&&(e=f),t.avail_out-=i,t.total_out+=i,null!=this.checkfn&&(t.adler=this.check=t._adler.adler32(this.check,this.window,a,i)),o(this.window,a,t.next_out,n,i),n+=i,a+=i),t.next_out_index=n,this.read=a,e};n.prototype.init=function(t,e,i,n,a,r,o){this.mode=0,this.lbits=t,this.dbits=e,this.ltree=i,this.ltree_index=n,this.dtree=a,this.dtree_index=r,this.tree=null},n.prototype.proc=function(t,e,i){var n,a,r,o,s,l,u,c=0,d=0,h=0;for(h=e.next_in_index,o=e.avail_in,c=t.bitb,d=t.bitk,s=t.write,l=s=258&&o>=10&&(t.bitb=c,t.bitk=d,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,i=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,t,e),h=e.next_in_index,o=e.avail_in,c=t.bitb,d=t.bitk,s=t.write,l=s>>=this.tree[a+1],d-=this.tree[a+1],0==(r=this.tree[a])){this.lit=this.tree[a+2],this.mode=6;break}if(0!=(16&r)){this.get=15&r,this.len=this.tree[a+2],this.mode=2;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}if(0!=(32&r)){this.mode=7;break}return this.mode=9,e.msg="invalid literal/length code",i=-3,t.bitb=c,t.bitk=d,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 2:for(n=this.get;d>=n,d-=n,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=3;case 3:for(n=this.need;d>=this.tree[a+1],d-=this.tree[a+1],0!=(16&(r=this.tree[a]))){this.get=15&r,this.dist=this.tree[a+2],this.mode=4;break}if(0==(64&r)){this.need=r,this.tree_index=a/3+this.tree[a+2];break}return this.mode=9,e.msg="invalid distance code",i=-3,t.bitb=c,t.bitk=d,e.avail_in=o,e.total_in+=h-e.next_in_index,e.next_in_index=h,t.write=s,t.inflate_flush(e,i);case 4:for(n=this.get;d>=n,d-=n,this.mode=5;case 5:for(u=s-this.dist;u<0;)u+=t.end;for(;0!=this.len;){if(0==l&&(s==t.end&&0!=t.read&&(s=0,l=s7&&(d-=8,o++,h--),t.write=s,i=t.inflate_flush(e,i),s=t.write,l=s>=c[S+1],v-=c[S+1],0!=(16&h)){for(h&=15,C=c[S+2]+(p&m[h]),p>>=h,v-=h;v<15;)w--,p|=(255&l.next_in[g++])<>=c[S+1],v-=c[S+1],0!=(16&h)){for(h&=15;v>=h,v-=h,y-=C,b>=M)T=b-M,s.window[b++]=s.window[T++],s.window[b++]=s.window[T++],C-=2;else{T=b-M;do{T+=s.end}while(T<0);if(h=s.end-T,C>h){if(C-=h,b-T>0&&h>b-T)do{s.window[b++]=s.window[T++]}while(0!=--h);else o(s.window,T,s.window,b,h),b+=h,T+=h,h=0;T=0}}do{s.window[b++]=s.window[T++]}while(0!=--C);break}if(0!=(64&h))return l.msg="invalid distance code",C=l.avail_in-w,C=v>>3>3:C,w+=C,g-=C,v-=C<<3,s.bitb=p,s.bitk=v,l.avail_in=w,l.total_in+=g-l.next_in_index,l.next_in_index=g,s.write=b,-3;u+=c[S+2],u+=p&m[h],S=3*(d+u),h=c[S]}break}if(0!=(64&h))return 0!=(32&h)?(C=l.avail_in-w,C=v>>3>3:C,w+=C,g-=C,v-=C<<3,s.bitb=p,s.bitk=v,l.avail_in=w,l.total_in+=g-l.next_in_index,l.next_in_index=g,s.write=b,_):(l.msg="invalid literal/length code",C=l.avail_in-w,C=v>>3>3:C,w+=C,g-=C,v-=C<<3,s.bitb=p,s.bitk=v,l.avail_in=w,l.total_in+=g-l.next_in_index,l.next_in_index=g,s.write=b,-3);if(u+=c[S+2],u+=p&m[h],S=3*(d+u),0==(h=c[S])){p>>=c[S+1],v-=c[S+1],s.window[b++]=c[S+2],y--;break}}else p>>=c[S+1],v-=c[S+1],s.window[b++]=c[S+2],y--}while(y>=258&&w>=10);return C=l.avail_in-w,C=v>>3>3:C,w+=C,g-=C,v-=C<<3,s.bitb=p,s.bitk=v,l.avail_in=w,l.total_in+=g-l.next_in_index,l.next_in_index=g,s.write=b,f},a.prototype.huft_build=function(t,e,i,n,a,r,s,l,u,c,h){var _,m,v,g,w,b,y,x,k,C,M,T,S,O,A;C=0,w=i;do{this.c[t[e+C]]++,C++,w--}while(0!=w);if(this.c[0]==i)return s[0]=-1,l[0]=0,f;for(x=l[0],b=1;b<=15&&0==this.c[b];b++);for(y=b,xw&&(x=w),l[0]=x,O=1<T+x;){if(g++,T+=x,A=v-T,A=A>x?x:A,(m=1<<(b=y-T))>_+1&&(m-=_+1,S=y,bd)return-3;this.u[g]=M=this.hn[0],this.hn[0]+=A,0!=g?(this.x[g]=w,this.r[0]=b,this.r[1]=x,b=w>>>T-x,this.r[2]=M-this.u[g-1]-b,o(this.r,0,u,3*(this.u[g-1]+b),3)):s[0]=M}for(this.r[1]=y-T,C>=i?this.r[0]=192:h[C]>>T;b>>=1)w^=b;for(w^=b,k=(1<257?(-3==u?l.msg="oversubscribed distance tree":u==p?(l.msg="incomplete distance tree",u=-3):-4!=u&&(l.msg="empty distance tree with lengths",u=-3),u):f)},a.prototype.initWorkArea=function(t){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(t),this.c=new Int32Array(16),this.r=new Int32Array(3),this.u=new Int32Array(15),this.x=new Int32Array(16)),this.v.length=this.options.errorAtPercent},_render_quota:function(){var e=this.model.toJSON(),i=e.quota_percent,n=t(this._templateQuotaMeter(e)),a=n.find(".progress-bar");return this.isOverQuota()?(a.attr("class","progress-bar bg-danger"),n.find(".quota-meter-text").css("color","white"),this.trigger("quota:over",e)):i>=this.options.warnAtPercent?(a.attr("class","progress-bar bg-warning"),this.trigger("quota:under quota:under:approaching",e)):(a.attr("class","progress-bar bg-success"),this.trigger("quota:under quota:under:ok",e)),n},_render_usage:function(){var e=t(this._templateUsage(this.model.toJSON()));return this.log(this+".rendering usage:",e),e},render:function(){var t=null;return this.log(this+".model.quota_percent:",this.model.get("quota_percent")),t=null===this.model.get("quota_percent")||void 0===this.model.get("quota_percent")?this._render_usage():this._render_quota(),this.$el.html(t),this.$el.find(".quota-meter-text").tooltip(),this},_templateQuotaMeter:function(t){return['"].join("")},_templateUsage:function(t){return['
','
',t.nice_total_disk_usage?(0,h.default)("Using ")+t.nice_total_disk_usage:"","
","
"].join("")},toString:function(){return"UserQuotaMeter("+this.model+")"}});e.default={UserQuotaMeter:f}}).call(e,i(0))},15:function(t,e,i){"use strict";(function(t,n){function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var r=i(3),o=a(r),s=i(1),l=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.prototype.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e}(s),u=i(14),c=a(u),d=i(18),h=a(d),f=i(33),_=a(f),p=i(24),m=a(p),v=i(80),g=a(v),w={toJSON:function(){var t=this,e={};return l.each(t.constructor.to_json_keys,function(i){var n=t.get(i);i in t.constructor.to_json_mappers&&(n=t.constructor.to_json_mappers[i](n,t)),e[i]=n}),e}},b=function(e,i){var n=new m.default({url_base:Galaxy.root+"visualization/list_history_datasets",filters:e,embedded:!0}),a=new m.default({url_base:Galaxy.root+"visualization/list_library_datasets",embedded:!0}),r=new g.default.View;r.add({id:"histories",title:(0,o.default)("Histories"),$el:t("
").append(n.$el)}),r.add({id:"libraries",title:(0,o.default)("Libraries"),$el:t("
").append(a.$el)}),Galaxy.modal.show({title:(0,o.default)("Select datasets for new tracks"),body:r.$el,closing_events:!0,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var e=[];r.$("input.grid-row-select-checkbox[name=id]:checked").each(function(){window.console.log(t(this).val()),e[e.length]=t.ajax({url:Galaxy.root+"api/datasets/"+t(this).val(),dataType:"json",data:{data_type:"track_config",hda_ldda:"histories"==r.current()?"hda":"ldda"}})}),t.when.apply(t,e).then(function(){var e=arguments[0]instanceof Array?t.map(arguments,function(t){return t[0]}):[arguments[0]];i(e)}),Galaxy.modal.hide()}}})},y=function(t){this.default_font=void 0!==t?t:"9px Monaco, Lucida Console, monospace",this.dummy_canvas=this.new_canvas(),this.dummy_context=this.dummy_canvas.getContext("2d"),this.dummy_context.font=this.default_font,this.char_width_px=this.dummy_context.measureText("A").width,this.patterns={},this.load_pattern("right_strand","/visualization/strand_right.png"),this.load_pattern("left_strand","/visualization/strand_left.png"),this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png"),this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};l.extend(y.prototype,{load_pattern:function(t,e){var i=this.patterns,n=this.dummy_context,a=new Image;a.src=Galaxy.root+"static/images"+e,a.onload=function(){i[t]=n.createPattern(a,"repeat")}},get_pattern:function(t){return this.patterns[t]},new_canvas:function(){var e=t("")[0];return e.manager=this,e}});var x=n.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(t){this.clear()},get_elt:function(t){var 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0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),k=x.extend({defaults:l.extend({},x.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(t,e){return!0},can_subset:function(t){return!1}}),initialize:function(t){x.prototype.initialize.call(this);var e=this.get("init_data");e&&this.add_data(e)},add_data:function(t){this.get("num_elements")d.get("start")?t.set("end",t.get("start")+this.attributes.min_region_size):t.set("start",t.get("end")-this.attributes.min_region_size),t.set("genome",this.attributes.genome),t.trim()}return this.load_data(t,e,i,n)},set_data:function(t,e){this.set_elt(t,e)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(e,i,n,a,r){var o=this._mark_stale(e);if(!o||!this.get("data_mode_compatible")(o,i))return void console.log("ERROR: problem with getting more data: current data is not compatible");var 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t.length()<=1e5?k.prototype.load_data.call(this,t,e,i,n):{data:null,region:t}}}),M=n.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(t){this.id=t.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(t){var e=l.find(this.get_chroms_info(),function(e){return e.chrom===t});return new T({chrom:e.chrom,end:e.len})},get_chrom_len:function(t){return l.find(this.get_chroms_info(),function(e){return e.chrom===t}).len}}),T=n.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(t){return this.attributes.chrom===t.get("chrom")&&this.attributes.start===t.get("start")&&this.attributes.end===t.get("end")},initialize:function(t){if(t.from_str){var e=t.from_str.split(":"),i=e[0],n=e[1].split("-");this.set({chrom:i,start:parseInt(n[0],10),end:parseInt(n[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new T({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(t){var e=this.get("chrom"),i=t.get("chrom"),n=this.get("start"),a=t.get("start"),r=this.get("end"),o=t.get("end");return e&&i&&e!==i?T.overlap_results.DIF_CHROMS:na?n>o?T.overlap_results.AFTER:r<=o?T.overlap_results.CONTAINED_BY:T.overlap_results.OVERLAP_END:r>=o?T.overlap_results.CONTAINS:T.overlap_results.CONTAINED_BY},trim:function(t){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var e=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>e&&(this.attributes.end=e-1)}return this},contains:function(t){return this.compute_overlap(t)===T.overlap_results.CONTAINS},overlaps:function(t){return 0===l.intersection([this.compute_overlap(t)],[T.overlap_results.DIF_CHROMS,T.overlap_results.BEFORE,T.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),S=n.Collection.extend({model:T}),O=n.Model.extend({defaults:{region:null,note:""},initialize:function(t){this.set("region",new T(t.region))}}),A=n.Collection.extend({model:O}),z=n.Model.extend(w).extend({defaults:{mode:"Auto"},initialize:function(t){this.set("dataset",new c.default.Dataset(t.dataset));var e=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",_.default.ConfigSettingCollection.from_models_and_saved_values(e,t.prefs));var i=this.get("preloaded_data");i=i?i.data:[],this.set("data_manager",new k({dataset:this.get("dataset"),init_data:i}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(t,e){return 0===l.size(t)&&(t={name:e.get("config").get("name").get("value"),color:e.get("config").get("color").get("value")}),t},dataset:function(t){return{id:t.id,hda_ldda:t.get("hda_ldda")}}}}),P=n.Collection.extend({model:z}),R=n.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return t.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),j=R.extend(w).extend({defaults:l.extend({},R.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(t){this.set("drawables",new P(t.tracks));var 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i=this,a=this;this.config=n.defaults(e.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:"",hide_panels:!1,hide_masthead:!1}),Galaxy.modal=this.modal=new d.default.View,Galaxy.router=this.router=e.Router&&new e.Router(a,e),this.masthead=new s.default.View(this.config),this.center=new 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"],"history");return e.extend(e.clone(p.prototype.templates),{quotaMsg:t})}(),t.default={CurrentHistoryView:_}}).call(t,i(1),i(0),i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),r=s(o),l=i(26),d=(s(l),i(10)),c=s(d),u=i(32),h=s(u),f=e.Model.extend({initialize:function(e){e=e||{},e.user_id=e.user_id||Galaxy.user.id,this.set({user_id:e.user_id,information:{title:(0,r.default)("Manage information"),description:"Edit your email, addresses and custom parameters or change your username.",url:"api/users/"+e.user_id+"/information/inputs",icon:"fa-user",redirect:"user"},password:{title:(0,r.default)("Change password"),description:(0,r.default)("Allows you to change your login credentials."),icon:"fa-unlock-alt",url:"api/users/"+e.user_id+"/password/inputs",submit_title:"Save password",redirect:"user"},communication:{title:(0,r.default)("Change communication settings"),description:(0,r.default)("Enable or disable the communication feature to chat with other users."),url:"api/users/"+e.user_id+"/communication/inputs",icon:"fa-comments-o",redirect:"user"},permissions:{title:(0,r.default)("Set dataset permissions for new histories"),description:"Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.",url:"api/users/"+e.user_id+"/permissions/inputs",icon:"fa-users",submit_title:"Save permissions",redirect:"user"},api_key:{title:(0,r.default)("Manage API key"),description:(0,r.default)("Access your current API key or create a new one."),url:"api/users/"+e.user_id+"/api_key/inputs",icon:"fa-key",submit_title:"Create a new key",submit_icon:"fa-check"},toolbox_filters:{title:(0,r.default)("Manage Toolbox filters"),description:(0,r.default)("Customize your Toolbox by displaying or omitting sets of Tools."),url:"api/users/"+e.user_id+"/toolbox_filters/inputs",icon:"fa-filter",submit_title:"Save filters",redirect:"user"},openids:{title:(0,r.default)("Manage OpenIDs"),description:(0,r.default)("Associate OpenIDs with your account."),icon:"fa-openid",onclick:function(){window.location.href=Galaxy.root+"openids/list"}},custom_builds:{title:(0,r.default)("Manage custom builds"),description:(0,r.default)("Add or remove custom builds using history datasets."),icon:"fa-cubes",onclick:function(){window.location.href=Galaxy.root+"custom_builds"}},logout:{title:(0,r.default)("Sign out"),description:(0,r.default)("Click here to sign out of all sessions."),icon:"fa-sign-out",onclick:function(){Galaxy.modal.show({title:(0,r.default)("Sign out"),body:"Do you want to continue and sign out of all active sessions?",buttons:{Cancel:function(){Galaxy.modal.hide()},"Sign out":function(){window.location.href=Galaxy.root+"user/logout?session_csrf_token="+Galaxy.session_csrf_token}}})}}})}}),p=e.View.extend({title:(0,r.default)("User Preferences"),active_tab:"user",initialize:function(){this.model=new f,this.setElement("
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You are using '+e.nice_total_disk_usage+" of disk space in this Galaxy instance. "+(Galaxy.config.enable_quotas?"Your disk quota is: "+e.quota+". ":"")+'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.

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").text("System Installed Builds").addClass("ui-margin-top")).append(this.installed_builds.$el)).append(n("

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Length Format

The length format is two-column, separated by whitespace, of the form:

chrom/contig   length of chrom/contig

For example, the first few entries of mm9.len are as follows:

chr1    197195432\nchr2    181748087\nchr3    159599783\nchr4    155630120\nchr5    152537259

Trackster uses this information to populate the select box for chrom/contig, andto set the maximum basepair of the track browser. You may either upload a .len fileof this format (Len File option), or directly enter the information into the box (Len Entry option).

"},_templateFasta:function(){return"

FASTA format

This is a multi-fasta file from your current history that provides the genomesequences for each chromosome/contig in your build.

Here is a snippet from an example multi-fasta file:

>chr1\nATTATATATAAGACCACAGAGAGAATATTTTGCCCGG...\n\n>chr2\nGGCGGCCGCGGCGATATAGAACTACTCATTATATATA...\n\n...

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t&&i&&t!==i?T.overlap_results.DIF_CHROMS:na?n>o?T.overlap_results.AFTER:s<=o?T.overlap_results.CONTAINED_BY:T.overlap_results.OVERLAP_END:s>=o?T.overlap_results.CONTAINS:T.overlap_results.CONTAINED_BY},trim:function(e){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var t=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>t&&(this.attributes.end=t-1)}return this},contains:function(e){return this.compute_overlap(e)===T.overlap_results.CONTAINS},overlaps:function(e){return 0===l.intersection([this.compute_overlap(e)],[T.overlap_results.DIF_CHROMS,T.overlap_results.BEFORE,T.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),M=n.Collection.extend({model:T}),$=n.Model.extend({defaults:{region:null,note:""},initialize:function(e){this.set("region",new T(e.region))}}),P=n.Collection.extend({model:$}),O=n.Model.extend(w).extend({defaults:{mode:"Auto"},initialize:function(e){this.set("dataset",new c.default.Dataset(e.dataset));var t=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",p.default.ConfigSettingCollection.from_models_and_saved_values(t,e.prefs));var i=this.get("preloaded_data");i=i?i.data:[],this.set("data_manager",new k({dataset:this.get("dataset"),init_data:i}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(e,t){return 0===l.size(e)&&(e={name:t.get("config").get("name").get("value"),color:t.get("config").get("color").get("value")}),e},dataset:function(e){return{id:e.id,hda_ldda:e.get("hda_ldda")}}}}),E=n.Collection.extend({model:O}),A=n.Model.extend({defaults:{title:"",type:""},urlRoot:Galaxy.root+"api/visualizations",save:function(){return e.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),D=A.extend(w).extend({defaults:l.extend({},A.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(e){this.set("drawables",new E(e.tracks));var t=[];this.set("config",p.default.ConfigSettingCollection.from_models_and_saved_values(t,e.prefs)),this.unset("tracks"),this.get("drawables").each(function(e){e.unset("preloaded_data")})},add_tracks:function(e){this.get("drawables").add(e)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(e,t){return{obj_type:"View",prefs:{name:t.get("title"),content_visible:!0},drawables:t.get("drawables")}}}}),z=n.Router.extend({initialize:function(e){var 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'].join("")},toString:function(){return"historyPanel"}});t.default=h}).call(t,i(2))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function a(e,t,i){return o.clone(_).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target=n.target||"galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}Object.defineProperty(t,"__esModule",{value:!0});var s=i(1),o=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(s),r=i(3),l=n(r),d=i(41),c=n(d),u=i(143),h=n(u),f=i(25),p=n(f),_=[{html:(0,l.default)("History Lists"),header:!0},{html:(0,l.default)("Saved Histories"),href:"histories/list",target:"_top"},{html:(0,l.default)("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:(0,l.default)("Current History"),header:!0,anon:!0},{html:(0,l.default)("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:(0,l.default)("Copy History"),func:function(){(0,h.default)(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Share or Publish"),href:"history/sharing"},{html:(0,l.default)("Show Structure"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/show_structure")}},{html:(0,l.default)("Extract Workflow"),href:"workflow/build_from_current_history"},{html:(0,l.default)("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete the current history?"))&&Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete the current history permanently? This cannot be undone."))&&Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Dataset Actions"),header:!0,anon:!0},{html:(0,l.default)("Copy Datasets"),href:"dataset/copy_datasets"},{html:(0,l.default)("Dataset Security"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/permissions?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,l.default)("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:(0,l.default)("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:(0,l.default)("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really unhide all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,l.default)("Really delete all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,l.default)("Purge Deleted Datasets"),confirm:(0,l.default)("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:(0,l.default)("Downloads"),header:!0},{html:(0,l.default)("Export Tool Citations"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/citations?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,l.default)("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:(0,l.default)("Other Actions"),header:!0},{html:(0,l.default)("Import from File"),href:"histories/import",target:"_top"}];p.default.load({type:"history-menu",async:!1,callback:function(t){var i=[];t.each(function(e){var t=e.toJSON();t.activate&&i.push({html:(0,l.default)(t.config.title),anon:!0})}),i.length>0&&(i.unshift({html:(0,l.default)("Webhooks"),header:!0}),e.merge(_,i))}});var m=function(e,t){t=t||{};var i=void 0===t.anonymous||t.anonymous,n=t.purgeAllowed||!1,s=a(i,n,Galaxy.root);return new c.default(e,s)};t.default=m}).call(t,i(0))},function(e,t,i){"use strict";(function(e,n,a){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(144),r=(s(o),i(176)),l=s(r),d=i(6),c=s(d),u=i(3),h=s(u),f=c.default.SessionStorageModel.extend({defaults:{tagsEditorShown:!1,annotationEditorShown:!1,scrollPosition:0},toString:function(){return"HistoryViewPrefs("+JSON.stringify(this.toJSON())+")"}});f.storageKey=function(){return"history-panel"};var p=l.default.HistoryViewEdit,_=p.extend({className:p.prototype.className+" current-history-panel",HDCAViewClass:p.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),emptyMsg:[(0,h.default)("This history is empty"),". ",(0,h.default)("You can "),'',(0,h.default)("load your own data"),"",(0,h.default)(" or "),'',(0,h.default)("get data from an external source"),""].join(""),initialize:function(t){t=t||{},this.preferences=new f(e.extend({id:f.storageKey()},e.pick(t,e.keys(f.prototype.defaults)))),p.prototype.initialize.call(this,t),this.panelStack=[],this.currentContentId=t.currentContentId||null},_setUpListeners:function(){p.prototype._setUpListeners.call(this);var e=this;this.on("new-model",function(){e.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(){return this.loadHistory(null,{url:Galaxy.root+"history/current_history_json"})},switchToHistory:function(e,t){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to switch histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(e,{url:Galaxy.root+"history/set_as_current?id="+e})},createNewHistory:function(e){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to create histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(null,{url:Galaxy.root+"history/create_new_current"})},setModel:function(e,t,i){return p.prototype.setModel.call(this,e,t,i),this.model&&this.model.id&&(this.log("checking for updates"),this.model.checkForUpdates()),this},_setUpModelListeners:function(){return p.prototype._setUpModelListeners.call(this),this.listenTo(this.model,{"change:nice_size change:size":function(){this.trigger("history-size-change",this,this.model,arguments)},"change:id":function(){this.once("loading-done",function(){this.model.checkForUpdates()})}})},_setUpCollectionListeners:function(){p.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,"state:ready",function(e,t,i){e.get("visible")||this.collection.storage.includeHidden()||this.removeItemView(e)})},_setUpBehaviors:function(t){t=t||this.$el;var i=this;return p.prototype._setUpBehaviors.call(i,t),this._debouncedScrollCaptureHandler||(this._debouncedScrollCaptureHandler=e.debounce(function(){i.$el.is(":visible")&&i.preferences.set("scrollPosition",n(this).scrollTop())},40)),i.$scrollContainer(t).off("scroll",this._debouncedScrollCaptureHandler).on("scroll",this._debouncedScrollCaptureHandler),i},_buildNewRender:function(){if(!this.model)return n();var e=p.prototype._buildNewRender.call(this);return e.find(".search").prependTo(e.find("> .controls")),this._renderQuotaMessage(e),e},_renderQuotaMessage:function(e){return e=e||this.$el,n(this.templates.quotaMsg({},this)).prependTo(e.find(".messages"))},_renderTags:function(e){var t=this;p.prototype._renderTags.call(t,e),t.preferences.get("tagsEditorShown")&&t.tagsEditor.toggle(!0),t.listenTo(t.tagsEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("tagsEditorShown",e.hidden)})},_renderAnnotation:function(e){var t=this;p.prototype._renderAnnotation.call(t,e),t.preferences.get("annotationEditorShown")&&t.annotationEditor.toggle(!0),t.listenTo(t.annotationEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("annotationEditorShown",e.hidden)})},_swapNewRender:function(t){p.prototype._swapNewRender.call(this,t);var i=this;return e.delay(function(){var e=i.preferences.get("scrollPosition");e&&i.scrollTo(e,0)},10),this},_attachItems:function(e){p.prototype._attachItems.call(this,e);var t=this;return t.currentContentId&&t._setCurrentContentById(t.currentContentId),this},addItemView:function(e,t,i){var n=p.prototype.addItemView.call(this,e,t,i);return n&&this.panelStack.length?this._collapseDrilldownPanel():n},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}})},setCurrentContent:function(e){this.$(".history-content.current-content").removeClass("current-content"),e?(e.$el.addClass("current-content"),this.currentContentId=e.model.id):this.currentContentId=null},_setCurrentContentById:function(e){var t=this.viewFromModelId(e)||null;this.setCurrentContent(t)},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$controls().add(this.$list()).hide(),e.parentName=this.model.get("name"),e.delegateEvents().render().$el.appendTo(this.$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.$controls().add(this.$list()).show()},events:e.extend(e.clone(p.prototype.events),{"click .uploader-link":function(e){Galaxy.upload.show(e)},"click .get-data-link":function(e){var t=n(".toolMenuContainer");t.parent().scrollTop(0),t.find('span:contains("Get Data")').click()}}),listenToGalaxy:function(t){this.listenTo(t,{"center-frame:load":function(t){var i=t.fullpath,n=null,a={display:/datasets\/([a-f0-9]+)\/display/,edit:/datasets\/([a-f0-9]+)\/edit/,report_error:/dataset\/errors\?id=([a-f0-9]+)/,rerun:/tool_runner\/rerun\?id=([a-f0-9]+)/,show_params:/datasets\/([a-f0-9]+)\/show_params/};e.find(a,function(t,a){return n=e.result(i.match(t),1)}),this._setCurrentContentById(n?"dataset-"+n:null)},"center-panel:load":function(e){this._setCurrentContentById()}})},connectToQuotaMeter:function(e){return e?(this.listenTo(e,"quota:over",this.showQuotaMessage),this.listenTo(e,"quota:under",this.hideQuotaMessage),this.on("rendered rendered:initial",function(){e&&e.isOverQuota()&&this.showQuotaMessage()}),this):this},clearMessages:function(t){var i=e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget);return 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t=this;document.addEventListener("copy",function(e){""===window.getSelection().toString()&&(t.app.workflow.active_node&&"subworkflow"!==t.app.workflow.active_node.type&&e.clipboardData.setData("application/json",JSON.stringify({nodeId:t.app.workflow.active_node.id})),e.preventDefault())}),document.addEventListener("paste",function(e){if(document.activeElement&&"textarea"!==document.activeElement.type&&"text"!==document.activeElement.type){var n;try{n=JSON.parse(e.clipboardData.getData("application/json")).nodeId}catch(t){}n&&t.app.workflow.nodes.hasOwnProperty(n)&&t.app.workflow.nodes[n].clone(),e.preventDefault()}})},update_viewport_overlay:function(){var t=this.cc,e=this.cv,n=this.oc,i=this.ov,r=t.width(),a=t.height(),o=n.width(),s=n.height(),l=t.position();i.css({left:-l.left/r*o,top:-l.top/a*s,width:e.width()/r*o-2,height:e.height()/a*s-2})},draw_overview:function(){var 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t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(5),s=a(o),l=n(720),c=a(l),d=t.Model.extend({initialize:function(t,e){this.app=t,this.element=e.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(t){return i.findWhere(this.workflow_outputs,{output_name:t})},isWorkflowOutput:function(t){return void 0!==this.getWorkflowOutput(t)},removeWorkflowOutput:function(t){for(;this.isWorkflowOutput(t);){var e=this.getWorkflowOutput(t);this.workflow_outputs.splice(i.indexOf(this.workflow_outputs,e),1)}},addWorkflowOutput:function(t,e){if(!this.isWorkflowOutput(t)){var n={output_name:t};return e&&(n.label=e),this.workflow_outputs.push(n),!0}return!1},labelWorkflowOutput:function(t,e){var n=!1,i=null;if(this.isWorkflowOutput(t)){var r=this.getWorkflowOutput(t);i=r.label,r.label=e,n=i!=e}else n=this.addWorkflowOutput(t,e);return 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r=Object.assign({},i,e);n.init_field_data(r),n.update_field_data(r),t.app.workflow.activate_node(n)}})},destroy:function(){r.each(this.input_terminals,function(t,e){e.destroy()}),r.each(this.output_terminals,function(t,e){e.destroy()}),this.app.workflow.remove_node(this),r(this.element).remove()},make_active:function(){r(this.element).addClass("toolForm-active")},make_inactive:function(){var t=this.element.get(0);!function(e){e.removeChild(t),e.appendChild(t)}(t.parentNode),r(t).removeClass("toolForm-active")},set_tool_version:function(){"tool"===this.type&&this.config_form&&(this.tool_version=this.config_form.version,this.content_id=this.config_form.id)},init_field_data:function(t){t.type&&(this.type=t.type),this.name=t.name,this.config_form=t.config_form,this.set_tool_version(),this.tool_state=t.tool_state,this.errors=t.errors,this.tooltip=t.tooltip?t.tooltip:"",this.annotation=t.annotation,this.post_job_actions=t.post_job_actions?t.post_job_actions:{},this.label=t.label,this.uuid=t.uuid,this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[];var e=this,n=new c.default({el:this.element[0],node:e});e.nodeView=n,r.each(t.data_inputs,function(t,e){n.addDataInput(e)}),t.data_inputs.length>0&&t.data_outputs.length>0&&n.addRule(),r.each(t.data_outputs,function(t,e){n.addDataOutput(e)}),n.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(t){var e=this,n=e.nodeView,a=[];if(r.each(n.outputViews,function(e,n){var r=n.output.name,o=t.data_outputs,s=!1;i.each(o,function(t){t.name==r&&(s=!0)}),!1===s&&a.push(r)}),i.each(a,function(t){i.each(n.outputViews[t].terminalElement.terminal.connectors,function(t){t&&t.destroy()}),n.outputViews[t].remove(),delete n.outputViews[t],delete e.output_terminals[t]}),r.each(e.workflow_outputs,function(t,n){n&&!e.output_terminals[n.output_name]&&e.workflow_outputs.splice(t,1)}),r.each(t.data_outputs,function(t,i){n.outputViews[i.name]?(e.output_terminals[i.name].datatypes=i.extensions,e.output_terminals[i.name].destroyInvalidConnections()):n.addDataOutput(i)}),this.tool_state=t.tool_state,this.config_form=t.config_form,this.set_tool_version(),this.errors=t.errors,this.annotation=t.annotation,this.label=t.label,"post_job_actions"in t){var o=t.post_job_actions;this.post_job_actions=o||{}}e.nodeView.renderToolErrors();var s=n.$("div.inputs"),l=n.newInputsDiv(),c={};i.each(t.data_inputs,function(t){var n=e.nodeView.addDataInput(t,l);c[t.name]=n}),i.each(i.difference(i.values(n.terminalViews),i.values(c)),function(t){t.el.terminal.destroy()}),n.terminalViews=c,e.nodeView.render(),1==t.data_outputs.length&&"collection_type"in t.data_outputs[0]&&n.updateDataOutput(t.data_outputs[0]),s.replaceWith(l),"workflow_outputs"in t&&(this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(t){var e=r(this.element).find(".toolFormBody");e.find("div").remove();var n="
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    ";this.config_form=n,e.html(n),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});e.default=d}).call(e,n(2),n(1),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var a=n(1),o=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(a),s=n(721),l=r(s),c=n(723),d=r(c);e.default=t.View.extend({initialize:function(t){this.node=t.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputViews={}},render:function(){this.renderToolLabel(),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolLabel:function(){this.$(".nodeTitle").text(this.node.label||this.node.name),this.$el.attr("node-label",this.node.label)},renderToolErrors:function(){this.node.errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return i("
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s.default.OutputCollectionTerminal({element:this.el,collection_type:e,collection_type_source:n,datatypes:t.extensions})}});e.default={InputTerminalView:p,OutputTerminalView:m,InputCollectionTerminalView:_,OutputCollectionTerminalView:v}}).call(e,n(2),n(1),n(0))},function(t,e,n){"use strict";(function(t,i,r){function a(t){this.collectionType=t,this.isCollection=!0,this.rank=t.split(":").length}Object.defineProperty(e,"__esModule",{value:!0});var o=n(20),s=function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}(o);window.workflow_globals=window.workflow_globals||{};var l={isCollection:!1,canMatch:function(){return!1},canMapOver:function(){return!1},toString:function(){return"NullCollectionType[]"},append:function(t){return t},equal:function(t){return t===this}},c={isCollection:!0,canMatch:function(t){return l!==t},canMapOver:function(){return!1},toString:function(){return"AnyCollectionType[]"},append:function(){return c},equal:function(t){return t===this}};t.extend(a.prototype,{append:function(t){return t===l?this:t===c?t:new a(this.collectionType+":"+t.collectionType)},canMatch:function(t){return t!==l&&(t===c||t.collectionType==this.collectionType)},canMapOver:function(t){if(t===l)return!1;if(t===c)return!1;if(this.rank<=t.rank)return!1;var e=t.collectionType;return this._endsWith(this.collectionType,e)},effectiveMapOver:function(t){var e=t.collectionType;return new a(this.collectionType.substring(0,this.collectionType.length-e.length-1))},equal:function(t){return t.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(t,e){return-1!==t.indexOf(e,t.length-e.length)}});var d=i.Model.extend({initialize:function(t){this.mapOver=t.mapOver||l,this.terminal=t.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(l)},setMapOver:function(t){this.mapOver=t,this.trigger("change")}}),u=i.Model.extend({initialize:function(t){this.element=t.element,this.connectors=[]},connect:function(t){this.connectors.push(t),this.node&&this.node.markChanged()},disconnect:function(e){this.connectors.splice(t.inArray(e,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){t.each(this.connectors,function(t,e){e.redraw()})},destroy:function(){t.each(this.connectors.slice(),function(t,e){e.destroy()})},destroyInvalidConnections:function(){r.each(this.connectors,function(t){t&&t.destroyIfInvalid()})},setMapOver:function(t){this.multiple||this.mapOver().equal(t)||(this.terminalMapping.setMapOver(t),r.each(this.node.output_terminals,function(e){e.setMapOver(t)}))},mapOver:function(){return this.terminalMapping?this.terminalMapping.mapOver:l},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){}}),h=u.extend({initialize:function(t){u.prototype.initialize.call(this,t),this.datatypes=t.datatypes},resetMappingIfNeeded:function(){this.node.hasConnectedOutputTerminals()||this.node.hasConnectedMappedInputTerminals()||r.each(this.node.mappedInputTerminals(),function(t){t.resetMappingIfNeeded()}),!this.node.hasMappedOverInputTerminals()&&this.resetMapping()},resetMapping:function(){this.terminalMapping.disableMapOver(),r.each(this.connectors,function(t){var e=t.handle2;e&&(e.resetMappingIfNeeded(),t.destroyIfInvalid())})}}),f=u.extend({initialize:function(t){u.prototype.initialize.call(this,t),this.update(t.input)},canAccept:function(t){return!this._inputFilled()&&this.attachable(t)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||r.each(this.node.output_terminals,function(t){t.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){return!!this.connected()&&(!this.multiple||!!this._collectionAttached())},_collectionAttached:function(){if(this.connected()){var t=this.connectors[0].handle1;return!!t&&!!(t.isCollection||t.isMappedOver()||t.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var t=this.mapOver();if(t.isCollection)return[t];var e=[];return this.node.hasConnectedOutputTerminals()?e.push(r.first(r.values(this.node.output_terminals)).mapOver()):r.each(this.node.connectedMappedInputTerminals(),function(t){e.push(t.mapOver())}),e},_producesAcceptableDatatype:function(t){for(var e in this.datatypes){var n=this.datatypes[e];if("input"==n)return!0;var i=[];if(i=i.concat(t.datatypes),t.node.post_job_actions)for(var r in t.node.post_job_actions){var a=t.node.post_job_actions[r];"ChangeDatatypeAction"!=a.action_type||""!==a.output_name&&a.output_name!=t.name||!a.action_arguments||i.push(a.action_arguments.newtype)}for(var o in i){var s=i[o];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(i[o],n))return!0}}return!1},_otherCollectionType:function(t){var e=l;t.isCollection&&(e=t.collectionType);var n=t.mapOver();return n.isCollection&&(e=n.append(e)),e}}),p=f.extend({update:function(t){this.datatypes=t.extensions,this.multiple=t.multiple,this.collection=!1},connect:function(t){f.prototype.connect.call(this,t);var e=t.handle1;if(e){var n=this._otherCollectionType(e);n.isCollection&&this.setMapOver(n)}},attachable:function(t){var e=this._otherCollectionType(t),n=this.mapOver();if(e.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==e.rank&&this._producesAcceptableDatatype(t));if(n.isCollection&&n.canMatch(e))return this._producesAcceptableDatatype(t);return!!this._mappingConstraints().every(r.bind(e.canMatch,e))&&this._producesAcceptableDatatype(t)}return!n.isCollection&&this._producesAcceptableDatatype(t)}}),_=f.extend({update:function(t){this.multiple=!1,this.collection=!0,this.datatypes=t.extensions;var e=[];t.collection_types?r.each(t.collection_types,function(t){e.push(new a(t))}):e.push(c),this.collectionTypes=e},connect:function(t){f.prototype.connect.call(this,t);var e=t.handle1;if(e){var n=this._effectiveMapOver(e);this.setMapOver(n)}},_effectiveMapOver:function(t){var e=this.collectionTypes,n=this._otherCollectionType(t);if(!r.some(e,function(t){return t.canMatch(n)}))for(var i in e){var a=e[i];if(n.canMapOver(a)){var o=n.effectiveMapOver(a);if(o!=l)return o}}return l},_effectiveCollectionTypes:function(){var t=this.mapOver();return r.map(this.collectionTypes,function(e){return t.append(e)})},attachable:function(t){var e=this._otherCollectionType(t);if(e.isCollection){var n=this._effectiveCollectionTypes(),i=this.mapOver();if(r.some(n,function(t){return t.canMatch(e)}))return this._producesAcceptableDatatype(t);if(i.isCollection)return!1;if(r.some(this.collectionTypes,function(t){return e.canMapOver(t)})){var a=this._effectiveMapOver(t);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return this._producesAcceptableDatatype(t)}}return!1}}),g=u.extend({initialize:function(t){if(u.prototype.initialize.call(this,t),this.datatypes=t.datatypes,t.collection_type)this.collectionType=new a(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),this.collectionType=c}this.isCollection=!0},update:function(t){var e;if(t.collection_type)e=new a(t.collection_type);else{t.collection_type_source||console.log("Warning: No collection type or collection type source defined."),e=c}e.collectionType!=this.collectionType.collectionType&&r.each(this.connectors,function(t){s.warning("Destroying a connection because collection type has changed."),t.destroy()}),this.collectionType=e}});e.default={InputTerminal:p,OutputTerminal:h,InputCollectionTerminal:_,OutputCollectionTerminal:g,TerminalMapping:d,CollectionTypeDescription:a,NULL_COLLECTION_TYPE_DESCRIPTION:l,ANY_COLLECTION_TYPE_DESCRIPTION:c}}).call(e,n(0),n(2),n(1))},function(t,e,n){"use strict";(function(t,n){Object.defineProperty(e,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var i=t.View.extend({className:"form-row dataRow input-data-row",initialize:function(t){this.input=t.input,this.nodeView=t.nodeView,this.terminalElement=t.terminalElement,this.$el.attr("name",this.input.name).html(this.input.label),t.skipResize||(this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),n("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()),this.$el.css({position:"",left:"",top:"",display:""}),this.$el.remove())}}),r=t.View.extend({className:"form-row dataRow",initialize:function(t){this.output=t.output,this.terminalElement=t.terminalElement,this.nodeView=t.nodeView;var e=this.output,i=e.name,r=this.nodeView.node;if(e.extensions.indexOf("input")>=0||e.extensions.indexOf("input_collection")>=0||(i=i+" ("+e.extensions.join(", ")+")"),this.$el.html(i),this.calloutView=null,["tool","subworkflow"].indexOf(r.type)>=0){var o=new a({label:i,output:e,node:r});this.calloutView=o,this.$el.append(o.el),this.$el.hover(function(){o.hoverImage()},function(){o.resetImage()})}this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),n("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()+17),this.$el.css({position:"",left:"",top:"",display:""}).detach()},redrawWorkflowOutput:function(){this.calloutView&&this.calloutView.resetImage()}}),a=t.View.extend({tagName:"div",initialize:function(t){this.label=t.label,this.node=t.node,this.output=t.output;var e=this,i=this.node;this.$el.attr("class","callout "+this.label).css({display:"none"}).append(n("
    ").append(n("").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png").click(function(){var t=e.output.name;i.isWorkflowOutput(t)?(i.removeWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")):(i.addWorkflowOutput(t),e.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png")),window.workflow_globals.workflow.has_changes=!0,window.workflow_globals.canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. All unmarked datasets will be hidden."}),this.$el.css({top:"50%",margin:"-8px 0px 0px 0px",right:8}),this.$el.show(),this.resetImage()},resetImage:function(){this.node.isWorkflowOutput(this.output.name)?this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"):this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")},hoverImage:function(){this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-yellow.png")}});e.default={DataInputView:i,DataOutputView:r}}).call(e,n(2),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){return t&&t.__esModule?t:{default:t}}function a(t){var e=t.model.attributes,n=e.workflow,i=e.node;e.inputs.unshift({type:"text",name:"__annotation",label:"Annotation",fixed:!0,value:i.annotation,area:!0,help:"Add an annotation or notes to this step. Annotations are available when a workflow is viewed."}),e.inputs.unshift({type:"text",name:"__label",label:"Label",value:i.label,help:(0,d.default)("Add a step label."),fixed:!0,onchange:function(e){var r=!1;for(var a in n.nodes){var o=n.nodes[a];if(o.label&&o.label==e&&o.id!=i.id){r=!0;break}}var s=t.data.match("__label");t.element_list[s].model.set("error_text",r&&"Duplicate label. Please fix this before saving the workflow."),t.trigger("change")}})}function o(t,e,n,i){var r=i.node.post_job_actions;e=e||[],e.push(t);for(var a in t.inputs){var s=t.inputs[a];if(s.action){if(s.name="pja__"+n+"__"+s.action,s.pja_arg&&(s.name+="__"+s.pja_arg),s.payload)for(var l in s.payload)s.payload[s.name+"__"+l]=s.payload[l],delete s.payload[l];var c=r[s.action+n];if(c){for(var d in e)e[d].expanded=!0;s.pja_arg?s.value=c.action_arguments&&c.action_arguments[s.pja_arg]||s.value:s.value="true"}}s.inputs&&o(s,e.slice(0),n,i)}}function s(t,e){var n=[],i=[],r=e.datatypes,a=e.node,s=e.workflow;for(var l in r)n.push({0:r[l],1:r[l]});for(l in a.input_terminals)i.push(a.input_terminals[l].name);n.sort(function(t,e){return t.label>e.label?1:t.labelhere     for more information. Valid inputs are: '+i.join(", ")+"."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:n,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Add Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{action:"RemoveTagDatasetAction",pja_arg:"tags",label:"Remove Tags",type:"text",value:"",ignore:"",help:"This action will remove tags for the dataset."},{title:(0,d.default)("Assign columns"),type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return o(u,[],t,e),u}function l(t){var e=t.model.attributes,n=e.inputs,i=e.node,r=i.post_job_actions,a=i.output_terminals&&Object.keys(i.output_terminals)[0];if(a){n.push({name:"pja__"+a+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(r["EmailAction"+a])),ignore:"false",help:(0,d.default)("An email notification will be sent when the job has completed."),payload:{host:window.location.host}}),n.push({name:"pja__"+a+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(r["DeleteIntermediatesAction"+a])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var o in i.output_terminals)n.push(s(o,e))}}Object.defineProperty(e,"__esModule",{value:!0});var c=n(3),d=r(c),u=n(5),h=r(u),f=n(26),p=r(f),_=n(55),g=r(_),m=t.View.extend({initialize:function(t){var e=this,n=t.node;this.form=new p.default(h.default.merge(t,{onchange:function(){h.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{id:n.id,type:n.type,content_id:n.content_id,inputs:e.form.data.create()},success:function(t){n.update_field_data(t)}})}})),a(this.form),this.form.render()}}),v=t.View.extend({initialize:function(t){var e=this,n=t.node;this.form=new g.default(h.default.merge(t,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",initialmodel:function(t,n){e._customize(n),t.resolve()},buildmodel:function(t,e){e.model.get("postchange")(t,e)},postchange:function(t,r){var a=r.model.attributes,o={tool_id:a.id,tool_version:a.version,type:"tool",inputs:i.extend(!0,{},r.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",o),h.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:o,success:function(i){r.model.set(i.config_form),e._customize(r),r.update(i.config_form),r.errors(i.config_form),n.update_field_data(i),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",i),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",e),t.reject()}})}}))},_customize:function(t){var e=t.model.attributes;h.default.deepeach(e.inputs,function(t){t.type&&(-1!=["data","data_collection"].indexOf(t.type)?(t.type="hidden",t.info="Data input '"+t.name+"' ("+h.default.textify(t.extensions)+")",t.value={__class__:"RuntimeValue"}):t.fixed||(t.collapsible_value={__class__:"RuntimeValue"},t.is_workflow=t.options&&0===t.options.length||-1!=["integer","float"].indexOf(t.type)))}),h.default.deepeach(e.inputs,function(t){"conditional"===t.type&&(t.test_param.collapsible_value=void 0)}),l(t),a(t)}});e.default={Default:m,Tool:v}}).call(e,n(2),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(1),c=r(l),d=n(224),u=r(d),h=n(15),f=a(h),p=n(5),_=a(p),g=n(33),m=a(g),v=n(31),y=a(v);n(150);var b=t.Model.extend({is_visible:function(t,e){var n=t.getBoundingClientRect(),r=i("svg")[0].getBoundingClientRect();return!(n.right<0||n.left>r.right||n.bottom<0||n.top>r.bottom)}}),w={drawTicks:function(t,e,n,i,r){var a=t.append("g").selectAll("g").data(e).enter().append("g").selectAll("g").data(n).enter().append("g").attr("class","tick").attr("transform",function(t){return"rotate("+(180*t.angle/Math.PI-90)+")translate("+t.radius+",0)"}),o=[],s=[],l=function(t){return t.angle>Math.PI?"end":null};return r?(o=[0,0,0,-4],s=[4,0,"",".35em"],l=null):(o=[1,0,4,0],s=[0,4,".35em",""]),a.append("line").attr("x1",o[0]).attr("y1",o[1]).attr("x2",o[2]).attr("y1",o[3]).style("stroke","#000"),a.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",l).attr("transform",i).text(function(t){return t.label})},formatNum:function(t,e){if(void 0===e&&(e=2),null===t)return null;var n=null;if(Math.abs(t)<1)n=t.toPrecision(e);else{var i=Math.round(t.toPrecision(e));t=Math.abs(t),t<1e3?n=i:t<1e6?n=Math.round((i/1e3).toPrecision(3)).toFixed(0)+"K":t<1e9&&(n=Math.round((i/1e6).toPrecision(3)).toFixed(0)+"M")}return n}},x=t.Model.extend({}),k=t.View.extend({className:"circster",initialize:function(t){this.genome=t.genome,this.label_arc_height=50,this.scale=1,this.circular_views=null,this.chords_views=null,this.model.get("drawables").on("add",this.add_track,this),this.model.get("drawables").on("remove",this.remove_track,this);var e=this.model.get("config");e.get("arc_dataset_height").on("change:value",this.update_track_bounds,this),e.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(t){return"DiagonalHeatmapTrack"!==t.get("track_type")})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(t){return"DiagonalHeatmapTrack"===t.get("track_type")})},get_tracks_bounds:function(){var t=this.get_circular_tracks(),e=this.model.get("config").get_value("arc_dataset_height"),n=this.model.get("config").get_value("track_gap"),i=Math.min(this.$el.width(),this.$el.height())-20,r=i/2-t.length*(e+n)+n-this.label_arc_height,a=u.range(r,i/2,e+n);return c.map(a,function(t){return[t,t+e]})},render:function(){var t=this,e=t.$el.width(),n=t.$el.height(),i=this.get_circular_tracks(),r=this.get_chord_tracks(),a=t.model.get("config").get_value("total_gap"),o=this.get_tracks_bounds(),s=u.select(t.$el[0]).append("svg").attr("width",e).attr("height",n).attr("pointer-events","all").append("svg:g").call(u.behavior.zoom().on("zoom",function(){var e=d.event.scale;s.attr("transform","translate("+d.event.translate+") scale("+e+")"),t.scale!==e&&(t.zoom_drag_timeout&&clearTimeout(t.zoom_drag_timeout),t.zoom_drag_timeout=setTimeout(function(){},400))})).attr("transform","translate("+e/2+","+n/2+")").append("svg:g").attr("class","tracks");this.circular_views=i.map(function(e,n){var i=new T({el:s.append("g")[0],track:e,radius_bounds:o[n],genome:t.genome,total_gap:a});return i.render(),i}),this.chords_views=r.map(function(e){var n=new A({el:s.append("g")[0],track:e,radius_bounds:o[0],genome:t.genome,total_gap:a});return n.render(),n});var l=this.circular_views[this.circular_views.length-1].radius_bounds[1],c=[l,l+this.label_arc_height];this.label_track_view=new C({el:s.append("g")[0],track:new x,radius_bounds:c,genome:t.genome,total_gap:a}),this.label_track_view.render()},add_track:function(t){var e=this.model.get("config").get_value("total_gap");if("DiagonalHeatmapTrack"===t.get("track_type")){var n=this.circular_views[0].radius_bounds,i=new A({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:n,genome:this.genome,total_gap:e});i.render(),this.chords_views.push(i)}else{var r=this.get_tracks_bounds();c.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])}),c.each(this.chords_views,function(t){t.update_radius_bounds(r[0])});var a=this.circular_views.length,o=new T({el:u.select("g.tracks").append("g")[0],track:t,radius_bounds:r[a],genome:this.genome,total_gap:e});o.render(),this.circular_views.push(o)}},remove_track:function(t,e,n){var i=this.circular_views[n.index];this.circular_views.splice(n.index,1),i.$el.remove();var r=this.get_tracks_bounds();c.each(this.circular_views,function(t,e){t.update_radius_bounds(r[e])})},update_track_bounds:function(){var t=this.get_tracks_bounds();c.each(this.circular_views,function(e,n){e.update_radius_bounds(t[n])}),c.each(this.chords_views,function(e){e.update_radius_bounds(t[0])})}}),M=t.View.extend({tagName:"g",initialize:function(t){this.bg_stroke="#ddd",this.loading_bg_fill="#ffc",this.bg_fill="#ddd",this.total_gap=t.total_gap,this.track=t.track,this.radius_bounds=t.radius_bounds,this.genome=t.genome,this.chroms_layout=this._chroms_layout(),this.data_bounds=[],this.scale=1,this.parent_elt=u.select(this.$el[0])},get_fill_color:function(){var t=this.track.get("config").get_value("block_color");return t||(t=this.track.get("config").get_value("color")),t},render:function(){var t=this.parent_elt,e=this.chroms_layout,n=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),r=t.selectAll("g").data(e).enter().append("svg:g"),a=r.append("path").attr("d",n).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);a.append("title").text(function(t){return t.data.chrom});var o=this,s=o.track.get("data_manager"),l=!s||s.data_is_ready();i.when(l).then(function(){i.when(o._render_data(t)).then(function(){a.style("fill",o.bg_fill),o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(t){this.radius_bounds=t;var e=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1e3).attr("d",e),this._transition_chrom_data(),this._transition_labels()},update_scale:function(t){var e=this.scale;if(this.scale=t,!(t<=e)){var n=this,r=new b;return this.parent_elt.selectAll("path.chrom-data").filter(function(t,e){return r.is_visible(this)}).each(function(e,r){var a,o=u.select(this),s=o.attr("chrom"),l=n.genome.get_chrom_region(s),d=n.track.get("data_manager");d.can_get_more_detailed_data(l)&&(a=n.track.get("data_manager").get_more_detailed_data(l,"Coverage",0,t),i.when(a).then(function(t){o.remove(),n._update_data_bounds();var e=c.find(n.chroms_layout,function(t){return t.data.chrom===s}),i=n.get_fill_color();n._render_chrom_data(n.parent_elt,e,t).style("stroke",i).style("fill",i)}))}),n}},_transition_chrom_data:function(){var t=this.track,e=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data");if(n[0].length>0){var r=this;i.when(t.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){var a=c.reject(c.map(i,function(t,n){var i=null,a=r._get_path_function(e[n],t);return a&&(i=a(t.data)),i}),function(t){return null===t}),o=t.get("config").get_value("color");n.each(function(t,e){u.select(this).transition().duration(1e3).style("stroke",o).style("fill",o).attr("d",a[e])})})}},_transition_labels:function(){},_update_data_bounds:function(t){this.data_bounds=t||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome)),this._transition_chrom_data()},_render_data:function(t){var e=this,n=this.chroms_layout,r=this.track,a=i.Deferred();return i.when(r.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){e.data_bounds=e.get_data_bounds(i),r.get("config").set_value("min_value",e.data_bounds[0],{silent:!0}),r.get("config").set_value("max_value",e.data_bounds[1],{silent:!0});var o=c.zip(n,i);c.each(o,function(n){var i=n[0],r=n[1];return e._render_chrom_data(t,i,r)});var s=e.get_fill_color();e.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s),a.resolve(t)}),a},_render_chrom_data:function(t,e,n){},_get_path_function:function(t,e){},_chroms_layout:function(){var t=this.genome.get_chroms_info(),e=u.layout.pie().value(function(t){return t.len}).sort(null),n=e(t),i=2*Math.PI*this.total_gap/t.length;return c.map(n,function(t,e){var n=t.endAngle-i;return t.endAngle=n>t.startAngle?n:t.startAngle,t})}}),C=M.extend({initialize:function(t){M.prototype.initialize.call(this,t),this.innerRadius=this.radius_bounds[0],this.radius_bounds[0]=this.radius_bounds[1],this.bg_stroke="#fff",this.bg_fill="#fff",this.min_arc_len=.05},_render_data:function(t){var e=this,n=t.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom}),n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>e.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").text(function(t){return t.data.chrom});var i=function(t){var n=(t.endAngle-t.startAngle)/t.value,i=u.range(0,t.value,25e6).map(function(i,r){return{radius:e.innerRadius,angle:i*n+t.startAngle,label:0===r?0:r%3?null:e.formatNum(i)}});return i.length<4&&(i[i.length-1].label=e.formatNum(Math.round((i[i.length-1].angle-t.startAngle)/n))),i},r=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null},a=c.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>e.min_arc_len});this.drawTicks(this.parent_elt,a,i,r)}});c.extend(C.prototype,w);var S=M.extend({initialize:function(t){M.prototype.initialize.call(this,t);var e=this.track.get("config");e.get("min_value").on("change:value",this._update_min_max,this),e.get("max_value").on("change:value",this._update_min_max,this),e.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var t=this.track.get("config"),e=[t.get_value("min_value"),t.get_value("max_value")];this._update_data_bounds(e),this.parent_elt.selectAll(".min_max").text(function(t,n){return e[n]})},_quantile:function(t,e){return t.sort(u.ascending),u.quantile(t,e)},_render_chrom_data:function(t,e,n){var i=this._get_path_function(e,n);return i?t.datum(n.data).append("path").attr("class","chrom-data").attr("chrom",e.data.chrom).attr("d",i):null},_get_path_function:function(t,e){if("string"==typeof e||!e.data||0===e.data.length)return null;var n=u.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(!0),i=u.scale.linear().domain([0,e.data.length]).range([t.startAngle,t.endAngle]),r=u.svg.line.radial().interpolate("linear").radius(function(t){return n(t[1])}).angle(function(t,e){return i(e)});return u.svg.area.radial().interpolate(r.interpolate()).innerRadius(n(0)).outerRadius(r.radius()).angle(r.angle())},render_labels:function(){var t=this,e=function(){return"rotate(90)"},n=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),e,!0).classed("min_max",!0);c.each(n,function(e){i(e).click(function(){new m.default.ConfigSettingCollectionView({collection:t.track.get("config")}).render_in_modal("Configure Track")})})},_transition_labels:function(){if(0!==this.data_bounds.length){var t=this,e=c.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>.08}),n=c.filter(e,function(t,e){return e%3==0}),i=c.flatten(c.map(n,function(e){return t._data_bounds_ticks_fn()(e)}));this.parent_elt.selectAll("g.tick").data(i).transition().attr("transform",function(t){return"rotate("+(180*t.angle/Math.PI-90)+")translate("+t.radius+",0)"})}},_data_bounds_ticks_fn:function(){var t=this;return function(e){return[{radius:t.radius_bounds[0],angle:e.startAngle,label:t.formatNum(t.data_bounds[0])},{radius:t.radius_bounds[1],angle:e.startAngle,label:t.formatNum(t.data_bounds[1])}]}},get_data_bounds:function(t){}});c.extend(S.prototype,w);var T=S.extend({get_data_bounds:function(t){var e=c.flatten(c.map(t,function(t){return t?c.map(t.data,function(t){return parseInt(t[1],10)||0}):0}));return[c.min(e),this._quantile(e,.98)||c.max(e)]}}),A=M.extend({render:function(){var t=this;i.when(t.track.get("data_manager").data_is_ready()).then(function(){i.when(t.track.get("data_manager").get_genome_wide_data(t.genome)).then(function(e){var n=[],i=t.genome.get_chroms_info();c.each(e,function(e,r){var a=i[r].chrom,o=c.map(e.data,function(e){var n=t._get_region_angle(a,e[1]),i=t._get_region_angle(e[3],e[4]);return{source:{startAngle:n,endAngle:n+.01},target:{startAngle:i,endAngle:i+.01}}});n=n.concat(o)}),t.parent_elt.append("g").attr("class","chord").selectAll("path").data(n).enter().append("path").style("fill",t.get_fill_color()).attr("d",u.svg.chord().radius(t.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(t){this.radius_bounds=t,this.parent_elt.selectAll("path").transition().attr("d",u.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(t,e){var n=c.find(this.chroms_layout,function(e){return e.data.chrom===t});return n.endAngle-(n.endAngle-n.startAngle)*(n.data.len-e)/n.data.len}}),j=t.View.extend({initialize:function(){_.default.cssLoadFile("static/style/circster.css");var t=new f.default.Genome(window.galaxy_config.app.genome),e=new f.default.GenomeVisualization(window.galaxy_config.app.viz_config);e.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset 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t=this;r("#PhyloViz").empty(),t.mainSVG=d.select("#PhyloViz").append("svg:svg").attr("width",t.width).attr("height",t.height).attr("pointer-events","all").call(t.zoomFunc.on("zoom",function(){t.zoomAndPan()})),t.boundingRect=t.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",t.width).attr("height",t.height).attr("stroke","black").attr("fill","white"),t.vis=t.mainSVG.append("svg:g").attr("class","vis"),t.layoutOptions={model:t.phyloTree,width:t.width,height:t.height,vis:t.vis,margins:t.margins},r("#title").text("Phylogenetic Tree from "+t.phyloTree.get("title")+":");new b(t.layoutOptions)},zoomAndPan:function(t){var e,n;void 0!==t&&(e=t.zoom,n=t.translate);var i=this,r=i.zoomFunc.scale(),a=i.zoomFunc.translate(),o="",s="";switch(e){case"reset":r=1,a=[0,0];break;case"+":r*=1.1;break;case"-":r*=.9;break;default:"number"==typeof e?r=e:null!==d.event&&(r=d.event.scale)}if(!(ri.MAX_SCALE)){if(i.zoomFunc.scale(r),o="translate("+i.margins[3]+","+i.margins[0]+") 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t=this;r.each(t.phyloTree.defaults,function(e,n){t.phyloTree.set(e,n)}),t.updateUI()},render:function(){}}),M=m.extend({className:"Settings",initialize:function(t){var e=this;e.el=r("#nodeSelectionView"),e.phyloTree=t.phyloTree,e.UI={enableEdit:r("#phylovizEditNodesCheck"),saveChanges:r("#phylovizNodeSaveChanges"),cancelChanges:r("#phylovizNodeCancelChanges"),name:r("#phyloVizSelectedNodeName"),dist:r("#phyloVizSelectedNodeDist"),annotation:r("#phyloVizSelectedNodeAnnotation")},e.valuesOfConcern={name:null,dist:null,annotation:null},r("#nodeSelCloseBtn").off().on("click",function(){e.el.hide()}),e.UI.saveChanges.off().on("click",function(){e.updateNodes()}),e.UI.cancelChanges.off().on("click",function(){e.cancelChanges()}),function(t){t.fn.enable=function(e){return t(this).each(function(){e?t(this).removeAttr("disabled"):t(this).attr("disabled","disabled")})}}(i),e.UI.enableEdit.off().on("click",function(){e.toggleUI()})},toggleUI:function(){var t=this,e=t.UI.enableEdit.is(":checked");e||t.cancelChanges(),r.each(t.valuesOfConcern,function(n,i){t.UI[n].enable(e)}),e?(t.UI.saveChanges.show(),t.UI.cancelChanges.show()):(t.UI.saveChanges.hide(),t.UI.cancelChanges.hide())},cancelChanges:function(){var t=this,e=t.phyloTree.get("selectedNode");e&&r.each(t.valuesOfConcern,function(n,i){t.UI[n].val(e[n])})},updateNodes:function(){var t=this,e=t.phyloTree.get("selectedNode");if(e){if(!t.isAcceptableValue(t.UI.dist,0,1)||t.hasIllegalJsonCharacters(t.UI.name)||t.hasIllegalJsonCharacters(t.UI.annotation))return;r.each(t.valuesOfConcern,function(n,i){e[n]=t.UI[n].val()}),t.phyloTree.set("nodeAttrChangedTime",new Date)}else alert("No node selected")}}),C=m.extend({initialize:function(){var t=this;r("#phyloVizSearchBtn").on("click",function(){var e=r("#phyloVizSearchTerm"),n=r("#phyloVizSearchCondition").val().split("-"),i=n[0],a=n[1];t.hasIllegalJsonCharacters(e),"dist"===i&&t.isAcceptableValue(e,0,1),t.searchTree(i,a,e.val())})},searchTree:function(t,e,n){d.selectAll("g.node").classed("searchHighlight",function(i){var r=i[t];if(void 0!==r&&null!==r)if("dist"===t)switch(e){case"greaterEqual":return r>=+n;case"lesserEqual":return r<=+n;default:return}else if("name"===t||"annotation"===t)return-1!==r.toLowerCase().indexOf(n.toLowerCase())})}});e.default={PhylovizView:w}}).call(e,n(2),n(0),n(0))},function(t,e,n){"use strict";(function(t,i){function r(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e.default=t,e}function a(t){return t&&t.__esModule?t:{default:t}}Object.defineProperty(e,"__esModule",{value:!0});var 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e=this.get("settings"),n=t.get("settings");for(var i in e)if(!n[i]||e[i]!==n[i])return!1;return!0},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}}),A=t.Collection.extend({model:T}),j=p.default.Visualization.extend({defaults:c.extend({},p.default.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),initialize:function(t){this.set("dataset",new b.default.Dataset(t.dataset)),this.set("tool",new v.default.Tool(t.tool)),this.set("regions",new p.default.GenomeRegionCollection(t.regions)),this.set("tracks",new A(t.tracks));var e=this.get("tool");this.set("tool_with_samplable_inputs",e),e.remove_inputs(["data","hidden_data","conditional","text"]),this.set("parameter_tree",new S({tool:e,config:t.tree_config}))},add_track:function(t){this.get("tracks").add(t)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset 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e=this.templatePaginator();r("body").find(".folder-paginator").html(e({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown,folder_page_size:Galaxy.libraries.preferences.get("folder_page_size")}))},configureElements:function(t){this.options=i.extend(this.options,t),!0===this.options.can_add_library_item?r(".add-library-items").show():r(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?(r(".dataset-manipulation").show(),r(".logged-dataset-manipulation").hide()):(r(".logged-dataset-manipulation").show(),r(".dataset-manipulation").show()):(r(".logged-dataset-manipulation").hide(),r(".dataset-manipulation").hide()),this.$el.find('[data-toggle="tooltip"]').tooltip({trigger:"hover"})},createFolderFromModal:function(t){var e=this;t.preventDefault(),t.stopPropagation();var n=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:(0,l.default)("Create New Folder"),body:n(),buttons:{Create:function(){e.createNewFolderEvent()},Close:function(){Galaxy.modal.hide()}}})},createNewFolderEvent:function(){var e=this.serializeNewFolder();if(this.validateNewFolder(e)){var n,i=new p.default.FolderAsModel,r=t.history.fragment.split("/");n=r.indexOf("page")>-1?r[r.length-3]:r[r.length-1],i.url=i.urlRoot+n,i.save(e,{success:function(t){Galaxy.modal.hide(),h.default.success("Folder created."),t.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(t)},error:function(t,e){Galaxy.modal.hide(),void 0!==e.responseJSON?h.default.error(e.responseJSON.err_msg):h.default.error("An error occurred.")}})}else h.default.error("Folder's name is 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e=this.modal.$("input[name=history_name]").val();if(""!==e)this.createNewHistory(e).done(function(e){t.processImportToHistory(e.id,e.name)}).fail(function(t,e,n){h.default.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var n=r("select[name=import_to_history] option:selected").val(),i=r("select[name=import_to_history] option:selected").text();this.processImportToHistory(n,i),this.modal.enableButton("Import")}},createNewHistory:function(t){return r.post(Galaxy.root+"api/histories",{name:t})},processImportToHistory:function(t,e){for(var n=this.findCheckedItems(),i=[],r=n.dataset_ids.length-1;r>=0;r--){var o=n.dataset_ids[r],s=new p.default.HistoryItem;s.url=s.urlRoot+t+"/contents",s.content=o,s.source="library",i.push(s)}for(var l=n.folder_ids.length-1;l>=0;l--){var c=n.folder_ids[l],s=new p.default.HistoryItem;s.url=s.urlRoot+t+"/contents",s.content=c,s.source="library_folder",i.push(s)}this.initChainCallControl({length:i.length,action:"to_history",history_name:e}),a.getJSON(Galaxy.root+"history/set_as_current?id="+t),this.chainCallImportingIntoHistory(i,e)},updateProgress:function(){this.progress+=this.progressStep,r(".progress-bar-import").width(Math.round(this.progress)+"%");var t=Math.round(this.progress)+"% Complete";r(".completion_span").text(t)},download:function(t){var e=this.findCheckedItems(),n=Galaxy.root+"api/libraries/datasets/download/"+t,i={ld_ids:e.dataset_ids,folder_ids:e.folder_ids};this.processDownload(n,i,"get")},processDownload:function(t,e,n){if(t&&e){e="string"==typeof e?e:r.param(e);var i="";r.each(e.split("&"),function(){var t=this.split("=");i+=''}),r('
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