From 85bf398fc33fb7ca230c51b09661176382923796 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 1 Dec 2017 15:31:09 -0500 Subject: [PATCH] change the default ot not add tags based on filename this is fairly confusing if you do not expect it and there is no way to revert --- .../scripts/mvc/library/library-foldertoolbar-view.js | 8 ++++---- static/scripts/bundled/library.bundled.js | 2 +- static/scripts/mvc/library/library-foldertoolbar-view.js | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js index 7eb7cc63516..512360922ad 100644 --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -1519,8 +1519,8 @@ var FolderToolbarView = Backbone.View.extend({ "
", "
", '", "
", "" @@ -1561,8 +1561,8 @@ var FolderToolbarView = Backbone.View.extend({ "", "
", '", "
", "" diff --git a/static/scripts/bundled/library.bundled.js b/static/scripts/bundled/library.bundled.js index 54232da2d83..f53862848c3 100644 --- a/static/scripts/bundled/library.bundled.js +++ b/static/scripts/bundled/library.bundled.js @@ -46,4 +46,4 @@ n=i,l=e("
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Date uploaded (UTC)<%= _.escape(ldda.get("date_uploaded")) %>
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Data Lines<%= _.escape(ldda.get("metadata_data_lines")) %>
Comment Lines<%= _.escape(ldda.get("metadata_comment_lines")) %>
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Column Types<%= _.escape(ldda.get("metadata_column_types")) %>
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Dataset: <%= _.escape(item.get("name")) %>

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Library-related permissions

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Roles that can modify the library item

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You can remove all access restrictions on this dataset.

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Roles that can manage permissions on the dataset

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changed.")},repaint:function(){a(".tooltip").hide();var e=this.$el;this.render(),e.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},templateRowFolder:function(){return s.template(['',"",'',"",'',"<% if(!edit_mode) { %>","",'<%- content_item.get("name") %>',"","",'<%- content_item.get("description") %>',"","<% } else if(edit_mode){ %>",'','',"<% } %>","folder","","",'<%= _.escape(content_item.get("update_time")) %>',"","","","<% if(edit_mode) { %>",'",'","<% } else if (!edit_mode){%>",'",'','","","<% } %>","",""].join(""))},templateRowFile:function(){return s.template(['',"",'',"",'','',"","",'/datasets/<%- content_item.id %>" class="library-dataset">','<%- content_item.get("name") %>',"","",'<%- content_item.get("message") %>','<%= _.escape(content_item.get("file_ext")) %>','<%= _.escape(content_item.get("file_size")) %>','<%= _.escape(content_item.get("update_time")) %>',"",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) 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n=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&nthis.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(i=[]),this.$el.html(t({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(i)):(this.$el.html(t({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),s("#center [data-toggle]").tooltip(),s("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var e=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){e.options.all_fetched=!0,e.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})}},renderRows:function(e){for(var t=0;t',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","
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","<% }%>","<% } else{ %>",'',"",'",'',' ','',"",'',"","
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this.setElement(t({library:e,button_config:this.element_visibility_config,edit_mode:this.edit_mode})),this.$el.show(),this},repaint:function(e){s(".tooltip").hide();var t=this.$el;this.render(),t.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){var t=this.element_visibility_config;!1===this.edit_mode?(t.save_library_btn=!1,t.cancel_library_btn=!1,t.delete_library_btn=!1,!0===e.get("deleted")?(t.undelete_library_btn=!0,t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1):!1===e.get("deleted")&&(t.save_library_btn=!1,t.cancel_library_btn=!1,t.undelete_library_btn=!1,!0===e.get("can_user_add")&&(t.upload_library_btn=!0),!0===e.get("can_user_modify")&&(t.edit_library_btn=!0),!0===e.get("can_user_manage")&&(t.permission_library_btn=!0))):!0===this.edit_mode&&(t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1,t.save_library_btn=!0,t.cancel_library_btn=!0,t.delete_library_btn=!0,t.undelete_library_btn=!1),this.element_visibility_config=t},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=!1,i=this.$el.find(".input_library_name").val();if(void 0!==i&&i!==e.get("name")){if(!(i.length>2))return void o.default.warning("Library name has to be at least 3 characters long.");e.set("name",i),t=!0}var s=this.$el.find(".input_library_description").val();void 0!==s&&s!==e.get("description")&&(e.set("description",s),t=!0);var a=this.$el.find(".input_library_synopsis").val();if(void 0!==a&&a!==e.get("synopsis")&&(e.set("synopsis",a),t=!0),t){var r=this;e.save(null,{patch:!0,success:function(e){r.edit_mode=!1,r.repaint(e),o.default.success("Changes to library saved.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(e),o.default.info("Nothing has changed.")},delete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.destroy({success:function(e){e.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?(s(".tooltip").hide(),t.repaint(e),t.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&t.repaint(e),o.default.success("Library has been marked deleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured during deleting the library.")}})},undelete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.url=e.urlRoot+e.id+"?undelete=true",e.destroy({success:function(e){e.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,t.repaint(e),o.default.success("Library has been undeleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while undeleting the library.")}})},templateRow:function(){return a.template(['" style="display:none;" data-id="<%- library.get("id") %>">',"<% if(!edit_mode) { %>",'<% if(library.get("deleted")) { %>','<%- library.get("name") %>',"<% } else { %>",'"><%- library.get("name") %>',"<% } %>",'<% if(library.get("description")) { %>','<% if( (library.get("description")).length> 80 ) { %>','"><%= _.escape(library.get("description")).substring(0, 80) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("description"))%>',"<% } %>","<% } else { %>","","<% } %>",'<% if(library.get("synopsis")) { %>','<% if( (library.get("synopsis")).length> 120 ) { %>','"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("synopsis"))%>',"<% } %>","<% } else { %>","","<% } %>","<% } else if(edit_mode){ %>",'','','',"<% } %>",'','<% if( (library.get("public")) 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e=this.templateToolBar(),t=!1,i=!0;Galaxy.user&&(t=Galaxy.user.isAdmin(),i=Galaxy.user.isAnonymous()),this.$el.html(e({admin_user:t,anon_user:i})),t&&(this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted"),this.$el.find("#exclude_restricted_chk")[0].checked=Galaxy.libraries.preferences.get("without_restricted"))},renderPaginator:function(e){this.options=s.extend(this.options,e);var t=this.templatePaginator();this.$el.find("#library_paginator").html(t({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown,library_page_size:Galaxy.libraries.preferences.get("library_page_size")}))},createLibraryFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this;this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New 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see?",Galaxy.libraries.preferences.get("library_page_size"));null!=t&&t==parseInt(t)&&(Galaxy.libraries.preferences.set({library_page_size:parseInt(t)}),Galaxy.libraries.libraryListView.render({show_page:1}))},clearLibraryModal:function(){a("input[name='Name']").val(""),a("input[name='Description']").val(""),a("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:a("input[name='Name']").val(),description:a("input[name='Description']").val(),synopsis:a("input[name='Synopsis']").val()}},validateNewLibrary:function(e){return""!==e.name},includeDeletedChecked:function(e){e.target.checked?(Galaxy.libraries.preferences.set({with_deleted:!0}),Galaxy.libraries.libraryListView.fetchDeleted()):(Galaxy.libraries.preferences.set({with_deleted:!1}),Galaxy.libraries.libraryListView.render())},excludeRestrictedChecked:function(e){e.target.checked?Galaxy.libraries.preferences.set({without_restricted:!0}):Galaxy.libraries.preferences.set({without_restricted:!1}),Galaxy.libraries.libraryListView.render()},searchLibraries:function(e){var t=a(".library-search-input").val();this.options.search_term=t,Galaxy.libraries.libraryListView.searchLibraries(t)},templateToolBar:function(){return s.template(['
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','
','
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','',"
","<% if(admin_user === true) { %>",'
',"","","
",'','',"","<% } %>",'','','',"","","
","
","
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',"
","
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",'','','',"
","
"].join(""))}});t.default={LibraryToolbarView:c}}).call(t,i(1),i(2),i(0))},306:function(e,t,i){"use strict";(function(e,s,a,r){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var n=i(3),l=o(n),d=i(42),c=o(d),h=i(156),_=o(h),p=i(139),u=o(p);i(198);var f=e.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedItems","click .toolbtn-show-locinfo":"showLocInfo","click .page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(e){this.options=s.defaults(e||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(e){this.options=s.extend(this.options,e);var t=this.templateToolBar(),i={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.user&&(i.is_admin=Galaxy.user.isAdmin(),i.is_anonym=Galaxy.user.isAnonymous(),null===Galaxy.config.user_library_import_dir&&!1===Galaxy.config.allow_library_path_paste&&null===Galaxy.config.library_import_dir||(i.mutiple_add_dataset_options=!0)),this.$el.html(t(i))},renderPaginator:function(e){this.options=s.extend(this.options,e);var t=this.templatePaginator();a("body").find(".folder-paginator").html(t({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown,folder_page_size:Galaxy.libraries.preferences.get("folder_page_size")}))},configureElements:function(e){this.options=s.extend(this.options,e),!0===this.options.can_add_library_item?a(".add-library-items").show():a(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?(a(".dataset-manipulation").show(),a(".logged-dataset-manipulation").hide()):(a(".logged-dataset-manipulation").show(),a(".dataset-manipulation").show()):(a(".logged-dataset-manipulation").hide(),a(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this,i=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:i(),buttons:{Create:function(){t.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var t=this.serialize_new_folder();if(this.validate_new_folder(t)){var i,s=new _.default.FolderAsModel,a=e.history.fragment.split("/");i=a.indexOf("page")>-1?a[a.length-3]:a[a.length-1],s.url=s.urlRoot+i,s.save(t,{success:function(e){Galaxy.modal.hide(),c.default.success("Folder created."),e.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(e)},error:function(e,t){Galaxy.modal.hide(),void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")}})}else c.default.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:a("input[name='Name']").val(),description:a("input[name='Description']").val()}},validate_new_folder:function(e){return""!==e.name},modalBulkImport:function(){if(0===this.findCheckedRows().length)c.default.info("You must select some datasets first.");else{var e=this;this.histories=new _.default.GalaxyHistories,this.histories.fetch().done(function(){var t=e.templateBulkImportInModal();e.modal=Galaxy.modal,e.modal.show({closing_events:!0,title:"Import into History",body:t({histories:e.histories.models}),buttons:{Import:function(){e.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})}).fail(function(e,t){void 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occurred.")})}},importAllIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),t=this;if(""!==e)a.post(Galaxy.root+"api/histories",{name:e}).done(function(e){t.options.last_used_history_id=e.id,t.processImportToHistory(e.id,e.name)}).fail(function(e,t,i){c.default.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var i=a("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=i;var s=a("select[name=dataset_import_bulk] option:selected").text();this.processImportToHistory(i,s),this.modal.enableButton("Import")}},processImportToHistory:function(e,t){var i=[],s=[];this.findCheckedRows().each(function(){var e=a(this).closest("tr").data("id");"F"==e.substring(0,1)?s.push(e):i.push(e)});for(var o=[],n=i.length-1;n>=0;n--){var l=i[n],d=new _.default.HistoryItem;d.url=d.urlRoot+e+"/contents",d.content=l,d.source="library",o.push(d)}for(var n=s.length-1;n>=0;n--){var c=s[n],d=new 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Click this to see it.","",{onclick:function(){var e=t.model.get("folder_id");window.location=Galaxy.root+"library/list#folders/"+e+"/datasets/"+t.id}})},error:function(e,t){void 0!==t.responseJSON?n.default.error("Dataset was not undeleted. "+t.responseJSON.err_msg):n.default.error("An error occured! Dataset was not undeleted. Please try again.")}})},undeleteFolder:function(e){a(".tooltip").hide();var t=a(e.target).closest("tr").data("id"),i=Galaxy.libraries.folderListView.collection.get(t);i.url=i.urlRoot+i.id+"?undelete=true",i.destroy({success:function(e,i){Galaxy.libraries.folderListView.collection.remove(t);var s=new d.default.FolderAsModel(i);Galaxy.libraries.folderListView.collection.add(s),Galaxy.libraries.folderListView.collection.sortFolder("name","asc"),n.default.success("Folder undeleted.")},error:function(e,t){void 0!==t.responseJSON?n.default.error("Folder was not undeleted. "+t.responseJSON.err_msg):n.default.error("An error occured! Folder was not undeleted. Please try again.")}})},startModifications:function(){this.options.edit_mode=!0,this.repaint()},cancelModifications:function(){this.options.edit_mode=!1,this.repaint()},saveModifications:function(){var e=Galaxy.libraries.folderListView.collection.get(this.$el.data("id")),t=!1,i=this.$el.find(".input_folder_name").val();if(void 0!==i&&i!==e.get("name")){if(!(i.length>2))return void n.default.warning("Folder name has to be at least 3 characters long.");e.set("name",i),t=!0}var s=this.$el.find(".input_folder_description").val();if(void 0!==s&&s!==e.get("description")&&(e.set("description",s),t=!0),t){var a=this;e.save(null,{patch:!0,success:function(e){a.options.edit_mode=!1,a.repaint(e),n.default.success("Changes to folder saved.")},error:function(e,t){void 0!==t.responseJSON?n.default.error(t.responseJSON.err_msg):n.default.error("An error occured while attempting to update the folder.")}})}else this.options.edit_mode=!1,this.repaint(e),n.default.info("Nothing has changed.")},repaint:function(){a(".tooltip").hide();var e=this.$el;this.render(),e.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},templateRowFolder:function(){return s.template(['',"",'',"",'',"<% if(!edit_mode) { %>","",'<%- content_item.get("name") %>',"","",'<%- content_item.get("description") %>',"","<% } else if(edit_mode){ %>",'','',"<% } %>","folder","","",'<%= _.escape(content_item.get("update_time")) %>',"","","","<% if(edit_mode) { %>",'",'","<% } else if (!edit_mode){%>",'",'','","","<% } %>","",""].join(""))},templateRowFile:function(){return s.template(['',"",'',"",'','',"","",'/datasets/<%- content_item.id %>" class="library-dataset">','<%- content_item.get("name") %>',"","",'<%- content_item.get("message") %>','<%= _.escape(content_item.get("file_ext")) %>','<%= _.escape(content_item.get("file_size")) %>','<%= _.escape(content_item.get("update_time")) %>',"",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>","","",'<% if (content_item.get("is_unrestricted")) { %>','',"<% } %>",'<% if (content_item.get("is_private")) { %>','',"<% } %>",'<% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %>','',"<% } %>",'<% if (content_item.get("can_manage")) { %>','/datasets/<%- content_item.id %>/permissions">','","","<% } %>","",""].join(""))},templateRowDeletedFile:function(){return s.template(['',"",'',"","",'','<%- content_item.get("name") %>',"","",'<%- content_item.get("message") %>',"","",'<%= _.escape(content_item.get("file_ext")) %>',"","",'<%= _.escape(content_item.get("file_size")) %>',"","",'<%= _.escape(content_item.get("update_time")) %>',"","",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>","","",'','","",""].join(""))},templateRowDeletedFolder:function(){return s.template(['',"",'',"","",'','<%- content_item.get("name") %>',"","",'<%- content_item.get("description") %>',"","","folder","","","",'<%= _.escape(content_item.get("update_time")) %>',"","","",'','","",""].join(""))}});t.default={FolderRowView:_}}).call(t,i(1),i(2),i(0))},303:function(e,t,i){"use strict";(function(e,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(42),o=a(r),n=i(156),l=a(n),d=i(304),c=a(d),h=i(2),_=a(h),p=e.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null,all_fetched:!1},initialize:function(e){this.options=_.default.defaults(this.options||{},e,this.defaults);var t=this;this.modal=null,this.collection=new l.default.Libraries,this.collection.url=this.collection.urlRoot+"?deleted=false",this.collection.fetch({success:function(){t.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})},render:function(e){this.options=_.default.extend(this.options,e),this.setElement("#libraries_element");var t=this.templateLibraryList(),i=null,a=null,r=function(e){return!0===e.get("public")};if(s(".tooltip").hide(),void 0!==e&&(a=void 0!==e.models?e.models:null),null!==this.collection&&null===a)this.sortLibraries(),i=Galaxy.libraries.preferences.get("with_deleted")?this.collection.models:this.collection.where({deleted:!1}),Galaxy.libraries.preferences.get("without_restricted")&&(i=_.default.filter(i,r));else if(null!==a){if(Galaxy.libraries.preferences.get("with_deleted"))i=a;else{var o=function(e){return!1===e.get("deleted")};i=_.default.filter(a,o)}Galaxy.libraries.preferences.get("without_restricted")&&(i=_.default.filter(i,r))}else i=[];(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_libraries_count=i.length;var n=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&nthis.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(i=[]),this.$el.html(t({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(i)):(this.$el.html(t({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),s("#center [data-toggle]").tooltip(),s("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var e=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){e.options.all_fetched=!0,e.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})}},renderRows:function(e){for(var t=0;t',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","
","There are no libraries matching your search. Try different keyword.","
","<% } else{ %>","
","There are no libraries visible to you here. If you expected some to show up please consult the",' library security wikipage',' or visit the Galaxy support site.',"
","<% }%>","<% } else{ %>",'',"",'",'',' ','',"",'',"","
','',"name","",'',"descriptionsynopsis
","<% }%>","
"].join(""))}});t.default={LibraryListView:p}}).call(t,i(1),i(0))},304:function(e,t,i){"use strict";(function(e,s,a){Object.defineProperty(t,"__esModule",{value:!0});var r=i(42),o=function(e){return e&&e.__esModule?e:{default:e}}(r),n=e.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},edit_mode:!1,element_visibility_config:{upload_library_btn:!1,edit_library_btn:!1,permission_library_btn:!1,save_library_btn:!1,cancel_library_btn:!1,delete_library_btn:!1,undelete_library_btn:!1},initialize:function(e){this.render(e)},render:function(e){void 0===e&&(e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))),this.prepareButtons(e);var t=this.templateRow();return this.setElement(t({library:e,button_config:this.element_visibility_config,edit_mode:this.edit_mode})),this.$el.show(),this},repaint:function(e){s(".tooltip").hide();var t=this.$el;this.render(),t.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){var t=this.element_visibility_config;!1===this.edit_mode?(t.save_library_btn=!1,t.cancel_library_btn=!1,t.delete_library_btn=!1,!0===e.get("deleted")?(t.undelete_library_btn=!0,t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1):!1===e.get("deleted")&&(t.save_library_btn=!1,t.cancel_library_btn=!1,t.undelete_library_btn=!1,!0===e.get("can_user_add")&&(t.upload_library_btn=!0),!0===e.get("can_user_modify")&&(t.edit_library_btn=!0),!0===e.get("can_user_manage")&&(t.permission_library_btn=!0))):!0===this.edit_mode&&(t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1,t.save_library_btn=!0,t.cancel_library_btn=!0,t.delete_library_btn=!0,t.undelete_library_btn=!1),this.element_visibility_config=t},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=!1,i=this.$el.find(".input_library_name").val();if(void 0!==i&&i!==e.get("name")){if(!(i.length>2))return void o.default.warning("Library name has to be at least 3 characters long.");e.set("name",i),t=!0}var s=this.$el.find(".input_library_description").val();void 0!==s&&s!==e.get("description")&&(e.set("description",s),t=!0);var a=this.$el.find(".input_library_synopsis").val();if(void 0!==a&&a!==e.get("synopsis")&&(e.set("synopsis",a),t=!0),t){var r=this;e.save(null,{patch:!0,success:function(e){r.edit_mode=!1,r.repaint(e),o.default.success("Changes to library saved.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(e),o.default.info("Nothing has changed.")},delete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.destroy({success:function(e){e.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?(s(".tooltip").hide(),t.repaint(e),t.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&t.repaint(e),o.default.success("Library has been marked deleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured during deleting the library.")}})},undelete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.url=e.urlRoot+e.id+"?undelete=true",e.destroy({success:function(e){e.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,t.repaint(e),o.default.success("Library has been undeleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while undeleting the library.")}})},templateRow:function(){return a.template(['" style="display:none;" data-id="<%- library.get("id") %>">',"<% if(!edit_mode) { %>",'<% if(library.get("deleted")) { %>','<%- library.get("name") %>',"<% } else { %>",'"><%- library.get("name") %>',"<% } %>",'<% if(library.get("description")) { %>','<% if( (library.get("description")).length> 80 ) { %>','"><%= _.escape(library.get("description")).substring(0, 80) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("description"))%>',"<% } %>","<% } else { %>","","<% } %>",'<% if(library.get("synopsis")) { %>','<% if( (library.get("synopsis")).length> 120 ) { %>','"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("synopsis"))%>',"<% } %>","<% } else { %>","","<% } %>","<% } else if(edit_mode){ %>",'','','',"<% } %>",'','<% if( (library.get("public")) && (library.get("deleted") === false) ) { %>',' ',"<% }%>",'','/permissions">','','','','" class="fa fa-ban fa-lg">','',"",""].join(""))}});t.default={LibraryRowView:n}}).call(t,i(1),i(0),i(2))},305:function(e,t,i){"use strict";(function(e,s,a){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(42),n=r(o),l=i(156),d=r(l),c=e.View.extend({el:"#center",defaults:{search_term:""},events:{"click #create_new_library_btn":"createLibraryFromModal","click #include_deleted_chk":"includeDeletedChecked","click #exclude_restricted_chk":"excludeRestrictedChecked","click .page_size_prompt":"showPageSizePrompt","keyup .library-search-input":"searchLibraries"},initialize:function(e){this.options=s.defaults(this.options||{},e,this.defaults),this.render()},render:function(){var e=this.templateToolBar(),t=!1,i=!0;Galaxy.user&&(t=Galaxy.user.isAdmin(),i=Galaxy.user.isAnonymous()),this.$el.html(e({admin_user:t,anon_user:i})),t&&(this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted"),this.$el.find("#exclude_restricted_chk")[0].checked=Galaxy.libraries.preferences.get("without_restricted"))},renderPaginator:function(e){this.options=s.extend(this.options,e);var t=this.templatePaginator();this.$el.find("#library_paginator").html(t({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown,library_page_size:Galaxy.libraries.preferences.get("library_page_size")}))},createLibraryFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this;this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){t.createNewLibrary()},Close:function(){t.modal.hide()}}})},createNewLibrary:function(){var e=this.serializeNewLibrary();if(this.validateNewLibrary(e)){var t=new d.default.Library,i=this;t.save(e,{success:function(e){Galaxy.libraries.libraryListView.collection.add(e),i.modal.hide(),i.clearLibraryModal(),Galaxy.libraries.libraryListView.render(),n.default.success("Library created.")},error:function(e,t){void 0!==t.responseJSON?n.default.error(t.responseJSON.err_msg):n.default.error("An error occured.")}})}else n.default.error("Library's name is missing.");return!1},showPageSizePrompt:function(e){e.preventDefault();var t=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));null!=t&&t==parseInt(t)&&(Galaxy.libraries.preferences.set({library_page_size:parseInt(t)}),Galaxy.libraries.libraryListView.render({show_page:1}))},clearLibraryModal:function(){a("input[name='Name']").val(""),a("input[name='Description']").val(""),a("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:a("input[name='Name']").val(),description:a("input[name='Description']").val(),synopsis:a("input[name='Synopsis']").val()}},validateNewLibrary:function(e){return""!==e.name},includeDeletedChecked:function(e){e.target.checked?(Galaxy.libraries.preferences.set({with_deleted:!0}),Galaxy.libraries.libraryListView.fetchDeleted()):(Galaxy.libraries.preferences.set({with_deleted:!1}),Galaxy.libraries.libraryListView.render())},excludeRestrictedChecked:function(e){e.target.checked?Galaxy.libraries.preferences.set({without_restricted:!0}):Galaxy.libraries.preferences.set({without_restricted:!1}),Galaxy.libraries.libraryListView.render()},searchLibraries:function(e){var t=a(".library-search-input").val();this.options.search_term=t,Galaxy.libraries.libraryListView.searchLibraries(t)},templateToolBar:function(){return s.template(['
','
','
','
','DATA LIBRARIES','',"",'
','',"
","<% if(admin_user === true) { %>",'
',"","","
",'','',"","<% } %>",'','','',"","","
","
","
",'
',"
","
"].join(""))},templatePaginator:function(){return s.template(['","",' <%- libraries_shown %> libraries shown (change)',"",""," <%- total_libraries_count %> total",""].join(""))},templateNewLibraryInModal:function(){return s.template(['
',"
",'','','',"
","
"].join(""))}});t.default={LibraryToolbarView:c}}).call(t,i(1),i(2),i(0))},306:function(e,t,i){"use strict";(function(e,s,a,r){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var n=i(3),l=o(n),d=i(42),c=o(d),h=i(156),_=o(h),p=i(139),u=o(p);i(198);var f=e.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedItems","click .toolbtn-show-locinfo":"showLocInfo","click .page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(e){this.options=s.defaults(e||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(e){this.options=s.extend(this.options,e);var t=this.templateToolBar(),i={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.user&&(i.is_admin=Galaxy.user.isAdmin(),i.is_anonym=Galaxy.user.isAnonymous(),null===Galaxy.config.user_library_import_dir&&!1===Galaxy.config.allow_library_path_paste&&null===Galaxy.config.library_import_dir||(i.mutiple_add_dataset_options=!0)),this.$el.html(t(i))},renderPaginator:function(e){this.options=s.extend(this.options,e);var t=this.templatePaginator();a("body").find(".folder-paginator").html(t({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(e){this.options=s.extend(this.options,e),!0===this.options.can_add_library_item?a(".add-library-items").show():a(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?(a(".dataset-manipulation").show(),a(".logged-dataset-manipulation").hide()):(a(".logged-dataset-manipulation").show(),a(".dataset-manipulation").show()):(a(".logged-dataset-manipulation").hide(),a(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(e){e.preventDefault(),e.stopPropagation();var 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l=s(t),r=s(i),n=s(a),d=s(o),c=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedItems","click .toolbtn-show-locinfo":"showLocInfo","click .page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(e){this.options=_.defaults(e||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(e){this.options=_.extend(this.options,e);var t=this.templateToolBar(),i={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.user&&(i.is_admin=Galaxy.user.isAdmin(),i.is_anonym=Galaxy.user.isAnonymous(),null===Galaxy.config.user_library_import_dir&&!1===Galaxy.config.allow_library_path_paste&&null===Galaxy.config.library_import_dir||(i.mutiple_add_dataset_options=!0)),this.$el.html(t(i))},renderPaginator:function(e){this.options=_.extend(this.options,e);var t=this.templatePaginator();$("body").find(".folder-paginator").html(t({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown,folder_page_size:Galaxy.libraries.preferences.get("folder_page_size")}))},configureElements:function(e){this.options=_.extend(this.options,e),!0===this.options.can_add_library_item?$(".add-library-items").show():$(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this,i=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:i(),buttons:{Create:function(){t.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var e=this.serialize_new_folder();if(this.validate_new_folder(e)){var t,i=new n.default.FolderAsModel,a=Backbone.history.fragment.split("/");t=a.indexOf("page")>-1?a[a.length-3]:a[a.length-1],i.url=i.urlRoot+t,i.save(e,{success:function(e){Galaxy.modal.hide(),r.default.success("Folder created."),e.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(e)},error:function(e,t){Galaxy.modal.hide(),void 0!==t.responseJSON?r.default.error(t.responseJSON.err_msg):r.default.error("An error occurred.")}})}else r.default.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(e){return""!==e.name},modalBulkImport:function(){if(0===this.findCheckedRows().length)r.default.info("You must select some datasets first.");else{var e=this;this.histories=new n.default.GalaxyHistories,this.histories.fetch().done(function(){var t=e.templateBulkImportInModal();e.modal=Galaxy.modal,e.modal.show({closing_events:!0,title:"Import into History",body:t({histories:e.histories.models}),buttons:{Import:function(){e.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})}).fail(function(e,t){void 0!==t.responseJSON?r.default.error(t.responseJSON.err_msg):r.default.error("An error occurred.")})}},importAllIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),t=this;if(""!==e)$.post(Galaxy.root+"api/histories",{name:e}).done(function(e){t.options.last_used_history_id=e.id,t.processImportToHistory(e.id,e.name)}).fail(function(e,t,i){r.default.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var i=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=i;var a=$("select[name=dataset_import_bulk] option:selected").text();this.processImportToHistory(i,a),this.modal.enableButton("Import")}},processImportToHistory:function(e,t){var i=[],a=[];this.findCheckedRows().each(function(){var e=$(this).closest("tr").data("id");"F"==e.substring(0,1)?a.push(e):i.push(e)});for(var o=[],s=i.length-1;s>=0;s--){var l=i[s];(d=new n.default.HistoryItem).url=d.urlRoot+e+"/contents",d.content=l,d.source="library",o.push(d)}for(s=a.length-1;s>=0;s--){var r=a[s],d=new n.default.HistoryItem;d.url=d.urlRoot+e+"/contents",d.content=r,d.source="library_folder",o.push(d)}this.initChainCallControl({length:o.length,action:"to_history",history_name:t}),jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+e),this.chainCallImportingIntoHistory(o,t)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%");var e=Math.round(this.progress)+"% Complete";$(".completion_span").text(e)},download:function(e,t){var i=[],a=[];this.findCheckedRows().each(function(){var e=$(this).closest("tr").data("id");"F"==e.substring(0,1)?a.push(e):i.push(e)});var o=Galaxy.root+"api/libraries/datasets/download/"+t,s={ld_ids:i,folder_ids:a};this.processDownload(o,s,"get")},processDownload:function(e,t,i){if(e&&t){t="string"==typeof t?t:$.param(t);var a="";$.each(t.split("&"),function(){var e=this.split("=");a+=''}),$('
'+a+"
").appendTo("body").submit().remove(),r.default.info("Your download will begin soon.")}else r.default.error("An error occurred.")},addFilesFromHistoryModal:function(){this.histories=new n.default.GalaxyHistories;var e=this;this.histories.fetch().done(function(){e.modal=Galaxy.modal;var t=e.templateAddFilesFromHistory();e.modal.show({closing_events:!0,title:"Adding datasets from your history",body:t({histories:e.histories.models}),buttons:{Add:function(){e.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),e.fetchAndDisplayHistoryContents(e.histories.models[0].id),$("#dataset_add_bulk").change(function(t){e.fetchAndDisplayHistoryContents(t.target.value)})}).fail(function(e,t){void 0!==t.responseJSON?r.default.error(t.responseJSON.err_msg):r.default.error("An error occurred.")})},importFilesFromPathModal:function(){var e=this;this.modal=Galaxy.modal;var t=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:t({}),buttons:{Import:function(){e.importFromPathsClicked(e)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var e=this;l.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(t){e.list_extensions=[];for(var i in t)e.list_extensions.push({id:t[i].extension,text:t[i].extension,description:t[i].description,description_url:t[i].description_url});e.list_extensions.sort(function(e,t){return e.id>t.id?1:e.idt.id?1:e.id=0;c--){var p=n[c].trim();0!==p.length&&d.push(p)}this.initChainCallControl({length:d.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:d,preserve_dirs:e,link_data:t,space_to_tab:i,to_posix_lines:a,source:"admin_path",file_type:s,tag_using_filenames:o,dbkey:l})}else r.default.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(e){var t;switch(e.action){case"adding_datasets":t=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(t({folder_name:this.options.folder_name}));break;case"deleting_datasets":t=this.templateDeletingItemsProgressBar(),this.modal.$el.find(".modal-body").html(t());break;case"to_history":t=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(t({history_name:e.history_name}));break;default:Galaxy.emit.error("Wrong action specified.","datalibs")}this.progress=0,this.progressStep=100/e.length,this.options.chain_call_control.total_number=e.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(e,t){var i=$("#jstree_browser").jstree().get_selected(!0),a=_.filter(i,function(e){return 0==e.state.disabled}),o=this.modal.$el.find(".preserve-checkbox").is(":checked"),s=this.modal.$el.find(".link-checkbox").is(":checked"),l=this.modal.$el.find(".spacetab-checkbox").is(":checked"),n=this.modal.$el.find(".posix-checkbox").is(":checked"),d=this.select_extension.value(),c=this.select_genome.value(),p=this.modal.$el.find(".tag-files").is(":checked"),h=a[0].type,u=[];if(a.length<1)r.default.info("Please select some items first.");else{this.modal.disableButton("Import");for(var m=a.length-1;m>=0;m--)void 0!==a[m].li_attr.full_path&&u.push(a[m].li_attr.full_path);if(this.initChainCallControl({length:u.length,action:"adding_datasets"}),"folder"===h){f=t.source+"_folder";this.chainCallImportingFolders({paths:u,preserve_dirs:o,link_data:s,space_to_tab:l,to_posix_lines:n,source:f,file_type:d,dbkey:c,tag_using_filenames:p})}else if("file"===h){var f=t.source+"_file";this.chainCallImportingUserdirFiles({paths:u,file_type:d,dbkey:c,link_data:s,space_to_tab:l,to_posix_lines:n,source:f,tag_using_filenames:p})}}},fetchAndDisplayHistoryContents:function(e){var t=this;new n.default.HistoryContents({id:e}).fetch({success:function(i){var a=t.templateHistoryContents();t.histories.get(e).set({contents:i}),t.modal.$el.find("#selected_history_content").html(a({history_contents:i.models.reverse()})),t.modal.$el.find(".history-import-select-all").bind("click",function(){$("#selected_history_content [type=checkbox]").prop("checked",!0)}),t.modal.$el.find(".history-import-unselect-all").bind("click",function(){$("#selected_history_content [type=checkbox]").prop("checked",!1)})},error:function(e,t){void 0!==t.responseJSON?r.default.error(t.responseJSON.err_msg):r.default.error("An error occurred.")}})},addAllDatasetsFromHistory:function(){var e=this.modal.$el.find("#selected_history_content").find(":checked"),t=[],i=[],a=[];if(e.length<1)r.default.info("You must select some datasets first.");else{this.modal.disableButton("Add"),e.each(function(){var e=$(this).closest("li").data("id");if(e){var a=$(this).closest("li").data("name");t.push(e),i.push(a)}});for(var o=t.length-1;o>=0;o--){var s=t[o],l=new n.default.Item;l.url=Galaxy.root+"api/folders/"+this.options.id+"/contents","collection"===i[o]?l.set({from_hdca_id:s}):l.set({from_hda_id:s}),a.push(l)}this.initChainCallControl({length:a.length,action:"adding_datasets"}),this.chainCallAddingHdas(a)}},chainCallImportingIntoHistory:function(e,t){var i=this,a=e.pop();if(void 0===a)return 0===this.options.chain_call_control.failed_number?r.default.success("Selected datasets imported into history. Click this to start analyzing it.","",{onclick:function(){window.location=Galaxy.root}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?r.default.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;l--){var d=new n.default.Item({id:e[l]});s.push(d)}for(l=t.length-1;l>=0;l--){var c=new n.default.FolderAsModel({id:t[l]});s.push(c)}this.options.chain_call_control.total_number=o,this.chainCallDeletingItems(s)}},showLocInfo:function(){var e=null,t=this;null!==Galaxy.libraries.libraryListView?(e=Galaxy.libraries.libraryListView.collection.get(this.options.parent_library_id),this.showLocInfoModal(e)):(e=new n.default.Library({id:this.options.parent_library_id})).fetch({success:function(){t.showLocInfoModal(e)},error:function(e,t){void 0!==t.responseJSON?r.default.error(t.responseJSON.err_msg):r.default.error("An error occurred.")}})},showLocInfoModal:function(e){var t=this,i=this.templateLocInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Location Details",body:i({library:e,options:t.options}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(e){switch(e.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),r.default.error("Invalid import source.")}},showPageSizePrompt:function(e){e.preventDefault();var t=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=t&&t==parseInt(t)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(t)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},findCheckedRows:function(){return $("#folder_list_body").find(":checked")},templateToolBar:function(){return _.template(['
','
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',"DATA LIBRARIES",'','",'","<% if(mutiple_add_dataset_options) { %>",'","<% } else { %>",'","<% } %>",'",'",'','",'','','","","","
","",'
',"
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id<%- library.get("id") %>
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',"
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","
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',"Select history: ",'","
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',"or create new: ",'',"","
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",'
','
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","
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",'
','
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","
"].join(""))},templateDeletingItemsProgressBar:function(){return _.template(['
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All files you select will be imported into the current folder ignoring their folder structure.
','','
','",'","
",'
','",'",'",'","
",'",'","
",'
',"
","
","

You can set extension type and genome for all imported datasets at once:

","
",'Type: ','Genome: ',"
","
","
",'","
","
"].join(""))},templateImportPathModal:function(){return _.template(['
','
All files within the given folders and their subfolders will be imported into the current folder.
','
','",'","
",'",'","
",'',"
","

You can set extension type and genome for all imported datasets at once:

","
",'Type: ','Genome: ',"
","
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"].join(""))},templatePaginator:function(){return _.template(['","",' <%- items_shown %> items shown (change)',"",""," <%- total_items_count %> total",""].join(""))}});e.default={FolderToolbarView:c}}); \ No newline at end of file +define("mvc/library/library-foldertoolbar-view",["exports","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select","libs/jquery/jstree"],function(e,t,i,a,o){"use strict";function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var l=s(t),r=s(i),n=s(a),d=s(o),c=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedItems","click .toolbtn-show-locinfo":"showLocInfo","click .page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(e){this.options=_.defaults(e||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(e){this.options=_.extend(this.options,e);var t=this.templateToolBar(),i={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.user&&(i.is_admin=Galaxy.user.isAdmin(),i.is_anonym=Galaxy.user.isAnonymous(),null===Galaxy.config.user_library_import_dir&&!1===Galaxy.config.allow_library_path_paste&&null===Galaxy.config.library_import_dir||(i.mutiple_add_dataset_options=!0)),this.$el.html(t(i))},renderPaginator:function(e){this.options=_.extend(this.options,e);var t=this.templatePaginator();$("body").find(".folder-paginator").html(t({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(e){this.options=_.extend(this.options,e),!0===this.options.can_add_library_item?$(".add-library-items").show():$(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this,i=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:i(),buttons:{Create:function(){t.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var e=this.serialize_new_folder();if(this.validate_new_folder(e)){var t,i=new n.default.FolderAsModel,a=Backbone.history.fragment.split("/");t=a.indexOf("page")>-1?a[a.length-3]:a[a.length-1],i.url=i.urlRoot+t,i.save(e,{success:function(e){Galaxy.modal.hide(),r.default.success("Folder created."),e.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(e)},error:function(e,t){Galaxy.modal.hide(),void 0!==t.responseJSON?r.default.error(t.responseJSON.err_msg):r.default.error("An error occurred.")}})}else r.default.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(e){return""!==e.name},modalBulkImport:function(){if(0===this.findCheckedRows().length)r.default.info("You must select some datasets first.");else{var e=this;this.histories=new n.default.GalaxyHistories,this.histories.fetch().done(function(){var t=e.templateBulkImportInModal();e.modal=Galaxy.modal,e.modal.show({closing_events:!0,title:"Import into History",body:t({histories:e.histories.models}),buttons:{Import:function(){e.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})}).fail(function(e,t){void 0!==t.responseJSON?r.default.error(t.responseJSON.err_msg):r.default.error("An error occurred.")})}},importAllIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),t=this;if(""!==e)$.post(Galaxy.root+"api/histories",{name:e}).done(function(e){t.options.last_used_history_id=e.id,t.processImportToHistory(e.id,e.name)}).fail(function(e,t,i){r.default.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var i=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=i;var a=$("select[name=dataset_import_bulk] option:selected").text();this.processImportToHistory(i,a),this.modal.enableButton("Import")}},processImportToHistory:function(e,t){var i=[],a=[];this.findCheckedRows().each(function(){var e=$(this).closest("tr").data("id");"F"==e.substring(0,1)?a.push(e):i.push(e)});for(var o=[],s=i.length-1;s>=0;s--){var l=i[s];(d=new n.default.HistoryItem).url=d.urlRoot+e+"/contents",d.content=l,d.source="library",o.push(d)}for(s=a.length-1;s>=0;s--){var r=a[s],d=new n.default.HistoryItem;d.url=d.urlRoot+e+"/contents",d.content=r,d.source="library_folder",o.push(d)}this.initChainCallControl({length:o.length,action:"to_history",history_name:t}),jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+e),this.chainCallImportingIntoHistory(o,t)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%");var e=Math.round(this.progress)+"% Complete";$(".completion_span").text(e)},download:function(e,t){var i=[],a=[];this.findCheckedRows().each(function(){var e=$(this).closest("tr").data("id");"F"==e.substring(0,1)?a.push(e):i.push(e)});var o=Galaxy.root+"api/libraries/datasets/download/"+t,s={ld_ids:i,folder_ids:a};this.processDownload(o,s,"get")},processDownload:function(e,t,i){if(e&&t){t="string"==typeof t?t:$.param(t);var a="";$.each(t.split("&"),function(){var e=this.split("=");a+=''}),$('
'+a+"
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t=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:t({}),buttons:{Import:function(){e.importFromPathsClicked(e)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var e=this;l.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(t){e.list_extensions=[];for(var i in t)e.list_extensions.push({id:t[i].extension,text:t[i].extension,description:t[i].description,description_url:t[i].description_url});e.list_extensions.sort(function(e,t){return e.id>t.id?1:e.idt.id?1:e.id=0;c--){var p=n[c].trim();0!==p.length&&d.push(p)}this.initChainCallControl({length:d.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:d,preserve_dirs:e,link_data:t,space_to_tab:i,to_posix_lines:a,source:"admin_path",file_type:s,tag_using_filenames:o,dbkey:l})}else r.default.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(e){var t;switch(e.action){case"adding_datasets":t=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(t({folder_name:this.options.folder_name}));break;case"deleting_datasets":t=this.templateDeletingItemsProgressBar(),this.modal.$el.find(".modal-body").html(t());break;case"to_history":t=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(t({history_name:e.history_name}));break;default:Galaxy.emit.error("Wrong action specified.","datalibs")}this.progress=0,this.progressStep=100/e.length,this.options.chain_call_control.total_number=e.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(e,t){var i=$("#jstree_browser").jstree().get_selected(!0),a=_.filter(i,function(e){return 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f=t.source+"_file";this.chainCallImportingUserdirFiles({paths:u,file_type:d,dbkey:c,link_data:s,space_to_tab:l,to_posix_lines:n,source:f,tag_using_filenames:p})}}},fetchAndDisplayHistoryContents:function(e){var t=this;new n.default.HistoryContents({id:e}).fetch({success:function(i){var a=t.templateHistoryContents();t.histories.get(e).set({contents:i}),t.modal.$el.find("#selected_history_content").html(a({history_contents:i.models.reverse()})),t.modal.$el.find(".history-import-select-all").bind("click",function(){$("#selected_history_content [type=checkbox]").prop("checked",!0)}),t.modal.$el.find(".history-import-unselect-all").bind("click",function(){$("#selected_history_content [type=checkbox]").prop("checked",!1)})},error:function(e,t){void 0!==t.responseJSON?r.default.error(t.responseJSON.err_msg):r.default.error("An error occurred.")}})},addAllDatasetsFromHistory:function(){var 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You can set extension type and genome for all imported datasets at once:

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