galaxy-commits May 2014

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commit/galaxy-central: martenson: data libraries: first take on shareable url for datasets
by commits-noreply＠bitbucket.org 03 May '14

03 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9dd03d95b91c/ Changeset: 9dd03d95b91c User: martenson Date: 2014-05-03 00:00:23 Summary: data libraries: first take on shareable url for datasets Affected #: 6 files diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -30,6 +30,7 @@ routes: { "" : "libraries", "folders/:id" : "folder_content", + "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", "folders/:folder_id/download/:format" : "download" } }); @@ -88,6 +89,15 @@ } }); + this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ + if (Galaxy.libraries.folderToolbarView){ + Galaxy.libraries.folderToolbarView.$el.unbind('click'); + } + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id}); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id, dataset_id: dataset_id}); + // Galaxy.libraries.folderListView.rowViews.get(dataset_id).showDatasetDetails(); + }); + Backbone.history.start({pushState: false}); } }); diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -32,10 +32,12 @@ 'click .dataset_row' : 'selectClickedRow', 'click .sort-folder-link' : 'sort_clicked' }, + + // cache of rendered views + rowViews: {}, initialize : function(options){ this.options = _.defaults(this.options || {}, options); - this.fetchFolder(); }, @@ -62,6 +64,9 @@ that.folder_container = folder_container; that.render(); that.addAll(folder_container.get('folder').models); + if (that.options.dataset_id){ + _.findWhere(that.rowViews, {id: that.options.dataset_id}).showDatasetDetails(); + } }, error: function(model, response){ if (typeof response.responseJSON !== "undefined"){ @@ -148,7 +153,12 @@ this.options.contains_file = true; model.set('readable_size', this.size_to_string(model.get('file_size'))); } + model.set('folder_id', this.id); var rowView = new mod_library_folderrow_view.FolderRowView(model); + + // save new rowView to cache + this.rowViews[model.get('id')] = rowView; + this.$el.find('#first_folder_item').after(rowView.el); $('.deleted_dataset').hover(function() { diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/mvc/library/library-folderrow-view.js --- a/static/scripts/mvc/library/library-folderrow-view.js +++ b/static/scripts/mvc/library/library-folderrow-view.js @@ -15,7 +15,7 @@ lastSelectedHistory: '', events: { - 'click .library-dataset' : 'showDatasetDetails', + // 'click .library-dataset' : 'showDatasetDetails', 'click .undelete_dataset_btn' : 'undelete_dataset' }, @@ -49,9 +49,10 @@ }, //show modal with current dataset info - showDatasetDetails : function(event){ + // showDatasetDetails : function(event){ + showDatasetDetails : function(){ // prevent default - event.preventDefault(); + // event.preventDefault(); var id = this.id; @@ -270,7 +271,7 @@ tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>'); tmpl_array.push(' </td>'); tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); - tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset + tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#folder_list_body").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#folder_list_body").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(n,m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:n});Galaxy.libraries.folderListView=new a.FolderListView({id:n,dataset_id:m})});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},initialize:function(g){this.options=_.defaults(this.options||{},g);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},render:function(g){this.options=_.defaults(this.options,g);var h=this.templateFolder();var i=this.folderContainer.attributes.metadata.full_path;var j;if(i.length===1){j=0}else{j=i[i.length-2][0]}this.$el.html(h({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:j,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var g=this.folderContainer.attributes.metadata;g.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(g);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)});this.postRender()},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}var g=new a.FolderRowView(h);this.$el.find("#first_folder_item").after(g.el);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(g){this.$el.find("#"+g.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th style="width:30%;"><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(' <th style="width:15%;"></th> ');g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");g.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents.</div>');return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},rowViews:{},initialize:function(g){this.options=_.defaults(this.options||{},g);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models);if(h.options.dataset_id){_.findWhere(h.rowViews,{id:h.options.dataset_id}).showDatasetDetails()}},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},render:function(g){this.options=_.defaults(this.options,g);var h=this.templateFolder();var i=this.folderContainer.attributes.metadata.full_path;var j;if(i.length===1){j=0}else{j=i[i.length-2][0]}this.$el.html(h({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:j,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var g=this.folderContainer.attributes.metadata;g.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(g);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)});this.postRender()},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}h.set("folder_id",this.id);var g=new a.FolderRowView(h);this.rowViews[h.get("id")]=g;this.$el.find("#first_folder_item").after(g.el);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(g){this.$el.find("#"+g.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th style="width:30%;"><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(' <th style="width:15%;"></th> ');g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");g.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents.</div>');return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/packed/mvc/library/library-folderrow-view.js --- a/static/scripts/packed/mvc/library/library-folderrow-view.js +++ b/static/scripts/packed/mvc/library/library-folderrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .library-dataset":"showDatasetDetails","click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(f){this.render(f)},render:function(f){var g=null;if(f.get("type")==="folder"){this.options.type="folder";g=this.templateRowFolder()}else{this.options.type="file";if(f.get("deleted")){g=this.templateRowDeletedFile()}else{g=this.templateRowFile()}}this.setElement(g({content_item:f}));this.$el.show();return this},showDatasetDetails:function(i){i.preventDefault();var j=this.id;var h=new c.Item();var g=new c.GalaxyHistories();h.id=j;var f=this;h.fetch({success:function(k){g.fetch({success:function(l){f.renderModalAfterFetch(k,l)},error:function(m,l){if(typeof l.responseJSON!=="undefined"){e.error(l.responseJSON.err_msg)}else{e.error("An error occured during fetching histories:(")}f.renderModalAfterFetch(k)}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error(k.responseJSON.err_msg)}else{e.error("An error occured during loading dataset details :(")}}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}}});$(".peek").html(k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};this.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var h=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=h;var f=$("#id_row").attr("data-id");var i=new c.HistoryItem();var g=this;i.url=i.urlRoot+h+"/contents";i.save({content:f,source:"library"},{success:function(){e.success("Dataset imported");g.modal.enableButton("Import");g.modal.enableButton("Download")},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error("Dataset not imported. "+j.responseJSON.err_msg)}else{e.error("An error occured! Dataset not imported. Please try again.")}g.modal.enableButton("Import");g.modal.enableButton("Download")}})},undelete_dataset:function(g){$(".tooltip").hide();var f=$(g.target).closest("tr")[0].id;var h=Galaxy.libraries.folderListView.collection.get(f);h.url=h.urlRoot+h.id+"?undelete=true";h.destroy({success:function(j,i){Galaxy.libraries.folderListView.collection.remove(f);var k=new c.Item(i);Galaxy.libraries.folderListView.collection.add(k);e.success("Dataset undeleted")},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error("Dataset was not undeleted. "+i.responseJSON.err_msg)}else{e.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>');tmpl_array.push(" <span>(empty folder)</span>");tmpl_array.push(" <% } %>");tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span></td>');tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td class="right-center"><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")}});return{FolderRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(f){this.render(f)},render:function(f){var g=null;if(f.get("type")==="folder"){this.options.type="folder";g=this.templateRowFolder()}else{this.options.type="file";if(f.get("deleted")){g=this.templateRowDeletedFile()}else{g=this.templateRowFile()}}this.setElement(g({content_item:f}));this.$el.show();return this},showDatasetDetails:function(){var i=this.id;var h=new c.Item();var g=new c.GalaxyHistories();h.id=i;var f=this;h.fetch({success:function(j){g.fetch({success:function(k){f.renderModalAfterFetch(j,k)},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error(k.responseJSON.err_msg)}else{e.error("An error occured during fetching histories:(")}f.renderModalAfterFetch(j)}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error occured during loading dataset details :(")}}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}}});$(".peek").html(k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};this.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var h=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=h;var f=$("#id_row").attr("data-id");var i=new c.HistoryItem();var g=this;i.url=i.urlRoot+h+"/contents";i.save({content:f,source:"library"},{success:function(){e.success("Dataset imported");g.modal.enableButton("Import");g.modal.enableButton("Download")},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error("Dataset not imported. "+j.responseJSON.err_msg)}else{e.error("An error occured! Dataset not imported. Please try again.")}g.modal.enableButton("Import");g.modal.enableButton("Download")}})},undelete_dataset:function(g){$(".tooltip").hide();var f=$(g.target).closest("tr")[0].id;var h=Galaxy.libraries.folderListView.collection.get(f);h.url=h.urlRoot+h.id+"?undelete=true";h.destroy({success:function(j,i){Galaxy.libraries.folderListView.collection.remove(f);var k=new c.Item(i);Galaxy.libraries.folderListView.collection.add(k);e.success("Dataset undeleted")},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error("Dataset was not undeleted. "+i.responseJSON.err_msg)}else{e.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>');tmpl_array.push(" <span>(empty folder)</span>");tmpl_array.push(" <% } %>");tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span></td>');tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td class="right-center"><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")}});return{FolderRowView:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Jeremy Goecks: Put converted datasets in history and add note to merge copied converter code.
by commits-noreply＠bitbucket.org 02 May '14

02 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b852505038a8/ Changeset: b852505038a8 User: Jeremy Goecks Date: 2014-05-02 22:32:38 Summary: Put converted datasets in history and add note to merge copied converter code. Affected #: 2 files diff -r 41bb60076082ea46686a4bb9db8cb593b8f35851 -r b852505038a8c3a05d0320ad7d00dccf7969a864 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1564,8 +1564,7 @@ raise NoConverterException("A dependency (%s) is missing a converter." % dependency) except KeyError: pass # No deps - new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] - new_dataset.name = self.name + new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=True ).values()[0] assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, dataset=new_dataset, metadata_safe=False ) session = trans.sa_session session.add( new_dataset ) diff -r 41bb60076082ea46686a4bb9db8cb593b8f35851 -r b852505038a8c3a05d0320ad7d00dccf7969a864 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -50,6 +50,7 @@ if converted_dataset: data = converted_dataset else: + # FIXME: merge with hda.get_converted_dataset() mode as it's nearly identical. #run converter here new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output=True, visible=False ).values()[0] new_data.hid = data.hid Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: devteam: Enhance the framework that supports discovery of tool dependencies' scripts that are in the same repository as the tool. This eliminates the requirement for setting a variable _SCRIPT_PATH in the tool_dependencies.xml and requirements tagset in a tool config. Now it only needs to be set in the tool config and it should look like: <requirement type="set_environment">PATH</requirement>
by commits-noreply＠bitbucket.org 02 May '14

02 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41bb60076082/ Changeset: 41bb60076082 User: devteam Date: 2014-05-02 21:55:45 Summary: Enhance the framework that supports discovery of tool dependencies' scripts that are in the same repository as the tool. This eliminates the requirement for setting a variable _SCRIPT_PATH in the tool_dependencies.xml and requirements tagset in a tool config. Now it only needs to be set in the tool config and it should look like: <requirement type="set_environment">PATH</requirement> Affected #: 5 files diff -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 -r 41bb60076082ea46686a4bb9db8cb593b8f35851 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -289,6 +289,55 @@ raise Exception( message ) return handled_tool_dependencies +def handle_env_vars_for_set_environment_tool_dependency( app, tool_shed_repository, tool_shed_repository_install_dir ): + env_var_name = 'PATH' + install_dir = \ + tool_dependency_util.get_tool_dependency_install_dir( app=app, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + repository_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dependency_type='set_environment', + tool_dependency_name=env_var_name, + tool_dependency_version=None ) + env_var_dict = dict( name=env_var_name, action='prepend_to', value=tool_shed_repository_install_dir ) + if not os.path.exists( install_dir ): + os.makedirs( install_dir ) + status = app.install_model.ToolDependency.installation_status.INSTALLING + tool_dependency = \ + tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=env_var_name, + version=None, + type='set_environment', + status=status, + set_status=True ) + env_file_builder = EnvFileBuilder( install_dir ) + return_code = env_file_builder.append_line( make_executable=True, **env_var_dict ) + if return_code: + error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \ + ( str( tool_dependency.name ), str( return_code ) ) + log.debug( error_message ) + status = app.install_model.ToolDependency.installation_status.ERROR + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=status, + error_message=error_message, + remove_from_disk=False ) + else: + if tool_dependency.status not in [ app.install_model.ToolDependency.installation_status.ERROR, + app.install_model.ToolDependency.installation_status.INSTALLED ]: + status = app.install_model.ToolDependency.installation_status.INSTALLED + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=status, + error_message=None, + remove_from_disk=False ) + log.debug( 'Environment variable %s set in %s for tool dependency %s.' % \ + ( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) ) + return tool_dependency + def install_and_build_package_via_fabric( app, tool_shed_repository, tool_dependency, actions_dict ): sa_session = app.install_model.context try: @@ -638,12 +687,20 @@ """ # TODO: Add support for a repository dependency definition within this tool dependency type's tag set. This should look something like # the following. See the implementation of support for this in the tool dependency package type's method above. + # This function is only called for set environment actions as defined below, not within an <install version="1.0"> tool + # dependency type. Here is an example of the tag set this function does handle: + # <action type="set_environment"> + # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + # </action> + # Here is an example of the tag set this function does not handle: # <set_environment version="1.0"> # <repository toolshed="<tool shed>" name="<repository name>" owner="<repository owner>" changeset_revision="<changeset revision>" /> # </set_environment> sa_session = app.install_model.context - tool_dependency = None + tool_dependencies = [] env_var_version = elem.get( 'version', '1.0' ) + tool_shed_repository_install_dir = fabric_util.get_tool_shed_repository_install_dir( app, tool_shed_repository ) + tool_shed_repository_install_dir_added_to_path = False for env_var_elem in elem: # Althoug we're in a loop here, this method will always return only a single ToolDependency or None. env_var_name = env_var_elem.get( 'name', None ) @@ -662,10 +719,10 @@ tool_dependency_type='set_environment', tool_dependency_name=env_var_name, tool_dependency_version=None ) - tool_shed_repository_install_dir = fabric_util.get_tool_shed_repository_install_dir( app, tool_shed_repository ) + install_environment = InstallEnvironment( tool_shed_repository_install_dir=tool_shed_repository_install_dir, + install_dir=install_dir ) env_var_dict = td_common_util.create_env_var_dict( elem=env_var_elem, - tool_dependency_install_dir=install_dir, - tool_shed_repository_install_dir=tool_shed_repository_install_dir ) + install_environment=install_environment ) if env_var_dict: if not os.path.exists( install_dir ): os.makedirs( install_dir ) @@ -714,7 +771,18 @@ status=status, error_message=error_message, remove_from_disk=False ) - return tool_dependency + if tool_dependency.status != app.install_model.ToolDependency.installation_status.ERROR: + if env_var_dict[ 'name' ] == 'PATH' and \ + env_var_dict[ 'action' ] in [ 'prepend_to', 'set_to', 'append_to' ] and \ + env_var_dict[ 'value' ] == install_environment.tool_shed_repository_install_dir: + tool_shed_repository_install_dir_added_to_path = True + tool_dependencies.append( tool_dependency ) + if not tool_shed_repository_install_dir_added_to_path: + tool_dependency = handle_env_vars_for_set_environment_tool_dependency( app, + tool_shed_repository, + tool_shed_repository_install_dir ) + tool_dependencies.append( tool_dependency ) + return tool_dependencies def strip_path( fpath ): if not fpath: diff -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 -r 41bb60076082ea46686a4bb9db8cb593b8f35851 lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -707,17 +707,22 @@ return env_var_dict def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + # This function is only called for set environment actions as defined above, not within a <set_environment> tool + # dependency type. Here is an example of the tag set this function does handle: # <action type="set_environment"> # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> # </action> + # Here is an example of the tag set this function does not handle: + # <action type="set_environment"> + # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + # </action> env_var_dicts = [] for env_elem in action_elem: if env_elem.tag == 'environment_variable': env_var_dict = \ td_common_util.create_env_var_dict( elem=env_elem, - tool_dependency_install_dir=install_environment.install_dir, - tool_shed_repository_install_dir=install_environment.tool_shed_repository_install_dir ) + install_environment=install_environment ) if env_var_dict: env_var_dicts.append( env_var_dict ) if env_var_dicts: diff -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 -r 41bb60076082ea46686a4bb9db8cb593b8f35851 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -168,10 +168,12 @@ return True return False -def create_env_var_dict( elem, tool_dependency_install_dir=None, tool_shed_repository_install_dir=None ): +def create_env_var_dict( elem, install_environment ): env_var_name = elem.get( 'name', 'PATH' ) env_var_action = elem.get( 'action', 'prepend_to' ) env_var_text = None + tool_dependency_install_dir = install_environment.install_dir + tool_shed_repository_install_dir = install_environment.tool_shed_repository_install_dir if elem.text and elem.text.find( 'REPOSITORY_INSTALL_DIR' ) >= 0: if tool_shed_repository_install_dir and elem.text.find( '$REPOSITORY_INSTALL_DIR' ) != -1: env_var_text = elem.text.replace( '$REPOSITORY_INSTALL_DIR', tool_shed_repository_install_dir ) diff -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 -r 41bb60076082ea46686a4bb9db8cb593b8f35851 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -349,9 +349,15 @@ requirement_dict[ 'status' ] = tool_dependency_status new_val.append( requirement_dict ) if tool_dependency_status in [ trans.install_model.ToolDependency.installation_status.INSTALLED ]: - installed_tool_dependencies[ td_key ] = new_val + if td_key in installed_tool_dependencies: + installed_tool_dependencies[ td_key ].extend( new_val ) + else: + installed_tool_dependencies[ td_key ] = new_val else: - missing_tool_dependencies[ td_key ] = new_val + if td_key in missing_tool_dependencies: + missing_tool_dependencies[ td_key ].extend( new_val ) + else: + missing_tool_dependencies[ td_key ] = new_val else: # The val dictionary looks something like this: # {'repository_name': 'xx', @@ -497,6 +503,7 @@ return installed_tool_dependencies root = tree.getroot() fabric_version_checked = False + set_environment_handled = False for elem in root: if elem.tag == 'package': # Only install the tool_dependency if it is not already installed and it is associated with a database record in the received @@ -556,21 +563,31 @@ # <set_environment version="1.0"> # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> # </set_environment> + set_environment_handled = True try: - tool_dependency = set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ) + tool_dependencies = set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ) except Exception, e: error_message = "Error setting environment for tool dependency: %s" % str( e ) log.debug( error_message ) - if tool_dependency: - # Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must - # be left False here. - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, - tool_dependency, - error_message, - remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, - app.install_model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) + for tool_dependency in tool_dependencies: + if tool_dependency and tool_dependency.status == app.install_model.ToolDependency.installation_status.ERROR: + # Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must + # be left False here. + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) + for tool_dependency in tool_dependencies: + if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, + app.install_model.ToolDependency.installation_status.ERROR ]: + installed_tool_dependencies.append( tool_dependency ) + if not set_environment_handled: + element_attributes = dict( name='PATH', action='prepend_to' ) + generated_elem = xml_util.create_element( 'environment_variable', attributes=element_attributes, sub_elements=None ) + generated_elem.text = '$REPOSITORY_INSTALL_DIR' + generated_attr_tups = [ ( 'PATH', None, 'set_environment' ) ] + tool_dependencies = set_environment( app, generated_elem, tool_shed_repository, generated_attr_tups ) + installed_tool_dependencies.extend( tool_dependencies ) return installed_tool_dependencies def repository_dependency_needed_only_for_compiling_tool_dependency( repository, repository_dependency ): diff -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 -r 41bb60076082ea46686a4bb9db8cb593b8f35851 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -23,6 +23,7 @@ from tool_shed.galaxy_install.tool_dependencies import install_util from tool_shed.galaxy_install.tool_dependencies import td_common_util import tool_shed.repository_types.util as rt_util +from xml.etree import ElementTree as XmlET eggs.require( 'mercurial' ) @@ -921,7 +922,28 @@ invalid_tool_dependencies_dict = {} valid_repository_dependency_tups = [] invalid_repository_dependency_tups = [] + needs_set_environment_tool_dependency_for_path = False + tools_metadata = metadata_dict.get( 'tools', None ) + if tools_metadata is not None: + for tools_dict in tools_metadata: + requirements = tools_dict.get( 'requirements', None ) + if requirements is not None: + for requirements_dict in requirements: + if requirements_dict[ 'type' ] == 'set_environment' and requirements_dict[ 'name' ] == 'PATH': + needs_set_environment_tool_dependency_for_path = True + break description = root.get( 'description' ) + if needs_set_environment_tool_dependency_for_path: + # Add this to the in-memory XML tree that is parsed to determine the database tool dependency records. This will not + # modify the on-disk tool dependency definitions, but is needed in order for the tool to correctly source the env.sh + # file that was generated for the PATH variable. + # <set_environment version="1.0"> + # <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + # </set_environment> + env_var_elem_attributes = dict( name='PATH', action='prepend_to' ) + set_environment_elem = xml_util.create_element( 'set_environment', attributes=dict( version='1.0' ) ) + XmlET.SubElement( set_environment_elem, 'environment_variable', attrib=env_var_elem_attributes ) + root.append( set_environment_elem ) for elem in root: if elem.tag == 'package': valid_tool_dependencies_dict, invalid_tool_dependencies_dict, repository_dependency_tup, repository_dependency_is_valid, message = \ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: History: cruft removal from controller and associated javascript
by commits-noreply＠bitbucket.org 02 May '14

02 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f79c07c4438/ Changeset: 2f79c07c4438 User: carlfeberhard Date: 2014-05-02 21:45:25 Summary: History: cruft removal from controller and associated javascript Affected #: 3 files diff -r 3f8e4852623187152ffaea5fd529fac2001c8316 -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -549,6 +549,7 @@ count += 1 return trans.show_ok_message( "%d datasets have been deleted permanently" % count, refresh_frames=['history'] ) + #TODO: use api instead @web.expose def delete_current( self, trans, purge=False ): """Delete just the active history -- this does not require a logged in user.""" @@ -604,6 +605,7 @@ trans.sa_session.add( history ) trans.sa_session.flush() return trans.show_ok_message( "Your datasets have been unhidden.", refresh_frames=refresh_frames ) + #TODO: used in index.mako @web.expose def resume_paused_jobs( self, trans, current=False, ids=None ): @@ -618,6 +620,7 @@ trans.sa_session.add( history ) trans.sa_session.flush() return trans.show_ok_message( "Your jobs have been resumed.", refresh_frames=refresh_frames ) + #TODO: used in index.mako @web.expose @web.require_login( "rate items" ) @@ -630,34 +633,7 @@ # Rate history. history_rating = self.rate_item( trans.sa_session, trans.get_user(), history, rating ) return self.get_ave_item_rating_data( trans.sa_session, history ) - - @web.expose - def rename_async( self, trans, id=None, new_name=None ): - history = self.get_history( trans, id ) - # Check that the history exists, and is either owned by the current - # user (if logged in) or the current history - assert history is not None - if history.user is None: - assert history == trans.get_history() - else: - assert history.user == trans.user - # Rename - new_name = sanitize_html( new_name ) - history.name = new_name - trans.sa_session.add( history ) - trans.sa_session.flush() - return new_name - - @web.expose - @web.require_login( "use Galaxy histories" ) - def annotate_async( self, trans, id, new_annotation=None, **kwargs ): - history = self.get_history( trans, id ) - if new_annotation: - # Sanitize annotation before adding it. - new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), history, new_annotation ) - trans.sa_session.flush() - return new_annotation + #TODO: used in display_base.mako @web.expose # TODO: Remove require_login when users are warned that, if they are not @@ -686,6 +662,7 @@ self.queue_history_import( trans, archive_type=archive_type, archive_source=archive_source ) return trans.show_message( "Importing history from '%s'. \ This history will be visible when the import is complete" % archive_source ) + #TODO: used in this file and index.mako @web.expose def export_archive( self, trans, id=None, gzip=True, include_hidden=False, include_deleted=False ): @@ -719,6 +696,7 @@ return trans.show_message( "Exporting History '%(n)s'. Use this link to download \ the archive or import it to another Galaxy server: \ <a href='%(u)s'>%(u)s</a>" % ( { 'n' : history.name, 'u' : url } ) ) + #TODO: used in this file and index.mako @web.expose @web.json @@ -733,6 +711,7 @@ "link" : url_for(controller='history', action="display_by_username_and_slug", username=history.user.username, slug=history.slug ) } return return_dict + #TODO: used in page/editor.mako @web.expose @web.require_login( "set history's accessible flag" ) @@ -748,6 +727,7 @@ history.importable = importable trans.sa_session.flush() return + #TODO: used in page/editor.mako @web.expose def get_item_content_async( self, trans, id ): @@ -764,6 +744,7 @@ for dataset in datasets: dataset.annotation = self.get_item_annotation_str( trans.sa_session, history.user, dataset ) return trans.stream_template_mako( "/history/item_content.mako", item = history, item_data = datasets ) + #TODO: used in embed_base.mako @web.expose def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): @@ -773,9 +754,12 @@ return ac_data = "" - for history in trans.sa_session.query( model.History ).filter_by( user=user ).filter( func.lower( model.History.name ) .like(q.lower() + "%") ): + for history in ( trans.sa_session.query( model.History ) + .filter_by( user=user ) + .filter( func.lower( model.History.name ).like(q.lower() + "%") ) ): ac_data = ac_data + history.name + "\n" return ac_data + #TODO: used in grid_base.mako @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): @@ -852,6 +836,7 @@ Warning! If you import this history, you will lose your current history. <br>You can <a href="%s">continue and import this history</a> or %s. """ % ( web.url_for(controller='history', action='imp', id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True ) + #TODO: used in history/view, display, embed @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): @@ -1390,51 +1375,4 @@ def get_item( self, trans, id ): return self.get_history( trans, id ) - - @web.json - def get_display_application_links( self, trans, hda_ids=None ): - """ - Returns external display application JSON data for all/given - HDAs within the current history. - """ - #TODO: fold into API and remove - try: - history = trans.get_history() - #TODO: allow id for more flexibility? (the following doesn't work if anonymous...) - #history = self.get_history( trans, id, check_ownership=True, check_accessible=True, deleted=None ) - if hda_ids: - unencoded_hda_ids = [ trans.security.decode_id( hda_id ) for hda_id in galaxy.util.listify( hda_ids ) ] - #TODO: this gets all - should narrow query by using hda_ids here - no way with this current method - hdas = self.get_history_datasets( trans, history, show_deleted=False, show_hidden=True, show_purged=False ) - - except Exception, exc: - log.error( 'Failed loading data for ids (%s): %s', hda_ids, str( exc ), exc_info=True ) - trans.response.status = 500 - return str( exc ) - - hda_display_links = [] - for hda in hdas: - # only get requested hdas - if hda_ids and hda.id not in unencoded_hda_ids: - continue - - hda_link_data = { 'id': trans.security.encode_id( hda.id ) } - # don't bail on entire list if one hda has an error; record and move on - try: - # 'old style': must be enabled in config (see universe_wsgi.ini) - if trans.app.config.enable_old_display_applications: - hda_link_data[ 'display_types' ] = self.get_old_display_applications( trans, hda ) - - # 'new style' - hda_link_data[ 'display_apps' ] = self.get_display_apps( trans, hda ) - - except Exception, exc: - log.error( 'Failed getting links, hda (%s): %s', hda_link_data[ 'id' ], str( exc ), exc_info=True ) - hda_link_data[ 'error' ] = str( exc ) - - hda_display_links.append( hda_link_data ) - - # send 'do not cache' headers to handle IE's caching of ajax get responses - trans.response.headers[ 'Cache-Control' ] = "max-age=0,no-cache,no-store" - trans.response.set_content_type( 'application/json' ) - return hda_display_links + #TODO: override of base ui controller? diff -r 3f8e4852623187152ffaea5fd529fac2001c8316 -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -34,26 +34,6 @@ // ........................................................................ urls urlRoot: galaxy_config.root + 'api/histories', - /** url for changing the name of the history */ - renameUrl : function(){ -//TODO: just use this.save() - var id = this.get( 'id' ); - if( !id ){ return undefined; } - return galaxy_config.root + 'history/rename_async?id=' + this.get( 'id' ); - }, - /** url for changing the annotation of the history */ - annotateUrl : function(){ - var id = this.get( 'id' ); - if( !id ){ return undefined; } - return galaxy_config.root + 'history/annotate_async?id=' + this.get( 'id' ); - }, - /** url for changing the tags of the history */ - tagUrl : function(){ - var id = this.get( 'id' ); - if( !id ){ return undefined; } - return galaxy_config.root + 'tag/get_tagging_elt_async?item_id=' + this.get( 'id' ) + '&item_class=History'; - }, - // ........................................................................ set up/tear down /** Set up the model * @param {Object} historyJSON model data for this History diff -r 3f8e4852623187152ffaea5fd529fac2001c8316 -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/base-mvc","utils/localization"],function(c,a,b){var e=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",renameUrl:function(){var g=this.get("id");if(!g){return undefined}return galaxy_config.root+"history/rename_async?id="+this.get("id")},annotateUrl:function(){var g=this.get("id");if(!g){return undefined}return galaxy_config.root+"history/annotate_async?id="+this.get("id")},tagUrl:function(){var g=this.get("id");if(!g){return undefined}return galaxy_config.root+"tag/get_tagging_elt_async?item_id="+this.get("id")+"&item_class=History"},initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.hdas=new c.HDACollection(i||[],{historyId:this.get("id")});if(i&&_.isArray(i)){this.hdas.reset(i)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.hdas){this.hdas.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||e.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.hdas.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});e.UPDATE_DELAY=4000;e.getHistoryData=function f(h,r){r=r||{};var l=r.hdaDetailIds||[];var n=jQuery.Deferred(),m=null;function i(s){return jQuery.ajax(galaxy_config.root+"api/histories/"+h)}function g(s){if(!s||!s.state_ids){return 0}return _.reduce(s.state_ids,function(t,v,u){return t+v.length},0)}function q(t){if(!g(t)){return[]}if(_.isFunction(l)){l=l(t)}var s=(l.length)?({details:l.join(",")}):({});return jQuery.ajax(galaxy_config.root+"api/histories/"+t.id+"/contents",{data:s})}var p=r.historyFn||i,o=r.hdaFn||q;var k=p(h);k.done(function(s){m=s;n.notify({status:"history data retrieved",historyJSON:m})});k.fail(function(u,s,t){n.reject(u,"loading the history")});var j=k.then(o);j.then(function(s){n.notify({status:"dataset data retrieved",historyJSON:m,hdaJSON:s});n.resolve(m,s)});j.fail(function(u,s,t){n.reject(u,"loading the datasets",{history:m})});return n};var d=Backbone.Collection.extend(a.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories"});return{History:e,HistoryCollection:d}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/base-mvc","utils/localization"],function(c,a,b){var e=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.hdas=new c.HDACollection(i||[],{historyId:this.get("id")});if(i&&_.isArray(i)){this.hdas.reset(i)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.hdas){this.hdas.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||e.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.hdas.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});e.UPDATE_DELAY=4000;e.getHistoryData=function f(h,r){r=r||{};var l=r.hdaDetailIds||[];var n=jQuery.Deferred(),m=null;function i(s){return jQuery.ajax(galaxy_config.root+"api/histories/"+h)}function g(s){if(!s||!s.state_ids){return 0}return _.reduce(s.state_ids,function(t,v,u){return t+v.length},0)}function q(t){if(!g(t)){return[]}if(_.isFunction(l)){l=l(t)}var s=(l.length)?({details:l.join(",")}):({});return jQuery.ajax(galaxy_config.root+"api/histories/"+t.id+"/contents",{data:s})}var p=r.historyFn||i,o=r.hdaFn||q;var k=p(h);k.done(function(s){m=s;n.notify({status:"history data retrieved",historyJSON:m})});k.fail(function(u,s,t){n.reject(u,"loading the history")});var j=k.then(o);j.then(function(s){n.notify({status:"dataset data retrieved",historyJSON:m,hdaJSON:s});n.resolve(m,s)});j.fail(function(u,s,t){n.reject(u,"loading the datasets",{history:m})});return n};var d=Backbone.Collection.extend(a.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories"});return{History:e,HistoryCollection:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: devteam: Fix for generating metadata when a tool dependency definition sets multiple environment variables within a single <set_environment> tool dependency type.
by commits-noreply＠bitbucket.org 02 May '14

02 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3f8e48526231/ Changeset: 3f8e48526231 User: devteam Date: 2014-05-02 18:50:57 Summary: Fix for generating metadata when a tool dependency definition sets multiple environment variables within a single <set_environment> tool dependency type. Affected #: 1 file diff -r 888cd02028b37f93beba8b175fec8c85a912ac9f -r 3f8e4852623187152ffaea5fd529fac2001c8316 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -563,14 +563,11 @@ # <set_environment version="1.0"> # <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> # </set_environment> - requirements_dict = {} for env_elem in elem: # <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> env_name = env_elem.get( 'name', None ) if env_name: - requirements_dict[ 'name' ] = env_name - requirements_dict[ 'type' ] = 'set_environment' - if requirements_dict: + requirements_dict = dict( name=env_name, type='set_environment' ) if 'set_environment' in valid_tool_dependencies_dict: valid_tool_dependencies_dict[ 'set_environment' ].append( requirements_dict ) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Small fixes for LWR.
by commits-noreply＠bitbucket.org 02 May '14

02 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/888cd02028b3/ Changeset: 888cd02028b3 User: jmchilton Date: 2014-05-02 18:21:10 Summary: Small fixes for LWR. Things added/modified for parameter rewriting at tool evaluatino time that regressed when implementing message queue stuff I guess. Affected #: 2 files diff -r 42b9fb317fdd9248154216530883603110905301 -r 888cd02028b37f93beba8b175fec8c85a912ac9f lib/galaxy/jobs/runners/lwr_client/setup_handler.py --- a/lib/galaxy/jobs/runners/lwr_client/setup_handler.py +++ b/lib/galaxy/jobs/runners/lwr_client/setup_handler.py @@ -32,7 +32,7 @@ def __init__(self, client, destination_args): self.client = client system_properties = self.__build_system_properties(destination_args) - system_properties["sep"] = client.job_directory.separator + system_properties["separator"] = client.job_directory.separator self.system_properties = system_properties self.jobs_directory = destination_args["jobs_directory"] diff -r 42b9fb317fdd9248154216530883603110905301 -r 888cd02028b37f93beba8b175fec8c85a912ac9f lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -251,7 +251,10 @@ if real_path in output_dataset_paths: dataset_path = output_dataset_paths[ real_path ] param_dict[name] = DatasetFilenameWrapper( hda, dataset_path=dataset_path ) - open( dataset_path.false_path, 'w' ).close() + try: + open( dataset_path.false_path, 'w' ).close() + except EnvironmentError: + pass # May well not exist - e.g. LWR. else: param_dict[name] = DatasetFilenameWrapper( hda ) # Provide access to a path to store additional files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: data libraries: bugfix, better UI changes role handling (stilll not _good_ but better)
by commits-noreply＠bitbucket.org 02 May '14

02 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/42b9fb317fdd/ Changeset: 42b9fb317fdd User: martenson Date: 2014-05-02 00:21:37 Summary: data libraries: bugfix, better UI changes role handling (stilll not _good_ but better) Affected #: 8 files diff -r bf94ed77f61a4fd6138ee098b675426f4a6fca97 -r 42b9fb317fdd9248154216530883603110905301 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -212,7 +212,7 @@ dataset.api_type = 'file' content_items.append( dataset ) else: - can_access, folder_ids = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) if can_access: dataset.api_type = 'file' content_items.append( dataset ) diff -r bf94ed77f61a4fd6138ee098b675426f4a6fca97 -r 42b9fb317fdd9248154216530883603110905301 static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -89,10 +89,6 @@ this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, id: this.options.id, upper_folder_id: upper_folder_id, order: this.sort})); - var fetched_metadata = this.folderContainer.attributes.metadata; - fetched_metadata.contains_file = this.options.contains_file; - Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata); - // initialize the library tooltips $("#center [data-toggle]").tooltip(); //hack to show scrollbars @@ -100,6 +96,22 @@ }, /** + * Call this after all models are added to the collection + * to ensure that the folder toolbar will show proper options + * and that event will be bound on all subviews. + */ + postRender: function(){ + var fetched_metadata = this.folderContainer.attributes.metadata; + fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined'; + Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata); + $('.deleted_dataset').hover(function() { + $(this).find('.show_on_hover').show(); + }, function () { + $(this).find('.show_on_hover').hide(); + }); + }, + + /** * Adds all given models to the collection. * @param {array of Item or FolderAsModel} array of models that should * be added to the view's collection. @@ -108,28 +120,23 @@ _.each(models.reverse(), function(model) { Galaxy.libraries.folderListView.collection.add(model); }); + $("#center [data-toggle]").tooltip(); this.checkEmptiness(); - $('.deleted_dataset').hover(function() { - $(this).find('.show_on_hover').show(); - }, function () { - $(this).find('.show_on_hover').hide(); - }); + + this.postRender(); }, /** - * Renders whole collection of models as views + * Iterates this view's collection and calls the render + * function for each. Also binds the hover behavior. */ renderAll: function(){ var that = this; _.each(this.collection.models.reverse(), function(model) { that.renderOne(model); }); - $('.deleted_dataset').hover(function() { - $(this).find('.show_on_hover').show(); - }, function () { - $(this).find('.show_on_hover').hide(); - }); + this.postRender(); }, /** @@ -145,12 +152,16 @@ this.$el.find('#first_folder_item').after(rowView.el); $('.deleted_dataset').hover(function() { - $(this).find('.show_on_hover').show(); + $(this).find('.show_on_hover').show(); }, function () { - $(this).find('.show_on_hover').hide(); + $(this).find('.show_on_hover').hide(); }); }, + /** + * removes the view of the given model from the DOM + * @param {Item or FolderAsModel} model of the view that will be removed + */ removeOne: function(model){ this.$el.find('#' + model.id).remove(); }, diff -r bf94ed77f61a4fd6138ee098b675426f4a6fca97 -r 42b9fb317fdd9248154216530883603110905301 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -40,23 +40,40 @@ render: function(options){ this.options = _.extend(this.options, options); - var toolbar_template = this.templateToolBar(); var is_admin = false; + var is_anonym = true; if (Galaxy.currUser){ is_admin = Galaxy.currUser.isAdmin(); + is_anonym = Galaxy.currUser.isAnonymous(); } - this.$el.html(toolbar_template({id: this.options.id, admin_user: is_admin})); + var toolbar_template = this.templateToolBar(); + this.$el.html(toolbar_template({id: this.options.id, admin_user: is_admin, anonym: is_anonym})); }, configureElements: function(options){ this.options = _.extend(this.options, options); + if (this.options.can_add_library_item === true){ - $('#toolbtn_create_folder').show(); - $('.toolbtn_add_files').show(); + $('.add-library-items').show(); + } else{ + $('.add-library-items').hide(); } if (this.options.contains_file === true){ - $('#toolbtn_bulk_import').show(); - $('#toolbtn_dl').show(); + if (Galaxy.currUser){ + if (!Galaxy.currUser.isAnonymous()){ + $('.logged-dataset-manipulation').show(); + $('.dataset-manipulation').show(); + } else { + $('.dataset-manipulation').show(); + $('.logged-dataset-manipulation').hide(); + } + } else { + $('.logged-dataset-manipulation').hide(); + $('.dataset-manipulation').hide(); + } + } else { + $('.logged-dataset-manipulation').hide(); + $('.dataset-manipulation').hide(); } this.$el.find('[data-toggle]').tooltip(); }, @@ -495,13 +512,13 @@ tmpl_array.push('<div class="library_style_container">'); // TOOLBAR tmpl_array.push('<div id="library_folder_toolbar">'); - tmpl_array.push('<span data-toggle="tooltip" data-placement="top" title="Include deleted datasets"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>'); - tmpl_array.push('<div class="btn-group">'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>'); + tmpl_array.push('<span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>'); + tmpl_array.push('<div class="btn-group add-library-items" style="display:none;">'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>'); tmpl_array.push('</div>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; " type="button"><span class="fa fa-book"></span> to history</button>'); - tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; ">'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to history</button>'); + tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">'); tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); tmpl_array.push(' </button>'); @@ -511,7 +528,7 @@ tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); tmpl_array.push(' </ul>'); tmpl_array.push(' </div>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button" style="margin-left: 0.5em; " type="button"><span class="fa fa-times"></span> delete</button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> delete</button>'); tmpl_array.push(' </div>'); tmpl_array.push(' <div id="folder_items_element">'); // library items will append here diff -r bf94ed77f61a4fd6138ee098b675426f4a6fca97 -r 42b9fb317fdd9248154216530883603110905301 static/scripts/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/mvc/library/library-librarytoolbar-view.js @@ -22,12 +22,10 @@ render: function(){ var toolbar_template = this.templateToolBar(); var is_admin = false; - var is_anonym = false; + var is_anonym = true; if (Galaxy.currUser){ is_admin = Galaxy.currUser.isAdmin(); is_anonym = Galaxy.currUser.isAnonymous(); - } else { - is_anonym = true; } this.$el.html(toolbar_template({admin_user: is_admin, anon_user: is_anonym})); if (is_admin){ diff -r bf94ed77f61a4fd6138ee098b675426f4a6fca97 -r 42b9fb317fdd9248154216530883603110905301 static/scripts/packed/galaxy.pages.js --- a/static/scripts/packed/galaxy.pages.js +++ b/static/scripts/packed/galaxy.pages.js @@ -1,1 +1,1 @@ -var Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case (Galaxy.ITEM_DATASET):f="Dataset";c="Datasets";b="dataset";item_class="HistoryDatasetAssociation";break;case (Galaxy.ITEM_WORKFLOW):f="Workflow";c="Workflows";b="workflow";item_class="StoredWorkflow";break;case (Galaxy.ITEM_PAGE):f="Page";c="Pages";b="page";item_class="Page";break;case (Galaxy.ITEM_VISUALIZATION):f="Visualization";c="Visualizations";b="visualization";item_class="Visualization";break}var e="list_"+c.toLowerCase()+"_for_selection";var a=list_objects_url.replace("LIST_ACTION",e);return{singular:f,plural:c,controller:b,iclass:item_class,list_ajax_url:a}}function make_item_importable(a,c,b){ajax_url=set_accessible_url.replace("ITEM_CONTROLLER",a);$.ajax({type:"POST",url:ajax_url,data:{id:c,accessible:"True"},error:function(){alert("Making "+b+" accessible failed")}})}WYMeditor.editor.prototype.dialog=function(i,e,g){var a=this;var b=a.uniqueStamp();var f=a.selected();function h(){$("#set_link_id").click(function(){$("#link_attribute_label").text("ID/Name");var k=$(".wym_href");k.addClass("wym_id").removeClass("wym_href");if(f){k.val($(f).attr("id"))}$(this).remove()})}if(i==WYMeditor.DIALOG_LINK){if(f){$(a._options.hrefSelector).val($(f).attr(WYMeditor.HREF));$(a._options.srcSelector).val($(f).attr(WYMeditor.SRC));$(a._options.titleSelector).val($(f).attr(WYMeditor.TITLE));$(a._options.altSelector).val($(f).attr(WYMeditor.ALT))}var c,d;if(f){c=$(f).attr("href");if(c==undefined){c=""}d=$(f).attr("title");if(d==undefined){d=""}}show_modal("Create Link","<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='"+c+"' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='"+d+"' size='40' /></div><div>",{"Make link":function(){var m=$(a._options.hrefSelector).val()||"",k=$(".wym_id").val()||"",n=$(a._options.titleSelector).val()||"";if(m||k){a._exec(WYMeditor.CREATE_LINK,b);var l=$("a[href="+b+"]",a._doc.body);l.attr(WYMeditor.HREF,m).attr(WYMeditor.TITLE,n).attr("id",k);if(l.text().indexOf("wym-")===0){l.text(n)}}hide_modal()},Cancel:function(){hide_modal()}},{},h)}if(i==WYMeditor.DIALOG_IMAGE){if(a._selected_image){$(a._options.dialogImageSelector+" "+a._options.srcSelector).val($(a._selected_image).attr(WYMeditor.SRC));$(a._options.dialogImageSelector+" "+a._options.titleSelector).val($(a._selected_image).attr(WYMeditor.TITLE));$(a._options.dialogImageSelector+" "+a._options.altSelector).val($(a._selected_image).attr(WYMeditor.ALT))}show_modal("Image","<div class='row'><label>URL</label><br><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>Alt text</label><br><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>Title</label><br><input type='text' class='wym_title' value='' size='40' /></div>",{Insert:function(){var k=$(a._options.srcSelector).val();if(k.length>0){a._exec(WYMeditor.INSERT_IMAGE,b);$("img[src$="+b+"]",a._doc.body).attr(WYMeditor.SRC,k).attr(WYMeditor.TITLE,$(a._options.titleSelector).val()).attr(WYMeditor.ALT,$(a._options.altSelector).val())}hide_modal()},Cancel:function(){hide_modal()}});return}if(i==WYMeditor.DIALOG_TABLE){show_modal("Table","<div class='row'><label>Caption</label><br><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>Summary</label><br><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>Number Of Rows<br></label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>Number Of Cols<br></label><input type='text' class='wym_cols' value='2' size='3' /></div>",{Insert:function(){var o=$(a._options.rowsSelector).val();var r=$(a._options.colsSelector).val();if(o>0&&r>0){var n=a._doc.createElement(WYMeditor.TABLE);var l=null;var q=null;var k=$(a._options.captionSelector).val();var p=n.createCaption();p.innerHTML=k;for(x=0;x<o;x++){l=n.insertRow(x);for(y=0;y<r;y++){l.insertCell(y)}}$(n).attr("summary",$(a._options.summarySelector).val());var m=$(a.findUp(a.container(),WYMeditor.MAIN_CONTAINERS)).get(0);if(!m||!m.parentNode){$(a._doc.body).append(n)}else{$(m).after(n)}}hide_modal()},Cancel:function(){hide_modal()}})}if(i==Galaxy.DIALOG_HISTORY_LINK||i==Galaxy.DIALOG_DATASET_LINK||i==Galaxy.DIALOG_WORKFLOW_LINK||i==Galaxy.DIALOG_PAGE_LINK||i==Galaxy.DIALOG_VISUALIZATION_LINK){var j;switch(i){case (Galaxy.DIALOG_HISTORY_LINK):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_DATASET_LINK):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_WORKFLOW_LINK):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_PAGE_LINK):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_VISUALIZATION_LINK):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){show_modal("Insert Link to "+j.singular,k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>",{Insert:function(){var m=false;if($("#make-importable:checked").val()!==null){m=true}var l=new Array();$("input[name=id]:checked").each(function(){var n=$(this).val();if(m){make_item_importable(j.controller,n,j.singular)}url_template=get_name_and_link_url+n;ajax_url=url_template.replace("ITEM_CONTROLLER",j.controller);$.getJSON(ajax_url,function(p){a._exec(WYMeditor.CREATE_LINK,b);var o=$("a[href="+b+"]",a._doc.body).text();if(o==""||o==b){a.insert("<a href='"+p.link+"'>"+j.singular+" '"+p.name+"'</a>")}else{$("a[href="+b+"]",a._doc.body).attr(WYMeditor.HREF,p.link).attr(WYMeditor.TITLE,j.singular+n)}})});hide_modal()},Cancel:function(){hide_modal()}})}})}if(i==Galaxy.DIALOG_EMBED_HISTORY||i==Galaxy.DIALOG_EMBED_DATASET||i==Galaxy.DIALOG_EMBED_WORKFLOW||i==Galaxy.DIALOG_EMBED_PAGE||i==Galaxy.DIALOG_EMBED_VISUALIZATION){var j;switch(i){case (Galaxy.DIALOG_EMBED_HISTORY):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_EMBED_DATASET):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_EMBED_WORKFLOW):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_EMBED_PAGE):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_EMBED_VISUALIZATION):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){if(i==Galaxy.DIALOG_EMBED_HISTORY||i==Galaxy.DIALOG_EMBED_WORKFLOW||i==Galaxy.DIALOG_EMBED_VISUALIZATION){k=k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>"}show_modal("Embed "+j.plural,k,{Embed:function(){var l=false;if($("#make-importable:checked").val()!=null){l=true}$("input[name=id]:checked").each(function(){var m=$(this).val();var p=$("label[for='"+m+"']:first").text();if(l){make_item_importable(j.controller,m,j.singular)}var n=j.iclass+"-"+m;var o=["<div id='",n,"' class='embedded-item ",j.singular.toLowerCase()," placeholder'>","<p class='title'>","Embedded Galaxy ",j.singular," '",p,"'","</p>","<p class='content'>","[Do not edit this block; Galaxy will fill it in with the annotated ",j.singular.toLowerCase()," when it is displayed.]","</p>","</div>"].join("");a.insert(o)});hide_modal()},Cancel:function(){hide_modal()}})}})}if(i==Galaxy.DIALOG_ANNOTATE_HISTORY){$.ajax({url:list_histories_for_selection_url,data:{},error:function(){alert("Grid refresh failed")},success:function(k){show_modal("Insert Link to History",k,{Annotate:function(){var l=new Array();$("input[name=id]:checked").each(function(){var m=$(this).val();$.ajax({url:get_history_annotation_table_url,data:{id:m},error:function(){alert("Grid refresh failed")},success:function(n){a.insert(n);init_galaxy_elts(a)}})});hide_modal()},Cancel:function(){hide_modal()}})}})}};$(function(){$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});$("[name=page_content]").wymeditor({skin:"galaxy",basePath:editor_base_path,iframeBasePath:iframe_base_path,boxHtml:"<table class='wym_box' width='100%' height='100%'><tr><td><div class='wym_area_top'>"+WYMeditor.TOOLS+"</div></td></tr><tr height='100%'><td><div class='wym_area_main' style='height: 100%;'>"+WYMeditor.IFRAME+WYMeditor.STATUS+"</div></div></td></tr></table>",toolsItems:[{name:"Bold",title:"Strong",css:"wym_tools_strong"},{name:"Italic",title:"Emphasis",css:"wym_tools_emphasis"},{name:"Superscript",title:"Superscript",css:"wym_tools_superscript"},{name:"Subscript",title:"Subscript",css:"wym_tools_subscript"},{name:"InsertOrderedList",title:"Ordered_List",css:"wym_tools_ordered_list"},{name:"InsertUnorderedList",title:"Unordered_List",css:"wym_tools_unordered_list"},{name:"Indent",title:"Indent",css:"wym_tools_indent"},{name:"Outdent",title:"Outdent",css:"wym_tools_outdent"},{name:"Undo",title:"Undo",css:"wym_tools_undo"},{name:"Redo",title:"Redo",css:"wym_tools_redo"},{name:"CreateLink",title:"Link",css:"wym_tools_link"},{name:"Unlink",title:"Unlink",css:"wym_tools_unlink"},{name:"InsertImage",title:"Image",css:"wym_tools_image"},{name:"InsertTable",title:"Table",css:"wym_tools_table"},]});var d=$.wymeditors(0);var f=function(g){show_modal("Saving page","progress");$.ajax({url:save_url,type:"POST",data:{id:page_id,content:d.xhtml(),annotations:JSON.stringify(new Object()),_:"true"},success:function(){g()}})};$("#save-button").click(function(){f(function(){hide_modal()})});$("#close-button").click(function(){var h=false;if(h){var g=function(){window.onbeforeunload=undefined;window.document.location=page_list_url};show_modal("Close editor","There are unsaved changes to your page which will be lost.",{Cancel:hide_modal,"Save Changes":function(){f(g)}},{"Don't Save":g})}else{window.document.location=page_list_url}});var a=$("<div class='galaxy-page-editor-button'><a id='insert-galaxy-link' class='action-button popup' href='#'>Paragraph type</a></div>");$(".wym_area_top").append(a);var b={};$.each(d._options.containersItems,function(h,g){var i=g.name;b[g.title.replace("_"," ")]=function(){d.container(i)}});make_popupmenu(a,b);var c=$("<div><a id='insert-galaxy-link' class='action-button popup' href='#'>Insert Link to Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(c);make_popupmenu(c,{"Insert History Link":function(){d.dialog(Galaxy.DIALOG_HISTORY_LINK)},"Insert Dataset Link":function(){d.dialog(Galaxy.DIALOG_DATASET_LINK)},"Insert Workflow Link":function(){d.dialog(Galaxy.DIALOG_WORKFLOW_LINK)},"Insert Page Link":function(){d.dialog(Galaxy.DIALOG_PAGE_LINK)},"Insert Visualization Link":function(){d.dialog(Galaxy.DIALOG_VISUALIZATION_LINK)},});var e=$("<div><a id='embed-galaxy-object' class='action-button popup' href='#'>Embed Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(e);make_popupmenu(e,{"Embed History":function(){d.dialog(Galaxy.DIALOG_EMBED_HISTORY)},"Embed Dataset":function(){d.dialog(Galaxy.DIALOG_EMBED_DATASET)},"Embed Workflow":function(){d.dialog(Galaxy.DIALOG_EMBED_WORKFLOW)},"Embed Visualization":function(){d.dialog(Galaxy.DIALOG_EMBED_VISUALIZATION)},})}); \ No newline at end of file +var Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization"};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case (Galaxy.ITEM_DATASET):f="Dataset";c="Datasets";b="dataset";item_class="HistoryDatasetAssociation";break;case (Galaxy.ITEM_WORKFLOW):f="Workflow";c="Workflows";b="workflow";item_class="StoredWorkflow";break;case (Galaxy.ITEM_PAGE):f="Page";c="Pages";b="page";item_class="Page";break;case (Galaxy.ITEM_VISUALIZATION):f="Visualization";c="Visualizations";b="visualization";item_class="Visualization";break}var e="list_"+c.toLowerCase()+"_for_selection";var a=list_objects_url.replace("LIST_ACTION",e);return{singular:f,plural:c,controller:b,iclass:item_class,list_ajax_url:a}}function make_item_importable(a,c,b){ajax_url=set_accessible_url.replace("ITEM_CONTROLLER",a);$.ajax({type:"POST",url:ajax_url,data:{id:c,accessible:"True"},error:function(){alert("Making "+b+" accessible failed")}})}WYMeditor.editor.prototype.dialog=function(i,e,g){var a=this;var b=a.uniqueStamp();var f=a.selected();function h(){$("#set_link_id").click(function(){$("#link_attribute_label").text("ID/Name");var k=$(".wym_href");k.addClass("wym_id").removeClass("wym_href");if(f){k.val($(f).attr("id"))}$(this).remove()})}if(i==WYMeditor.DIALOG_LINK){if(f){$(a._options.hrefSelector).val($(f).attr(WYMeditor.HREF));$(a._options.srcSelector).val($(f).attr(WYMeditor.SRC));$(a._options.titleSelector).val($(f).attr(WYMeditor.TITLE));$(a._options.altSelector).val($(f).attr(WYMeditor.ALT))}var c,d;if(f){c=$(f).attr("href");if(c==undefined){c=""}d=$(f).attr("title");if(d==undefined){d=""}}show_modal("Create Link","<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='"+c+"' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='"+d+"' size='40' /></div><div>",{"Make link":function(){var m=$(a._options.hrefSelector).val()||"",k=$(".wym_id").val()||"",n=$(a._options.titleSelector).val()||"";if(m||k){a._exec(WYMeditor.CREATE_LINK,b);var l=$("a[href="+b+"]",a._doc.body);l.attr(WYMeditor.HREF,m).attr(WYMeditor.TITLE,n).attr("id",k);if(l.text().indexOf("wym-")===0){l.text(n)}}hide_modal()},Cancel:function(){hide_modal()}},{},h)}if(i==WYMeditor.DIALOG_IMAGE){if(a._selected_image){$(a._options.dialogImageSelector+" "+a._options.srcSelector).val($(a._selected_image).attr(WYMeditor.SRC));$(a._options.dialogImageSelector+" "+a._options.titleSelector).val($(a._selected_image).attr(WYMeditor.TITLE));$(a._options.dialogImageSelector+" "+a._options.altSelector).val($(a._selected_image).attr(WYMeditor.ALT))}show_modal("Image","<div class='row'><label>URL</label><br><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>Alt text</label><br><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>Title</label><br><input type='text' class='wym_title' value='' size='40' /></div>",{Insert:function(){var k=$(a._options.srcSelector).val();if(k.length>0){a._exec(WYMeditor.INSERT_IMAGE,b);$("img[src$="+b+"]",a._doc.body).attr(WYMeditor.SRC,k).attr(WYMeditor.TITLE,$(a._options.titleSelector).val()).attr(WYMeditor.ALT,$(a._options.altSelector).val())}hide_modal()},Cancel:function(){hide_modal()}});return}if(i==WYMeditor.DIALOG_TABLE){show_modal("Table","<div class='row'><label>Caption</label><br><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>Summary</label><br><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>Number Of Rows<br></label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>Number Of Cols<br></label><input type='text' class='wym_cols' value='2' size='3' /></div>",{Insert:function(){var o=$(a._options.rowsSelector).val();var r=$(a._options.colsSelector).val();if(o>0&&r>0){var n=a._doc.createElement(WYMeditor.TABLE);var l=null;var q=null;var k=$(a._options.captionSelector).val();var p=n.createCaption();p.innerHTML=k;for(x=0;x<o;x++){l=n.insertRow(x);for(y=0;y<r;y++){l.insertCell(y)}}$(n).attr("summary",$(a._options.summarySelector).val());var m=$(a.findUp(a.container(),WYMeditor.MAIN_CONTAINERS)).get(0);if(!m||!m.parentNode){$(a._doc.body).append(n)}else{$(m).after(n)}}hide_modal()},Cancel:function(){hide_modal()}})}if(i==Galaxy.DIALOG_HISTORY_LINK||i==Galaxy.DIALOG_DATASET_LINK||i==Galaxy.DIALOG_WORKFLOW_LINK||i==Galaxy.DIALOG_PAGE_LINK||i==Galaxy.DIALOG_VISUALIZATION_LINK){var j;switch(i){case (Galaxy.DIALOG_HISTORY_LINK):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_DATASET_LINK):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_WORKFLOW_LINK):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_PAGE_LINK):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_VISUALIZATION_LINK):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){show_modal("Insert Link to "+j.singular,k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>",{Insert:function(){var m=false;if($("#make-importable:checked").val()!==null){m=true}var l=new Array();$("input[name=id]:checked").each(function(){var n=$(this).val();if(m){make_item_importable(j.controller,n,j.singular)}url_template=get_name_and_link_url+n;ajax_url=url_template.replace("ITEM_CONTROLLER",j.controller);$.getJSON(ajax_url,function(p){a._exec(WYMeditor.CREATE_LINK,b);var o=$("a[href="+b+"]",a._doc.body).text();if(o==""||o==b){a.insert("<a href='"+p.link+"'>"+j.singular+" 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bf94ed77f61a4fd6138ee098b675426f4a6fca97 -r 42b9fb317fdd9248154216530883603110905301 static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},initialize:function(g){this.options=_.defaults(this.options||{},g);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},render:function(g){this.options=_.defaults(this.options,g);var i=this.templateFolder();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));var h=this.folderContainer.attributes.metadata;h.contains_file=this.options.contains_file;Galaxy.libraries.folderToolbarView.configureElements(h);$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness();$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)});$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}var g=new a.FolderRowView(h);this.$el.find("#first_folder_item").after(g.el);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(g){this.$el.find("#"+g.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th style="width:30%;"><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(' <th style="width:15%;"></th> ');g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");g.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents.</div>');return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},initialize:function(g){this.options=_.defaults(this.options||{},g);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},render:function(g){this.options=_.defaults(this.options,g);var h=this.templateFolder();var i=this.folderContainer.attributes.metadata.full_path;var j;if(i.length===1){j=0}else{j=i[i.length-2][0]}this.$el.html(h({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:j,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var g=this.folderContainer.attributes.metadata;g.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(g);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)});this.postRender()},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}var g=new a.FolderRowView(h);this.$el.find("#first_folder_item").after(g.el);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(g){this.$el.find("#"+g.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th style="width:30%;"><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(' <th style="width:15%;"></th> ');g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");g.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents.</div>');return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r bf94ed77f61a4fd6138ee098b675426f4a6fca97 -r 42b9fb317fdd9248154216530883603110905301 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g=false;if(Galaxy.currUser){g=Galaxy.currUser.isAdmin()}this.$el.html(h({id:this.options.id,admin_user:g}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$("#toolbtn_create_folder").show();$(".toolbtn_add_files").show()}if(this.options.contains_file===true){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var j=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=j;var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(n({history_name:m}));var k=100/o.length;this.initProgress(k);var f=[];for(var g=o.length-1;g>=0;g--){var h=o[g];var l=new c.HistoryItem();l.url=l.urlRoot+j+"/contents";l.content=h;l.source="library";f.push(l)}this.options.chain_call_control.total_number=f.length;this.chainCall(f,m)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history")}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('<div id="library_folder_toolbar">');tmpl_array.push('<span data-toggle="tooltip" data-placement="top" title="Include deleted datasets"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push('<div class="btn-group">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("</div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; " type="button"><span class="fa fa-book"></span> to history</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button" style="margin-left: 0.5em; " type="button"><span class="fa fa-times"></span> delete</button>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=false;var f=true;if(Galaxy.currUser){i=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}var h=this.templateToolBar();this.$el.html(h({id:this.options.id,admin_user:i,anonym:f}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var j=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=j;var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(n({history_name:m}));var k=100/o.length;this.initProgress(k);var f=[];for(var g=o.length-1;g>=0;g--){var h=o[g];var l=new c.HistoryItem();l.url=l.urlRoot+j+"/contents";l.content=h;l.source="library";f.push(l)}this.options.chain_call_control.total_number=f.length;this.chainCall(f,m)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history")}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('<div id="library_folder_toolbar">');tmpl_array.push('<span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push('<div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("</div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to history</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> delete</button>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file diff -r bf94ed77f61a4fd6138ee098b675426f4a6fca97 -r 42b9fb317fdd9248154216530883603110905301 static/scripts/packed/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/packed/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-librarytoolbar-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=false;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}else{d=true}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},show_library_modal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.create_new_library_event()},Close:function(){d.modal.hide()}}})},create_new_library_event:function(){var f=this.serialize_new_library();if(this.validate_new_library(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clear_library_modal();Galaxy.libraries.libraryListView.render();b.success("Library created")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured :(")}}})}else{b.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(d){return d.name!==""},check_include_deleted:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');tmpl_array.push(" </div>");tmpl_array.push(" <% } %>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},show_library_modal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.create_new_library_event()},Close:function(){d.modal.hide()}}})},create_new_library_event:function(){var f=this.serialize_new_library();if(this.validate_new_library(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clear_library_modal();Galaxy.libraries.libraryListView.render();b.success("Library created")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured :(")}}})}else{b.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(d){return d.name!==""},check_include_deleted:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');tmpl_array.push(" </div>");tmpl_array.push(" <% } %>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Heatmaps fix tab-spacing, code cleanup
by commits-noreply＠bitbucket.org 01 May '14

01 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bf94ed77f61a/ Changeset: bf94ed77f61a User: guerler Date: 2014-05-01 23:16:54 Summary: Charts: Heatmaps fix tab-spacing, code cleanup Affected #: 1 file diff -r a924f00f31589ab8568a7e9c3b1f4f27a5916d42 -r bf94ed77f61a4fd6138ee098b675426f4a6fca97 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js @@ -58,15 +58,21 @@ // data indexing // - // labels in alphabetical order + // labels (in alphabetical order) this.rowLabel = []; this.colLabel = []; + // index (order from original dataset) + this.rowIndex = []; + this.colIndex = []; + // unique keys (key indices are unique per label and indicate the labels rank in the alphabetical sorting) this.colRank = {}; this.rowRank = {}; - // identify unqiue labels + // + // identify and parse labels + // for (var i in this.data) { var cell = this.data[i]; @@ -75,14 +81,20 @@ if (this.colRank[col_label] === undefined) { this.colRank[col_label] = true; this.colLabel.push(col_label); + this.colIndex.push(col_label); } var row_label = cell.row_label; if (this.rowRank[row_label] === undefined) { this.rowRank[row_label] = true; this.rowLabel.push(row_label); + this.rowIndex.push(row_label); } } + // + // sort labels and update rank dictionary + // + // set sizes this.rowNumber = this.rowLabel.length this.colNumber = this.colLabel.length @@ -92,29 +104,22 @@ this.colLabel.sort(); // generate sorted key list for rows - this.rowIndex = [] for (var i in this.rowLabel) { var row_label = this.rowLabel[i]; - var row_index = parseInt(i); - this.rowRank[row_label] = row_index; - - // should contain clustering - this.rowIndex.push(row_index); + var row_rank = parseInt(i); + this.rowRank[row_label] = row_rank; } // generate sorted key list for columns - this.colIndex = [] for (var i in this.colLabel) { var col_label = this.colLabel[i]; - var col_index = parseInt(i); - this.colRank[col_label] = col_index; - - // should contain clustering - this.colIndex.push(col_index); + var col_rank = parseInt(i); + this.colRank[col_label] = col_rank; } // - // parse indexing to cells, identify data range + // parse indexing from rank dictionary to cells + // identify data range // // min/max @@ -139,12 +144,26 @@ } } + // + // translate original create cluster from order in original data + // + + // generate sorted key list for columns + for (var i in this.colIndex) { + this.colIndex[i] = this.colRank[this.colIndex[i]]; + } + // generate sorted key list for columns + for (var i in this.rowIndex) { + this.rowIndex[i] = this.rowRank[this.rowIndex[i]]; + } + // middle this.mid = (this.max + this.min) / 2; // // set colors // + // identify buckets this.nColors = this.options.colors.length; @@ -166,11 +185,11 @@ // add event to select field this.$select.on('change', function(){ - self._order(this.value); + self._sortByOrder(this.value); }); // - // draw + // finally draw the heatmap // this._draw(); }, @@ -217,6 +236,346 @@ this.heatMap = this._buildHeatMap(); this.legend = this._buildLegend(); }, + + // build legend + _buildLegend: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var height = this.height; + var legendCellWidth = this.width / this.nColors; + + // create range labels + var dataRange = []; + for(var i = 0; i < this.nColors; i++) { + dataRange.push(''); + } + + // prepare indices + var dataRangeMin = 0; + var dataRangeMid = parseInt((dataRange.length - 1) / 2); + var dataRangeMax = dataRange.length - 1; + + // add labels + dataRange[dataRangeMin] = this.min; + dataRange[dataRangeMid] = this.mid; + dataRange[dataRangeMax] = this.max; + + // create legend + var legend = this.svg.selectAll(".legend") + .data(dataRange) + .enter().append("g") + .attr("class", "legend"); + + // add boxes + legend.append("rect") + .attr("x", function(d, i) { + return legendCellWidth * i; + }) + .attr("y", height + cellSize) + .attr("width", legendCellWidth) + .attr("height", cellSize) + .style("fill", function(d, i) { + return self.options.colors[i]; + }); + + // add text + legend.append("text") + .attr("class", "mono") + .text(function(d) { + return d; + }) + .attr("width", legendCellWidth) + .attr("x", function(d, i) { + return legendCellWidth * i; + }) + .attr("y", height + cellSize) + .style("font-size", cellSize + "px"); + }, + + // build column labels + _buildColLabels: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var colIndex = this.colIndex; + var colLabel = this.colLabel; + + // column labels + var colLabels = this.svg.append("g") + .selectAll(".colLabelg") + .data(colLabel) + .enter() + .append("text") + .text(function (d) { + return d; + }) + .attr("x", 0) + .attr("y", function (d, i) { + return colIndex.indexOf(i) * cellSize; + }) + .style("font-size", cellSize + "px") + .style("text-anchor", "left") + .attr("transform", "translate(" + cellSize / 2 + ", -17) rotate (-90)") + .attr("class", function (d, i) { + return "colLabel mono c" + i; + }) + .on("mouseover", function(d) { + d3.select(this).classed("text-hover",true); + d3.select(this).style("font-size", parseInt(cellSize * 1.3) + "px"); + }) + .on("mouseout" , function(d) { + d3.select(this).classed("text-hover",false); + d3.select(this).style("font-size", parseInt(cellSize) + "px"); + }) + .on("click", function(d, i) { + self.colSortOrder=!self.colSortOrder; + self._sortByLabel("c", i, self.colSortOrder); + d3.select("#order").property("selectedIndex", 4).node().focus(); + }); + }, + + // build row labels + _buildRowLabels: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var rowIndex = this.rowIndex; + var rowLabel = this.rowLabel; + + // draw labels + var rowLabels = this.svg.append("g") + .selectAll(".rowLabelg") + .data(rowLabel) + .enter() + .append("text") + .text(function (d) { + return d; + }) + .attr("x", 0) + .attr("y", function (d, i) { + return rowIndex.indexOf(i) * cellSize; + }) + .style("font-size", cellSize + "px") + .style("text-anchor", "end") + .attr("transform", "translate(-10," + cellSize / 1.5 + ")") + .attr("class", function (d, i) { + return "rowLabel mono r" + i; + } ) + .on("mouseover", function(d) { + d3.select(this).classed("text-hover",true); + d3.select(this).style("font-size", parseInt(cellSize * 1.3) + "px"); + }) + .on("mouseout" , function(d) { + d3.select(this).classed("text-hover",false); + d3.select(this).style("font-size", parseInt(cellSize) + "px"); + }) + .on("click", function(d, i) { + self.rowSortOrder=!self.rowSortOrder; + self._sortByLabel("r", i, self.rowSortOrder); + d3.select("#order").property("selectedIndex", 4).node().focus(); + }); + }, + + // build heat map + _buildHeatMap: function() { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var rowIndex = this.rowIndex; + var rowLabel = this.rowLabel; + var colIndex = this.colIndex; + var colLabel = this.colLabel; + + // heat map + var heatMap = this.svg.append("g").attr("class","g3") + .selectAll(".cellg") + .data(self.data, function(d) { + return d.row_rank + ":" + d.col_rank; + }) + .enter() + .append("rect") + .attr("x", function(d) { + return colIndex.indexOf(d.col_rank) * cellSize; + }) + .attr("y", function(d) { + return rowIndex.indexOf(d.row_rank) * cellSize; + }) + .attr("class", function(d){ + return "cell cell-border cr" + d.row_rank + " cc" + d.col_rank; + }) + .attr("width", cellSize) + .attr("height", cellSize) + .style("fill", function(d) { + return self.colorScale(d.value); + }) + .on("mouseover", function(d){ + // highlight text + d3.select(this).classed("cell-hover",true); + d3.selectAll(".rowLabel").classed("text-highlight",function(r,ri){ return ri==(d.row_rank);}); + d3.selectAll(".colLabel").classed("text-highlight",function(c,ci){ return ci==(d.col_rank);}); + + // update the tooltip position and value + d3.select("#heatmap-tooltip") + .style("left", (d3.event.pageX+10) + "px") + .style("top", (d3.event.pageY-10) + "px") + .select("#value") + .text("Label: " + rowLabel[d.row_rank] + " | " + colLabel[d.col_rank] + ", Value: " + d.value); + // show the tooltip + d3.select("#heatmap-tooltip").classed("hidden", false); + }) + .on("mouseout", function(){ + d3.select(this).classed("cell-hover",false); + d3.selectAll(".rowLabel").classed("text-highlight",false); + d3.selectAll(".colLabel").classed("text-highlight",false); + d3.select("#heatmap-tooltip").classed("hidden", true); + }); + }, + + // change ordering of cells + _sortByLabel: function(rORc, i, sortOrder) { + // get cell size + var cellSize = this.cellSize; + + // define transition / prepare element + var t = this.svg.transition().duration(this.options.pace); + + // collect cells + var cells=[]; + t.selectAll(".c" + rORc + i) + .filter(function(ce){ + cells.push(ce); + }); + + // sort cells + cells.sort(function(a, b) { + if (sortOrder) { + return b.value - a.value; + } else { + return a.value - b.value; + } + }); + + // rows or columns + if(rORc == "r") { + // get sorted key list + var sorted = []; + for (var i in cells) { + sorted.push(cells[i].col_rank); + } + + // sort cells + t.selectAll(".cell") + .attr("x", function(d) { + return sorted.indexOf(d.col_rank) * cellSize; + }); + + // sort labels + t.selectAll(".colLabel") + .attr("y", function (d, i) { + return sorted.indexOf(i) * cellSize; + }); + } else { + // get sorted key list + sorted = []; + for (var i in cells) { + sorted.push(cells[i].row_rank); + } + + // sort cells + t.selectAll(".cell") + .attr("y", function(d) { + return sorted.indexOf(d.row_rank) * cellSize; + }); + + // sort labels + t.selectAll(".rowLabel") + .attr("y", function (d, i) { + return sorted.indexOf(i) * cellSize; + }); + } + }, + + // sort function + _sortByOrder: function (value) { + // link this + var self = this; + + // gather data + var cellSize = this.cellSize; + var rowIndex = this.rowIndex; + var rowLabel = this.rowLabel; + var colIndex = this.colIndex; + var colLabel = this.colLabel; + + // set duration / select element + var t = this.svg.transition().duration(this.options.pace); + if(value=="hclust"){ + t.selectAll(".cell") + .attr("x", function(d) { + return colIndex.indexOf(d.col_rank) * cellSize; + }) + .attr("y", function(d) { + return rowIndex.indexOf(d.row_rank) * cellSize; + }); + + t.selectAll(".rowLabel") + .attr("y", function(d, i) { + return rowIndex.indexOf(i) * cellSize; + }); + + t.selectAll(".colLabel") + .attr("y", function(d, i) { + return colIndex.indexOf(i) * cellSize; + }); + + } else if (value=="byboth") { + t.selectAll(".cell") + .attr("x", function(d) { + return d.col_rank * cellSize; + }) + .attr("y", function(d) { + return d.row_rank * cellSize; + }); + + t.selectAll(".rowLabel") + .attr("y", function (d, i) { + return i * cellSize; + }); + + t.selectAll(".colLabel") + .attr("y", function (d, i) { + return i * cellSize; + }); + } else if (value=="byrow") { + t.selectAll(".cell") + .attr("y", function(d) { + return d.row_rank * cellSize; + }); + + t.selectAll(".rowLabel") + .attr("y", function (d, i) { + return i * cellSize; + }); + } else if (value=="bycol"){ + t.selectAll(".cell") + .attr("x", function(d) { + return d.col_rank * cellSize; + }); + t.selectAll(".colLabel") + .attr("y", function (d, i) { + return i * cellSize; + }); + } + }, // selection of cells _addSelectionTool: function() { @@ -224,455 +583,115 @@ // selection // var sa=d3.select(".g3") - .on("mousedown", function() { - if( !d3.event.altKey) { - d3.selectAll(".cell-selected").classed("cell-selected", false); - d3.selectAll(".rowLabel").classed("text-selected", false); - d3.selectAll(".colLabel").classed("text-selected", false); + .on("mousedown", function() { + if( !d3.event.altKey) { + d3.selectAll(".cell-selected").classed("cell-selected", false); + d3.selectAll(".rowLabel").classed("text-selected", false); + d3.selectAll(".colLabel").classed("text-selected", false); + } + var p = d3.mouse(this); + sa.append("rect") + .attr({ + rx : 0, + ry : 0, + class : "selection", + x : p[0], + y : p[1], + width : 1, + height : 1 + }) + }) + .on("mousemove", function() { + var s = sa.select("rect.selection"); + + if(!s.empty()) { + var p = d3.mouse(this), + d = { + x : parseInt(s.attr("x"), 10), + y : parseInt(s.attr("y"), 10), + width : parseInt(s.attr("width"), 10), + height : parseInt(s.attr("height"), 10) + }, + move = { + x : p[0] - d.x, + y : p[1] - d.y + }; + + if(move.x < 1 || (move.x*2<d.width)) { + d.x = p[0]; + d.width -= move.x; + } else { + d.width = move.x; } - var p = d3.mouse(this); - sa.append("rect") - .attr({ - rx : 0, - ry : 0, - class : "selection", - x : p[0], - y : p[1], - width : 1, - height : 1 - }) - }) - .on("mousemove", function() { - var s = sa.select("rect.selection"); - - if(!s.empty()) { - var p = d3.mouse(this), - d = { - x : parseInt(s.attr("x"), 10), - y : parseInt(s.attr("y"), 10), - width : parseInt(s.attr("width"), 10), - height : parseInt(s.attr("height"), 10) - }, - move = { - x : p[0] - d.x, - y : p[1] - d.y - }; - - if(move.x < 1 || (move.x*2<d.width)) { - d.x = p[0]; - d.width -= move.x; - } else { - d.width = move.x; - } - if(move.y < 1 || (move.y*2<d.height)) { - d.y = p[1]; - d.height -= move.y; - } else { - d.height = move.y; - } - s.attr(d); - - // deselect all temporary selected state objects - d3.selectAll(".cell-selection.cell-selected").classed("cell-selected", false); - d3.selectAll(".text-selection.text-selected").classed("text-selected",false); - d3.selectAll(".cell").filter(function(cell_d, i) { - if(!d3.select(this).classed("cell-selected") && - // inner circle inside selection frame - (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width && - (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height) - { - d3.select(this) - .classed("cell-selection", true) - .classed("cell-selected", true); + if(move.y < 1 || (move.y*2<d.height)) { + d.y = p[1]; + d.height -= move.y; + } else { + d.height = move.y; + } + s.attr(d); + + // deselect all temporary selected state objects + d3.selectAll(".cell-selection.cell-selected").classed("cell-selected", false); + d3.selectAll(".text-selection.text-selected").classed("text-selected",false); + d3.selectAll(".cell").filter(function(cell_d, i) { + if(!d3.select(this).classed("cell-selected") && + // inner circle inside selection frame + (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width && + (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height) + { + d3.select(this) + .classed("cell-selection", true) + .classed("cell-selected", true); - d3.select(".r"+(cell_d.row_rank)) - .classed("text-selection",true) - .classed("text-selected",true); + d3.select(".r"+(cell_d.row_rank)) + .classed("text-selection",true) + .classed("text-selected",true); - d3.select(".c"+(cell_d.col_rank)) - .classed("text-selection",true) - .classed("text-selected",true); - } - }); - } - }) - .on("mouseup", function() { + d3.select(".c"+(cell_d.col_rank)) + .classed("text-selection",true) + .classed("text-selected",true); + } + }); + } + }) + .on("mouseup", function() { + // remove selection frame + sa.selectAll("rect.selection").remove(); + + // remove temporary selection marker class + d3.selectAll(".cell-selection").classed("cell-selection", false); + d3.selectAll(".text-selection").classed("text-selection",false); + }) + .on("mouseout", function() { + if(d3.event.relatedTarget.tagName=='html') { // remove selection frame sa.selectAll("rect.selection").remove(); - + // remove temporary selection marker class d3.selectAll(".cell-selection").classed("cell-selection", false); - d3.selectAll(".text-selection").classed("text-selection",false); - }) - .on("mouseout", function() { - if(d3.event.relatedTarget.tagName=='html') { - // remove selection frame - sa.selectAll("rect.selection").remove(); - - // remove temporary selection marker class - d3.selectAll(".cell-selection").classed("cell-selection", false); - d3.selectAll(".rowLabel").classed("text-selected",false); - d3.selectAll(".colLabel").classed("text-selected",false); - } - }); - }, - - // build legend - _buildLegend: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var height = this.height; - var legendCellWidth = this.width / this.nColors; - - // create range labels - var dataRange = []; - for(var i = 0; i < this.nColors; i++) { - dataRange.push(''); + d3.selectAll(".rowLabel").classed("text-selected",false); + d3.selectAll(".colLabel").classed("text-selected",false); } - - // prepare indices - var dataRangeMin = 0; - var dataRangeMid = parseInt((dataRange.length - 1) / 2); - var dataRangeMax = dataRange.length - 1; - - // add labels - dataRange[dataRangeMin] = this.min; - dataRange[dataRangeMid] = this.mid; - dataRange[dataRangeMax] = this.max; - - // create legend - var legend = this.svg.selectAll(".legend") - .data(dataRange) - .enter().append("g") - .attr("class", "legend"); + }); + }, - // add boxes - legend.append("rect") - .attr("x", function(d, i) { - return legendCellWidth * i; - }) - .attr("y", height + cellSize) - .attr("width", legendCellWidth) - .attr("height", cellSize) - .style("fill", function(d, i) { - return self.options.colors[i]; - }); - - // add text - legend.append("text") - .attr("class", "mono") - .text(function(d) { - return d; - }) - .attr("width", legendCellWidth) - .attr("x", function(d, i) { - return legendCellWidth * i; - }) - .attr("y", height + cellSize) - .style("font-size", cellSize + "px"); - }, - - // build column labels - _buildColLabels: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // column labels - var colLabels = this.svg.append("g") - .selectAll(".colLabelg") - .data(colLabel) - .enter() - .append("text") - .text(function (d) { - return d; - }) - .attr("x", 0) - .attr("y", function (d, i) { - return colIndex.indexOf(i) * cellSize; - }) - .style("font-size", cellSize + "px") - .style("text-anchor", "left") - .attr("transform", "translate(" + cellSize / 2 + ", -17) rotate (-90)") - .attr("class", function (d, i) { - return "colLabel mono c" + i; - }) - .on("mouseover", function(d) { - d3.select(this).classed("text-hover",true); - d3.select(this).style("font-size", parseInt(cellSize * 1.3) + "px"); - }) - .on("mouseout" , function(d) { - d3.select(this).classed("text-hover",false); - d3.select(this).style("font-size", parseInt(cellSize) + "px"); - }) - .on("click", function(d, i) { - self.colSortOrder=!self.colSortOrder; - self._sortByLabel("c", i, self.colSortOrder); - d3.select("#order").property("selectedIndex", 4).node().focus(); - }); - }, - - // build row labels - _buildRowLabels: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - - // draw labels - var rowLabels = this.svg.append("g") - .selectAll(".rowLabelg") - .data(rowLabel) - .enter() - .append("text") - .text(function (d) { - return d; - }) - .attr("x", 0) - .attr("y", function (d, i) { - return rowIndex.indexOf(i) * cellSize; - }) - .style("font-size", cellSize + "px") - .style("text-anchor", "end") - .attr("transform", "translate(-10," + cellSize / 1.5 + ")") - .attr("class", function (d, i) { - return "rowLabel mono r" + i; - } ) - .on("mouseover", function(d) { - d3.select(this).classed("text-hover",true); - d3.select(this).style("font-size", parseInt(cellSize * 1.3) + "px"); - }) - .on("mouseout" , function(d) { - d3.select(this).classed("text-hover",false); - d3.select(this).style("font-size", parseInt(cellSize) + "px"); - }) - .on("click", function(d, i) { - self.rowSortOrder=!self.rowSortOrder; - self._sortByLabel("r", i, self.rowSortOrder); - d3.select("#order").property("selectedIndex", 4).node().focus(); - }); - }, - - // build heat map - _buildHeatMap: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // heat map - var heatMap = this.svg.append("g").attr("class","g3") - .selectAll(".cellg") - .data(self.data, function(d) { - return d.row_rank + ":" + d.col_rank; - }) - .enter() - .append("rect") - .attr("x", function(d) { - return colIndex.indexOf(d.col_rank) * cellSize; - }) - .attr("y", function(d) { - return rowIndex.indexOf(d.row_rank) * cellSize; - }) - .attr("class", function(d){ - return "cell cell-border cr" + d.row_rank + " cc" + d.col_rank; - }) - .attr("width", cellSize) - .attr("height", cellSize) - .style("fill", function(d) { - return self.colorScale(d.value); - }) - .on("mouseover", function(d){ - // highlight text - d3.select(this).classed("cell-hover",true); - d3.selectAll(".rowLabel").classed("text-highlight",function(r,ri){ return ri==(d.row_rank);}); - d3.selectAll(".colLabel").classed("text-highlight",function(c,ci){ return ci==(d.col_rank);}); - - // update the tooltip position and value - d3.select("#heatmap-tooltip") - .style("left", (d3.event.pageX+10) + "px") - .style("top", (d3.event.pageY-10) + "px") - .select("#value") - .text("Label: " + rowLabel[d.row_rank] + " | " + colLabel[d.col_rank] + ", Value: " + d.value); - // show the tooltip - d3.select("#heatmap-tooltip").classed("hidden", false); - }) - .on("mouseout", function(){ - d3.select(this).classed("cell-hover",false); - d3.selectAll(".rowLabel").classed("text-highlight",false); - d3.selectAll(".colLabel").classed("text-highlight",false); - d3.select("#heatmap-tooltip").classed("hidden", true); - }); - }, - - // change ordering of cells - _sortByLabel: function(rORc, i, sortOrder) { - // get cell size - var cellSize = this.cellSize; - - // define transition / prepare element - var t = this.svg.transition().duration(this.options.pace); - - // collect cells - var cells=[]; - t.selectAll(".c" + rORc + i) - .filter(function(ce){ - cells.push(ce); - }); - - // sort cells - cells.sort(function(a, b) { - if (sortOrder) { - return b.value - a.value; - } else { - return a.value - b.value; - } - }); - - // rows or columns - if(rORc == "r") { - // get sorted key list - var sorted = []; - for (var i in cells) { - sorted.push(cells[i].col_rank); - } - - // sort cells - t.selectAll(".cell") - .attr("x", function(d) { - return sorted.indexOf(d.col_rank) * cellSize; - }); - - // sort labels - t.selectAll(".colLabel") - .attr("y", function (d, i) { - return sorted.indexOf(i) * cellSize; - }); - } else { - // get sorted key list - sorted = []; - for (var i in cells) { - sorted.push(cells[i].row_rank); - } - - // sort cells - t.selectAll(".cell") - .attr("y", function(d) { - return sorted.indexOf(d.row_rank) * cellSize; - }); - - // sort labels - t.selectAll(".rowLabel") - .attr("y", function (d, i) { - return sorted.indexOf(i) * cellSize; - }); - } - }, - - // sort function - _order: function (value) { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // set duration / select element - var t = this.svg.transition().duration(this.options.pace); - if(value=="hclust"){ - t.selectAll(".cell") - .attr("x", function(d) { - return colIndex.indexOf(d.col_rank) * cellSize; - }) - .attr("y", function(d) { - return rowIndex.indexOf(d.row_rank) * cellSize; - }); - - t.selectAll(".rowLabel") - .attr("y", function(d, i) { - return rowIndex.indexOf(i) * cellSize; - }); - - t.selectAll(".colLabel") - .attr("y", function(d, i) { - return colIndex.indexOf(i) * cellSize; - }); - - } else if (value=="byboth") { - t.selectAll(".cell") - .attr("x", function(d) { - return d.col_rank * cellSize; - }) - .attr("y", function(d) { - return d.row_rank * cellSize; - }); - - t.selectAll(".rowLabel") - .attr("y", function (d, i) { - return i * cellSize; - }); - - t.selectAll(".colLabel") - .attr("y", function (d, i) { - return i * cellSize; - }); - } else if (value=="byrow") { - t.selectAll(".cell") - .attr("y", function(d) { - return d.row_rank * cellSize; - }); - - t.selectAll(".rowLabel") - .attr("y", function (d, i) { - return i * cellSize; - }); - } else if (value=="bycol"){ - t.selectAll(".cell") - .attr("x", function(d) { - return d.col_rank * cellSize; - }); - t.selectAll(".colLabel") - .attr("y", function (d, i) { - return i * cellSize; - }); - } - }, - - // template - _templateSelect: function() { - return '<select id="order">' + - '<option value="hclust">Cluster</option>' + - '<option value="byboth">Sort by row and column</option>' + - '<option value="byrow">Sort by row label</option>' + - '<option value="bycol">Sort by column label</option>' + - '</select>'; - }, - - // template - _templateTooltip: function() { - return '<div id="heatmap-tooltip" class="hidden">' + - '<p><span id="value"></p>' - '</div>'; - } - }); + // template + _templateSelect: function() { + return '<select id="order">' + + '<option value="hclust">Cluster</option>' + + '<option value="byboth">Sort by row and column</option>' + + '<option value="byrow">Sort by row label</option>' + + '<option value="bycol">Sort by column label</option>' + + '</select>'; + }, + + // template + _templateTooltip: function() { + return '<div id="heatmap-tooltip" class="hidden">' + + '<p><span id="value"></p>' + '</div>'; + } +}); }); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Tweaks to the recent Tool Shed API enhancements, making them more RESTful.
by commits-noreply＠bitbucket.org 01 May '14

01 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a924f00f3158/ Changeset: a924f00f3158 User: greg Date: 2014-05-01 22:44:44 Summary: Tweaks to the recent Tool Shed API enhancements, making them more RESTful. Affected #: 5 files diff -r f337aefda5c6c709760c51019df777c083b036bb -r a924f00f31589ab8568a7e9c3b1f4f27a5916d42 lib/galaxy/webapps/tool_shed/api/categories.py --- a/lib/galaxy/webapps/tool_shed/api/categories.py +++ b/lib/galaxy/webapps/tool_shed/api/categories.py @@ -17,9 +17,9 @@ return value_mapper @web.expose_api - def create_category( self, trans, payload, **kwd ): + def create( self, trans, payload, **kwd ): """ - POST /api/categories/create_category + POST /api/categories Returns a dictionary of information about the created category. : param key: the current Galaxy admin user's API key diff -r f337aefda5c6c709760c51019df777c083b036bb -r a924f00f31589ab8568a7e9c3b1f4f27a5916d42 lib/galaxy/webapps/tool_shed/api/users.py --- a/lib/galaxy/webapps/tool_shed/api/users.py +++ b/lib/galaxy/webapps/tool_shed/api/users.py @@ -16,9 +16,9 @@ """RESTful controller for interactions with users in the Tool Shed.""" @web.expose_api - def create_user( self, trans, payload, **kwd ): + def create( self, trans, payload, **kwd ): """ - POST /api/users/create_user + POST /api/users Returns a dictionary of information about the created user. : param key: the current Galaxy admin user's API key diff -r f337aefda5c6c709760c51019df777c083b036bb -r a924f00f31589ab8568a7e9c3b1f4f27a5916d42 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -85,7 +85,6 @@ controller='categories', name_prefix='category_', path_prefix='/api', - new={ 'create_category' : 'POST' }, parent_resources=dict( member_name='category', collection_name='categories' ) ) webapp.mapper.resource( 'repository', 'repositories', @@ -112,7 +111,6 @@ controller='users', name_prefix='user_', path_prefix='/api', - new={ 'create_user' : 'POST' }, parent_resources=dict( member_name='user', collection_name='users' ) ) webapp.finalize_config() # Wrap the webapp in some useful middleware diff -r f337aefda5c6c709760c51019df777c083b036bb -r a924f00f31589ab8568a7e9c3b1f4f27a5916d42 lib/tool_shed/scripts/api/create_categories.py --- a/lib/tool_shed/scripts/api/create_categories.py +++ b/lib/tool_shed/scripts/api/create_categories.py @@ -39,7 +39,7 @@ if name is not None and description is not None: data = dict( name=name, description=description ) - url = '%s/api/categories/new/create_category' % to_tool_shed + url = '%s/api/categories' % to_tool_shed try: response = submit( url, data, api_key ) except Exception, e: diff -r f337aefda5c6c709760c51019df777c083b036bb -r a924f00f31589ab8568a7e9c3b1f4f27a5916d42 lib/tool_shed/scripts/api/create_users.py --- a/lib/tool_shed/scripts/api/create_users.py +++ b/lib/tool_shed/scripts/api/create_users.py @@ -42,7 +42,7 @@ data = dict( email=email, password=password, username=username ) - url = '%s/api/users/new/create_user' % to_tool_shed + url = '%s/api/users' % to_tool_shed try: response = submit( url, data, api_key ) except Exception, e: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Enhance the Tool Shed API to provide information about users that is public (i.e., public username) and to include a function for creating a new user. Add a Tool Shed API script that retrieves all of the pubic information about users from a Tool Shed, automatically generates test email accounts and test passwords, and creates the list of users in another Tool Shed. This script streamlines the process of populating a development Tool Shed with users, enabling imp
by commits-noreply＠bitbucket.org 01 May '14

01 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f337aefda5c6/ Changeset: f337aefda5c6 User: greg Date: 2014-05-01 22:07:48 Summary: Enhance the Tool Shed API to provide information about users that is public (i.e., public username) and to include a function for creating a new user. Add a Tool Shed API script that retrieves all of the pubic information about users from a Tool Shed, automatically generates test email accounts and test passwords, and creates the list of users in another Tool Shed. This script streamlines the process of populating a development Tool Shed with users, enabling import of a repository capsule exportied from the specified Tool Shed. This simplifies the process of developing new repository hierarchies in a local development Tool Shed. Affected #: 5 files diff -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 -r f337aefda5c6c709760c51019df777c083b036bb lib/galaxy/webapps/tool_shed/api/users.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/api/users.py @@ -0,0 +1,128 @@ +import logging +import os + +from galaxy import util +from galaxy import web +from galaxy.web.base.controller import BaseAPIController +from galaxy.security.validate_user_input import validate_email +from galaxy.security.validate_user_input import validate_publicname +from galaxy.security.validate_user_input import validate_password +import tool_shed.util.shed_util_common as suc + +log = logging.getLogger( __name__ ) + + +class UsersController( BaseAPIController ): + """RESTful controller for interactions with users in the Tool Shed.""" + + @web.expose_api + def create_user( self, trans, payload, **kwd ): + """ + POST /api/users/create_user + Returns a dictionary of information about the created user. + +: param key: the current Galaxy admin user's API key + + The following parameters are included in the payload. + :param username (required): the public username of the user + """ + user_dict = dict( message = '', + status = 'ok' ) + # Make sure the current user's API key proves he is an admin user in this Tool Shed. + if trans.user_is_admin(): + # Get the information about the user to be created from the payload. + email = payload.get( 'email', '' ) + password = payload.get( 'password', '' ) + username = payload.get( 'username', '' ) + message = self.__validate( trans, + email=email, + password=password, + confirm=password, + username=username ) + if message: + message = 'email: %s, username: %s - %s' % ( email, username, message ) + user_dict[ 'message' ] = message + user_dict[ 'status' ] = 'error' + else: + # Create the user. + user = self.__create_user( trans, email, username, password ) + user_dict = user.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans ) ) + user_dict[ 'message' ] = "User '%s' has been created." % str( user.username ) + user_dict[ 'url' ] = web.url_for( controller='users', + action='show', + id=trans.security.encode_id( user.id ) ) + else: + user_dict[ 'message' ] = 'You are not authorized to create a user in this Tool Shed.' + user_dict[ 'status' ] = 'error' + return user_dict + + def __create_user( self, trans, email, username, password ): + user = trans.app.model.User( email=email ) + user.set_password_cleartext( password ) + user.username = username + if trans.app.config.user_activation_on: + user.active = False + else: + user.active = True # Activation is off, every new user is active by default. + trans.sa_session.add( user ) + trans.sa_session.flush() + trans.app.security_agent.create_private_user_role( user ) + return user + + def __get_value_mapper( self, trans ): + value_mapper = { 'id' : trans.security.encode_id } + return value_mapper + + @web.expose_api_anonymous + def index( self, trans, deleted=False, **kwd ): + """ + GET /api/users + Returns a list of dictionaries that contain information about each user. + """ + # Example URL: http://localhost:9009/api/users + user_dicts = [] + deleted = util.asbool( deleted ) + for user in trans.sa_session.query( trans.app.model.User ) \ + .filter( trans.app.model.User.table.c.deleted == deleted ) \ + .order_by( trans.app.model.User.table.c.username ): + user_dict = user.to_dict( view='collection', + value_mapper=self.__get_value_mapper( trans ) ) + user_dict[ 'url' ] = web.url_for( controller='users', + action='show', + id=trans.security.encode_id( user.id ) ) + user_dicts.append( user_dict ) + return user_dicts + + @web.expose_api_anonymous + def show( self, trans, id, **kwd ): + """ + GET /api/users/{encoded_user_id} + Returns a dictionary of information about a user. + + :param id: the encoded id of the User object. + """ + # Example URL: http://localhost:9009/api/users/f9cad7b01a472135 + user = suc.get_user( trans, id ) + if user is None: + user_dict = dict( message = 'Unable to locate user record for id %s.' % ( str( id ) ), + status = 'error' ) + return user_dict + user_dict = user.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans ) ) + user_dict[ 'url' ] = web.url_for( controller='users', + action='show', + id=trans.security.encode_id( user.id ) ) + return user_dict + + def __validate( self, trans, email, password, confirm, username ): + if not username: + return "A public user name is required in the Tool Shed." + if username in [ 'repos' ]: + return "The term <b>%s</b> is a reserved word in the Tool Shed, so it cannot be used as a public user name." % username + message = validate_email( trans, email ) + if not message: + message = validate_password( trans, password, confirm ) + if not message and username: + message = validate_publicname( trans, username ) + return message diff -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 -r f337aefda5c6c709760c51019df777c083b036bb lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -107,6 +107,13 @@ name_prefix='repository_revision_', path_prefix='/api', parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) ) + webapp.mapper.resource( 'user', + 'users', + controller='users', + name_prefix='user_', + path_prefix='/api', + new={ 'create_user' : 'POST' }, + parent_resources=dict( member_name='user', collection_name='users' ) ) webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): diff -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 -r f337aefda5c6c709760c51019df777c083b036bb lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -20,8 +20,8 @@ class User( object, Dictifiable ): - dict_collection_visible_keys = ( 'id', 'email' ) - dict_element_visible_keys = ( 'id', 'email', 'username' ) + dict_collection_visible_keys = ( 'id', 'username' ) + dict_element_visible_keys = ( 'id', 'username' ) def __init__( self, email=None, password=None ): self.email = email diff -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 -r f337aefda5c6c709760c51019df777c083b036bb lib/tool_shed/scripts/api/create_categories.py --- a/lib/tool_shed/scripts/api/create_categories.py +++ b/lib/tool_shed/scripts/api/create_categories.py @@ -9,10 +9,10 @@ This script is very useful for populating a new development Tool Shed with the set of categories that currently exist in either the test or main public Galaxy Tool Sheds. This will streamline building -new repository hierarchies in the development Tool Shed and exportin gthem into a capsule that can be +new repository hierarchies in the development Tool Shed and exporting them into a capsule that can be imported into one of the public Tool Sheds. -Here is a working example of how to use this script to retrieve the current set of repositories that are +Here is a working example of how to use this script to retrieve the current set of categories that are available in the test public Tool Shed and create each of them in a local development Tool Shed. ./create_categories.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009 diff -r f6561aae5484240c8b76cc32a7b4b1f501b0e660 -r f337aefda5c6c709760c51019df777c083b036bb lib/tool_shed/scripts/api/create_users.py --- /dev/null +++ b/lib/tool_shed/scripts/api/create_users.py @@ -0,0 +1,60 @@ +#!/usr/bin/env python +""" +This script will retrieve a list of dictionaries (one for each user) from the Tool Shed defined +by the --from_tool_shed parameter, which should be a base Tool Shed URL. It will retrieve the +username from each dictionary and create a new user with that username in the Tool Shed defined +by the --to_tool_shed parameter (a different base Tool Shed URL). An email and password value +will automatically be provided for each user. Email addresses will be <username>@test.org and +passwords will be testuser. Users that already exist with a specified username in the Tool Shed +in which the users are being created will not be affected. + +This script is very useful for populating a new development Tool Shed with the set of users that +currently exist in either the test or main public Galaxy Tool Sheds. This will streamline building +new repository hierarchies in the development Tool Shed and exporting them into a capsule that can +be imported into one of the public Tool Sheds. + +Here is a working example of how to use this script to retrieve the current set of users that +are available in the test public Tool Shed and create each of them in a local development Tool Shed. + +./create_users.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009 +""" + +import os +import sys +import argparse +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import get +from common import submit + +def main( options ): + api_key = options.api + from_tool_shed = options.from_tool_shed.rstrip( '/' ) + to_tool_shed = options.to_tool_shed.rstrip( '/' ) + # Get the users from the specified Tool Shed. + url = '%s/api/users' % from_tool_shed + user_dicts = get( url ) + create_response_dicts = [] + for user_dict in user_dicts: + username = user_dict.get( 'username', None ) + if username is not None: + email = '%s(a)test.org' % username + password = 'testuser' + data = dict( email=email, + password=password, + username=username ) + url = '%s/api/users/new/create_user' % to_tool_shed + try: + response = submit( url, data, api_key ) + except Exception, e: + response = str( e ) + log.exception( str( e ) ) + create_response_dict = dict( response=response ) + create_response_dicts.append( create_response_dict ) + +if __name__ == '__main__': + parser = argparse.ArgumentParser( description='Retrieve a list of users from a Tool Shed and create them in another Tool Shed.' ) + parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which users will be created" ) + parser.add_argument( "-f", "--from_tool_shed", dest="from_tool_shed", required=True, help="URL of Tool Shed from which to retrieve the users" ) + parser.add_argument( "-t", "--to_tool_shed", dest="to_tool_shed", required=True, help="URL of Tool Shed in which to create the users" ) + options = parser.parse_args() + main( options ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits May 2014