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commit/galaxy-central: Jeremy Goecks: Do not propagate keyboard events in JS editable text plugin; this prevents unwanted side effects with other elmements on the page using keyboard events.
by commits-noreply＠bitbucket.org 25 Apr '14

25 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/de882c903511/ Changeset: de882c903511 User: Jeremy Goecks Date: 2014-04-25 22:58:21 Summary: Do not propagate keyboard events in JS editable text plugin; this prevents unwanted side effects with other elmements on the page using keyboard events. Affected #: 1 file diff -r 986d7190844d5f7b68804242699a8049af80a937 -r de882c9035116eccd7563c9f89aec586a017ce2f static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -356,6 +356,9 @@ // Enter key. set_text($(this).val()); } + + // Do not propogate event to avoid unwanted side effects. + e.stopPropagation(); }); } 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: improved folder rendering flow
by commits-noreply＠bitbucket.org 25 Apr '14

25 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/986d7190844d/ Changeset: 986d7190844d User: martenson Date: 2014-04-25 21:36:39 Summary: data libraries: improved folder rendering flow Affected #: 8 files diff -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c -r 986d7190844d5f7b68804242699a8049af80a937 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 @@ -12,7 +12,6 @@ mod_library_folderrow_view) { var FolderListView = Backbone.View.extend({ - // main element definition el : '#folder_items_element', // progress percentage progress: 0, @@ -32,29 +31,31 @@ }, initialize : function(options){ - var that = this; - this.options = _.defaults(this.options || {}, options); - this.collection = new mod_library_model.Folder(); + this.options = _.defaults(this.options || {}, options); + this.collection = new mod_library_model.Folder(); + // start to listen if someone adds a model to the collection + this.listenTo(this.collection, 'add', this.renderOne); + this.fetchFolder(); + }, - // start to listen if someone adds a model to the collection - this.listenTo(this.collection, 'add', this.addOne); - - this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id}); - this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents'; - this.folderContainer.fetch({ - success: function (folder_container) { - that.render(); - var items = folder_container.get('folder').models; - that.addAll(items); - }, - error: function(model, response){ - if (typeof response.responseJSON !== "undefined"){ - mod_toastr.error(response.responseJSON.err_msg); - } else { - mod_toastr.error('An error ocurred :('); - } + fetchFolder: function(){ + var that = this; + this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id}); + this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents'; + this.folderContainer.fetch({ + success: function(folder_container) { + that.folder_container = folder_container; + that.render(); + that.addAll(folder_container.get('folder').models) + }, + error: function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error(response.responseJSON.err_msg); + } else { + mod_toastr.error('An error ocurred :('); } - }); + } + }); }, render: function (options) { @@ -83,16 +84,33 @@ $("#center").css('overflow','auto'); }, - /** Adds all given models to the collection. */ - addAll:function(items){ - _.each(items.reverse(), function(item) { - Galaxy.libraries.folderListView.collection.add(item); + /** + * 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. + */ + addAll: function(models){ + _.each(models.reverse(), function(model) { + Galaxy.libraries.folderListView.collection.add(model); }); this.checkEmptiness(); }, - /** Creates a view for the given model and adds it to the folder view. */ - addOne: function(model){ + /** + * Renders whole collection of models as views + */ + renderAll: function(){ + var that = this; + _.each(this.collection.models.reverse(), function(model) { + that.renderOne(model); + }); + }, + + /** + * Creates a view for the given model and adds it to the folder view. + * @param {Item or FolderAsModel} model of the view that will be rendered + */ + renderOne: function(model){ if (model.get('data_type') !== 'folder'){ this.options.contains_file = true; model.set('readable_size', this.size_to_string(model.get('file_size'))); @@ -124,34 +142,42 @@ this.sort = 'asc'; } this.render(); + this.renderAll(); }, - /** Sorts the underlying collection according to the parameters received. - * Currently supports only sorting by name. */ + /** + * Sorts the underlying collection according to the parameters received. + * Currently supports only sorting by name. + */ sortFolder: function(sort_by, order){ if (sort_by === 'name'){ if (order === 'asc'){ - this.collection.sortByNameAsc(); + return this.collection.sortByNameAsc(); } else if (order === 'desc'){ - this.collection.sortByNameDesc(); + return this.collection.sortByNameDesc(); } } }, - /** convert size to nice string */ + /** + * convert size to nice string + * @param {int} size + * @return {string} readable representation of size with units + */ size_to_string : function (size){ - // identify unit var unit = ""; if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else if (size >= 100000) { size = size / 100000; unit = "MB"; } else if (size >= 100) { size = size / 100; unit = "KB"; } else { size = size * 10; unit = "b"; } - // return formatted string return (Math.round(size) / 10) + unit; }, - /** User clicked the checkbox in the table heading */ + /** + * User clicked the checkbox in the table heading + * @param {context} event + */ selectAll : function (event) { var selected = event.target.checked; that = this; @@ -168,8 +194,10 @@ }); }, - /** Check checkbox if user clicks on the whole row or - * on the checkbox itself */ + /** + * Check checkbox if user clicks on the whole row or + * on the checkbox itself + */ selectClickedRow : function (event) { var checkbox = ''; var $row; diff -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c -r 986d7190844d5f7b68804242699a8049af80a937 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 @@ -396,14 +396,15 @@ tmpl_array.push('<div class="library_style_container">'); 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>'); // TOOLBAR - tmpl_array.push('<div id="library_folder_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('</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" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); + 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">'); @@ -412,6 +413,7 @@ 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-trash-o"></span> delete</button>'); tmpl_array.push(' </div>'); tmpl_array.push(' <div id="folder_items_element">'); // library items will append here diff -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c -r 986d7190844d5f7b68804242699a8049af80a937 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 @@ -1,6 +1,9 @@ define([], function() { - +/** + * This view represents the top part of the library page. + * It contains the tool bar with buttons. + */ var LibraryToolbarView = Backbone.View.extend({ el: '#center', @@ -30,7 +33,7 @@ }, delegate_modal: function(event){ - // probably should refactor to have this functionality in this view, not in the library list view + // TODO probably should refactor to have this functionality in this view, not in the library list view Galaxy.libraries.libraryListView.show_library_modal(event); }, diff -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c -r 986d7190844d5f7b68804242699a8049af80a937 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",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){var h=this;this.options=_.defaults(this.options||{},g);this.collection=new d.Folder();this.listenTo(this.collection,"add",this.addOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";this.folderContainer.fetch({success:function(i){h.render();var j=i.get("folder").models;h.addAll(j)},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)});this.checkEmptiness()},addOne: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.$el.find("#first_folder_item").after(g.el);this.checkEmptiness()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){var g=this.templateEmptyFolder();this.$el.find("#folder_list_body").append(g())}else{this.$el.find("#empty_folder_message").remove()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){this.collection.sortByNameAsc()}else{if(g==="desc"){this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox").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><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(" </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(" </tr>");g.push(" </tbody>");g.push("</table>");return _.template(g.join(""))},templateEmptyFolder:function(){var g=[];g.push('<tr id="empty_folder_message">');g.push('<td colspan="6" style="text-align:center">');g.push("This folder is either empty or you do not have proper access permissions to see the contents.");g.push("</td>");g.push("</tr>");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",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.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.fetchFolder()},fetchFolder:function(){var g=this;this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";this.folderContainer.fetch({success:function(h){g.folder_container=h;g.render();g.addAll(h.get("folder").models)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){f.error(h.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)});this.checkEmptiness()},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)})},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.$el.find("#first_folder_item").after(g.el);this.checkEmptiness()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){var g=this.templateEmptyFolder();this.$el.find("#folder_list_body").append(g())}else{this.$el.find("#empty_folder_message").remove()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox").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><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(" </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(" </tr>");g.push(" </tbody>");g.push("</table>");return _.template(g.join(""))},templateEmptyFolder:function(){var g=[];g.push('<tr id="empty_folder_message">');g.push('<td colspan="6" style="text-align:center">');g.push("This folder is either empty or you do not have proper access permissions to see the contents.");g.push("</td>");g.push("</tr>");return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c -r 986d7190844d5f7b68804242699a8049af80a937 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"},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)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');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('<div id="library_folder_toolbar" >');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" 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(" </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(""))},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"},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)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');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('<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-trash-o"></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(""))},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 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c -r 986d7190844d5f7b68804242699a8049af80a937 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1309,7 +1309,7 @@ .modal_table th{border:none !important} .modal_table td{border:none !important} th.button_heading{width:2em} -#library_folder_toolbar{margin-bottom:1em} +#library_folder_toolbar{margin-bottom:1em}#library_folder_toolbar span{margin-right:0.2em} #library_toolbar{margin-bottom:1em}#library_toolbar span{margin-right:0.2em} img.expanderIcon{padding-right:4px} input.datasetCheckbox,li,ul{padding:0;margin:0} diff -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c -r 986d7190844d5f7b68804242699a8049af80a937 static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -20,7 +20,7 @@ .modal_table th{border:none !important} .modal_table td{border:none !important} th.button_heading{width:2em} -#library_folder_toolbar{margin-bottom:1em} +#library_folder_toolbar{margin-bottom:1em}#library_folder_toolbar span{margin-right:0.2em} #library_toolbar{margin-bottom:1em}#library_toolbar span{margin-right:0.2em} img.expanderIcon{padding-right:4px} input.datasetCheckbox,li,ul{padding:0;margin:0} diff -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c -r 986d7190844d5f7b68804242699a8049af80a937 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -99,6 +99,9 @@ #library_folder_toolbar { margin-bottom: 1em; + span { + margin-right: 0.2em; + } } #library_toolbar { margin-bottom: 1em; 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: davebgx: Fix library security functional tests.
by commits-noreply＠bitbucket.org 25 Apr '14

25 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4fa2b864adca/ Changeset: 4fa2b864adca User: davebgx Date: 2014-04-25 21:29:56 Summary: Fix library security functional tests. Affected #: 4 files diff -r 267d03b5c9cdcad228fd40e12340f01c45f12c60 -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c test-data/library/3.bed --- /dev/null +++ b/test-data/library/3.bed @@ -0,0 +1,25 @@ +chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547, +chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310, +chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235, +chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252, +chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903, +chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0, +chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572, +chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269, +chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884, +chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015, +chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087, +chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331, +chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568, +chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243, +chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, +chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402, +chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455, +chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679, +chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945, +chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681, +chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718, +chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260, +chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0, +chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804, +chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057, diff -r 267d03b5c9cdcad228fd40e12340f01c45f12c60 -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c test-data/library/4.bed --- /dev/null +++ b/test-data/library/4.bed @@ -0,0 +1,1 @@ +chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + diff -r 267d03b5c9cdcad228fd40e12340f01c45f12c60 -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c test-data/library/5.bed --- /dev/null +++ b/test-data/library/5.bed @@ -0,0 +1,134 @@ +chr7 115444712 115444739 CCDS5763.1_cds_0_0_chr7_115444713_f 0 + +chr7 115468538 115468624 CCDS5763.1_cds_1_0_chr7_115468539_f 0 + +chr7 115483024 115483277 CCDS5763.1_cds_2_0_chr7_115483025_f 0 + +chr7 115484165 115484501 CCDS5763.1_cds_3_0_chr7_115484166_f 0 + +chr7 115485764 115485980 CCDS5763.1_cds_4_0_chr7_115485765_f 0 + +chr7 115486322 115486481 CCDS5763.1_cds_5_0_chr7_115486323_f 0 + +chr7 115491298 115491487 CCDS5763.1_cds_6_0_chr7_115491299_f 0 + +chr7 115468538 115468624 CCDS5764.1_cds_0_0_chr7_115468539_f 0 + +chr7 115483024 115483277 CCDS5764.1_cds_1_0_chr7_115483025_f 0 + +chr7 115484165 115484501 CCDS5764.1_cds_2_0_chr7_115484166_f 0 + +chr7 115485764 115485980 CCDS5764.1_cds_3_0_chr7_115485765_f 0 + +chr7 115486322 115486481 CCDS5764.1_cds_4_0_chr7_115486323_f 0 + +chr7 115491298 115491487 CCDS5764.1_cds_5_0_chr7_115491299_f 0 + +chr7 115733786 115733936 CCDS5766.1_cds_0_0_chr7_115733787_f 0 + +chr7 115734264 115734452 CCDS5766.1_cds_1_0_chr7_115734265_f 0 + +chr7 115739975 115740126 CCDS5766.1_cds_2_0_chr7_115739976_f 0 + +chr7 115733786 115733936 CCDS5765.1_cds_0_0_chr7_115733787_f 0 + +chr7 115739975 115740164 CCDS5765.1_cds_1_0_chr7_115739976_f 0 + +chr7 115759067 115759097 CCDS5767.1_cds_0_0_chr7_115759068_f 0 + +chr7 115760529 115760694 CCDS5767.1_cds_1_0_chr7_115760530_f 0 + +chr7 115792950 115793292 CCDS5767.1_cds_2_0_chr7_115792951_f 0 + +chr7 116096616 116096655 CCDS5768.1_cds_0_0_chr7_116096617_f 0 + +chr7 116122131 116122195 CCDS5768.1_cds_1_0_chr7_116122132_f 0 + +chr7 116126998 116127050 CCDS5768.1_cds_2_0_chr7_116126999_f 0 + +chr7 116132776 116132840 CCDS5768.1_cds_3_0_chr7_116132777_f 0 + +chr7 116138181 116138388 CCDS5768.1_cds_4_0_chr7_116138182_f 0 + +chr7 116140267 116140347 CCDS5768.1_cds_5_0_chr7_116140268_f 0 + +chr7 116144237 116144316 CCDS5768.1_cds_6_0_chr7_116144238_f 0 + +chr7 116146073 116146145 CCDS5768.1_cds_7_0_chr7_116146074_f 0 + +chr7 116150064 116150127 CCDS5768.1_cds_8_0_chr7_116150065_f 0 + +chr7 116151731 116151872 CCDS5768.1_cds_9_0_chr7_116151732_f 0 + +chr7 116187545 116187696 CCDS5770.1_cds_0_0_chr7_116187546_f 0 + +chr7 116333766 116333849 CCDS5770.1_cds_1_0_chr7_116333767_f 0 + +chr7 116353565 116353725 CCDS5770.1_cds_2_0_chr7_116353566_f 0 + +chr7 116363797 116363852 CCDS5770.1_cds_3_0_chr7_116363798_f 0 + +chr7 116364495 116364611 CCDS5770.1_cds_4_0_chr7_116364496_f 0 + +chr7 116365889 116365965 CCDS5770.1_cds_5_0_chr7_116365890_f 0 + +chr7 116368128 116368197 CCDS5770.1_cds_6_0_chr7_116368129_f 0 + +chr7 116370085 116370240 CCDS5770.1_cds_7_0_chr7_116370086_f 0 + +chr7 116372439 116372537 CCDS5770.1_cds_8_0_chr7_116372440_f 0 + +chr7 116404866 116404981 CCDS5770.1_cds_9_0_chr7_116404867_f 0 + +chr7 116423325 116423398 CCDS5770.1_cds_10_0_chr7_116423326_f 0 + +chr7 116424838 116424941 CCDS5770.1_cds_11_0_chr7_116424839_f 0 + +chr7 116443791 116443942 CCDS5770.1_cds_12_0_chr7_116443792_f 0 + +chr7 116453088 116453181 CCDS5770.1_cds_13_0_chr7_116453089_f 0 + +chr7 116455927 116456067 CCDS5770.1_cds_14_0_chr7_116455928_f 0 + +chr7 116456865 116456985 CCDS5770.1_cds_15_0_chr7_116456866_f 0 + +chr7 116187545 116187696 CCDS5769.1_cds_0_0_chr7_116187546_f 0 + +chr7 116333766 116333849 CCDS5769.1_cds_1_0_chr7_116333767_f 0 + +chr7 116353565 116353725 CCDS5769.1_cds_2_0_chr7_116353566_f 0 + +chr7 116363797 116363852 CCDS5769.1_cds_3_0_chr7_116363798_f 0 + +chr7 116364495 116364611 CCDS5769.1_cds_4_0_chr7_116364496_f 0 + +chr7 116365889 116365965 CCDS5769.1_cds_5_0_chr7_116365890_f 0 + +chr7 116370085 116370240 CCDS5769.1_cds_6_0_chr7_116370086_f 0 + +chr7 116372439 116372537 CCDS5769.1_cds_7_0_chr7_116372440_f 0 + +chr7 116404866 116404981 CCDS5769.1_cds_8_0_chr7_116404867_f 0 + +chr7 116423325 116423398 CCDS5769.1_cds_9_0_chr7_116423326_f 0 + +chr7 116424838 116424941 CCDS5769.1_cds_10_0_chr7_116424839_f 0 + +chr7 116443791 116443942 CCDS5769.1_cds_11_0_chr7_116443792_f 0 + +chr7 116453088 116453181 CCDS5769.1_cds_12_0_chr7_116453089_f 0 + +chr7 116455927 116456067 CCDS5769.1_cds_13_0_chr7_116455928_f 0 + +chr7 116463766 116463862 CCDS5769.1_cds_14_0_chr7_116463767_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116531616 116531881 CCDS5771.1_cds_1_0_chr7_116531617_r 0 - +chr7 116549075 116549353 CCDS5771.1_cds_2_0_chr7_116549076_r 0 - +chr7 116554571 116554798 CCDS5771.1_cds_3_0_chr7_116554572_r 0 - +chr7 116556911 116556994 CCDS5771.1_cds_4_0_chr7_116556912_r 0 - +chr7 116597600 116597753 CCDS5772.1_cds_0_0_chr7_116597601_r 0 - +chr7 116601356 116601470 CCDS5772.1_cds_1_0_chr7_116601357_r 0 - +chr7 116602616 116602722 CCDS5772.1_cds_2_0_chr7_116602617_r 0 - +chr7 116613942 116614052 CCDS5772.1_cds_3_0_chr7_116613943_r 0 - +chr7 116615015 116615072 CCDS5772.1_cds_4_0_chr7_116615016_r 0 - +chr7 116616073 116616149 CCDS5772.1_cds_5_0_chr7_116616074_r 0 - +chr7 116616990 116617115 CCDS5772.1_cds_6_0_chr7_116616991_r 0 - +chr7 116618730 116618865 CCDS5772.1_cds_7_0_chr7_116618731_r 0 - +chr7 116619702 116619814 CCDS5772.1_cds_8_0_chr7_116619703_r 0 - +chr7 116654167 116654279 CCDS5772.1_cds_9_0_chr7_116654168_r 0 - +chr7 116656241 116656364 CCDS5772.1_cds_10_0_chr7_116656242_r 0 - +chr7 116660840 116660940 CCDS5772.1_cds_11_0_chr7_116660841_r 0 - +chr7 116661360 116661465 CCDS5772.1_cds_12_0_chr7_116661361_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116738257 116738368 CCDS5773.1_cds_1_0_chr7_116738258_f 0 + +chr7 116743038 116743147 CCDS5773.1_cds_2_0_chr7_116743039_f 0 + +chr7 116764903 116765119 CCDS5773.1_cds_3_0_chr7_116764904_f 0 + +chr7 116768280 116768370 CCDS5773.1_cds_4_0_chr7_116768281_f 0 + +chr7 116769252 116769416 CCDS5773.1_cds_5_0_chr7_116769253_f 0 + +chr7 116770552 116770678 CCDS5773.1_cds_6_0_chr7_116770553_f 0 + +chr7 116774104 116774351 CCDS5773.1_cds_7_0_chr7_116774105_f 0 + +chr7 116776020 116776113 CCDS5773.1_cds_8_0_chr7_116776021_f 0 + +chr7 116782645 116782828 CCDS5773.1_cds_9_0_chr7_116782646_f 0 + +chr7 116793468 116793660 CCDS5773.1_cds_10_0_chr7_116793469_f 0 + +chr7 116821743 116821838 CCDS5773.1_cds_11_0_chr7_116821744_f 0 + +chr7 116824357 116824444 CCDS5773.1_cds_12_0_chr7_116824358_f 0 + +chr7 116825938 116826662 CCDS5773.1_cds_13_0_chr7_116825939_f 0 + +chr7 116828934 116829063 CCDS5773.1_cds_14_0_chr7_116828935_f 0 + +chr7 116836830 116836868 CCDS5773.1_cds_15_0_chr7_116836831_f 0 + +chr7 116837536 116837787 CCDS5773.1_cds_16_0_chr7_116837537_f 0 + +chr7 116840678 116840758 CCDS5773.1_cds_17_0_chr7_116840679_f 0 + +chr7 116844523 116844674 CCDS5773.1_cds_18_0_chr7_116844524_f 0 + +chr7 116845585 116845813 CCDS5773.1_cds_19_0_chr7_116845586_f 0 + +chr7 116848617 116848718 CCDS5773.1_cds_20_0_chr7_116848618_f 0 + +chr7 116861526 116861775 CCDS5773.1_cds_21_0_chr7_116861527_f 0 + +chr7 116876442 116876598 CCDS5773.1_cds_22_0_chr7_116876443_f 0 + +chr7 116886846 116886936 CCDS5773.1_cds_23_0_chr7_116886847_f 0 + +chr7 116898692 116898865 CCDS5773.1_cds_24_0_chr7_116898693_f 0 + +chr7 116899463 116899569 CCDS5773.1_cds_25_0_chr7_116899464_f 0 + +chr7 116900912 116901113 CCDS5773.1_cds_26_0_chr7_116900913_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr7 116952022 116952124 CCDS5774.1_cds_1_0_chr7_116952023_r 0 - +chr7 116953508 116953641 CCDS5774.1_cds_2_0_chr7_116953509_r 0 - +chr7 116955071 116955135 CCDS5774.1_cds_3_0_chr7_116955072_r 0 - +chr7 116958551 116958737 CCDS5774.1_cds_4_0_chr7_116958552_r 0 - +chr7 116959056 116959262 CCDS5774.1_cds_5_0_chr7_116959057_r 0 - +chr7 116962093 116962272 CCDS5774.1_cds_6_0_chr7_116962094_r 0 - +chr7 116968917 116969105 CCDS5774.1_cds_7_0_chr7_116968918_r 0 - +chr7 116969273 116969426 CCDS5774.1_cds_8_0_chr7_116969274_r 0 - +chr7 116979835 116979935 CCDS5774.1_cds_9_0_chr7_116979836_r 0 - +chr7 116980017 116980104 CCDS5774.1_cds_10_0_chr7_116980018_r 0 - +chr7 116990559 116990639 CCDS5774.1_cds_11_0_chr7_116990560_r 0 - +chr7 116991879 116991975 CCDS5774.1_cds_12_0_chr7_116991880_r 0 - +chr7 116994439 116994715 CCDS5774.1_cds_13_0_chr7_116994440_r 0 - +chr7 117001063 117001181 CCDS5774.1_cds_14_0_chr7_117001064_r 0 - +chr7 117011515 117011770 CCDS5774.1_cds_15_0_chr7_117011516_r 0 - +chr7 117014445 117014596 CCDS5774.1_cds_16_0_chr7_117014446_r 0 - +chr7 117016866 117016966 CCDS5774.1_cds_17_0_chr7_117016867_r 0 - +chr7 117018255 117018459 CCDS5774.1_cds_18_0_chr7_117018256_r 0 - +chr7 117025132 117026786 CCDS5774.1_cds_19_0_chr7_117025133_r 0 - +chr7 117044769 117044994 CCDS5774.1_cds_20_0_chr7_117044770_r 0 - +chr7 117095213 117095321 CCDS5774.1_cds_21_0_chr7_117095214_r 0 - +chr7 117107339 117107420 CCDS5774.1_cds_22_0_chr7_117107340_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131424558 131424600 CCDS4149.1_cds_1_0_chr5_131424559_f 0 + +chr5 131425903 131425993 CCDS4149.1_cds_2_0_chr5_131425904_f 0 + +chr5 131426117 131426159 CCDS4149.1_cds_3_0_chr5_131426118_f 0 + diff -r 267d03b5c9cdcad228fd40e12340f01c45f12c60 -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -2254,7 +2254,7 @@ # NOTE: due to the library_wait() method call at the end of this method, no tests should be done # for strings_displayed_after_submit. params = dict( cntrller=cntrller, library_id=library_id, folder_id=folder_id ) - url = "%s/library_common/upload_library_dataset" % self.url + url = "/library_common/upload_library_dataset" if replace_id: # If we're uploading a new version of a library dataset, we have to include the replace_id param in the # request because the form field named replace_id will not be displayed on the upload form if we dont. @@ -2309,17 +2309,15 @@ def ldda_permissions( self, cntrller, library_id, folder_id, id, role_ids_str, permissions_in=[], permissions_out=[], strings_displayed=[], ldda_name='' ): # role_ids_str must be a comma-separated string of role ids - url = "%s/library_common/ldda_permissions?cntrller=%s&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, cntrller, library_id, folder_id, id ) + params = dict( cntrller=cntrller, library_id=library_id, folder_id=folder_id, id=id ) + url = "/library_common/ldda_permissions" for po in permissions_out: - key = '%s_out' % po - url = "%s&%s=%s" % ( url, key, role_ids_str ) + params[ '%s_out' % po ] = role_ids_str for pi in permissions_in: - key = '%s_in' % pi - url = "%s&%s=%s" % ( url, key, role_ids_str ) + params[ '%s_in' % pi ] = role_ids_str if permissions_in or permissions_out: - url += "&update_roles_button=Save" - self.visit_url( url ) + params[ 'update_roles_button' ] = 'Save' + self.visit_url( url, params ) if not strings_displayed: strings_displayed = [ "Permissions updated for dataset '%s'." % ldda_name ] for check_str in strings_displayed: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: davebgx: Fix tool shed functional test for repository dependency handling.
by commits-noreply＠bitbucket.org 25 Apr '14

25 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/267d03b5c9cd/ Changeset: 267d03b5c9cd User: davebgx Date: 2014-04-25 20:28:17 Summary: Fix tool shed functional test for repository dependency handling. Affected #: 1 file diff -r 666a75d94ee91091d94b65ffbfe700224ad58f15 -r 267d03b5c9cdcad228fd40e12340f01c45f12c60 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -18,6 +18,7 @@ from galaxy.web import security from galaxy.web.framework.helpers import iff from galaxy.util.json import from_json_string +from galaxy.util import asbool from base.asserts import verify_assertions from galaxy import eggs @@ -1325,11 +1326,25 @@ params[ key ] = value if params: url += '?%s' % urllib.urlencode( params ) + checked_boxes = dict() + unchecked_boxes = dict() if checkbox_params is not None: + for checkbox_field in checkbox_params: + if checkbox_field in checked_boxes or checkbox_field in unchecked_boxes: + continue + if asbool( checkbox_params[ checkbox_field ] ): + checked_boxes[ checkbox_field ] = True + else: + unchecked_boxes[ checkbox_field ] = False + # Any checkbox field that is found twice in the controller's incoming parameters is considered checked, + # while any field that only appears once is considered unchecked. + checkbox_params = '&'.join( [ urllib.urlencode( checked_boxes ), + urllib.urlencode( checked_boxes ), + urllib.urlencode( unchecked_boxes ) ] ) if params or parsed_url.query: - url += '&%s&%s' % ( urllib.urlencode( checkbox_params ), urllib.urlencode( checkbox_params ) ) + url += '&%s' % checkbox_params else: - url += '?%s&%s' % ( urllib.urlencode( checkbox_params ), urllib.urlencode( checkbox_params ) ) + url += '?%s' % checkbox_params new_url = tc.go( url ) return_code = tc.browser.get_code() assert return_code in allowed_codes, 'Invalid HTTP return code %s, allowed codes: %s' % \ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Fix for persisting data table entries generated by installed data managers.
by commits-noreply＠bitbucket.org 25 Apr '14

25 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/666a75d94ee9/ Changeset: 666a75d94ee9 User: davebgx Date: 2014-04-25 19:21:32 Summary: Fix for persisting data table entries generated by installed data managers. Affected #: 1 file diff -r dda514ffa5e99b1b13bc3d88dbf35c1fb336742d -r 666a75d94ee91091d94b65ffbfe700224ad58f15 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -134,15 +134,15 @@ tool_shed_url = tool_elem.find( 'tool_shed' ).text # Handle protocol changes. tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.data_managers.app, tool_shed_url ) + # The protocol is not stored in the database. + tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url ) repository_name = tool_elem.find( 'repository_name' ).text repository_owner = tool_elem.find( 'repository_owner' ).text installed_changeset_revision = tool_elem.find( 'installed_changeset_revision' ).text - self.tool_shed_repository_info_dict = dict( tool_shed_url=tool_shed_url, + self.tool_shed_repository_info_dict = dict( tool_shed=tool_shed, name=repository_name, owner=repository_owner, installed_changeset_revision=installed_changeset_revision ) - # The protocol is not stored in the database. - tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url ) tool_shed_repository = \ suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.data_managers.app, tool_shed, 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: Add support for 3 new tool dependency installation recipe action tag types: assert_directory_exists, assert_file_exists and assert_file_executable.
by commits-noreply＠bitbucket.org 25 Apr '14

25 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dda514ffa5e9/ Changeset: dda514ffa5e9 User: greg Date: 2014-04-25 16:58:15 Summary: Add support for 3 new tool dependency installation recipe action tag types: assert_directory_exists, assert_file_exists and assert_file_executable. Affected #: 4 files diff -r 2edce562ccaa8bdd12e40b2263646f7b9cf93966 -r dda514ffa5e99b1b13bc3d88dbf35c1fb336742d lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -4,6 +4,8 @@ from galaxy import eggs eggs.require( 'Fabric' ) +eggs.require( 'ssh' ) +eggs.require( 'paramiko' ) from fabric.api import env from fabric.api import lcd diff -r 2edce562ccaa8bdd12e40b2263646f7b9cf93966 -r dda514ffa5e99b1b13bc3d88dbf35c1fb336742d lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py @@ -13,6 +13,8 @@ # TODO: eliminate the use of fabric here. from galaxy import eggs eggs.require( 'Fabric' ) +eggs.require( 'ssh' ) +eggs.require( 'paramiko' ) from fabric.operations import _AttributeString from fabric import state @@ -412,7 +414,10 @@ return tool_dependency, filtered_actions, dir def load_step_handlers( self ): - step_handlers_by_type = dict( autoconf=step_handler.Autoconf(), + step_handlers_by_type = dict( assert_directory_exists=step_handler.AssertDirectoryExists(), + assert_file_executable=step_handler.AssertFileExecutable(), + assert_file_exists=step_handler.AssertFileExists(), + autoconf=step_handler.Autoconf(), change_directory=step_handler.ChangeDirectory(), chmod=step_handler.Chmod(), download_binary=step_handler.DownloadBinary(), diff -r 2edce562ccaa8bdd12e40b2263646f7b9cf93966 -r dda514ffa5e99b1b13bc3d88dbf35c1fb336742d 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 @@ -14,6 +14,9 @@ # TODO: eliminate the use of fabric here. from galaxy import eggs eggs.require( 'Fabric' ) +eggs.require( 'ssh' ) +eggs.require( 'paramiko' ) + from fabric.api import settings from fabric.api import lcd @@ -33,6 +36,105 @@ raise "Unimplemented Method" +class AssertDirectoryExists( RecipeStep ): + + def __init__( self ): + self.type = 'assert_directory_exists' + + def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + install_environment, work_dir, install_dir, current_dir=None, initial_download=False ): + """ + Make sure a directory on disk exists. Since this class is not used in the initial download stage, + no recipe step filtering is performed here, and None values are always returned for filtered_actions + and dir. + """ + if os.path.isabs( action_dict[ 'full_path' ] ): + full_path = action_dict[ 'full_path' ] + else: + full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) + if not td_common_util.assert_directory_exists( full_path=full_path ): + status = app.install_model.ToolDependency.installation_status.ERROR + error_message = 'The required directory %s does not exist.' % str( full_path ) + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency, + status=status, + error_message=error_message, + remove_from_disk=False ) + return tool_dependency, None, None + + def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_dir, is_binary_download ): + # <action type="make_directory">$INSTALL_DIR/mira</action> + if action_elem.text: + action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir ) + return action_dict + + +class AssertFileExecutable( RecipeStep ): + + def __init__( self ): + self.type = 'assert_file_executable' + + def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + install_environment, work_dir, install_dir, current_dir=None, initial_download=False ): + """ + Make sure a file on disk exists and is executable. Since this class is not used in the initial + download stage, no recipe step filtering is performed here, and None values are always returned + for filtered_actions and dir. + """ + if os.path.isabs( action_dict[ 'full_path' ] ): + full_path = action_dict[ 'full_path' ] + else: + full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) + if not td_common_util.assert_file_executable( full_path=full_path ): + status = app.install_model.ToolDependency.installation_status.ERROR + error_message = 'The file %s is not executable by the owner.' % str( full_path ) + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency, + status=status, + error_message=error_message, + remove_from_disk=False ) + return tool_dependency, None, None + + def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_dir, is_binary_download ): + # <action type="assert_executable">$INSTALL_DIR/mira/my_file</action> + if action_elem.text: + action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir ) + return action_dict + + +class AssertFileExists( RecipeStep ): + + def __init__( self ): + self.type = 'assert_file_exists' + + def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder, + install_environment, work_dir, install_dir, current_dir=None, initial_download=False ): + """ + Make sure a file on disk exists. Since this class is not used in the initial download stage, + no recipe step filtering is performed here, and None values are always returned for + filtered_actions and dir. + """ + if os.path.isabs( action_dict[ 'full_path' ] ): + full_path = action_dict[ 'full_path' ] + else: + full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) + if not td_common_util.assert_file_exists( full_path=full_path ): + status = app.install_model.ToolDependency.installation_status.ERROR + error_message = 'The required file %s does not exist.' % str( full_path ) + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency, + status=status, + error_message=error_message, + remove_from_disk=False ) + return tool_dependency, None, None + + def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_dir, is_binary_download ): + # <action type="assert_on_path">$INSTALL_DIR/mira/my_file</action> + if action_elem.text: + action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir ) + return action_dict + + class Autoconf( RecipeStep ): def __init__( self ): diff -r 2edce562ccaa8bdd12e40b2263646f7b9cf93966 -r dda514ffa5e99b1b13bc3d88dbf35c1fb336742d 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 @@ -2,6 +2,7 @@ import os import re import shutil +import stat import sys import tarfile import time @@ -110,6 +111,31 @@ def open_zip( self, filepath, mode ): return zipfile.ZipFile( filepath, mode ) +def assert_directory_exists( full_path ): + """Return True if a directory exists and is not a symbolic link.""" + if os.path.islink( full_path ): + return False + if os.path.is_dir( full_path ): + return True + return False + +def assert_file_exists( full_path ): + """Return True if a file exists. This will work for both symbolic linke and files.""" + if os.path.exists( full_path ): + return True + return False + +def assert_file_executable( full_path ): + """Return True if a file exists and is executable.""" + if os.path.islink( full_path ): + return False + if os.path.is_file( full_path ): + # Make sure the owner has execute permission on the file. + # See http://docs.python.org/2/library/stat.html + if stat.S_IXUSR & os.stat( full_path )[ stat.ST_MODE ] == 64: + return True + return False + def create_env_var_dict( elem, tool_dependency_install_dir=None, tool_shed_repository_install_dir=None ): env_var_name = elem.get( 'name', 'PATH' ) env_var_action = elem.get( 'action', 'prepend_to' ) @@ -155,6 +181,10 @@ regex = regex.replace( r"\'", "'" ) return regex +def evaluate_template( text, install_dir ): + """ Substitute variables defined in XML blocks from dependencies file.""" + return Template( text ).safe_substitute( get_env_var_values( install_dir ) ) + def format_traceback(): ex_type, ex, tb = sys.exc_info() return ''.join( traceback.format_tb( tb ) ) @@ -444,6 +474,10 @@ continue return actions_elem_tuples +def __shellquote( s ): + """Quote and escape the supplied string for use in shell expressions.""" + return "'" + s.replace( "'", "'\\''" ) + "'" + def url_download( install_dir, downloaded_file_name, download_url, extract=True ): file_path = os.path.join( install_dir, downloaded_file_name ) src = None @@ -494,11 +528,3 @@ if not member_path.startswith( basename ): return False return True - -def __shellquote(s): - """Quote and escape the supplied string for use in shell expressions.""" - return "'" + s.replace( "'", "'\\''" ) + "'" - -def evaluate_template( text, install_dir ): - """ Substitute variables defined in XML blocks from dependencies file.""" - return Template( text ).safe_substitute( get_env_var_values( install_dir ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: Jeremy Goecks: BAM data provider: hash to create read guids. This is line with other data providers and decreases payload size slightly.
by commits-noreply＠bitbucket.org 25 Apr '14

25 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2edce562ccaa/ Changeset: 2edce562ccaa User: Jeremy Goecks Date: 2014-04-25 16:50:47 Summary: BAM data provider: hash to create read guids. This is line with other data providers and decreases payload size slightly. Affected #: 1 file diff -r 611117ed0a88654c736bc5722016b81874475c95 -r 2edce562ccaa8bdd12e40b2263646f7b9cf93966 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -1018,7 +1018,7 @@ if qname in paired_pending: # Found pair. pair = paired_pending[qname] - results.append( [ "%i_%s" % ( pair['start'], qname ), + results.append( [ hash( "%i_%s" % ( pair['start'], qname ) ), pair['start'], read.pos + read_len, qname, @@ -1033,7 +1033,7 @@ 'rlen': read_len, 'strand': strand, 'cigar': read.cigar, 'mapq': read.mapq } count += 1 else: - results.append( [ "%i_%s" % ( read.pos, qname ), + results.append( [ hash( "%i_%s" % ( read.pos, qname ) ), read.pos, read.pos + read_len, qname, read.cigar, strand, read.seq, read.mapq ] ) count += 1 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 Apr '14

25 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/09c44c3db98c/ Changeset: 09c44c3db98c User: davebgx Date: 2014-04-25 16:41:34 Summary: Fix tool shed functional tests for roles and email notifications. Affected #: 1 file diff -r 880974da3ca4d3d76bcf8b11184cb42c4aee95b7 -r 09c44c3db98cef9fa33b8e511e52928dcec5d2f5 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -525,7 +525,7 @@ def enable_email_alerts( self, repository, strings_displayed=[], strings_not_displayed=[] ): repository_id = self.security.encode_id( repository.id ) params = dict( operation='Receive email alerts', id=repository_id ) - self.visit_url( '/repository/browse_repositories' ) + self.visit_url( '/repository/browse_repositories', params ) self.check_for_strings( strings_displayed ) def escape_html( self, string, unescape=False ): @@ -796,7 +796,7 @@ self.check_for_strings( strings_displayed, strings_not_displayed ) params = dict( operation='manage users and groups', id=self.security.encode_id( role.id ) ) url = '/admin/roles' - self.visit_url( url ) + self.visit_url( url, params ) strings_displayed = [ common.test_user_1_email, common.test_user_2_email ] self.check_for_strings( strings_displayed, strings_not_displayed ) # As elsewhere, twill limits the possibility of submitting the form, this time due to not executing the javascript https://bitbucket.org/galaxy/galaxy-central/commits/611117ed0a88/ Changeset: 611117ed0a88 User: davebgx Date: 2014-04-25 16:41:53 Summary: Fix functional tests for library templates. Affected #: 2 files diff -r 09c44c3db98cef9fa33b8e511e52928dcec5d2f5 -r 611117ed0a88654c736bc5722016b81874475c95 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -2040,16 +2040,13 @@ dis-inherit your template, call the manage_library_template_inheritance() below immediately after you call this method in your test code. Templates added to Requesttype objects are always inherited to samples. """ - if item_type == 'library': - url = "%s/library_common/add_template?cntrller=%s&item_type=%s&form_type=%s&library_id=%s" % \ - ( self.url, cntrller, item_type, form_type, library_id ) - elif item_type == 'folder': - url = "%s/library_common/add_template?cntrller=%s&item_type=%s&form_type=%s&library_id=%s&folder_id=%s" % \ - ( self.url, cntrller, item_type, form_type, library_id, folder_id ) + params = dict( cntrller=cntrller, item_type=item_type, form_type=form_type, library_id=library_id ) + url = "/library_common/add_template" + if item_type == 'folder': + params[ 'folder_id' ] = folder_id elif item_type == 'ldda': - url = "%s/library_common/add_template?cntrller=%s&item_type=%s&form_type=%s&library_id=%s&folder_id=%s&ldda_id=%s" % \ - ( self.url, cntrller, item_type, form_type, library_id, folder_id, ldda_id ) - self.visit_url( url ) + params[ 'ldda_id' ] = ldda_id + self.visit_url( url, params ) self.check_page_for_string ( "Select a template for the" ) self.refresh_form( "form_id", form_id ) # For some unknown reason, twill barfs if the form number ( 1 ) is used in the following diff -r 09c44c3db98cef9fa33b8e511e52928dcec5d2f5 -r 611117ed0a88654c736bc5722016b81874475c95 test/functional/test_library_templates.py --- a/test/functional/test_library_templates.py +++ b/test/functional/test_library_templates.py @@ -72,12 +72,14 @@ # Pass number of options we want in our SelectField num_options = 2 # Create form for library template + strings_displayed_after_submit = [ "The form '%s' has been updated with the changes." % type ] self.create_form( name=type, description=form_desc, form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE, field_type=type, num_options=num_options, - field_name=field_name ) + field_name=field_name, + strings_displayed_after_submit=strings_displayed_after_submit ) # Get all of the new form definitions for later use global AddressField_form AddressField_form = get_form( 'AddressField' ) @@ -145,7 +147,7 @@ # Add a template containing an AddressField to library1 self.add_template( cntrller='library_admin', item_type='library', - form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE.replace( ' ', '+' ), + form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE, form_id=self.security.encode_id( AddressField_form.id ), form_name=AddressField_form.name, library_id=self.security.encode_id( library1.id ) ) @@ -287,7 +289,7 @@ # Add a template containing an CheckboxField to library1 self.add_template( cntrller='library_admin', item_type='library', - form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE.replace( ' ', '+' ), + form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE, form_id=self.security.encode_id( CheckboxField_form.id ), form_name=CheckboxField_form.name, library_id=self.security.encode_id( library2.id ) ) @@ -363,7 +365,7 @@ # Logged in as admin_user self.add_template( cntrller='library_admin', item_type='library', - form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE.replace( ' ', '+' ), + form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE, form_id=self.security.encode_id( SelectField_form.id ), form_name=SelectField_form.name, library_id=self.security.encode_id( library3.id ) ) @@ -464,7 +466,7 @@ # Add an inheritable template to library4 self.add_template( cntrller='library_admin', item_type='library', - form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE.replace( ' ', '+' ), + form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE, form_id=self.security.encode_id( TextArea_form.id ), form_name=TextArea_form.name, library_id=self.security.encode_id( library4.id ) ) @@ -533,7 +535,7 @@ # Add an inheritable template to library5 self.add_template( cntrller='library_admin', item_type='library', - form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE.replace( ' ', '+' ), + form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE, form_id=self.security.encode_id( TextField_form.id ), form_name=TextField_form.name, library_id=self.security.encode_id( library5.id ) ) @@ -602,7 +604,7 @@ # Currently there is only a TextField, and we'll add a TextArea. self.edit_template( cntrller='library_admin', item_type='library', - form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE.replace( ' ', '+' ), + form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE, library_id=self.security.encode_id( library5.id ), field_type='TextArea', field_label_1=TextArea_form.name, @@ -647,7 +649,7 @@ # We won't select an option since we have no workflow to select self.add_template( cntrller='library_admin', item_type='library', - form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE.replace( ' ', '+' ), + form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE, form_id=self.security.encode_id( WorkflowField_form.id ), form_name=WorkflowField_form.name, library_id=self.security.encode_id( library6.id ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: Jeremy Goecks: Simplification for dowsampler in bam data provider
by commits-noreply＠bitbucket.org 25 Apr '14

25 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/880974da3ca4/ Changeset: 880974da3ca4 User: Jeremy Goecks Date: 2014-04-25 03:24:33 Summary: Simplification for dowsampler in bam data provider Affected #: 1 file diff -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 -r 880974da3ca4d3d76bcf8b11184cb42c4aee95b7 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -952,8 +952,7 @@ # Convert threshold to N for stepping through iterator. n = int( 1/threshold ) - for e in itertools.islice( read_iterator, None, None, n ): - yield e + return itertools.islice( read_iterator, None, None, n ) # Alternatate and much slower implementation that looks for pending pairs. ''' 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: Move some hg utility functions out of shed_util_common and into hg_util.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1dd573cdce2/ Changeset: d1dd573cdce2 User: greg Date: 2014-04-24 21:45:55 Summary: Move some hg utility functions out of shed_util_common and into hg_util. Affected #: 12 files diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1855,7 +1855,7 @@ repo = hg.repository( hg_util.get_configured_ui(), path=repo_files_dir ) repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) repository_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) - suc.update_repository( repo, latest_ctx_rev ) + hg_util.update_repository( repo, latest_ctx_rev ) # Remove old Data Manager entries if repository.includes_data_managers: data_manager_util.remove_from_data_manager( trans.app, repository ) diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -2,7 +2,7 @@ from galaxy import web from galaxy.web.base.controller import BaseUIController from tool_shed.util.shed_util_common import get_repository_by_name_and_owner -from tool_shed.util.shed_util_common import update_repository +from tool_shed.util.hg_util import update_repository from tool_shed.util.metadata_util import set_repository_metadata from galaxy import eggs diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -722,7 +722,7 @@ repository = suc.get_repository_in_tool_shed( trans, id ) repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) # Update repository files for browsing. - suc.update_repository( repo ) + hg_util.update_repository( repo ) changeset_revision = repository.tip( trans.app ) metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, changeset_revision, metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) @@ -2743,7 +2743,7 @@ commands.commit( repo.ui, repo, repo_dir, user=trans.user.username, message=commit_message ) suc.handle_email_alerts( trans, repository ) # Update the repository files for browsing. - suc.update_repository( repo ) + hg_util.update_repository( repo ) # Get the new repository tip. repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) if tip == repository.tip( trans.app ): @@ -3117,7 +3117,7 @@ else: ctx_child = None diffs = [] - options_dict = suc.get_mercurial_default_options_dict( 'diff' ) + options_dict = hg_util.get_mercurial_default_options_dict( 'diff' ) # Not quite sure if the following settings make any difference, but with a combination of them and the size check on each # diff, we don't run out of memory when viewing the changelog of the cisortho2 repository on the test tool shed. options_dict[ 'maxfile' ] = suc.MAXDIFFSIZE @@ -3252,7 +3252,11 @@ else: message += malicious_error status = 'error' - containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) + containers_dict = container_util.build_repository_containers_for_tool_shed( trans, + repository, + changeset_revision, + repository_dependencies, + repository_metadata ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) heads = suc.get_repository_heads( repo ) return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -226,7 +226,7 @@ admin_only=admin_only ) if ok: # Update the repository files for browsing. - suc.update_repository( repo ) + hg_util.update_repository( repo ) # Get the new repository tip. if tip == repository.tip( trans.app ): message = 'No changes to repository. ' diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -2,6 +2,7 @@ Manage automatic installation of tools configured in the xxx.xml files in ~/scripts/migrate_tools (e.g., 0002_tools.xml). All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed. """ +import json import os import shutil import tempfile @@ -9,12 +10,11 @@ import logging from galaxy import util from galaxy.tools import ToolSection -from galaxy.util.json import from_json_string -from galaxy.util.json import to_json_string import tool_shed.util.shed_util_common as suc from tool_shed.util import common_install_util from tool_shed.util import common_util from tool_shed.util import datatype_util +from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util @@ -505,8 +505,10 @@ tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) if not cloned_ok: - suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.install_model.ToolShedRepository.installation_status.CLONING ) - cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) + suc.update_tool_shed_repository_status( self.app, + tool_shed_repository, + self.app.install_model.ToolShedRepository.installation_status.CLONING ) + cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) if cloned_ok and not is_installed: self.handle_repository_contents( tool_shed_repository=tool_shed_repository, repository_clone_url=repository_clone_url, @@ -525,7 +527,7 @@ ( self.tool_shed_url, tool_shed_repository.name, self.repository_owner, tool_shed_repository.installed_changeset_revision ) text = common_util.tool_shed_get( self.app, self.tool_shed_url, url ) if text: - tool_version_dicts = from_json_string( text ) + tool_version_dicts = json.loads( text ) tool_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository ) else: # Set the tool versions since they seem to be missing for this repository in the tool shed. diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -560,14 +560,17 @@ if isinstance( repo_info_dict, basestring ): repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) # Clone each repository to the configured location. - suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.install_model.ToolShedRepository.installation_status.CLONING ) + suc.update_tool_shed_repository_status( trans.app, + tool_shed_repository, + trans.install_model.ToolShedRepository.installation_status.CLONING ) repo_info_tuple = repo_info_dict[ tool_shed_repository.name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple - relative_clone_dir = suc.generate_tool_shed_repository_install_dir( repository_clone_url, tool_shed_repository.installed_changeset_revision ) + relative_clone_dir = suc.generate_tool_shed_repository_install_dir( repository_clone_url, + tool_shed_repository.installed_changeset_revision ) clone_dir = os.path.join( tool_path, relative_clone_dir ) relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name ) install_dir = os.path.join( tool_path, relative_install_dir ) - cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) + cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) if cloned_ok: if reinstalling: # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated. @@ -577,7 +580,7 @@ if current_ctx_rev != ctx_rev: repo = hg.repository( hg_util.get_configured_ui(), path=os.path.abspath( install_dir ) ) pull_repository( repo, repository_clone_url, current_changeset_revision ) - suc.update_repository( repo, ctx_rev=current_ctx_rev ) + hg_util.update_repository( repo, ctx_rev=current_ctx_rev ) handle_repository_contents( trans, tool_shed_repository=tool_shed_repository, tool_path=tool_path, diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -112,7 +112,7 @@ repo_dir = repository.repo_path( app ) repo = hg.repository( hg_util.get_configured_ui(), repo_dir ) work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-cafr" ) - cloned_ok, error_message = suc.clone_repository( repo_dir, work_dir, changeset_revision ) + cloned_ok, error_message = hg_util.clone_repository( repo_dir, work_dir, changeset_revision ) if cloned_ok: # Iterate through all the directories in the cloned changeset revision and determine whether there's a # directory named test-data. If this directory is not present update the metadata record for the changeset diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ b/lib/tool_shed/util/export_util.py @@ -39,7 +39,7 @@ def archive_repository_revision( trans, ui, repository, archive_dir, changeset_revision ): '''Create an un-versioned archive of a repository.''' repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( trans.app ) ) - options_dict = suc.get_mercurial_default_options_dict( 'archive' ) + options_dict = hg_util.get_mercurial_default_options_dict( 'archive' ) options_dict[ 'rev' ] = changeset_revision error_message = '' return_code = None diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/tool_shed/util/hg_util.py --- a/lib/tool_shed/util/hg_util.py +++ b/lib/tool_shed/util/hg_util.py @@ -3,6 +3,7 @@ from time import gmtime from time import strftime +from galaxy.util import listify from galaxy import eggs eggs.require( 'mercurial' ) @@ -11,6 +12,26 @@ from mercurial import hg from mercurial import ui +log = logging.getLogger( __name__ ) + +def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): + """ + Clone the repository up to the specified changeset_revision. No subsequent revisions will be + present in the cloned repository. + """ + try: + commands.clone( get_configured_ui(), + str( repository_clone_url ), + dest=str( repository_file_dir ), + pull=True, + noupdate=False, + rev=listify( str( ctx_rev ) ) ) + return True, None + except Exception, e: + error_message = 'Error cloning repository: %s' % str( e ) + log.debug( error_message ) + return False, error_message + def get_changectx_for_changeset( repo, changeset_revision, **kwd ): """Retrieve a specified changectx from a repository.""" for changeset in repo.changelog: @@ -28,7 +49,19 @@ # quiet = True _ui.setconfig( 'ui', 'quiet', True ) return _ui - + +def get_mercurial_default_options_dict( command, command_table=None, **kwd ): + '''Borrowed from repoman - get default parameters for a mercurial command.''' + if command_table is None: + command_table = commands.table + possible = cmdutil.findpossible( command, command_table ) + if len( possible ) != 1: + raise Exception, 'unable to find mercurial command "%s"' % command + default_options_dict = dict( ( r[ 1 ].replace( '-', '_' ), r[ 2 ] ) for r in possible[ possible.keys()[ 0 ] ][ 1 ][ 1 ] ) + for option in kwd: + default_options_dict[ option ] = kwd[ option ] + return default_options_dict + def get_readable_ctx_date( ctx ): """Convert the date of the changeset (the received ctx) to a human-readable date.""" t, tz = ctx.date() @@ -106,3 +139,21 @@ rev = '-1' label = "-1:%s" % changeset_revision return rev, label + +def update_repository( repo, ctx_rev=None ): + """ + Update the cloned repository to changeset_revision. It is critical that the installed repository is updated to the desired + changeset_revision before metadata is set because the process for setting metadata uses the repository files on disk. + """ + # TODO: We may have files on disk in the repo directory that aren't being tracked, so they must be removed. + # The codes used to show the status of files are as follows. + # M = modified + # A = added + # R = removed + # C = clean + # ! = deleted, but still tracked + # ? = not tracked + # I = ignored + # It would be nice if we could use mercurial's purge extension to remove untracked files. The problem is that + # purging is not supported by the mercurial API. + commands.update( get_configured_ui(), repo, rev=ctx_rev ) diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1799,7 +1799,7 @@ current_changeset_revision = str( repo.changectx( changeset ) ) ctx = repo.changectx( changeset ) log.debug( "Cloning repository changeset revision: %s", str( ctx.rev() ) ) - cloned_ok, error_message = suc.clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) + cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) if cloned_ok: log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) current_metadata_dict, invalid_tups = generate_metadata_for_changeset_revision( app=trans.app, @@ -1811,7 +1811,8 @@ resetting_all_metadata_on_repository=True, updating_installed_repository=False, persist=False ) - # We'll only display error messages for the repository tip (it may be better to display error messages for each installable changeset revision). + # We'll only display error messages for the repository tip (it may be better to display error + # messages for each installable changeset revision). if current_changeset_revision == repository.tip( trans.app ): invalid_file_tups.extend( invalid_tups ) if current_metadata_dict: diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -25,10 +25,7 @@ from galaxy import eggs eggs.require( 'mercurial' ) -from mercurial import cmdutil -from mercurial import commands from mercurial import hg -from mercurial import ui eggs.require( 'markupsafe' ) import markupsafe @@ -139,15 +136,6 @@ return repository_metadata.malicious return False -def changeset_is_valid( app, repository, changeset_revision ): - """Make sure a changeset hash is valid for a specified repository.""" - repo = hg.repository( hg_util.get_configured_ui(), repository.repo_path( app ) ) - for changeset in repo.changelog: - changeset_hash = str( repo.changectx( changeset ) ) - if changeset_revision == changeset_hash: - return True - return False - def check_or_update_tool_shed_status_for_installed_repository( trans, repository ): updated = False tool_shed_status_dict = get_tool_shed_status_for_installed_repository( trans.app, repository ) @@ -162,21 +150,6 @@ ok = False return ok, updated -def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): - """Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository.""" - try: - commands.clone( hg_util.get_configured_ui(), - str( repository_clone_url ), - dest=str( repository_file_dir ), - pull=True, - noupdate=False, - rev=util.listify( str( ctx_rev ) ) ) - return True, None - except Exception, e: - error_message = 'Error cloning repository: %s' % str( e ) - log.debug( error_message ) - return False, error_message - def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ): """Persist the current in-memory list of config_elems to a file named by the value of config_filename.""" fd, filename = tempfile.mkstemp( prefix="tmp-toolshed-cetxf" ) @@ -655,18 +628,6 @@ return changeset_revisions[ -1 ] return INITIAL_CHANGELOG_HASH -def get_mercurial_default_options_dict( command, command_table=None, **kwd ): - '''Borrowed from repoman - get default parameters for a mercurial command.''' - if command_table is None: - command_table = commands.table - possible = cmdutil.findpossible( command, command_table ) - if len( possible ) != 1: - raise Exception, 'unable to find mercurial command "%s"' % command - default_options_dict = dict( ( r[ 1 ].replace( '-', '_' ), r[ 2 ] ) for r in possible[ possible.keys()[ 0 ] ][ 1 ][ 1 ] ) - for option in kwd: - default_options_dict[ option ] = kwd[ option ] - return default_options_dict - def get_named_tmpfile_from_ctx( ctx, filename, dir ): """Return a named temporary file created from a specified file with a given name included in a repository changeset revision.""" filename = strip_path( filename ) @@ -1784,24 +1745,6 @@ config_elems.append( elem ) config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) -def update_repository( repo, ctx_rev=None ): - """ - Update the cloned repository to changeset_revision. It is critical that the installed repository is updated to the desired - changeset_revision before metadata is set because the process for setting metadata uses the repository files on disk. - """ - # TODO: We may have files on disk in the repo directory that aren't being tracked, so they must be removed. - # The codes used to show the status of files are as follows. - # M = modified - # A = added - # R = removed - # C = clean - # ! = deleted, but still tracked - # ? = not tracked - # I = ignored - # It would be nice if we could use mercurial's purge extension to remove untracked files. The problem is that - # purging is not supported by the mercurial API. - commands.update( hg_util.get_configured_ui(), repo, rev=ctx_rev ) - def update_tool_shed_repository_status( app, tool_shed_repository, status, error_message=None ): """Update the status of a tool shed repository in the process of being installed into Galaxy.""" context = app.install_model.context diff -r 203623b931507dcd182e2521911ab036021faf61 -r d1dd573cdce2bd122cbb0e98e947dc7992fe3ed0 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -19,6 +19,7 @@ from galaxy.web import security from tool_shed.util.encoding_util import tool_shed_encode from tool_shed.util import shed_util_common as suc +from tool_shed.util import hg_util from tool_shed.util import xml_util from galaxy import eggs @@ -260,7 +261,7 @@ def clone_repository( self, repository, destination_path ): url = '%s/repos/%s/%s' % ( self.url, repository.user.username, repository.name ) - success, message = suc.clone_repository( url, destination_path, self.get_repository_tip( repository ) ) + success, message = hg_util.clone_repository( url, destination_path, self.get_repository_tip( repository ) ) assert success is True, message def commit_and_push( self, repository, hgrepo, options, username, password ): 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: Fix for the execute_step() method in the SetEnvironment class.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/203623b93150/ Changeset: 203623b93150 User: greg Date: 2014-04-24 21:11:43 Summary: Fix for the execute_step() method in the SetEnvironment class. Affected #: 1 file diff -r 99056011d2dbbfa64f8b9ab56871e1d4da279f69 -r 203623b931507dcd182e2521911ab036021faf61 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 @@ -450,14 +450,20 @@ env_var_dicts = action_dict[ 'environment_variable' ] for env_var_dict in env_var_dicts: # Check for the presence of the $ENV[] key string and populate it if possible. - env_var_dict = self.handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, cmds ) + env_var_dict = self.handle_environment_variables( app=app, + install_environment=install_environment, + tool_dependency=tool_dependency, + install_dir=install_dir, + env_var_dict=env_var_dict, + set_prior_environment_commands=cmds ) env_file_builder.append_line( **env_var_dict ) # The caller should check the status of the returned tool_dependency since return_code is not # returned by this function. return_code = env_file_builder.return_code return tool_dependency, None, None - def handle_environment_variables( self, app, tool_dependency, install_dir, env_var_dict, set_prior_environment_commands ): + def handle_environment_variables( self, app, install_environment, tool_dependency, install_dir, env_var_dict, + set_prior_environment_commands ): """ This method works with with a combination of three tool dependency definition tag sets, which are defined in the tool_dependencies.xml file in the order discussed here. The example for this discussion is the @@ -539,7 +545,6 @@ set_prior_environment_commands.append( 'echo %s: $%s' % ( inherited_env_var_name, inherited_env_var_name ) ) command = ' ; '.join( set_prior_environment_commands ) # Run the command and capture the output. - install_environment = recipe_manager.InstallEnvironment() command_return = install_environment.handle_command( app, tool_dependency, install_dir, command, return_output=True ) # And extract anything labeled with the name of the environment variable we're populating here. if '%s: ' % inherited_env_var_name in command_return: 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: Fix tool shed unit tests I broke with my last commit.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/99056011d2db/ Changeset: 99056011d2db User: greg Date: 2014-04-24 19:45:04 Summary: Fix tool shed unit tests I broke with my last commit. Affected #: 2 files diff -r ffafb6350791453b31c841e5462314bcd04ffa88 -r 99056011d2dbbfa64f8b9ab56871e1d4da279f69 test/unit/tool_shed_unit_tests/test_fabric_util.py --- a/test/unit/tool_shed_unit_tests/test_fabric_util.py +++ b/test/unit/tool_shed_unit_tests/test_fabric_util.py @@ -1,6 +1,5 @@ from contextlib import contextmanager -from tool_shed.galaxy_install.recipe.recipe_manager import EnvFileBuilder -from tool_shed.galaxy_install.tool_dependencies import fabric_util +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import EnvFileBuilder def test_env_file_builder(): @@ -10,10 +9,10 @@ mock_return = dict(value=0) def mock_file_append( text, file_path, **kwds ): - added_lines.append(text) - return mock_return["value"] + added_lines.append( text ) + return mock_return[ "value" ] - with __mock_fabric_util_method("file_append", mock_file_append): + with __mock_env_file_builder_method( env_file_builder, "file_append", mock_file_append ): env_file_builder.append_line( name="PATH", action="prepend_to", value="/usr/bin/local/R" ) assert added_lines == [ "PATH=/usr/bin/local/R:$PATH; export PATH" ] assert env_file_builder.return_code == 0 @@ -37,10 +36,10 @@ ## Poor man's mocking. Need to get a real mocking library as real Galaxy development ## dependnecy. @contextmanager -def __mock_fabric_util_method(name, mock_method): - real_method = getattr(fabric_util, name) +def __mock_env_file_builder_method( env_file_builder, name, mock_method ): + real_method = getattr( env_file_builder, name ) try: - setattr(fabric_util, name, mock_method) + setattr( env_file_builder, name, mock_method ) yield finally: - setattr(fabric_util, name, real_method) + setattr( env_file_builder, name, real_method ) diff -r ffafb6350791453b31c841e5462314bcd04ffa88 -r 99056011d2dbbfa64f8b9ab56871e1d4da279f69 test/unit/tool_shed_unit_tests/test_td_common_util.py --- a/test/unit/tool_shed_unit_tests/test_td_common_util.py +++ b/test/unit/tool_shed_unit_tests/test_td_common_util.py @@ -4,7 +4,8 @@ from tool_shed.galaxy_install.tool_dependencies import fabric_util from tool_shed.galaxy_install.tool_dependencies import td_common_util -from tool_shed.galaxy_install.recipe.recipe_manager import EnvFileBuilder +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import EnvFileBuilder + TEST_DEPENDENCIES_DIR = "/opt/galaxy/dependencies" TEST_INSTALL_DIR = "%s/test_install_dir" % TEST_DEPENDENCIES_DIR 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: davebgx: Get tool dependency status from the install model.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ffafb6350791/ Changeset: ffafb6350791 User: davebgx Date: 2014-04-24 17:24:24 Summary: Get tool dependency status from the install model. Affected #: 1 file diff -r cf9cd1027e2a7e3f29201125fbbacf929ef55d0b -r ffafb6350791453b31c841e5462314bcd04ffa88 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -86,7 +86,7 @@ install_dir=install_dir, current_dir=current_dir, initial_download=False ) - if tool_dependency.status in [ app.model.ToolDependency.installation_status.ERROR ]: + if tool_dependency.status in [ app.install_model.ToolDependency.installation_status.ERROR ]: # If the tool_dependency status is in an error state, return it with no additional # processing. return tool_dependency 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: davebgx: Update tool shed twilltestcase methods to reflect changes in the base twilltestcase's visit_url method. Fix functional tests for the tool shed. Update test tool dependencies to not actually compile EMBOSS and freebayes.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cf9cd1027e2a/ Changeset: cf9cd1027e2a User: davebgx Date: 2014-04-24 17:23:03 Summary: Update tool shed twilltestcase methods to reflect changes in the base twilltestcase's visit_url method. Fix functional tests for the tool shed. Update test tool dependencies to not actually compile EMBOSS and freebayes. Affected #: 4 files diff -r f1cb12e876c659c456c0b10f577494f79211b7f4 -r cf9cd1027e2a7e3f29201125fbbacf929ef55d0b test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -284,30 +284,6 @@ category = test_db_util.get_category_by_name( kwd[ 'name' ] ) return category - def create_checkbox_query_string( self, field_name, value ): - ''' - From galaxy.web.form_builder.CheckboxField: - The hidden field is necessary because if the check box is not checked on the form, it will - not be included in the request params. The hidden field ensure that this will happen. When - parsing the request, the value 'true' in the hidden field actually means it is NOT checked. - See the is_checked() method below. The prefix is necessary in each case to ensure functional - correctness when the param is inside a conditional. - - This may look strange upon initial inspection, but see the comments in the get_html() method - above for clarification. Basically, if value is not True, then it will always be a list with - 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not - checked, then value will be only the hidden field. - - The create_checkbox_query_string method emulates the described behavior with URL query parameters. - This is currently necessary because twill does not correctly parse certain forms, so the test - method has to visit the intended form target "manually". - ''' - field_value = str( value ).lower() - if value: - return '%s=%s&%s=%s' % ( field_name, field_value, field_name, field_value ) - else: - return '%s=%s' % ( field_name, field_value ) - def create_repository_dependency( self, repository=None, repository_tuples=[], @@ -547,7 +523,8 @@ def enable_email_alerts( self, repository, strings_displayed=[], strings_not_displayed=[] ): repository_id = self.security.encode_id( repository.id ) - self.visit_url( '/repository/browse_repositories?operation=Receive+email+alerts&id=%s' % repository_id ) + params = dict( operation='Receive email alerts', id=repository_id ) + self.visit_url( '/repository/browse_repositories' ) self.check_for_strings( strings_displayed ) def escape_html( self, string, unescape=False ): @@ -816,15 +793,19 @@ strings_not_displayed = [] self.visit_url( '/admin/roles' ) self.check_for_strings( strings_displayed, strings_not_displayed ) - url = '/admin/roles?operation=manage+users+and+groups&id=%s' % self.security.encode_id( role.id ) + params = dict( operation='manage users and groups', id=self.security.encode_id( role.id ) ) + url = '/admin/roles' self.visit_url( url ) strings_displayed = [ common.test_user_1_email, common.test_user_2_email ] self.check_for_strings( strings_displayed, strings_not_displayed ) # As elsewhere, twill limits the possibility of submitting the form, this time due to not executing the javascript # attached to the role selection form. Visit the action url directly with the necessary parameters. - url = '/admin/manage_users_and_groups_for_role?id=%s&in_users=%d&operation=manage+users+and+groups&role_members_edit_button=Save' % \ - ( self.security.encode_id( role.id ), user.id ) - self.visit_url( url ) + params = dict( id=self.security.encode_id( role.id ), + in_users=user.id, + operation='manage users and groups', + role_members_edit_button='Save' ) + url = '/admin/manage_users_and_groups_for_role' + self.visit_url( url, params ) strings_displayed = [ "Role '%s' has been updated" % role.name ] self.check_for_strings( strings_displayed, strings_not_displayed ) @@ -1050,8 +1031,9 @@ self.check_for_strings( strings_displayed, strings_not_displayed ) def reactivate_repository( self, installed_repository ): - url = '/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=%s' % self.security.encode_id( installed_repository.id ) - self.visit_galaxy_url( url ) + params = dict( operation='activate or reinstall', id=self.security.encode_id( installed_repository.id ) ) + url = '/admin_toolshed/browse_repositories' + self.visit_galaxy_url( url, params ) strings_displayed = [ installed_repository.name, 'repository has been activated' ] self.check_for_strings( strings_displayed, [] ) @@ -1068,12 +1050,12 @@ self.check_for_strings( strings_displayed, strings_not_displayed=[] ) # Build the url that will simulate a filled-out form being submitted. Due to a limitation in twill, the reselect_tool_panel_section # form doesn't get parsed correctly. - repo_dependencies = self.create_checkbox_query_string( field_name='install_repository_dependencies', value=install_repository_dependencies ) - tool_dependencies = self.create_checkbox_query_string( field_name='install_tool_dependencies', value=install_tool_dependencies ) encoded_repository_id = self.security.encode_id( installed_repository.id ) - url = '/admin_toolshed/reinstall_repository?id=%s&%s&%s&no_changes=%s&new_tool_panel_section_label=%s' % \ - ( encoded_repository_id, repo_dependencies, tool_dependencies, str( no_changes ), new_tool_panel_section_label ) - self.visit_galaxy_url( url ) + params = dict( id=encoded_repository_id, no_changes=no_changes, new_tool_panel_section_label=new_tool_panel_section_label ) + checkbox_params = dict( install_repository_dependencies=install_repository_dependencies, + install_tool_dependencies=install_tool_dependencies ) + url = '/admin_toolshed/reinstall_repository' + self.visit_galaxy_url( url, params=params, checkbox_params=checkbox_params ) # Manually initiate the install process, as with installing a repository. See comments in the # initiate_installation_process method for details. repository_ids = self.initiate_installation_process( install_tool_dependencies, @@ -1429,8 +1411,9 @@ for tool in installed_repository.metadata[ 'tools' ]: strings = list( strings_displayed ) strings.extend( [ tool[ 'id' ], tool[ 'description' ], tool[ 'version' ], tool[ 'guid' ], tool[ 'name' ] ] ) - url = '/admin_toolshed/view_tool_metadata?repository_id=%s&tool_id=%s' % ( repository_id, urllib.quote_plus( tool[ 'id' ] ) ) - self.visit_galaxy_url( url ) + params = dict( repository_id=repository_id, tool_id=tool[ 'id' ] ) + url = '/admin_toolshed/view_tool_metadata' + self.visit_galaxy_url( url, params ) self.check_for_strings( strings, strings_not_displayed ) def verify_unchanged_repository_metadata( self, repository ): @@ -1451,9 +1434,9 @@ self.visit_galaxy_url( url ) self.check_for_strings( strings, strings_not_displayed ) - def visit_galaxy_url( self, url ): + def visit_galaxy_url( self, url, params=None, checkbox_params=None ): url = '%s%s' % ( self.galaxy_url, url ) - self.visit_url( url ) + self.visit_url( url, params=params, checkbox_params=checkbox_params ) def wait_for_repository_installation( self, repository_ids ): final_states = [ galaxy_model.ToolShedRepository.installation_status.ERROR, diff -r f1cb12e876c659c456c0b10f577494f79211b7f4 -r cf9cd1027e2a7e3f29201125fbbacf929ef55d0b test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py --- a/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -111,8 +111,9 @@ convert_repository = self.test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) strings_displayed=[ 'Handle repository dependencies', 'convert_chars_1087', self.get_repository_tip( convert_repository ) ] # Due to twill's limitations, only check for strings on the (redirected) reselect tool panel section page, don't actually reinstall. - url = '/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=%s' % self.security.encode_id( installed_column_repository.id ) - self.visit_galaxy_url( url ) + params = dict( operation='activate or reinstall', id=self.security.encode_id( installed_column_repository.id ) ) + url = '/admin_toolshed/browse_repositories' + self.visit_galaxy_url( url, params ) self.check_for_strings( strings_displayed ) strings_not_displayed = [ 'column_maker_1087' ] - self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) \ No newline at end of file diff -r f1cb12e876c659c456c0b10f577494f79211b7f4 -r cf9cd1027e2a7e3f29201125fbbacf929ef55d0b test/tool_shed/test_data/emboss/emboss.tar Binary file test/tool_shed/test_data/emboss/emboss.tar has changed diff -r f1cb12e876c659c456c0b10f577494f79211b7f4 -r cf9cd1027e2a7e3f29201125fbbacf929ef55d0b test/tool_shed/test_data/freebayes/tool_dependencies.xml --- a/test/tool_shed/test_data/freebayes/tool_dependencies.xml +++ b/test/tool_shed/test_data/freebayes/tool_dependencies.xml @@ -3,13 +3,7 @@ <package name="freebayes" version="0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8"><install version="1.0"><actions> - <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> - <action type="shell_command">git reset --hard 9696d0ce8a962f7bb61c4791be5ce44312b81cf8</action> - <action type="shell_command">make</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> + <action type="shell_command">echo "Success."</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> @@ -23,17 +17,7 @@ <package name="samtools" version="0.1.18"><install version="1.0"><actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> - <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>misc/maq2sam-long</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="shell_command">echo "Success."</action><action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> 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: davebgx: Fix typo in step handler.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f1cb12e876c6/ Changeset: f1cb12e876c6 User: davebgx Date: 2014-04-24 17:06:59 Summary: Fix typo in step handler. Affected #: 1 file diff -r 3b6e94371b8a8e996cc8e317de8cbfe45790b94e -r f1cb12e876c659c456c0b10f577494f79211b7f4 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 @@ -592,7 +592,7 @@ install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) return tool_dependency, None, None - def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_dir, is_binary_downloa ): + def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_dir, is_binary_download ): # <action type="set_environment_for_install"> # <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056"> # <package name="numpy" version="1.7.1" /> 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: dannon: Add simplejson back again until 'anyjson' changes are pushed through bioblend.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b6e94371b8a/ Changeset: 3b6e94371b8a User: dannon Date: 2014-04-24 17:03:23 Summary: Add simplejson back again until 'anyjson' changes are pushed through bioblend. Affected #: 1 file diff -r de54998e192b99bd70751d692969b508463e1805 -r 3b6e94371b8a8e996cc8e317de8cbfe45790b94e eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -61,6 +61,7 @@ pytz = 2013.9 requests = 2.2.1 Routes = 1.12.3 +simplejson = 2.1.1 sqlalchemy_migrate = 0.7.2 ssh = 1.7.14 SVGFig = 1.1.6 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: Add a new recipe manager to support tool dependency package installation. Create new classes for each recipe step where classes contain both a prepare_step() and an execute_step() function. This implementation breaks up the very large loops in install_util.py (where recipe steps are prepared) and fabric_util.py (where recipe steps are executed). The recipe manager currently loads all of the recipe step classes when it is instantiated - this approach could be twe
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/de54998e192b/ Changeset: de54998e192b User: greg Date: 2014-04-24 16:46:56 Summary: Add a new recipe manager to support tool dependency package installation. Create new classes for each recipe step where classes contain both a prepare_step() and an execute_step() function. This implementation breaks up the very large loops in install_util.py (where recipe steps are prepared) and fabric_util.py (where recipe steps are executed). The recipe manager currently loads all of the recipe step classes when it is instantiated - this approach could be tweaked if desired. Affected #: 11 files diff -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 -r de54998e192b99bd70751d692969b508463e1805 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -1,765 +1,64 @@ -# For Python 2.5 -from __future__ import with_statement - import logging import os -import Queue -import shutil -import stat -import subprocess -import sys -import tempfile -import td_common_util -import threading -import time -import shlex -from contextlib import contextmanager -from galaxy.util import DATABASE_MAX_STRING_SIZE -from galaxy.util import DATABASE_MAX_STRING_SIZE_PRETTY -from galaxy.util import shrink_string_by_size -from galaxy.util import unicodify -from galaxy.util.template import fill_template from galaxy import eggs -eggs.require( 'ssh' ) -eggs.require( 'paramiko' ) eggs.require( 'Fabric' ) -from fabric import state from fabric.api import env -from fabric.api import hide from fabric.api import lcd -from fabric.api import settings -from fabric.api import prefix -from fabric.operations import _AttributeString + +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import EnvFileBuilder +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import InstallEnvironment +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import RecipeManager log = logging.getLogger( __name__ ) -INSTALLATION_LOG = 'INSTALLATION.log' -VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' - - -class AsynchronousReader( threading.Thread ): - """ - A helper class to implement asynchronous reading of a stream in a separate thread. Read lines are pushed - onto a queue to be consumed in another thread. - """ - - def __init__( self, fd, queue ): - threading.Thread.__init__( self ) - self._fd = fd - self._queue = queue - self.lines = [] - - def run( self ): - """Read lines and put them on the queue.""" - thread_lock = threading.Lock() - thread_lock.acquire() - for line in iter( self._fd.readline, '' ): - stripped_line = line.rstrip() - self.lines.append( stripped_line ) - self._queue.put( stripped_line ) - thread_lock.release() - - def installation_complete( self ): - """Make sure there is more installation and compilation logging content expected.""" - return not self.is_alive() and self._queue.empty() - - -class EnvFileBuilder( object ): - - def __init__( self, install_dir ): - self.install_dir = install_dir - self.return_code = 0 - - def append_line( self, make_executable=True, **kwd ): - env_var_dict = dict( **kwd ) - env_entry, env_file = self.create_or_update_env_shell_file( self.install_dir, env_var_dict ) - return_code = file_append( env_entry, env_file, make_executable=make_executable ) - self.return_code = self.return_code or return_code - return self.return_code - - @staticmethod - def create_or_update_env_shell_file( install_dir, env_var_dict ): - env_var_action = env_var_dict[ 'action' ] - env_var_value = env_var_dict[ 'value' ] - if env_var_action in [ 'prepend_to', 'set_to', 'append_to' ]: - env_var_name = env_var_dict[ 'name' ] - if env_var_action == 'prepend_to': - changed_value = '%s:$%s' % ( env_var_value, env_var_name ) - elif env_var_action == 'set_to': - changed_value = '%s' % env_var_value - elif env_var_action == 'append_to': - changed_value = '$%s:%s' % ( env_var_name, env_var_value ) - line = "%s=%s; export %s" % ( env_var_name, changed_value, env_var_name ) - elif env_var_action == "source": - line = "if [ -f %s ] ; then . %s ; fi" % ( env_var_value, env_var_value ) - else: - raise Exception( "Unknown shell file action %s" % env_var_action ) - env_shell_file_path = os.path.join( install_dir, 'env.sh' ) - return line, env_shell_file_path - - -class InstallEnvironment( object ): - """Object describing the environment built up as part of the process of building and installing a package.""" - - def add_env_shell_file_paths( self, paths ): - for path in paths: - self.env_shell_file_paths.append( str( path ) ) - - def build_command( self, command, action_type='shell_command' ): - """ - Build command line for execution from simple command, but - configuring environment described by this object. - """ - env_cmds = self.environment_commands( action_type ) - return '\n'.join( env_cmds + [ command ] ) - - def __call__( self, install_dir ): - with settings( warn_only=True, **td_common_util.get_env_var_values( install_dir ) ): - with prefix( self.__setup_environment() ): - yield - - def environment_commands( self, action_type ): - """Build a list of commands used to construct the environment described by this object.""" - cmds = [] - for env_shell_file_path in self.env_shell_file_paths: - if os.path.exists( env_shell_file_path ): - for env_setting in open( env_shell_file_path ): - cmds.append( env_setting.strip( '\n' ) ) - else: - log.debug( 'Invalid file %s specified, ignoring %s action.' % ( str( env_shell_file_path ), str( action_type ) ) ) - return cmds - - def environment_dict( self, action_type='template_command' ): - env_vars = dict() - for env_shell_file_path in self.env_shell_file_paths: - if os.path.exists( env_shell_file_path ): - for env_setting in open( env_shell_file_path ): - env_string = env_setting.split( ';' )[ 0 ] - env_name, env_path = env_string.split( '=' ) - env_vars[ env_name ] = env_path - else: - log.debug( 'Invalid file %s specified, ignoring template_command action.' % str( env_shell_file_path ) ) - return env_vars - - def __init__( self ): - self.env_shell_file_paths = [] - - def __setup_environment( self ): - return "&&".join( [ ". %s" % file for file in self.__valid_env_shell_file_paths() ] ) - - def __valid_env_shell_file_paths( self ): - return [ file for file in self.env_shell_file_paths if os.path.exists( file ) ] +INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environmnet', + 'setup_r_environmnet', 'setup_ruby_environmnet', 'shell_command' ] def check_fabric_version(): version = env.version if int( version.split( "." )[ 0 ] ) < 1: raise NotImplementedError( "Install Fabric version 1.0 or later." ) -def close_file_descriptor( fd ): - """Attempt to close a file descriptor.""" - start_timer = time.time() - error = '' - while True: - try: - fd.close() - break - except IOError, e: - # Undoubtedly close() was called during a concurrent operation on the same file object. - log.debug( 'Error closing file descriptor: %s' % str( e ) ) - time.sleep( .5 ) - current_wait_time = time.time() - start_timer - if current_wait_time >= 600: - error = 'Error closing file descriptor: %s' % str( e ) - break - return error - -def enqueue_output( stdout, stdout_queue, stderr, stderr_queue ): - """ - This method places streamed stdout and stderr into a threaded IPC queue target. Received data - is printed and saved to that thread's queue. The calling thread can then retrieve the data using - thread.stdout and thread.stderr. - """ - stdout_logger = logging.getLogger( 'fabric_util.STDOUT' ) - stderr_logger = logging.getLogger( 'fabric_util.STDERR' ) - for line in iter( stdout.readline, '' ): - output = line.rstrip() - stdout_logger.debug( output ) - stdout_queue.put( output ) - stdout_queue.put( None ) - for line in iter( stderr.readline, '' ): - output = line.rstrip() - stderr_logger.debug( output ) - stderr_queue.put( output ) - stderr_queue.put( None ) - -def file_append( text, file_path, make_executable=True ): - """ - Append a line to a file unless the line already exists in the file. This method creates the file if - it doesn't exist. If make_executable is True, the permissions on the file are set to executable by - the owner. - """ - file_dir = os.path.dirname( file_path ) - if not os.path.exists( file_dir ): - try: - os.makedirs( file_dir ) - except Exception, e: - log.exception( str( e ) ) - return 1 - if os.path.exists( file_path ): - try: - new_env_file_contents = [] - env_file_contents = file( file_path, 'r' ).readlines() - # Clean out blank lines from the env.sh file. - for line in env_file_contents: - line = line.rstrip() - if line: - new_env_file_contents.append( line ) - env_file_contents = new_env_file_contents - except Exception, e: - log.exception( str( e ) ) - return 1 - else: - env_file_handle = open( file_path, 'w' ) - env_file_handle.close() - env_file_contents = [] - if make_executable: - # Explicitly set the file's executable bits. - try: - os.chmod( file_path, int( '111', base=8 ) | os.stat( file_path )[ stat.ST_MODE ] ) - except Exception, e: - log.exception( str( e ) ) - return 1 - # Convert the received text to a list, in order to support adding one or more lines to the file. - if isinstance( text, basestring ): - text = [ text ] - for line in text: - line = line.rstrip() - if line and line not in env_file_contents: - env_file_contents.append( line ) - try: - file( file_path, 'w' ).write( '\n'.join( env_file_contents ) ) - except Exception, e: - log.exception( str( e ) ) - return 1 - return 0 - -def filter_actions_after_binary_installation( actions ): - '''Filter out actions that should not be processed if a binary download succeeded.''' - filtered_actions = [] - for action in actions: - action_type, action_dict = action - if action_type in [ 'set_environment', 'chmod', 'download_binary' ]: - filtered_actions.append( action ) - return filtered_actions - -def handle_action_shell_file_paths( env_file_builder, action_dict ): - shell_file_paths = action_dict.get( 'action_shell_file_paths', [] ) - for shell_file_path in shell_file_paths: - env_file_builder.append_line( action="source", value=shell_file_path ) - -def handle_command( app, tool_dependency, install_dir, cmd, return_output=False ): - """ - Handle a command by determining if it is "simple" or "complex" and redirecting appropriately and then - logging the results. - """ - context = app.install_model.context - command = str( cmd ) - output = handle_complex_command( command ) - log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) - stdout = output.stdout - stderr = output.stderr - if len( stdout ) > DATABASE_MAX_STRING_SIZE: - print "Length of stdout > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) - stdout = shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) - if len( stderr ) > DATABASE_MAX_STRING_SIZE: - print "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) - stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) - if output.return_code not in [ 0 ]: - tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR - if stderr: - tool_dependency.error_message = unicodify( stderr ) - elif stdout: - tool_dependency.error_message = unicodify( stdout ) - else: - # We have a problem if there was no stdout and no stderr. - tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \ - ( str( cmd ), str( output.return_code ) ) - context.add( tool_dependency ) - context.flush() - if return_output: - return output - return output.return_code - -def handle_complex_command( command ): - """ - Wrap subprocess.Popen in such a way that the stderr and stdout from running a shell command will - be captured and logged in nearly real time. This is similar to fabric.local, but allows us to - retain control over the process. This method is named "complex" because it uses queues and - threads to execute a command while capturing and displaying the output. - """ - # Launch the command as subprocess. A bufsize of 1 means line buffered. - process_handle = subprocess.Popen( str( command ), - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, - bufsize=1, - close_fds=False, - shell=True, - cwd=state.env[ 'lcwd' ] ) - pid = process_handle.pid - # Launch the asynchronous readers of the process' stdout and stderr. - stdout_queue = Queue.Queue() - stdout_reader = AsynchronousReader( process_handle.stdout, stdout_queue ) - stdout_reader.start() - stderr_queue = Queue.Queue() - stderr_reader = AsynchronousReader( process_handle.stderr, stderr_queue ) - stderr_reader.start() - # Place streamed stdout and stderr into a threaded IPC queue target so it can - # be printed and stored for later retrieval when generating the INSTALLATION.log. - stdio_thread = threading.Thread( target=enqueue_output, - args=( process_handle.stdout, - stdout_queue, - process_handle.stderr, - stderr_queue ) ) - thread_lock = threading.Lock() - thread_lock.acquire() - stdio_thread.start() - # Check the queues for output until there is nothing more to get. - start_timer = time.time() - while not stdout_reader.installation_complete() or not stderr_reader.installation_complete(): - # Show what we received from standard output. - while not stdout_queue.empty(): - try: - line = stdout_queue.get() - except Queue.Empty: - line = None - break - if line: - print line - start_timer = time.time() - else: - break - # Show what we received from standard error. - while not stderr_queue.empty(): - try: - line = stderr_queue.get() - except Queue.Empty: - line = None - break - if line: - print line - start_timer = time.time() - else: - stderr_queue.task_done() - break - # Sleep a bit before asking the readers again. - time.sleep( .1 ) - current_wait_time = time.time() - start_timer - if stdout_queue.empty() and stderr_queue.empty() and current_wait_time > td_common_util.NO_OUTPUT_TIMEOUT: - err_msg = "\nShutting down process id %s because it generated no output for the defined timeout period of %.1f seconds.\n" % \ - ( pid, td_common_util.NO_OUTPUT_TIMEOUT ) - stderr_reader.lines.append( err_msg ) - process_handle.kill() - break - thread_lock.release() - # Wait until each of the threads we've started terminate. The following calls will block each thread - # until it terminates either normally, through an unhandled exception, or until the timeout occurs. - stdio_thread.join( td_common_util.NO_OUTPUT_TIMEOUT ) - stdout_reader.join( td_common_util.NO_OUTPUT_TIMEOUT ) - stderr_reader.join( td_common_util.NO_OUTPUT_TIMEOUT ) - # Close subprocess' file descriptors. - error = close_file_descriptor( process_handle.stdout ) - error = close_file_descriptor( process_handle.stderr ) - stdout = '\n'.join( stdout_reader.lines ) - stderr = '\n'.join( stderr_reader.lines ) - # Handle error condition (deal with stdout being None, too) - output = _AttributeString( stdout.strip() if stdout else "" ) - errors = _AttributeString( stderr.strip() if stderr else "" ) - # Make sure the process has finished. - process_handle.poll() - output.return_code = process_handle.returncode - output.stderr = errors - return output - -def handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, set_prior_environment_commands ): - """ - This method works with with a combination of three tool dependency definition tag sets, which are defined - in the tool_dependencies.xml file in the order discussed here. The example for this discussion is the - tool_dependencies.xml file contained in the osra repository, which is available at: - - http://testtoolshed.g2.bx.psu.edu/view/bgruening/osra - - The first tag set defines a complex repository dependency like this. This tag set ensures that changeset - revision XXX of the repository named package_graphicsmagick_1_3 owned by YYY in the tool shed ZZZ has been - previously installed. - - <tool_dependency> - <package name="graphicsmagick" version="1.3.18"> - <repository changeset_revision="XXX" name="package_graphicsmagick_1_3" owner="YYY" prior_installation_required="True" toolshed="ZZZ" /> - </package> - ... - - * By the way, there is an env.sh file associated with version 1.3.18 of the graphicsmagick package which looks - something like this (we'll reference this file later in this discussion. - ---- - GRAPHICSMAGICK_ROOT_DIR=/<my configured tool dependency path>/graphicsmagick/1.3.18/YYY/package_graphicsmagick_1_3/XXX/gmagick; - export GRAPHICSMAGICK_ROOT_DIR - ---- - - The second tag set defines a specific package dependency that has been previously installed (guaranteed by the - tag set discussed above) and compiled, where the compiled dependency is needed by the tool dependency currently - being installed (osra version 2.0.0 in this case) and complied in order for its installation and compilation to - succeed. This tag set is contained within the <package name="osra" version="2.0.0"> tag set, which implies that - version 2.0.0 of the osra package requires version 1.3.18 of the graphicsmagick package in order to successfully - compile. When this tag set is handled, one of the effects is that the env.sh file associated with graphicsmagick - version 1.3.18 is "sourced", which undoubtedly sets or alters certain environment variables (e.g. PATH, PYTHONPATH, - etc). - -  - <action type="set_environment_for_install"> - <repository changeset_revision="XXX" name="package_graphicsmagick_1_3" owner="YYY" toolshed="ZZZ"> - <package name="graphicsmagick" version="1.3.18" /> - </repository> - </action> - - The third tag set enables discovery of the same required package dependency discussed above for correctly compiling - the osra version 2.0.0 package, but in this case the package can be discovered at tool execution time. Using the - $ENV[] option as shown in this example, the value of the environment variable named GRAPHICSMAGICK_ROOT_DIR (which - was set in the environment using the second tag set described above) will be used to automatically alter the env.sh - file associated with the osra version 2.0.0 tool dependency when it is installed into Galaxy. * Refer to where we - discussed the env.sh file for version 1.3.18 of the graphicsmagick package above. - - <action type="set_environment"> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> -  - <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable> - </action> - - The above tag will produce an env.sh file for version 2.0.0 of the osra package when it it installed into Galaxy - that looks something like this. Notice that the path to the gmagick binary is included here since it expands the - defined $ENV[GRAPHICSMAGICK_ROOT_DIR] value in the above tag set. - - ---- - LD_LIBRARY_PATH=/<my configured tool dependency path>/graphicsmagick/1.3.18/YYY/package_graphicsmagick_1_3/XXX/gmagick/lib/:$LD_LIBRARY_PATH; - export LD_LIBRARY_PATH - LD_LIBRARY_PATH=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/potrace/build/lib/:$LD_LIBRARY_PATH; - export LD_LIBRARY_PATH - PATH=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/bin:$PATH; - export PATH - OSRA_DATA_FILES=/<my configured tool dependency path>/osra/1.4.0/YYY/depends_on/XXX/share; - export OSRA_DATA_FILES - ---- - """ - env_var_value = env_var_dict[ 'value' ] - # env_var_value is the text of an environment variable tag like this: <environment_variable action="prepend_to" name="LD_LIBRARY_PATH"> - # Here is an example of what env_var_value could look like: $ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/ - if '$ENV[' in env_var_value and ']' in env_var_value: - # Pull out the name of the environment variable to populate. - inherited_env_var_name = env_var_value.split( '[' )[1].split( ']' )[0] - to_replace = '$ENV[%s]' % inherited_env_var_name - # Build a command line that outputs VARIABLE_NAME: <the value of the variable>. - set_prior_environment_commands.append( 'echo %s: $%s' % ( inherited_env_var_name, inherited_env_var_name ) ) - command = ' ; '.join( set_prior_environment_commands ) - # Run the command and capture the output. - command_return = handle_command( app, tool_dependency, install_dir, command, return_output=True ) - # And extract anything labeled with the name of the environment variable we're populating here. - if '%s: ' % inherited_env_var_name in command_return: - environment_variable_value = command_return.split( '\n' ) - for line in environment_variable_value: - if line.startswith( inherited_env_var_name ): - inherited_env_var_value = line.replace( '%s: ' % inherited_env_var_name, '' ) - log.info( 'Replacing %s with %s in env.sh for this repository.', to_replace, inherited_env_var_value ) - env_var_value = env_var_value.replace( to_replace, inherited_env_var_value ) - else: - # If the return is empty, replace the original $ENV[] with nothing, to avoid any shell misparsings later on. - log.error( 'Environment variable %s not found, removing from set_environment.', inherited_env_var_name ) - env_var_value = env_var_value.replace( to_replace, '$%s' % inherited_env_var_name ) - env_var_dict[ 'value' ] = env_var_value - return env_var_dict - -def install_virtualenv( app, venv_dir ): - if not os.path.exists( venv_dir ): - with make_tmp_dir() as work_dir: - downloaded_filename = VIRTUALENV_URL.rsplit('/', 1)[-1] - try: - dir = td_common_util.url_download( work_dir, downloaded_filename, VIRTUALENV_URL ) - except: - log.error( "Failed to download virtualenv: td_common_util.url_download( '%s', '%s', '%s' ) threw an exception", work_dir, downloaded_filename, VIRTUALENV_URL ) - return False - full_path_to_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - shutil.move( full_path_to_dir, venv_dir ) - return True - def install_and_build_package( app, tool_dependency, actions_dict ): """Install a Galaxy tool dependency package either via a url or a mercurial or git clone command.""" install_dir = actions_dict[ 'install_dir' ] package_name = actions_dict[ 'package_name' ] actions = actions_dict.get( 'actions', None ) filtered_actions = [] + env_file_builder = EnvFileBuilder( install_dir ) install_environment = InstallEnvironment() + recipe_manager = RecipeManager() if actions: - with make_tmp_dir() as work_dir: + with install_environment.make_tmp_dir() as work_dir: with lcd( work_dir ): - # The first action in the list of actions will be the one that defines the installation process. There - # are currently three supported processes; download_binary, download_by_url and clone via a "shell_command" - # action type. + # The first action in the list of actions will be the one that defines the initial download process. + # There are currently three supported actions; download_binary, download_by_url and clone via a + # shell_command action type. The recipe steps will be filtered at this stage in the process, with + # the filtered actions being used in the next stage below. The installation directory (i.e., dir) + # is also defined in this stage and is used in the next stage below when defining current_dir. action_type, action_dict = actions[ 0 ] - if action_type == 'download_binary': - url = action_dict[ 'url' ] - # Get the target directory for this download, if the user has specified one. Default to the root of $INSTALL_DIR. - target_directory = action_dict.get( 'target_directory', None ) - # Attempt to download a binary from the specified URL. - log.debug( 'Attempting to download from %s to %s', url, str( target_directory ) ) - downloaded_filename = None - try: - downloaded_filename = td_common_util.download_binary( url, work_dir ) - # Filter out any actions that are not download_binary, chmod, or set_environment. - filtered_actions = filter_actions_after_binary_installation( actions[ 1: ] ) - # Set actions to the same, so that the current download_binary doesn't get re-run in the - # filtered actions below. - actions = filtered_actions - except Exception, e: - log.exception( str( e ) ) - # No binary exists, or there was an error downloading the binary from the generated URL. - # Proceed with the remaining actions. - filtered_actions = actions[ 1: ] - action_type, action_dict = filtered_actions[ 0 ] - # If the downloaded file exists, move it to $INSTALL_DIR. Put this outside the try/catch above so that - # any errors in the move step are correctly sent to the tool dependency error handler. - if downloaded_filename and os.path.exists( os.path.join( work_dir, downloaded_filename ) ): - if target_directory: - target_directory = os.path.realpath( os.path.normpath( os.path.join( install_dir, target_directory ) ) ) - # Make sure the target directory is not outside of $INSTALL_DIR. - if target_directory.startswith( os.path.realpath( install_dir ) ): - full_path_to_dir = os.path.abspath( os.path.join( install_dir, target_directory ) ) - else: - full_path_to_dir = os.path.abspath( install_dir ) - else: - full_path_to_dir = os.path.abspath( install_dir ) - td_common_util.move_file( current_dir=work_dir, - source=downloaded_filename, - destination=full_path_to_dir ) - if action_type == 'download_by_url': - # Eliminate the download_by_url action so remaining actions can be processed correctly. - filtered_actions = actions[ 1: ] - url = action_dict[ 'url' ] - is_binary = action_dict.get( 'is_binary', False ) - log.debug( 'Attempting to download via url: %s', url ) - if 'target_filename' in action_dict: - # Sometimes compressed archives extract their content to a folder other than the default - # defined file name. Using this attribute will ensure that the file name is set appropriately - # and can be located after download, decompression and extraction. - downloaded_filename = action_dict[ 'target_filename' ] - else: - downloaded_filename = os.path.split( url )[ -1 ] - dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True ) - if is_binary: - log_file = os.path.join( install_dir, INSTALLATION_LOG ) - if os.path.exists( log_file ): - logfile = open( log_file, 'ab' ) - else: - logfile = open( log_file, 'wb' ) - logfile.write( 'Successfully downloaded from url: %s\n' % action_dict[ 'url' ] ) - logfile.close() - log.debug( 'Successfully downloaded from url: %s' % action_dict[ 'url' ] ) - elif action_type == 'shell_command': - # <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> - # Eliminate the shell_command clone action so remaining actions can be processed correctly. - filtered_actions = actions[ 1: ] - return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] ) - if return_code: - return tool_dependency - dir = package_name - elif action_type == 'download_file': - # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> - # Download a single file to the working directory. - filtered_actions = actions[ 1: ] - url = action_dict[ 'url' ] - if 'target_filename' in action_dict: - # Sometimes compressed archives extracts their content to a folder other than the default - # defined file name. Using this attribute will ensure that the file name is set appropriately - # and can be located after download, decompression and extraction. - filename = action_dict[ 'target_filename' ] - else: - filename = url.split( '/' )[ -1 ] - td_common_util.url_download( work_dir, filename, url ) - dir = os.path.curdir - elif action_type == 'setup_r_environment': - # setup an R environment - # <action type="setup_r_environment"> - # <repository name="package_r_3_0_1" owner="bgruening"> - # <package name="R" version="3.0.1" /> - # </repository> - #  - # <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</package> - # </action> - filtered_actions = actions[ 1: ] - env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None ) - if env_shell_file_paths is None: - log.debug( 'Missing R environment. Please check your specified R installation exists.' ) - return tool_dependency - else: - install_environment.add_env_shell_file_paths( env_shell_file_paths ) - log.debug( 'Handling setup_r_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' % \ - ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) ) - tarball_names = [] - for url in action_dict[ 'r_packages' ]: - filename = url.split( '/' )[ -1 ] - tarball_names.append( filename ) - td_common_util.url_download( work_dir, filename, url, extract=False ) - dir = os.path.curdir - current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - with lcd( current_dir ): - with settings( warn_only=True ): - for tarball_name in tarball_names: - # Use raw strings so that python won't automatically unescape the quotes before passing the command - # to subprocess.Popen. - cmd = r'''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; - Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % \ - ( str( tarball_name ) ) - cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - # R libraries are installed to $INSTALL_DIR (install_dir), we now set the R_LIBS path to that directory - env_file_builder = EnvFileBuilder( install_dir ) - # Pull in R environment (runtime). - handle_action_shell_file_paths( env_file_builder, action_dict ) - env_file_builder.append_line( name="R_LIBS", action="prepend_to", value=install_dir ) - return_code = env_file_builder.return_code - if return_code: - return tool_dependency - elif action_type == 'setup_ruby_environment': - # setup an Ruby environment - # <action type="setup_ruby_environment"> - # <repository name="package_ruby_2_0" owner="bgruening"> - # <package name="ruby" version="2.0" /> - # </repository> - #  - # <package>protk</package> - # <package>protk=1.2.4</package> - # <package>http://url-to-some-gem-file.de/protk.gem</package> - # </action> - filtered_actions = actions[ 1: ] - env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None ) - if env_shell_file_paths is None: - log.debug( 'Missing Ruby environment, make sure your specified Ruby installation exists.' ) - return tool_dependency - else: - install_environment.add_env_shell_file_paths( env_shell_file_paths ) - log.debug( 'Handling setup_ruby_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' % \ - ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) ) - dir = os.path.curdir - current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - with lcd( current_dir ): - with settings( warn_only=True ): - ruby_package_tups = action_dict.get( 'ruby_package_tups', [] ) - for ruby_package_tup in ruby_package_tups: - gem, gem_version = ruby_package_tup - if os.path.isfile( gem ): - # we assume a local shipped gem file - cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; - gem install --local %s''' % ( gem ) - elif gem.find( '://' ) != -1: - # We assume a URL to a gem file. - url = gem - gem_name = url.split( '/' )[ -1 ] - td_common_util.url_download( work_dir, gem_name, url, extract=False ) - cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; - gem install --local %s ''' % ( gem_name ) - else: - # gem file from rubygems.org with or without version number - if gem_version: - # Specific ruby gem version was requested. - # Use raw strings so that python won't automatically unescape the quotes before passing the command - # to subprocess.Popen. - cmd = r'''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; - gem install %s --version "=%s"''' % ( gem, gem_version) - else: - # no version number given - cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; - gem install %s''' % ( gem ) - cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - env_file_builder = EnvFileBuilder( install_dir ) - # Pull in ruby dependencies (runtime). - handle_action_shell_file_paths( env_file_builder, action_dict ) - env_file_builder.append_line( name="GEM_PATH", action="prepend_to", value=install_dir ) - env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join(install_dir, 'bin') ) - return_code = env_file_builder.return_code - if return_code: - return tool_dependency - elif action_type == 'setup_perl_environment': - # setup an Perl environment - # <action type="setup_perl_environment"> - # <repository name="package_perl_5_18" owner="bgruening"> - # <package name="perl" version="5.18.1" /> - # </repository> - #  - # <package>XML::Parser</package> - # <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package> - # </action> - filtered_actions = actions[ 1: ] - env_shell_file_paths = action_dict.get( 'env_shell_file_paths', None ) - if env_shell_file_paths is None: - log.debug( 'Missing Rerl environment, make sure your specified Rerl installation exists.' ) - return tool_dependency - else: - install_environment.add_env_shell_file_paths( env_shell_file_paths ) - log.debug( 'Handling setup_perl_environment for tool dependency %s with install_environment.env_shell_file_paths:\n%s' % \ - ( str( tool_dependency.name ), str( install_environment.env_shell_file_paths ) ) ) - dir = os.path.curdir - current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - with lcd( current_dir ): - with settings( warn_only=True ): - perl_packages = action_dict.get( 'perl_packages', [] ) - for perl_package in perl_packages: - # If set to a true value then MakeMaker's prompt function will always - # return the default without waiting for user input. - cmd = '''PERL_MM_USE_DEFAULT=1; export PERL_MM_USE_DEFAULT; ''' - if perl_package.find( '://' ) != -1: - # We assume a URL to a gem file. - url = perl_package - perl_package_name = url.split( '/' )[ -1 ] - dir = td_common_util.url_download( work_dir, perl_package_name, url, extract=True ) - # Search for Build.PL or Makefile.PL (ExtUtils::MakeMaker vs. Module::Build). - tmp_work_dir = os.path.join( work_dir, dir ) - if os.path.exists( os.path.join( tmp_work_dir, 'Makefile.PL' ) ): - cmd += '''perl Makefile.PL INSTALL_BASE=$INSTALL_DIR && make && make install''' - elif os.path.exists( os.path.join( tmp_work_dir, 'Build.PL' ) ): - cmd += '''perl Build.PL --install_base $INSTALL_DIR && perl Build && perl Build install''' - else: - log.debug( 'No Makefile.PL or Build.PL file found in %s. Skipping installation of %s.' % \ - ( url, perl_package_name ) ) - return tool_dependency - with lcd( tmp_work_dir ): - cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - else: - # perl package from CPAN without version number. - # cpanm should be installed with the parent perl distribution, otherwise this will not work. - cmd += '''cpanm --local-lib=$INSTALL_DIR %s''' % ( perl_package ) - cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - env_file_builder = EnvFileBuilder( install_dir ) - # Pull in perl dependencies (runtime). - handle_action_shell_file_paths( env_file_builder, action_dict ) - # Recursively add dependent PERL5LIB and PATH to env.sh & anything else needed. - env_file_builder.append_line( name="PERL5LIB", action="prepend_to", value=os.path.join( install_dir, 'lib', 'perl5' ) ) - env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join( install_dir, 'bin' ) ) - return_code = env_file_builder.return_code - if return_code: - return tool_dependency + if action_type in INSTALL_ACTIONS: + # Some of the parameters passed here are needed only by a subset of the step handler classes, + # but to allow for a standard method signature we'll pass them along. We don't check the + # tool_dependency status in this stage because it should not have been changed based on a + # download. + tool_dependency, filtered_actions, dir = \ + recipe_manager.execute_step( app=app, + tool_dependency=tool_dependency, + package_name=package_name, + actions=actions, + action_type=action_type, + action_dict=action_dict, + filtered_actions=filtered_actions, + env_file_builder=env_file_builder, + install_environment=install_environment, + work_dir=work_dir, + install_dir=install_dir, + current_dir=None, + initial_download=True ) else: # We're handling a complex repository dependency where we only have a set_environment tag set. # <action type="set_environment"> @@ -767,207 +66,33 @@ # </action> filtered_actions = [ a for a in actions ] dir = install_dir - full_path_to_dir = os.path.abspath( os.path.join( work_dir, dir ) ) - if not os.path.exists( full_path_to_dir ): - os.makedirs( full_path_to_dir ) - # The package has been down-loaded, so we can now perform all of the actions defined for building it. + # We're in stage 2 of the installation process. The package has been down-loaded, so we can + # now perform all of the actions defined for building it. for action_tup in filtered_actions: current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) with lcd( current_dir ): action_type, action_dict = action_tup - if action_type == 'make_directory': - if os.path.isabs( action_dict[ 'full_path' ] ): - full_path = action_dict[ 'full_path' ] - else: - full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) - td_common_util.make_directory( full_path=full_path ) - elif action_type == 'move_directory_files': - td_common_util.move_directory_files( current_dir=current_dir, - source_dir=os.path.join( action_dict[ 'source_directory' ] ), - destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) - elif action_type == 'move_file': - td_common_util.move_file( current_dir=current_dir, - source=os.path.join( action_dict[ 'source' ] ), - destination=os.path.join( action_dict[ 'destination' ] ), - rename_to=action_dict[ 'rename_to' ] ) - elif action_type == 'set_environment': - # Currently the only action supported in this category is "environment_variable". - # Build a command line from the prior_installation_required, in case an environment variable is referenced - # in the set_environment action. - cmds = install_environment.environment_commands( 'set_environment' ) - env_var_dicts = action_dict[ 'environment_variable' ] - env_file_builder = EnvFileBuilder( install_dir ) - for env_var_dict in env_var_dicts: - # Check for the presence of the $ENV[] key string and populate it if possible. - env_var_dict = handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, cmds ) - env_file_builder.append_line( **env_var_dict ) - return_code = env_file_builder.return_code - if return_code: - return tool_dependency - elif action_type == 'set_environment_for_install': - # Currently the only action supported in this category is a list of paths to one or more tool dependency env.sh files, - # the environment setting in each of which will be injected into the environment for all <action type="shell_command"> - # tags that follow this <action type="set_environment_for_install"> tag set in the tool_dependencies.xml file. - install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) - elif action_type == 'setup_virtualenv': - # TODO: maybe should be configurable - venv_src_directory = os.path.abspath( os.path.join( app.config.tool_dependency_dir, '__virtualenv_src' ) ) - if not install_virtualenv( app, venv_src_directory ): - log.error( 'Unable to install virtualenv' ) - return tool_dependency - requirements = action_dict[ 'requirements' ] - if os.path.exists( os.path.join( dir, requirements ) ): - # requirements specified as path to a file - requirements_path = requirements - else: - # requirements specified directly in XML, create a file with these for pip. - requirements_path = os.path.join( install_dir, "requirements.txt" ) - with open( requirements_path, "w" ) as f: - f.write( requirements ) - venv_directory = os.path.join( install_dir, "venv" ) - # TODO: Consider making --no-site-packages optional. - setup_command = "python %s/virtualenv.py --no-site-packages '%s'" % (venv_src_directory, venv_directory) - # POSIXLY_CORRECT forces shell commands . and source to have the same - # and well defined behavior in bash/zsh. - activate_command = "POSIXLY_CORRECT=1; . %s" % os.path.join( venv_directory, "bin", "activate" ) - install_command = "python '%s' install -r '%s'" % ( os.path.join( venv_directory, "bin", "pip" ), requirements_path ) - full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command ) - return_code = handle_command( app, tool_dependency, install_dir, full_setup_command ) - if return_code: - return tool_dependency - # Use raw strings so that python won't automatically unescape the quotes before passing the command - # to subprocess.Popen. - site_packages_command = r"""%s -c 'import os, sys; print os.path.join(sys.prefix, "lib", "python" + sys.version[:3], "site-packages")'""" % os.path.join( venv_directory, "bin", "python" ) - output = handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) - if output.return_code: - return tool_dependency - if not os.path.exists( output.stdout ): - log.debug( "virtualenv's site-packages directory '%s' does not exist", output.stdout ) - return tool_dependency - env_file_builder = EnvFileBuilder( install_dir ) - env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=output.stdout ) - env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) ) - return_code = env_file_builder.return_code - if return_code: - return tool_dependency - elif action_type == 'shell_command': - with settings( warn_only=True ): - cmd = install_environment.build_command( action_dict[ 'command' ] ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - elif action_type == 'template_command': - env_vars = dict() - env_vars = install_environment.environment_dict() - env_vars.update( td_common_util.get_env_var_values( install_dir ) ) - language = action_dict[ 'language' ] - with settings( warn_only=True, **env_vars ): - if language == 'cheetah': - # We need to import fabric.api.env so that we can access all collected environment variables. - cmd = fill_template( '#from fabric.api import env\n%s' % action_dict[ 'command' ], context=env_vars ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - elif action_type == 'make_install': - # make; make install; allow providing make options - with settings( warn_only=True ): - make_opts = action_dict.get( 'make_opts', '' ) - cmd = install_environment.build_command( 'make %s && make install' % make_opts ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - elif action_type == 'autoconf': - # Handle configure, make and make install allow providing configuration options - with settings( warn_only=True ): - configure_opts = action_dict.get( 'configure_opts', '' ) - if 'prefix=' in configure_opts: - pre_cmd = './configure %s && make && make install' % configure_opts - else: - pre_cmd = './configure --prefix=$INSTALL_DIR %s && make && make install' % configure_opts - cmd = install_environment.build_command( td_common_util.evaluate_template( pre_cmd, install_dir ) ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) - if return_code: - return tool_dependency - elif action_type == 'download_file': - # Download a single file to the current working directory. - url = action_dict[ 'url' ] - if 'target_filename' in action_dict: - filename = action_dict[ 'target_filename' ] - else: - filename = url.split( '/' )[ -1 ] - extract = action_dict.get( 'extract', False ) - td_common_util.url_download( current_dir, filename, url, extract=extract ) - elif action_type == 'change_directory': - target_directory = os.path.realpath( os.path.normpath( os.path.join( current_dir, action_dict[ 'directory' ] ) ) ) - if target_directory.startswith( os.path.realpath( current_dir ) ) and os.path.exists( target_directory ): - # Change directory to a directory within the current working directory. - dir = target_directory - elif target_directory.startswith( os.path.realpath( work_dir ) ) and os.path.exists( target_directory ): - # Change directory to a directory above the current working directory, but within the defined work_dir. - dir = target_directory.replace( os.path.realpath( work_dir ), '' ).lstrip( '/' ) - else: - log.error( 'Invalid or nonexistent directory %s specified, ignoring change_directory action.', target_directory ) - elif action_type == 'chmod': - for target_file, mode in action_dict[ 'change_modes' ]: - if os.path.exists( target_file ): - os.chmod( target_file, mode ) - else: - log.error( 'Invalid file %s specified, ignoring %s action.', target_file, action_type ) - elif action_type == 'download_binary': - url = action_dict[ 'url' ] - target_directory = action_dict.get( 'target_directory', None ) - try: - downloaded_filename = td_common_util.download_binary( url, work_dir ) - except Exception, e: - log.exception( str( e ) ) - # If the downloaded file exists, move it to $INSTALL_DIR. Put this outside the try/catch above so that - # any errors in the move step are correctly sent to the tool dependency error handler. - if downloaded_filename and os.path.exists( os.path.join( work_dir, downloaded_filename ) ): - if target_directory: - target_directory = os.path.realpath( os.path.normpath( os.path.join( install_dir, target_directory ) ) ) - # Make sure the target directory is not outside of $INSTALL_DIR. - if target_directory.startswith( os.path.realpath( install_dir ) ): - full_path_to_dir = os.path.abspath( os.path.join( install_dir, target_directory ) ) - else: - full_path_to_dir = os.path.abspath( install_dir ) - else: - full_path_to_dir = os.path.abspath( install_dir ) - td_common_util.move_file( current_dir=work_dir, - source=downloaded_filename, - destination=full_path_to_dir ) + tool_dependency, tmp_filtered_actions, tmp_dir = \ + recipe_manager.execute_step( app=app, + tool_dependency=tool_dependency, + package_name=package_name, + actions=actions, + action_type=action_type, + action_dict=action_dict, + filtered_actions=filtered_actions, + env_file_builder=env_file_builder, + install_environment=install_environment, + work_dir=work_dir, + install_dir=install_dir, + current_dir=current_dir, + initial_download=False ) + if tool_dependency.status in [ app.model.ToolDependency.installation_status.ERROR ]: + # If the tool_dependency status is in an error state, return it with no additional + # processing. + return tool_dependency + # Make sure to handle the special case where the value of dir is reset (this happens when + # the action_type is change_directiory). In all other action types, dir will be returned as + # None. + if tmp_dir is not None: + dir = tmp_dir return tool_dependency - -def log_results( command, fabric_AttributeString, file_path ): - """Write attributes of fabric.operations._AttributeString to a specified log file.""" - if os.path.exists( file_path ): - logfile = open( file_path, 'ab' ) - else: - logfile = open( file_path, 'wb' ) - logfile.write( "\n#############################################\n" ) - logfile.write( '%s\nSTDOUT\n' % command ) - logfile.write( str( fabric_AttributeString.stdout ) ) - logfile.write( "\n#############################################\n" ) - logfile.write( "\n#############################################\n" ) - logfile.write( '%s\nSTDERR\n' % command ) - logfile.write( str( fabric_AttributeString.stderr ) ) - logfile.write( "\n#############################################\n" ) - logfile.close() - -@contextmanager -def make_tmp_dir(): - work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-mtd" ) - yield work_dir - if os.path.exists( work_dir ): - try: - shutil.rmtree( work_dir ) - except Exception, e: - log.exception( str( e ) ) - -def set_galaxy_environment( galaxy_user, tool_dependency_dir, host='localhost', shell='/bin/bash -l -c' ): - """General Galaxy environment configuration. This method is not currently used.""" - env.user = galaxy_user - env.install_dir = tool_dependency_dir - env.host_string = host - env.shell = shell - env.use_sudo = False - return env diff -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 -r de54998e192b99bd70751d692969b508463e1805 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 @@ -5,9 +5,10 @@ import subprocess import sys import tempfile -from string import Template import fabric_util import td_common_util +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import EnvFileBuilder +from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import RecipeManager import tool_shed.util.shed_util_common as suc from tool_shed.util import common_util from tool_shed.util import encoding_util @@ -94,7 +95,7 @@ package_name, package_version, required_repository ) - env_file_builder = fabric_util.EnvFileBuilder( tool_dependency.installation_directory( app ) ) + env_file_builder = EnvFileBuilder( tool_dependency.installation_directory( app ) ) env_file_builder.append_line( action="source", value=required_tool_dependency_env_file_path ) return_code = env_file_builder.return_code if return_code: @@ -497,19 +498,24 @@ elif package_elem.tag == 'readme': # Nothing to be done. continue - #elif package_elem.tag == 'proprietary_fabfile': + #elif package_elem.tag == 'custom_fabfile': # # TODO: This is not yet supported or functionally correct... - # # Handle tool dependency installation where the repository includes one or more proprietary fabric scripts. + # # Handle tool dependency installation where the repository includes one or more custom fabric scripts. # if not fabric_version_checked: # check_fabric_version() # fabric_version_checked = True # fabfile_name = package_elem.get( 'name', None ) - # proprietary_fabfile_path = os.path.abspath( os.path.join( os.path.split( tool_dependencies_config )[ 0 ], fabfile_name ) ) - # print 'Installing tool dependencies via fabric script ', proprietary_fabfile_path + # custom_fabfile_path = os.path.abspath( os.path.join( os.path.split( tool_dependencies_config )[ 0 ], fabfile_name ) ) + # print 'Installing tool dependencies via fabric script ', custom_fabfile_path return tool_dependency -def install_via_fabric( app, tool_dependency, install_dir, package_name=None, proprietary_fabfile_path=None, actions_elem=None, action_elem=None, **kwd ): - """Parse a tool_dependency.xml file's <actions> tag set to gather information for the installation via fabric.""" +def install_via_fabric( app, tool_dependency, install_dir, package_name=None, custom_fabfile_path=None, + actions_elem=None, action_elem=None, **kwd ): + """ + Parse a tool_dependency.xml file's <actions> tag set to gather information for installation using the + fabric_util.install_and_build_package() method. The use of fabric is being eliminated, so some of these + functions may need to be renamed at some point. + """ sa_session = app.install_model.context if not os.path.exists( install_dir ): os.makedirs( install_dir ) @@ -517,278 +523,30 @@ if package_name: actions_dict[ 'package_name' ] = package_name actions = [] - all_env_shell_file_paths = [] - env_var_dicts = [] + is_binary_download = False if actions_elem is not None: elems = actions_elem if elems.get( 'os' ) is not None and elems.get( 'architecture' ) is not None: is_binary_download = True - else: - is_binary_download = False elif action_elem is not None: # We were provided with a single <action> element to perform certain actions after a platform-specific tarball was downloaded. elems = [ action_elem ] else: elems = [] + recipe_manager = RecipeManager() for action_elem in elems: # Make sure to skip all comments, since they are now included in the XML tree. if action_elem.tag != 'action': continue action_dict = {} action_type = action_elem.get( 'type', 'shell_command' ) - if action_type == 'download_binary': - platform_info_dict = tool_dependency_util.get_platform_info_dict() - platform_info_dict[ 'name' ] = tool_dependency.name - platform_info_dict[ 'version' ] = tool_dependency.version - url_template_elems = action_elem.findall( 'url_template' ) - # Check if there are multiple url_template elements, each with attrib entries for a specific platform. - if len( url_template_elems ) > 1: - # <base_url os="darwin" extract="false">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/faToTwoBit</base_url> - # This method returns the url_elem that best matches the current platform as received from os.uname(). - # Currently checked attributes are os and architecture. - # These correspond to the values sysname and processor from the Python documentation for os.uname(). - url_template_elem = tool_dependency_util.get_download_url_for_platform( url_template_elems, platform_info_dict ) - else: - url_template_elem = url_template_elems[ 0 ] - action_dict[ 'url' ] = Template( url_template_elem.text ).safe_substitute( platform_info_dict ) - action_dict[ 'target_directory' ] = action_elem.get( 'target_directory', None ) - elif action_type == 'shell_command': - # <action type="shell_command">make</action> - action_elem_text = td_common_util.evaluate_template( action_elem.text, install_dir ) - if action_elem_text: - action_dict[ 'command' ] = action_elem_text - else: - continue - elif action_type == 'template_command': - # Default to Cheetah as it's the first template language supported. - language = action_elem.get( 'language', 'cheetah' ).lower() - if language == 'cheetah': - # Cheetah template syntax. - # <action type="template_command" language="cheetah"> - # #if env.PATH: - # make - # #end if - # </action> - action_elem_text = action_elem.text.strip() - if action_elem_text: - action_dict[ 'language' ] = language - action_dict[ 'command' ] = action_elem_text - else: - continue - else: - log.debug( "Unsupported template language '%s'. Not proceeding." % str( language ) ) - raise Exception( "Unsupported template language '%s' in tool dependency definition." % str( language ) ) - elif action_type == 'download_by_url': - # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> - if is_binary_download: - action_dict[ 'is_binary' ] = True - if action_elem.text: - action_dict[ 'url' ] = action_elem.text - target_filename = action_elem.get( 'target_filename', None ) - if target_filename: - action_dict[ 'target_filename' ] = target_filename - else: - continue - elif action_type == 'download_file': - # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> - if action_elem.text: - action_dict[ 'url' ] = action_elem.text - target_filename = action_elem.get( 'target_filename', None ) - if target_filename: - action_dict[ 'target_filename' ] = target_filename - action_dict[ 'extract' ] = asbool( action_elem.get( 'extract', False ) ) - else: - continue - elif action_type == 'make_directory': - # <action type="make_directory">$INSTALL_DIR/lib/python</action> - if action_elem.text: - action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir ) - else: - continue - elif action_type == 'change_directory': - # <action type="change_directory">PHYLIP-3.6b</action> - if action_elem.text: - action_dict[ 'directory' ] = action_elem.text - else: - continue - elif action_type == 'move_directory_files': - # <action type="move_directory_files"> - # <source_directory>bin</source_directory> - # <destination_directory>$INSTALL_DIR/bin</destination_directory> - # </action> - for move_elem in action_elem: - move_elem_text = td_common_util.evaluate_template( move_elem.text, install_dir ) - if move_elem_text: - action_dict[ move_elem.tag ] = move_elem_text - elif action_type == 'move_file': - # <action type="move_file" rename_to="new_file_name"> - # <source>misc/some_file</source> - # <destination>$INSTALL_DIR/bin</destination> - # </action> - action_dict[ 'source' ] = td_common_util.evaluate_template( action_elem.find( 'source' ).text, install_dir ) - action_dict[ 'destination' ] = td_common_util.evaluate_template( action_elem.find( 'destination' ).text, install_dir ) - action_dict[ 'rename_to' ] = action_elem.get( 'rename_to' ) - elif action_type == 'set_environment': - # <action type="set_environment"> - # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> - # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - # </action> - for env_elem in action_elem: - if env_elem.tag == 'environment_variable': - env_var_dict = td_common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir ) - if env_var_dict: - env_var_dicts.append( env_var_dict ) - if env_var_dicts: - # The last child of an <action type="set_environment"> might be a comment, so manually set it to be 'environment_variable'. - action_dict[ 'environment_variable' ] = env_var_dicts - else: - continue - elif action_type == 'set_environment_for_install': - # <action type="set_environment_for_install"> - # <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056"> - # <package name="numpy" version="1.7.1" /> - # </repository> - # </action> - # This action type allows for defining an environment that will properly compile a tool dependency. Currently, tag set definitions like - # that above are supported, but in the future other approaches to setting environment variables or other environment attributes can be - # supported. The above tag set will result in the installed and compiled numpy version 1.7.1 binary to be used when compiling the current - # tool dependency package. See the package_matplotlib_1_2 repository in the test tool shed for a real-world example. - for env_elem in action_elem: - if env_elem.tag == 'repository': - env_shell_file_paths = td_common_util.get_env_shell_file_paths( app, env_elem ) - if env_shell_file_paths: - all_env_shell_file_paths.extend( env_shell_file_paths ) - if all_env_shell_file_paths: - action_dict[ 'env_shell_file_paths' ] = all_env_shell_file_paths - else: - continue - elif action_type == 'setup_virtualenv': - # <action type="setup_virtualenv" /> - ## Install requirements from file requirements.txt of downloaded bundle - or - - # <action type="setup_virtualenv">tools/requirements.txt</action> - ## Install requirements from specified file from downloaded bundle -or - - # <action type="setup_virtualenv">pyyaml==3.2.0 - # lxml==2.3.0</action> - ## Manually specify contents of requirements.txt file to create dynamically. - action_dict[ 'requirements' ] = td_common_util.evaluate_template( action_elem.text or 'requirements.txt', install_dir ) - elif action_type == 'autoconf': - # Handle configure, make and make install allow providing configuration options - if action_elem.text: - configure_opts = td_common_util.evaluate_template( action_elem.text, install_dir ) - action_dict[ 'configure_opts' ] = configure_opts - elif action_type == 'setup_r_environment': - # setup an R environment. - # <action type="setup_r_environment"> - # <repository name="package_r_3_0_1" owner="bgruening"> - # <package name="R" version="3.0.1" /> - # </repository> - #  - # <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</package> - # </action> - # Discover all child repository dependency tags and define the path to an env.sh file associated with each repository. - # This will potentially update the value of the 'env_shell_file_paths' entry in action_dict. - action_dict = td_common_util.get_env_shell_file_paths_from_setup_environment_elem( app, all_env_shell_file_paths, action_elem, action_dict ) - r_packages = list() - for env_elem in action_elem: - if env_elem.tag == 'package': - r_packages.append( env_elem.text.strip() ) - if r_packages: - action_dict[ 'r_packages' ] = r_packages - else: - continue - elif action_type == 'setup_ruby_environment': - # setup a Ruby environment. - # <action type="setup_ruby_environment"> - # <repository name="package_ruby_2_0" owner="bgruening"> - # <package name="ruby" version="2.0" /> - # </repository> - #  - # <package>protk</package> - # <package>protk=1.2.4</package> - # <package>http://url-to-some-gem-file.de/protk.gem</package> - # </action> - # Discover all child repository dependency tags and define the path to an env.sh file associated with each repository. - # This will potentially update the value of the 'env_shell_file_paths' entry in action_dict. - action_dict = td_common_util.get_env_shell_file_paths_from_setup_environment_elem( app, all_env_shell_file_paths, action_elem, action_dict ) - ruby_package_tups = [] - for env_elem in action_elem: - if env_elem.tag == 'package': - #A valid gem definition can be: - # protk=1.2.4 - # protk - # ftp://ftp.gruening.de/protk.gem - gem_token = env_elem.text.strip().split( '=' ) - if len( gem_token ) == 2: - # version string - gem_name = gem_token[ 0 ] - gem_version = gem_token[ 1 ] - ruby_package_tups.append( ( gem_name, gem_version ) ) - else: - # gem name for rubygems.org without version number - gem = env_elem.text.strip() - ruby_package_tups.append( ( gem, None ) ) - if ruby_package_tups: - action_dict[ 'ruby_package_tups' ] = ruby_package_tups - else: - continue - elif action_type == 'setup_perl_environment': - # setup a Perl environment. - # <action type="setup_perl_environment"> - # <repository name="package_perl_5_18" owner="bgruening"> - # <package name="perl" version="5.18.1" /> - # </repository> - #  - # <package>XML::Parser</package> - # <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package> - # </action> - # Discover all child repository dependency tags and define the path to an env.sh file associated with each repository. - # This will potentially update the value of the 'env_shell_file_paths' entry in action_dict. - action_dict = td_common_util.get_env_shell_file_paths_from_setup_environment_elem( app, all_env_shell_file_paths, action_elem, action_dict ) - perl_packages = [] - for env_elem in action_elem: - if env_elem.tag == 'package': - # A valid package definition can be: - # XML::Parser - # http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz - # Unfortunately CPAN does not support versioning, so if you want real reproducibility you need to specify - # the tarball path and the right order of different tarballs manually. - perl_packages.append( env_elem.text.strip() ) - if perl_packages: - action_dict[ 'perl_packages' ] = perl_packages - else: - continue - elif action_type == 'make_install': - # make; make install; allow providing make options - if action_elem.text: - make_opts = td_common_util.evaluate_template( action_elem.text, install_dir ) - action_dict[ 'make_opts' ] = make_opts - elif action_type == 'chmod': - # Change the read, write, and execute bits on a file. - # <action type="chmod"> - # <file mode="750">$INSTALL_DIR/bin/faToTwoBit</file> - # </action> - file_elems = action_elem.findall( 'file' ) - chmod_actions = [] - # A unix octal mode is the sum of the following values: - # Owner: - # 400 Read 200 Write 100 Execute - # Group: - # 040 Read 020 Write 010 Execute - # World: - # 004 Read 002 Write 001 Execute - for file_elem in file_elems: - # So by the above table, owner read/write/execute and group read permission would be 740. - # Python's os.chmod uses base 10 modes, convert received unix-style octal modes to base 10. - received_mode = int( file_elem.get( 'mode', 600 ), base=8 ) - # For added security, ensure that the setuid and setgid bits are not set. - mode = received_mode & ~( stat.S_ISUID | stat.S_ISGID ) - file = td_common_util.evaluate_template( file_elem.text, install_dir ) - chmod_tuple = ( file, mode ) - chmod_actions.append( chmod_tuple ) - action_dict[ 'change_modes' ] = chmod_actions - else: - log.debug( "Unsupported action type '%s'. Not proceeding." % str( action_type ) ) - raise Exception( "Unsupported action type '%s' in tool dependency definition." % str( action_type ) ) + action_dict = recipe_manager.prepare_step( app=app, + tool_dependency=tool_dependency, + action_type=action_type, + action_elem=action_elem, + action_dict=action_dict, + install_dir=install_dir, + is_binary_download=is_binary_download ) action_tuple = ( action_type, action_dict ) if action_type == 'set_environment': if action_tuple not in actions: @@ -797,15 +555,15 @@ actions.append( action_tuple ) if actions: actions_dict[ 'actions' ] = actions - if proprietary_fabfile_path: + if custom_fabfile_path is not None: # TODO: this is not yet supported or functional, but when it is handle it using the fabric api. - # run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=package_name ) + # execute_custom_fabric_script( app, elem, custom_fabfile_path, install_dir, package_name=package_name ) raise Exception( 'Tool dependency installation using proprietary fabric scripts is not yet supported.' ) else: tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) return tool_dependency -def run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=None, **kwd ): +def execute_custom_fabric_script( app, elem, custom_fabfile_path, install_dir, package_name=None, **kwd ): """ TODO: Handle this using the fabric api. Parse a tool_dependency.xml file's fabfile <method> tag set to build the method parameters and execute the method. @@ -834,10 +592,10 @@ else: params_str = params_str.rstrip( ',' ) try: - cmd = 'fab -f %s %s:%s' % ( proprietary_fabfile_path, method_name, params_str ) + cmd = 'fab -f %s %s:%s' % ( custom_fabfile_path, method_name, params_str ) returncode, message = run_subprocess( app, cmd ) except Exception, e: - return "Exception executing fabric script %s: %s. " % ( str( proprietary_fabfile_path ), str( e ) ) + return "Exception executing fabric script %s: %s. " % ( str( custom_fabfile_path ), str( e ) ) if returncode: return message handle_environment_settings( app, tool_dependency, install_dir, cmd ) @@ -913,7 +671,7 @@ set_status=True ) if env_var_version == '1.0': # Create this tool dependency's env.sh file. - env_file_builder = fabric_util.EnvFileBuilder( install_dir ) + 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' % \ diff -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 -r de54998e192b99bd70751d692969b508463e1805 lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py @@ -0,0 +1,449 @@ +import logging +import os +import Queue +import shutil +import stat +import subprocess +import tempfile +import threading +import time + +from contextlib import contextmanager + +# TODO: eliminate the use of fabric here. +from galaxy import eggs +eggs.require( 'Fabric' ) + +from fabric.operations import _AttributeString +from fabric import state +from fabric.api import prefix + +from galaxy.util import DATABASE_MAX_STRING_SIZE +from galaxy.util import DATABASE_MAX_STRING_SIZE_PRETTY +from galaxy.util import shrink_string_by_size +from galaxy.util import unicodify + +from tool_shed.galaxy_install.tool_dependencies import td_common_util +from tool_shed.galaxy_install.tool_dependencies.recipe import step_handler + +log = logging.getLogger( __name__ ) + + +class AsynchronousReader( threading.Thread ): + """ + A helper class to implement asynchronous reading of a stream in a separate thread. Read lines are pushed + onto a queue to be consumed in another thread. + """ + + def __init__( self, fd, queue ): + threading.Thread.__init__( self ) + self._fd = fd + self._queue = queue + self.lines = [] + + def run( self ): + """Read lines and put them on the queue.""" + thread_lock = threading.Lock() + thread_lock.acquire() + for line in iter( self._fd.readline, '' ): + stripped_line = line.rstrip() + self.lines.append( stripped_line ) + self._queue.put( stripped_line ) + thread_lock.release() + + def installation_complete( self ): + """Make sure there is more installation and compilation logging content expected.""" + return not self.is_alive() and self._queue.empty() + + +class EnvFileBuilder( object ): + + def __init__( self, install_dir ): + self.install_dir = install_dir + self.return_code = 0 + + def append_line( self, make_executable=True, **kwd ): + env_var_dict = dict( **kwd ) + env_entry, env_file = self.create_or_update_env_shell_file( self.install_dir, env_var_dict ) + return_code = self.file_append( env_entry, env_file, make_executable=make_executable ) + self.return_code = self.return_code or return_code + return self.return_code + + @staticmethod + def create_or_update_env_shell_file( install_dir, env_var_dict ): + env_var_action = env_var_dict[ 'action' ] + env_var_value = env_var_dict[ 'value' ] + if env_var_action in [ 'prepend_to', 'set_to', 'append_to' ]: + env_var_name = env_var_dict[ 'name' ] + if env_var_action == 'prepend_to': + changed_value = '%s:$%s' % ( env_var_value, env_var_name ) + elif env_var_action == 'set_to': + changed_value = '%s' % env_var_value + elif env_var_action == 'append_to': + changed_value = '$%s:%s' % ( env_var_name, env_var_value ) + line = "%s=%s; export %s" % ( env_var_name, changed_value, env_var_name ) + elif env_var_action == "source": + line = "if [ -f %s ] ; then . %s ; fi" % ( env_var_value, env_var_value ) + else: + raise Exception( "Unknown shell file action %s" % env_var_action ) + env_shell_file_path = os.path.join( install_dir, 'env.sh' ) + return line, env_shell_file_path + + def file_append( self, text, file_path, make_executable=True ): + """ + Append a line to a file unless the line already exists in the file. This method creates the file if + it doesn't exist. If make_executable is True, the permissions on the file are set to executable by + the owner. + """ + file_dir = os.path.dirname( file_path ) + if not os.path.exists( file_dir ): + try: + os.makedirs( file_dir ) + except Exception, e: + log.exception( str( e ) ) + return 1 + if os.path.exists( file_path ): + try: + new_env_file_contents = [] + env_file_contents = file( file_path, 'r' ).readlines() + # Clean out blank lines from the env.sh file. + for line in env_file_contents: + line = line.rstrip() + if line: + new_env_file_contents.append( line ) + env_file_contents = new_env_file_contents + except Exception, e: + log.exception( str( e ) ) + return 1 + else: + env_file_handle = open( file_path, 'w' ) + env_file_handle.close() + env_file_contents = [] + if make_executable: + # Explicitly set the file's executable bits. + try: + os.chmod( file_path, int( '111', base=8 ) | os.stat( file_path )[ stat.ST_MODE ] ) + except Exception, e: + log.exception( str( e ) ) + return 1 + # Convert the received text to a list, in order to support adding one or more lines to the file. + if isinstance( text, basestring ): + text = [ text ] + for line in text: + line = line.rstrip() + if line and line not in env_file_contents: + env_file_contents.append( line ) + try: + file( file_path, 'w' ).write( '\n'.join( env_file_contents ) ) + except Exception, e: + log.exception( str( e ) ) + return 1 + return 0 + + def handle_action_shell_file_paths( self, action_dict ): + shell_file_paths = action_dict.get( 'action_shell_file_paths', [] ) + for shell_file_path in shell_file_paths: + self.append_line( action="source", value=shell_file_path ) + + +class InstallEnvironment( object ): + """Object describing the environment built up as part of the process of building and installing a package.""" + + + def __init__( self ): + self.env_shell_file_paths = [] + + def __call__( self, install_dir ): + with settings( warn_only=True, **td_common_util.get_env_var_values( install_dir ) ): + with prefix( self.__setup_environment() ): + yield + + def add_env_shell_file_paths( self, paths ): + for path in paths: + self.env_shell_file_paths.append( str( path ) ) + + def build_command( self, command, action_type='shell_command' ): + """ + Build command line for execution from simple command, but + configuring environment described by this object. + """ + env_cmds = self.environment_commands( action_type ) + return '\n'.join( env_cmds + [ command ] ) + + def close_file_descriptor( self, fd ): + """Attempt to close a file descriptor.""" + start_timer = time.time() + error = '' + while True: + try: + fd.close() + break + except IOError, e: + # Undoubtedly close() was called during a concurrent operation on the same file object. + log.debug( 'Error closing file descriptor: %s' % str( e ) ) + time.sleep( .5 ) + current_wait_time = time.time() - start_timer + if current_wait_time >= 600: + error = 'Error closing file descriptor: %s' % str( e ) + break + return error + + def enqueue_output( self, stdout, stdout_queue, stderr, stderr_queue ): + """ + This method places streamed stdout and stderr into a threaded IPC queue target. Received data + is printed and saved to that thread's queue. The calling thread can then retrieve the data using + thread.stdout and thread.stderr. + """ + stdout_logger = logging.getLogger( 'fabric_util.STDOUT' ) + stderr_logger = logging.getLogger( 'fabric_util.STDERR' ) + for line in iter( stdout.readline, '' ): + output = line.rstrip() + stdout_logger.debug( output ) + stdout_queue.put( output ) + stdout_queue.put( None ) + for line in iter( stderr.readline, '' ): + output = line.rstrip() + stderr_logger.debug( output ) + stderr_queue.put( output ) + stderr_queue.put( None ) + + def environment_commands( self, action_type ): + """Build a list of commands used to construct the environment described by this object.""" + cmds = [] + for env_shell_file_path in self.env_shell_file_paths: + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + cmds.append( env_setting.strip( '\n' ) ) + else: + log.debug( 'Invalid file %s specified, ignoring %s action.' % ( str( env_shell_file_path ), str( action_type ) ) ) + return cmds + + def environment_dict( self, action_type='template_command' ): + env_vars = dict() + for env_shell_file_path in self.env_shell_file_paths: + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + env_string = env_setting.split( ';' )[ 0 ] + env_name, env_path = env_string.split( '=' ) + env_vars[ env_name ] = env_path + else: + log.debug( 'Invalid file %s specified, ignoring template_command action.' % str( env_shell_file_path ) ) + return env_vars + + def handle_command( self, app, tool_dependency, install_dir, cmd, return_output=False ): + """Handle a command and log the results.""" + context = app.install_model.context + command = str( cmd ) + output = self.handle_complex_command( command ) + self.log_results( cmd, output, os.path.join( install_dir, td_common_util.INSTALLATION_LOG ) ) + stdout = output.stdout + stderr = output.stderr + if len( stdout ) > DATABASE_MAX_STRING_SIZE: + print "Length of stdout > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) + stdout = shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + if len( stderr ) > DATABASE_MAX_STRING_SIZE: + print "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) + stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + if output.return_code not in [ 0 ]: + tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR + if stderr: + tool_dependency.error_message = unicodify( stderr ) + elif stdout: + tool_dependency.error_message = unicodify( stdout ) + else: + # We have a problem if there was no stdout and no stderr. + tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \ + ( str( cmd ), str( output.return_code ) ) + context.add( tool_dependency ) + context.flush() + if return_output: + return output + return output.return_code + + def handle_complex_command( self, command ): + """ + Wrap subprocess.Popen in such a way that the stderr and stdout from running a shell command will + be captured and logged in nearly real time. This is similar to fabric.local, but allows us to + retain control over the process. This method is named "complex" because it uses queues and + threads to execute a command while capturing and displaying the output. + """ + # Launch the command as subprocess. A bufsize of 1 means line buffered. + process_handle = subprocess.Popen( str( command ), + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + bufsize=1, + close_fds=False, + shell=True, + cwd=state.env[ 'lcwd' ] ) + pid = process_handle.pid + # Launch the asynchronous readers of the process' stdout and stderr. + stdout_queue = Queue.Queue() + stdout_reader = AsynchronousReader( process_handle.stdout, stdout_queue ) + stdout_reader.start() + stderr_queue = Queue.Queue() + stderr_reader = AsynchronousReader( process_handle.stderr, stderr_queue ) + stderr_reader.start() + # Place streamed stdout and stderr into a threaded IPC queue target so it can + # be printed and stored for later retrieval when generating the INSTALLATION.log. + stdio_thread = threading.Thread( target=self.enqueue_output, + args=( process_handle.stdout, + stdout_queue, + process_handle.stderr, + stderr_queue ) ) + thread_lock = threading.Lock() + thread_lock.acquire() + stdio_thread.start() + # Check the queues for output until there is nothing more to get. + start_timer = time.time() + while not stdout_reader.installation_complete() or not stderr_reader.installation_complete(): + # Show what we received from standard output. + while not stdout_queue.empty(): + try: + line = stdout_queue.get() + except Queue.Empty: + line = None + break + if line: + print line + start_timer = time.time() + else: + break + # Show what we received from standard error. + while not stderr_queue.empty(): + try: + line = stderr_queue.get() + except Queue.Empty: + line = None + break + if line: + print line + start_timer = time.time() + else: + stderr_queue.task_done() + break + # Sleep a bit before asking the readers again. + time.sleep( .1 ) + current_wait_time = time.time() - start_timer + if stdout_queue.empty() and stderr_queue.empty() and current_wait_time > td_common_util.NO_OUTPUT_TIMEOUT: + err_msg = "\nShutting down process id %s because it generated no output for the defined timeout period of %.1f seconds.\n" % \ + ( pid, td_common_util.NO_OUTPUT_TIMEOUT ) + stderr_reader.lines.append( err_msg ) + process_handle.kill() + break + thread_lock.release() + # Wait until each of the threads we've started terminate. The following calls will block each thread + # until it terminates either normally, through an unhandled exception, or until the timeout occurs. + stdio_thread.join( td_common_util.NO_OUTPUT_TIMEOUT ) + stdout_reader.join( td_common_util.NO_OUTPUT_TIMEOUT ) + stderr_reader.join( td_common_util.NO_OUTPUT_TIMEOUT ) + # Close subprocess' file descriptors. + error = self.close_file_descriptor( process_handle.stdout ) + error = self.close_file_descriptor( process_handle.stderr ) + stdout = '\n'.join( stdout_reader.lines ) + stderr = '\n'.join( stderr_reader.lines ) + # Handle error condition (deal with stdout being None, too) + output = _AttributeString( stdout.strip() if stdout else "" ) + errors = _AttributeString( stderr.strip() if stderr else "" ) + # Make sure the process has finished. + process_handle.poll() + output.return_code = process_handle.returncode + output.stderr = errors + return output + + def log_results( self, command, fabric_AttributeString, file_path ): + """Write attributes of fabric.operations._AttributeString to a specified log file.""" + if os.path.exists( file_path ): + logfile = open( file_path, 'ab' ) + else: + logfile = open( file_path, 'wb' ) + logfile.write( "\n#############################################\n" ) + logfile.write( '%s\nSTDOUT\n' % command ) + logfile.write( str( fabric_AttributeString.stdout ) ) + logfile.write( "\n#############################################\n" ) + logfile.write( "\n#############################################\n" ) + logfile.write( '%s\nSTDERR\n' % command ) + logfile.write( str( fabric_AttributeString.stderr ) ) + logfile.write( "\n#############################################\n" ) + logfile.close() + + @contextmanager + def make_tmp_dir( self ): + work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-mtd" ) + yield work_dir + if os.path.exists( work_dir ): + try: + shutil.rmtree( work_dir ) + except Exception, e: + log.exception( str( e ) ) + + def __setup_environment( self ): + return "&&".join( [ ". %s" % file for file in self.__valid_env_shell_file_paths() ] ) + + def __valid_env_shell_file_paths( self ): + return [ file for file in self.env_shell_file_paths if os.path.exists( file ) ] + + +class RecipeManager( object ): + + def __init__( self ): + self.step_handlers_by_type = self.load_step_handlers() + + def get_step_handler_by_type( self, type ): + return self.step_handlers_by_type.get( type, None ) + + def execute_step( self, app, tool_dependency, package_name, actions, action_type, action_dict, filtered_actions, + env_file_builder, install_environment, work_dir, install_dir, current_dir=None, initial_download=False ): + if actions: + step_handler = self.get_step_handler_by_type( action_type ) + tool_dependency, filtered_actions, dir = step_handler.execute_step( app=app, + tool_dependency=tool_dependency, + package_name=package_name, + actions=actions, + action_dict=action_dict, + filtered_actions=filtered_actions, + env_file_builder=env_file_builder, + install_environment=install_environment, + work_dir=work_dir, + install_dir=install_dir, + current_dir=current_dir, + initial_download=initial_download ) + else: + dir = None + return tool_dependency, filtered_actions, dir + + def load_step_handlers( self ): + step_handlers_by_type = dict( autoconf=step_handler.Autoconf(), + change_directory=step_handler.ChangeDirectory(), + chmod=step_handler.Chmod(), + download_binary=step_handler.DownloadBinary(), + download_by_url=step_handler.DownloadByUrl(), + download_file=step_handler.DownloadFile(), + make_directory=step_handler.MakeDirectory(), + make_install=step_handler.MakeInstall(), + move_directory_files=step_handler.MoveDirectoryFiles(), + move_file=step_handler.MoveFile(), + set_environment=step_handler.SetEnvironment(), + set_environment_for_install=step_handler.SetEnvironmentForInstall(), + setup_perl_environment=step_handler.SetupPerlEnvironment(), + setup_r_environment=step_handler.SetupREnvironment(), + setup_ruby_environment=step_handler.SetupRubyEnvironment(), + setup_virtual_env=step_handler.SetupVirtualEnv(), + shell_command=step_handler.ShellCommand(), + template_command=step_handler.TemplateCommand() ) + return step_handlers_by_type + + def prepare_step( self, app, tool_dependency, action_type, action_elem, action_dict, install_dir, is_binary_download ): + """ + Prepare the recipe step for later execution. This generally alters the received action_dict + with new information needed during this step's execution. + """ + if action_elem is not None: + step_handler = self.get_step_handler_by_type( action_type ) + action_dict = step_handler.prepare_step( app=app, + tool_dependency=tool_dependency, + action_elem=action_elem, + action_dict=action_dict, + install_dir=install_dir, + is_binary_download=is_binary_download ) + return action_dict + \ No newline at end of file This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Client app: extract method on client app init to javascript_app so it isn't called twice when using parent.javascripts()
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/369bb0f7ebef/ Changeset: 369bb0f7ebef User: carlfeberhard Date: 2014-04-24 16:34:24 Summary: Client app: extract method on client app init to javascript_app so it isn't called twice when using parent.javascripts() Affected #: 5 files diff -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -12,6 +12,7 @@ ${self.metas()} ${self.stylesheets()} ${self.javascripts()} + ${self.javascript_app()} </head><body class="inbound"> ${next.body()} @@ -83,8 +84,6 @@ }); </script> - ${ galaxy_client.load( app=self.js_app ) } - %if not form_input_auto_focus is UNDEFINED and form_input_auto_focus: <script type="text/javascript"> $(document).ready( function() { @@ -98,5 +97,9 @@ </%def> +<%def name="javascript_app()"> + ${ galaxy_client.load( app=self.js_app ) } +</%def> + ## Additional metas can be defined by templates inheriting from this one. <%def name="metas()"></%def> diff -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -1,6 +1,6 @@ <!DOCTYPE HTML> +<%namespace name="galaxy_client" file="/galaxy_client_app.mako" /> -<%namespace name="galaxy_client" file="/galaxy_client_app.mako" /><% self.has_left_panel = hasattr( self, 'left_panel' ) self.has_right_panel = hasattr( self, 'right_panel' ) @@ -20,7 +20,10 @@ ## Default stylesheets <%def name="stylesheets()"> - ${h.css('base','jquery.rating')} + ${h.css( + 'base', + 'jquery.rating' + )} <style type="text/css"> #center { %if not self.has_left_panel: @@ -67,9 +70,9 @@ root: '${h.url_for( "/" )}' }; - ## load additional style sheet - if (window != window.top) - $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head'); + //## load additional style sheet + //if (window != window.top) + // $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head'); // console protection window.console = window.console || { @@ -91,16 +94,24 @@ }); </script> +</%def> + +<%def name="javascript_app()"> ## load the Galaxy global js var ${ galaxy_client.load() } - </%def> ## Default late-load javascripts <%def name="late_javascripts()"> ## Scripts can be loaded later since they progressively add features to ## the panels, but do not change layout - ${h.js( 'libs/jquery/jquery.event.drag', 'libs/jquery/jquery.event.hover', 'libs/jquery/jquery.form', 'libs/jquery/jquery.rating', 'galaxy.panels' )} + ${h.js( + 'libs/jquery/jquery.event.drag', + 'libs/jquery/jquery.event.hover', + 'libs/jquery/jquery.form', + 'libs/jquery/jquery.rating', + 'galaxy.panels' + )} <script type="text/javascript"> ensure_dd_helper(); @@ -295,6 +306,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1"> ${self.stylesheets()} ${self.javascripts()} + ${self.javascript_app()} </head><% diff -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -1,4 +1,5 @@ <%inherit file="/base/base_panels.mako"/> +<%namespace name="mod_masthead" file="/webapps/galaxy/galaxy.masthead.mako"/> ## Default title @@ -17,4 +18,4 @@ <% mod_masthead.load(self.active_view); %> -</%def> \ No newline at end of file +</%def> diff -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -101,6 +101,11 @@ }); var galaxy_config = ${ h.to_json_string( self.galaxy_config ) }; + </script> +</%def> + +<%def name="javascript_app()"> + <script type="text/javascript"> // load any app configured define( 'app', function(){ var jscript = galaxy_config.app.jscript; @@ -116,6 +121,7 @@ } }); </script> + ## load the Galaxy global js var and run 'app' from above ${ galaxy_client.load( app='app' ) } @@ -125,7 +131,6 @@ ##${ galaxy_client.load( app=( app_config[ 'jscript' ] if 'jscript' in app_config else None )) } ##TODO: at that point, we can think about optimizing the various apps - </%def> ## default late-load javascripts @@ -165,6 +170,7 @@ ## load scripts ${self.javascripts()} + ${self.javascript_app()} </head><body scroll="no" class="full-content"> diff -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c -r 369bb0f7ebef50a72f36cf2f74d23f7d351d61c4 templates/webapps/galaxy/root/history.mako --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -8,13 +8,16 @@ ## ----------------------------------------------------------------------------- <%def name="javascripts()"> ${ parent.javascripts() } - <script type="text/javascript"> $(function(){ $( 'body' ).addClass( 'historyPage' ).addClass( 'history-panel' ) .css({ margin: '0px', padding: '0px' }); }); +</script> +</%def> +<%def name="javascript_app()"> +<script type="text/javascript"> define( 'app', function(){ require([ 'mvc/history/current-history-panel' @@ -34,8 +37,7 @@ }); }); }); -}) +}); </script> ${ galaxy_client.load( app='app', history=history, hdas=hdas, show_deleted=show_deleted, show_hidden=show_hidden ) } - </%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Update LWR client through LWR changeset bd8d1cc.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/641f7063ce3c/ Changeset: 641f7063ce3c User: jmchilton Date: 2014-04-24 07:31:57 Summary: Update LWR client through LWR changeset bd8d1cc. Needed for LWR runner to be able to use env tags from job conf file. Affected #: 4 files diff -r b172ca94e169ccf2450432398d67623f79c5588f -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -39,6 +39,7 @@ ) else: job_directory = None + self.env = destination_params.get( "env", [] ) self.files_endpoint = destination_params.get("files_endpoint", None) self.job_directory = job_directory @@ -81,7 +82,7 @@ super(JobClient, self).__init__(destination_params, job_id) self.job_manager_interface = job_manager_interface - def launch(self, command_line, requirements=[], remote_staging=[], job_config=None): + def launch(self, command_line, requirements=[], env=[], remote_staging=[], job_config=None): """ Queue up the execution of the supplied `command_line` on the remote server. Called launch for historical reasons, should be renamed to @@ -98,6 +99,8 @@ launch_params['params'] = dumps(submit_params_dict) if requirements: launch_params['requirements'] = dumps([requirement.to_dict() for requirement in requirements]) + if env: + launch_params['env'] = dumps(env) if remote_staging: launch_params['remote_staging'] = dumps(remote_staging) if job_config and self.setup_handler.local: @@ -291,7 +294,7 @@ raise Exception(error_message) self.client_manager = client_manager - def launch(self, command_line, requirements=[], remote_staging=[], job_config=None): + def launch(self, command_line, requirements=[], env=[], remote_staging=[], job_config=None): """ """ launch_params = dict(command_line=command_line, job_id=self.job_id) @@ -300,6 +303,8 @@ launch_params['params'] = submit_params_dict if requirements: launch_params['requirements'] = [requirement.to_dict() for requirement in requirements] + if env: + launch_params['env'] = env if remote_staging: launch_params['remote_staging'] = remote_staging if job_config and self.setup_handler.local: diff -r b172ca94e169ccf2450432398d67623f79c5588f -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c lib/galaxy/jobs/runners/lwr_client/staging/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/__init__.py @@ -32,6 +32,8 @@ Local path created by Galaxy for running this job. requirements : list List of requirements for tool execution. + env: list + List of dict object describing environment variables to populate. version_file : str Path to version file expected on the client server arbitrary_files : dict() @@ -54,6 +56,7 @@ client_outputs, working_directory, requirements, + env=[], arbitrary_files=None, rewrite_paths=True, ): @@ -64,6 +67,7 @@ self.client_outputs = client_outputs self.working_directory = working_directory self.requirements = requirements + self.env = env self.rewrite_paths = rewrite_paths self.arbitrary_files = arbitrary_files or {} @@ -156,5 +160,5 @@ return join(output_directory, self.path_helper.local_name(name)) files_directory = "%s_files%s" % (basename(output_file)[0:-len(".dat")], self.path_helper.separator) - names = filter(lambda o: o.startswith(files_directory), self.output_directory_contents) + names = filter(lambda o: o.startswith(files_directory), self.output_directory_contents) return dict(map(lambda name: (local_path(name), name), names)) diff -r b172ca94e169ccf2450432398d67623f79c5588f -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c lib/galaxy/jobs/runners/lwr_client/staging/down.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/down.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/down.py @@ -80,7 +80,10 @@ if self._attempt_collect_output('output_workdir', path=output_file, name=lwr_name): self.downloaded_working_directory_files.append(lwr_name) # Remove from full output_files list so don't try to download directly. - self.output_files.remove(output_file) + try: + self.output_files.remove(output_file) + except ValueError: + raise Exception("Failed to remove %s from %s" % (output_file, self.output_files)) def __collect_outputs(self): # Legacy LWR not returning list of files, iterate over the list of diff -r b172ca94e169ccf2450432398d67623f79c5588f -r 641f7063ce3c5dcf375aafdd9a65a2e3f7ccfa4c lib/galaxy/jobs/runners/lwr_client/staging/up.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/up.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/up.py @@ -25,6 +25,7 @@ launch_kwds = dict( command_line=rebuilt_command_line, requirements=client_job_description.requirements, + env=client_job_description.env, ) if file_stager.job_config: launch_kwds["job_config"] = file_stager.job_config Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Fix Python 3 incompat in galaxy.jobs.runners.util.
by commits-noreply＠bitbucket.org 24 Apr '14

24 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b172ca94e169/ Changeset: b172ca94e169 User: jmchilton Date: 2014-04-24 03:33:41 Summary: Fix Python 3 incompat in galaxy.jobs.runners.util. Module shared with LWR so hoping for Python 3 compat. Affected #: 2 files diff -r 776e13962bbc861a94242e142e73278c9499dc70 -r b172ca94e169ccf2450432398d67623f79c5588f lib/galaxy/jobs/runners/util/__init__.py --- a/lib/galaxy/jobs/runners/util/__init__.py +++ b/lib/galaxy/jobs/runners/util/__init__.py @@ -3,7 +3,5 @@ processes and interfacing with job managers. This module should contain functionality shared between Galaxy and the LWR. """ -try: - from galaxy.util.bunch import Bunch -except ImportError: - from lwr.util import Bunch + +from galaxy.util.bunch import Bunch diff -r 776e13962bbc861a94242e142e73278c9499dc70 -r b172ca94e169ccf2450432398d67623f79c5588f lib/galaxy/jobs/runners/util/condor/__init__.py --- a/lib/galaxy/jobs/runners/util/condor/__init__.py +++ b/lib/galaxy/jobs/runners/util/condor/__init__.py @@ -20,7 +20,8 @@ def submission_params(prefix=SUBMIT_PARAM_PREFIX, **kwds): submission_params = {} - for key, value in kwds.iteritems(): + for key in kwds: + value = kwds[key] key = key.lower() if key.startswith(prefix): condor_key = key[len(prefix):] 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: default sorting; cleanup; refactor; jslint; start on getting rid of modals for library/folder creation
by commits-noreply＠bitbucket.org 23 Apr '14

23 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/776e13962bbc/ Changeset: 776e13962bbc User: martenson Date: 2014-04-23 23:31:01 Summary: data libraries: default sorting; cleanup; refactor; jslint; start on getting rid of modals for library/folder creation Affected #: 15 files diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -79,7 +79,7 @@ this.library_router.on('route:download', function(folder_id, format) { if ($('#center').find(':checked').length === 0) { - mod_toastr.info('You have to select some datasets to download') + mod_toastr.info('You have to select some datasets to download'); } else { Galaxy.libraries.folderToolbarView.download(folder_id, format); Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 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 @@ -25,253 +25,257 @@ sort: 'asc', - // event binding events: { 'click #select-all-checkboxes' : 'selectAll', 'click .dataset_row' : 'selectClickedRow', 'click .sort-folder-link' : 'sort_clicked' }, - // initialize - initialize : function(options){ - var that = this; - this.options = _.defaults(this.options || {}, options); - this.queue = jQuery.Deferred(); - this.queue.resolve(); - this.collection = new mod_library_model.Folder(); - this.listenTo(this.collection, 'add', this.addOne); - - this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id}); - this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents'; - this.folderContainer.fetch({ - success: function (folder_container) { - that.render(); + + initialize : function(options){ + var that = this; + this.options = _.defaults(this.options || {}, options); + this.collection = new mod_library_model.Folder(); - var items = folder_container.get('folder').models; - that.addAll(items); + // start to listen if someone adds a model to the collection + this.listenTo(this.collection, 'add', this.addOne); + + this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id}); + this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents'; + this.folderContainer.fetch({ + success: function (folder_container) { + that.render(); + var items = folder_container.get('folder').models; + that.addAll(items); + }, + error: function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error(response.responseJSON.err_msg); + } else { + mod_toastr.error('An error ocurred :('); + } + } + }); + }, - }, - error: function(){ - mod_toastr.error('An error occured :('); - } - }); - }, + render: function (options) { + this.options = _.defaults(this.options || {}, options); + var template = this.templateFolder(); - render: function (options) { - this.options = _.defaults(this.options || {}, options); - var template = this.templateFolder(); - var contains_file = false; + // TODO move to server + // find the upper id in the full path + var path = this.folderContainer.attributes.metadata.full_path; + var upper_folder_id; + if (path.length === 1){ // the library is above us + upper_folder_id = 0; + } else { + upper_folder_id = path[path.length-2][0]; + } - // TODO move to server - // prepare nice size strings - // for (var i = 0; i < this.collection.models.length; i++) { - // var model = this.collection.models[i]; - // if (model.get('type') === 'file'){ - // contains_file = true; - // model.set('readable_size', this.size_to_string(model.get('file_size'))); - // } - // } + this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, id: this.options.id, upper_folder_id: upper_folder_id, order: this.sort})); - // TODO move to server - // find the upper id in the full path - var path = this.folderContainer.attributes.metadata.full_path; - var upper_folder_id; - if (path.length === 1){ // the library is above us - upper_folder_id = 0; - } else { - upper_folder_id = path[path.length-2][0]; + 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 + $("#center").css('overflow','auto'); + }, + + /** Adds all given models to the collection. */ + addAll:function(items){ + _.each(items.reverse(), function(item) { + Galaxy.libraries.folderListView.collection.add(item); + }); + this.checkEmptiness(); + }, + + /** Creates a view for the given model and adds it to the folder view. */ + addOne: function(model){ + if (model.get('data_type') !== 'folder'){ + this.options.contains_file = true; + model.set('readable_size', this.size_to_string(model.get('file_size'))); } - // TODO add template when folder is empty + var rowView = new mod_library_folderrow_view.FolderRowView(model); + this.$el.find('#first_folder_item').after(rowView.el); + this.checkEmptiness(); + }, - this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, id: this.options.id, upper_folder_id: upper_folder_id, order: this.sort})); - // this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, items: this.folderContainer.attributes.folder.models, id: this.options.id, upper_folder_id: upper_folder_id })); + /** Checks whether the list is empty and adds/removes the message */ + // TODO needs refactor + checkEmptiness : function(){ + if ((this.$el.find('.dataset_row').length === 0) && (this.$el.find('.folder_row').length === 0)){ + var empty_folder_tmpl = this.templateEmptyFolder(); + this.$el.find('#folder_list_body').append(empty_folder_tmpl()); + } else { + this.$el.find('#empty_folder_message').remove(); + } + }, - if (this.collection.models.length > 0){ - this.renderRows(); + /** User clicked the table heading = he wants to sort stuff */ + sort_clicked : function(event){ + event.preventDefault(); + if (this.sort === 'asc'){ + this.sortFolder('name','desc'); + this.sort = 'desc'; + } else { + this.sortFolder('name','asc'); + this.sort = 'asc'; + } + this.render(); + }, + + /** Sorts the underlying collection according to the parameters received. + * Currently supports only sorting by name. */ + sortFolder: function(sort_by, order){ + if (sort_by === 'name'){ + if (order === 'asc'){ + this.collection.sortByNameAsc(); + } else if (order === 'desc'){ + this.collection.sortByNameDesc(); + } } - // if (this.folderContainer.attributes.metadata.can_add_library_item === true){ - var options = this.folderContainer.attributes.metadata; - options.contains_file = this.options.contains_file; - Galaxy.libraries.folderToolbarView.configureElements(options); - // Galaxy.libraries.folderToolbarView.configureElements({ can_add_library_item: this.folderContainer.attributes.metadata.can_add_library_item, contains_file: contains_file }); - // } + }, - // initialize the library tooltips - $("#center [data-toggle]").tooltip(); - //hack to show scrollbars - $("#center").css('overflow','auto'); - }, + /** convert size to nice string */ + size_to_string : function (size){ + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, - renderRows: function(){ - for (var i = 0; i < this.collection.models.length; i++) { - var folder_item = this.collection.models[i]; - var rowView = new mod_library_folderrow_view.FolderRowView(folder_item); - this.$el.find('#folder_list_body').append(rowView.el); - } - }, + /** User clicked the checkbox in the table heading */ + selectAll : function (event) { + var selected = event.target.checked; + that = this; + // Iterate each checkbox + $(':checkbox').each(function() { + this.checked = selected; + $row = $(this.parentElement.parentElement); + // Change color of selected/unselected + if (selected) { + that.makeDarkRow($row); + } else { + that.makeWhiteRow($row); + } + }); + }, - addAll:function(items){ - _.each(items.reverse(), function(item) { - Galaxy.libraries.folderListView.collection.add(item); - }); - }, + /** Check checkbox if user clicks on the whole row or + * on the checkbox itself */ + selectClickedRow : function (event) { + var checkbox = ''; + var $row; + var source; + if (event.target.localName === 'input'){ + checkbox = event.target; + $row = $(event.target.parentElement.parentElement); + source = 'input'; + } else if (event.target.localName === 'td') { + checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0]; + $row = $(event.target.parentElement); + source = 'td'; + } + if (checkbox.checked){ + if (source==='td'){ + checkbox.checked = ''; + this.makeWhiteRow($row); + } else if (source==='input') { + this.makeDarkRow($row); + } + } else { + if (source==='td'){ + checkbox.checked = 'selected'; + this.makeDarkRow($row); + } else if (source==='input') { + this.makeWhiteRow($row); + } + } + }, - addOne: function(model){ - if (model.get('data_type') !== 'folder'){ - this.options.contains_file = true; - model.set('readable_size', this.size_to_string(model.get('file_size'))); - } - var rowView = new mod_library_folderrow_view.FolderRowView(model); - this.$el.find('#first_folder_item').after(rowView.el); - }, + makeDarkRow: function($row){ + $row.removeClass('light'); + $row.find('a').removeClass('light'); + $row.addClass('dark'); + $row.find('a').addClass('dark'); + $row.find('span').removeClass('fa-file-o'); + $row.find('span').addClass('fa-file'); + }, - sort_clicked : function(event){ - event.preventDefault(); - if (this.sort === 'asc'){ - this.sortFolder('name','desc'); - this.sort = 'desc'; - } else { - this.sortFolder('name','asc'); - this.sort = 'asc'; - } - this.render(); - }, - - /** Sorts the underlying collection according to the parameters received. - Currently supports only sorting by name. */ - sortFolder: function(sort_by, order){ - if (sort_by === 'name'){ - if (order === 'asc'){ - this.collection.sortByNameAsc(); - } else if (order === 'desc'){ - this.collection.sortByNameDesc(); - } - } - }, - - // convert size to nice string - size_to_string : function (size){ - // identify unit - var unit = ""; - if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else - if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else - if (size >= 100000) { size = size / 100000; unit = "MB"; } else - if (size >= 100) { size = size / 100; unit = "KB"; } else - { size = size * 10; unit = "b"; } - // return formatted string - return (Math.round(size) / 10) + unit; - }, - - // select all datasets - selectAll : function (event) { - var selected = event.target.checked; - that = this; - // Iterate each checkbox - $(':checkbox').each(function() { - this.checked = selected; - $row = $(this.parentElement.parentElement); - // Change color of selected/unselected - (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row); - }); - // Show the tools in menu - // this.checkTools(); - }, - - // Check checkbox on row itself or row checkbox click - selectClickedRow : function (event) { - var checkbox = ''; - var $row; - var source; - if (event.target.localName === 'input'){ - checkbox = event.target; - $row = $(event.target.parentElement.parentElement); - source = 'input'; - } else if (event.target.localName === 'td') { - checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0]; - $row = $(event.target.parentElement); - source = 'td'; - } - if (checkbox.checked){ - if (source==='td'){ - checkbox.checked = ''; - this.makeWhiteRow($row); - } else if (source==='input') { - this.makeDarkRow($row); - } - } else { - if (source==='td'){ - checkbox.checked = 'selected'; - this.makeDarkRow($row); - } else if (source==='input') { - this.makeWhiteRow($row); - } - } - }, - - makeDarkRow: function($row){ - $row.removeClass('light'); - $row.find('a').removeClass('light'); - $row.addClass('dark'); - $row.find('a').addClass('dark'); - $row.find('span').removeClass('fa-file-o'); - $row.find('span').addClass('fa-file'); - }, - - makeWhiteRow: function($row){ - $row.removeClass('dark'); - $row.find('a').removeClass('dark'); - $row.addClass('light'); - $row.find('a').addClass('light'); - $row.find('span').addClass('fa-file-o'); - $row.find('span').removeClass('fa-file'); - }, + makeWhiteRow: function($row){ + $row.removeClass('dark'); + $row.find('a').removeClass('dark'); + $row.addClass('light'); + $row.find('a').addClass('light'); + $row.find('span').addClass('fa-file-o'); + $row.find('span').removeClass('fa-file'); + }, // MMMMMMMMMMMMMMMMMM // === TEMPLATES ==== // MMMMMMMMMMMMMMMMMM - // main template for folder browsing - templateFolder : function (){ - var tmpl_array = []; + templateFolder : function (){ + var tmpl_array = []; - // BREADCRUMBS - tmpl_array.push('<ol class="breadcrumb">'); - tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>'); - tmpl_array.push(' <% _.each(path, function(path_item) { %>'); - tmpl_array.push(' <% if (path_item[0] != id) { %>'); - tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> '); - tmpl_array.push( '<% } else { %>'); - tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push('</ol>'); + // BREADCRUMBS + tmpl_array.push('<ol class="breadcrumb">'); + tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>'); + tmpl_array.push(' <% _.each(path, function(path_item) { %>'); + tmpl_array.push(' <% if (path_item[0] != id) { %>'); + tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> '); + tmpl_array.push( '<% } else { %>'); + tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</ol>'); - // FOLDER CONTENT - tmpl_array.push('<table id="folder_table" class="grid table table-condensed">'); - tmpl_array.push(' <thead>'); - tmpl_array.push(' <th class="button_heading"></th>'); - tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); - tmpl_array.push(' <th><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>'); - tmpl_array.push(' <th>data type</th>'); - tmpl_array.push(' <th>size</th>'); - tmpl_array.push(' <th>time updated (UTC)</th>'); - tmpl_array.push(' </thead>'); - tmpl_array.push(' <tbody id="folder_list_body">'); - tmpl_array.push(' <tr id="first_folder_item">'); - tmpl_array.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>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' </tr>'); + // FOLDER CONTENT + tmpl_array.push('<table id="folder_table" class="grid table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th class="button_heading"></th>'); + tmpl_array.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>'); + tmpl_array.push(' <th><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>'); + tmpl_array.push(' <th>data type</th>'); + tmpl_array.push(' <th>size</th>'); + tmpl_array.push(' <th>time updated (UTC)</th>'); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody id="folder_list_body">'); + tmpl_array.push(' <tr id="first_folder_item">'); + tmpl_array.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>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' </tr>'); - tmpl_array.push(' </tbody>'); - tmpl_array.push('</table>'); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); - return _.template(tmpl_array.join('')); - } + return _.template(tmpl_array.join('')); + }, - }); + templateEmptyFolder: function(){ + var tmpl_array = []; + + tmpl_array.push('<tr id="empty_folder_message">'); + tmpl_array.push('<td colspan="6" style="text-align:center">'); + tmpl_array.push('This folder is either empty or you do not have proper access permissions to see the contents.'); + tmpl_array.push('</td>'); + tmpl_array.push('</tr>'); + + return _.template(tmpl_array.join('')); + } + + }); return { FolderListView: FolderListView diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 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 @@ -221,12 +221,12 @@ } var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})); - promise.done(function(a1){ + promise.done(function(){ // we are fine self.updateProgress(); self.chainCall(history_item_set, history_name); }) - .fail(function(a1){ + .fail(function(){ // we have a problem self.options.chain_call_control.failed_number += 1; self.updateProgress(); @@ -315,7 +315,7 @@ self.histories.get(history_id).set({'contents' : history_contents}); self.modal.$el.find('#selected_history_content').html(history_contents_template({history_contents: history_contents.models.reverse()})); }, - error: function(model, response){ + error: function(){ mod_toastr.error('An error ocurred :('); } }); @@ -381,7 +381,7 @@ self.updateProgress(); self.chainCallAddingHdas(hdas_set); }) - .fail(function(data){ + .fail(function(){ // we have a problem self.options.chain_call_control.failed_number += 1; self.updateProgress(); diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 static/scripts/mvc/library/library-librarylist-view.js --- a/static/scripts/mvc/library/library-librarylist-view.js +++ b/static/scripts/mvc/library/library-librarylist-view.js @@ -27,7 +27,6 @@ // map of library model ids to library views = cache rowViews: {}, - // initialize initialize : function(options){ this.options = _.defaults(this.options || {}, options); var viewContext = this; @@ -37,18 +36,18 @@ this.collection = new mod_library_model.Libraries(); this.collection.fetch({ - success: function(libraries){ + success: function(){ viewContext.render(); }, - error: function(model, response){ + error: function(){ mod_toastr.error('An error occured. Please try again.'); } }); }, /** Renders the libraries table either from the object's own collection, - or from a given array of library models, - or renders an empty list in case no data is given. */ + * or from a given array of library models, + * or renders an empty list in case no data is given. */ render: function (options) { var template = this.templateLibraryList(); var libraries_to_render = null; @@ -60,6 +59,7 @@ } if (this.collection !== null && models === null){ + this.sortLibraries(); if (include_deleted){ // show all the libraries libraries_to_render = this.collection.models; } else{ // show only undeleted libraries @@ -82,6 +82,7 @@ $("#center").css('overflow','auto'); }, + /** Render all given models as rows in the library list */ renderRows: function(libraries_to_render){ for (var i = 0; i < libraries_to_render.length; i++) { var library = libraries_to_render[i]; @@ -98,12 +99,11 @@ } }, + /** Table heading was clicked, update sorting preferences and re-render */ sort_clicked : function(){ if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){ - this.sortLibraries('name','desc'); Galaxy.libraries.preferences.set({'sort_order': 'desc'}); } else { - this.sortLibraries('name','asc'); Galaxy.libraries.preferences.set({'sort_order': 'asc'}); } this.render(); @@ -111,11 +111,11 @@ /** Sorts the underlying collection according to the parameters received. Currently supports only sorting by name. */ - sortLibraries: function(sort_by, order){ - if (sort_by === 'name'){ - if (order === 'asc'){ + sortLibraries: function(){ + if (Galaxy.libraries.preferences.get('sort_by') === 'name'){ + if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){ this.collection.sortByNameAsc(); - } else if (order === 'desc'){ + } else if (Galaxy.libraries.preferences.get('sort_order') === 'desc'){ this.collection.sortByNameDesc(); } } @@ -220,7 +220,7 @@ $("input[name='Synopsis']").val(''); }, - // serialize data from the form + // serialize data from the new library form serialize_new_library : function(){ return { name: $("input[name='Name']").val(), diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 static/scripts/mvc/library/library-libraryrow-view.js --- a/static/scripts/mvc/library/library-libraryrow-view.js +++ b/static/scripts/mvc/library/library-libraryrow-view.js @@ -2,12 +2,10 @@ define([ "galaxy.masthead", "utils/utils", - "libs/toastr", - "mvc/library/library-model"], + "libs/toastr"], function(mod_masthead, mod_utils, - mod_toastr, - mod_library_model) { + mod_toastr) { // galaxy library row view var LibraryRowView = Backbone.View.extend({ @@ -161,7 +159,7 @@ row_view.repaint(library); mod_toastr.success('Changes to library saved'); }, - error: function(model, response){ + error: function(){ mod_toastr.error('An error occured during updating the library :('); } }); @@ -237,7 +235,7 @@ tmpl_array.push(' <% } else if(library.get("public") === true) { %>'); tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>'); tmpl_array.push(' <% }%>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Upload to library" class="primary-button btn-xs upload_library_btn" type="button" style="<% if(button_config.upload_library_btn === false) { print("display:none;") } %>"><span class="fa fa-upload"></span></button>'); + // tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Upload to library" class="primary-button btn-xs upload_library_btn" type="button" style="<% if(button_config.upload_library_btn === false) { print("display:none;") } %>"><span class="fa fa-upload"></span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>'); diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 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 @@ -1,12 +1,5 @@ -define([ - "galaxy.masthead", - "utils/utils", - "libs/toastr", - "mvc/library/library-model"], -function(mod_masthead, - mod_utils, - mod_toastr, - mod_library_model) { +define([], +function() { var LibraryToolbarView = Backbone.View.extend({ el: '#center', diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 static/scripts/mvc/library/library-model.js --- a/static/scripts/mvc/library/library-model.js +++ b/static/scripts/mvc/library/library-model.js @@ -11,7 +11,7 @@ */ isVisible : function(show_deleted){ var isVisible = true; - if( (!show_delete) && (this.get('deleted')) ){ + if( (!show_deleted) && (this.get('deleted')) ){ isVisible = false; } return isVisible; diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 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",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){var h=this;this.options=_.defaults(this.options||{},g);this.queue=jQuery.Deferred();this.queue.resolve();this.collection=new d.Folder();this.listenTo(this.collection,"add",this.addOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";this.folderContainer.fetch({success:function(i){h.render();var j=i.get("folder").models;h.addAll(j)},error:function(){f.error("An error occured :(")}})},render:function(g){this.options=_.defaults(this.options||{},g);var h=this.templateFolder();var i=false;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(h({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));if(this.collection.models.length>0){this.renderRows()}var g=this.folderContainer.attributes.metadata;g.contains_file=this.options.contains_file;Galaxy.libraries.folderToolbarView.configureElements(g);$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(){for(var j=0;j<this.collection.models.length;j++){var h=this.collection.models[j];var g=new a.FolderRowView(h);this.$el.find("#folder_list_body").append(g.el)}},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)})},addOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}var g=new a.FolderRowView(h);this.$el.find("#first_folder_item").after(g.el)},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()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){this.collection.sortByNameAsc()}else{if(g==="desc"){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;$(":checkbox").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);(g)?that.makeDarkRow($row):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; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th><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(" </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(" </tr>");g.push(" </tbody>");g.push("</table>");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",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){var h=this;this.options=_.defaults(this.options||{},g);this.collection=new d.Folder();this.listenTo(this.collection,"add",this.addOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";this.folderContainer.fetch({success:function(i){h.render();var j=i.get("folder").models;h.addAll(j)},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();$("#center").css("overflow","auto")},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});this.checkEmptiness()},addOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}var g=new a.FolderRowView(h);this.$el.find("#first_folder_item").after(g.el);this.checkEmptiness()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){var g=this.templateEmptyFolder();this.$el.find("#folder_list_body").append(g())}else{this.$el.find("#empty_folder_message").remove()}},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()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){this.collection.sortByNameAsc()}else{if(g==="desc"){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;$(":checkbox").each(function(){this.checked=g;$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><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(" </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(" </tr>");g.push(" </tbody>");g.push("</table>");return _.template(g.join(""))},templateEmptyFolder:function(){var g=[];g.push('<tr id="empty_folder_message">');g.push('<td colspan="6" style="text-align:center">');g.push("This folder is either empty or you do not have proper access permissions to see the contents.");g.push("</td>");g.push("</tr>");return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 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"},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(k){f.updateProgress();f.chainCall(g,j)}).fail(function(k){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(j,i){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(j){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');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('<div id="library_folder_toolbar" >');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" 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(" </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(""))},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"},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)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');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('<div id="library_folder_toolbar" >');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" 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(" </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(""))},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 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 static/scripts/packed/mvc/library/library-librarylist-view.js --- a/static/scripts/packed/mvc/library/library-librarylist-view.js +++ b/static/scripts/packed/mvc/library/library-librarylist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(j){h.render()},error:function(k,j){e.error("An error occured. Please try again.")}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(m){for(var l=0;l<m.length;l++){var k=m[l];var j=_.findWhere(this.rowViews,{id:k.get("id")});if(j!==undefined&&this instanceof Backbone.View){j.delegateEvents();this.$el.find("#library_list_body").append(j.el)}else{var h=new a.LibraryRowView(k);this.$el.find("#library_list_body").append(h.el);this.rowViews[k.get("id")]=h}}},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.sortLibraries("name","desc");Galaxy.libraries.preferences.set({sort_order:"desc"})}else{this.sortLibraries("name","asc");Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(i,h){if(i==="name"){if(h==="asc"){this.collection.sortByNameAsc()}else{if(h==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");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("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(i){i.preventDefault();i.stopPropagation();var h=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){h.create_new_library_event()},Close:function(){h.modal.hide()}}})},create_new_library_event:function(){var j=this.serialize_new_library();if(this.validate_new_library(j)){var i=new c.Library();var h=this;i.save(j,{success:function(k){h.collection.add(k);h.modal.hide();h.clear_library_modal();h.render();e.success("Library created")},error:function(){e.error("An error occured :(")}})}else{e.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:$("input[name='Synopsis']").val()}},validate_new_library:function(h){return h.name!==""}});return{LibraryListView:f}}); \ No newline at end of file +define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){h.render()},error:function(){e.error("An error occured. Please try again.")}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(m){for(var l=0;l<m.length;l++){var k=m[l];var j=_.findWhere(this.rowViews,{id:k.get("id")});if(j!==undefined&&this instanceof Backbone.View){j.delegateEvents();this.$el.find("#library_list_body").append(j.el)}else{var h=new a.LibraryRowView(k);this.$el.find("#library_list_body").append(h.el);this.rowViews[k.get("id")]=h}}},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");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("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(i){i.preventDefault();i.stopPropagation();var h=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){h.create_new_library_event()},Close:function(){h.modal.hide()}}})},create_new_library_event:function(){var j=this.serialize_new_library();if(this.validate_new_library(j)){var i=new c.Library();var h=this;i.save(j,{success:function(k){h.collection.add(k);h.modal.hide();h.clear_library_modal();h.render();e.success("Library created")},error:function(){e.error("An error occured :(")}})}else{e.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(h){return h.name!==""}});return{LibraryListView:f}}); \ No newline at end of file diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 static/scripts/packed/mvc/library/library-libraryrow-view.js --- a/static/scripts/packed/mvc/library/library-libraryrow-view.js +++ b/static/scripts/packed/mvc/library/library-libraryrow-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({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .upload_library_btn":"upload_to_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(f){this.render(f)},render:function(g){if(typeof g==="undefined"){g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(g);var f=this.templateRow();this.setElement(f({library:g,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(f){$(".tooltip").hide();var g=this.$el;this.render(f);g.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(f){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(f.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(f.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(f.get("can_user_add")===true){vis_config.upload_library_btn=true}if(f.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(f.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true}}this.element_visibility_config=vis_config},upload_to_library:function(){e.info("Coming soon. Stay tuned.")},permissions_on_library:function(){e.info("Coming soon. Stay tuned.")},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){e.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var h=false;var j=this.$el.find(".input_library_name").val();if(typeof j!=="undefined"&&j!==g.get("name")){if(j.length>2){g.set("name",j);h=true}else{e.warning("Library name has to be at least 3 characters long");return}}var i=this.$el.find(".input_library_description").val();if(typeof i!=="undefined"&&i!==g.get("description")){g.set("description",i);h=true}var k=this.$el.find(".input_library_synopsis").val();if(typeof k!=="undefined"&&k!==g.get("synopsis")){g.set("synopsis",k);h=true}if(h){var f=this;g.save(null,{patch:true,success:function(l){f.edit_mode=false;f.repaint(l);e.success("Changes to library saved")},error:function(m,l){e.error("An error occured during updating the library :(")}})}else{this.edit_mode=false;this.repaint(g);e.info("Nothing has changed")}},delete_library:function(){var g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var f=this;g.destroy({success:function(h){h.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(h);f.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();f.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){f.repaint(h)}}e.success("Library has been marked deleted")},error:function(){e.error("An error occured during deleting the library :(")}})},undelete_library:function(){var g=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var f=this;g.url=g.urlRoot+g.id+"?undelete=true";g.destroy({success:function(h){h.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(h);f.edit_mode=false;f.repaint(h);e.success("Library has been undeleted")},error:function(){e.error("An error occured while undeleting the library :(")}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if(library.get("deleted") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span>');tmpl_array.push(' <% } else if(library.get("public") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Upload to library" class="primary-button btn-xs upload_library_btn" type="button" style="<% if(button_config.upload_library_btn === false) { print("display:none;") } %>"><span class="fa fa-upload"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .upload_library_btn":"upload_to_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true}}this.element_visibility_config=vis_config},upload_to_library:function(){d.info("Coming soon. Stay tuned.")},permissions_on_library:function(){d.info("Coming soon. Stay tuned.")},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){d.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(){d.error("An error occured during updating the library :(")}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(){d.error("An error occured during deleting the library :(")}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(){d.error("An error occured while undeleting the library :(")}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if(library.get("deleted") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span>');tmpl_array.push(' <% } else if(library.get("public") === true) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 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(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(a,c,d,b){var e=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var h=this.templateToolBar();var g=false;var f=false;if(Galaxy.currUser){g=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}else{f=true}this.$el.html(h({admin_user:g,anon_user:f}));if(g){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},delegate_modal:function(f){Galaxy.libraries.libraryListView.show_library_modal(f)},check_include_deleted:function(f){if(f.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(""))}});return{LibraryToolbarView:e}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var d=this.templateToolBar();var c=false;var b=false;if(Galaxy.currUser){c=Galaxy.currUser.isAdmin();b=Galaxy.currUser.isAnonymous()}else{b=true}this.$el.html(d({admin_user:c,anon_user:b}));if(c){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},delegate_modal:function(b){Galaxy.libraries.libraryListView.show_library_modal(b)},check_include_deleted:function(b){if(b.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(""))}});return{LibraryToolbarView:a}}); \ No newline at end of file diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 static/scripts/packed/mvc/library/library-model.js --- a/static/scripts/packed/mvc/library/library-model.js +++ b/static/scripts/packed/mvc/library/library-model.js @@ -1,1 +1,1 @@ -define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(l){var k=true;if((!show_delete)&&(this.get("deleted"))){k=false}return k}});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(k){k=k||{}},getVisible:function(l,m){m=m||[];var k=new i(this.filter(function(n){return n.isVisible(l)}));return k},sortByNameAsc:function(){this.comparator=function(l,k){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}return 0};this.sort();return this},sortByNameDesc:function(){this.comparator=function(l,k){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}return 0};this.sort();return this}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var c=Backbone.Collection.extend({model:g,sortByNameAsc:function(){this.comparator=function(l,k){if(l.get("type")===k.get("type")){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}return 0}else{if(l.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this},sortByNameDesc:function(){this.comparator=function(l,k){if(l.get("type")===k.get("type")){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}return 0}else{if(l.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this}});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(k){this.get("folder").reset(k.folder_contents);return k}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(k){this.id=k.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Collection.extend({url:"/api/histories",model:h});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:j}}); \ No newline at end of file +define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(l){var k=true;if((!l)&&(this.get("deleted"))){k=false}return k}});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(k){k=k||{}},getVisible:function(l,m){m=m||[];var k=new i(this.filter(function(n){return n.isVisible(l)}));return k},sortByNameAsc:function(){this.comparator=function(l,k){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}return 0};this.sort();return this},sortByNameDesc:function(){this.comparator=function(l,k){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}return 0};this.sort();return this}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var c=Backbone.Collection.extend({model:g,sortByNameAsc:function(){this.comparator=function(l,k){if(l.get("type")===k.get("type")){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}return 0}else{if(l.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this},sortByNameDesc:function(){this.comparator=function(l,k){if(l.get("type")===k.get("type")){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}return 0}else{if(l.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this}});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(k){this.get("folder").reset(k.folder_contents);return k}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(k){this.id=k.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Collection.extend({url:"/api/histories",model:h});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:j}}); \ No newline at end of file diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var DrawResults=function(options){this.incomplete_features=options.incomplete_features;this.feature_mapper=options.feature_mapper};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords,incomplete_features=[];for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((this.mode==="Dense"||slot!==null)&&(feature_start<view_end&&feature_end>view_start)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1]);if(feature_start<view_start||feature_end>view_end){incomplete_features.push(feature)}}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return new DrawResults({incomplete_features:incomplete_features,feature_mapper:feature_mapper})},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start+(pack_mode?1:4),cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var DrawResults=function(options){this.incomplete_features=options.incomplete_features;this.feature_mapper=options.feature_mapper};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords,incomplete_features=[];for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((this.mode==="Dense"||slot!==null)&&(feature_start<view_end&&feature_end>view_start)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1]);if(feature_start<view_start||feature_end>view_end){incomplete_features.push(feature)}}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return new DrawResults({incomplete_features:incomplete_features,feature_mapper:feature_mapper})},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.detail_block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start+(pack_mode?1:4),cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file diff -r 51643642564f214f09c2eff32307360f5e09dfaf -r 776e13962bbc861a94242e142e73278c9499dc70 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:"#DDDDDD"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:"#AAAAAA"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ 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: dannon: Add mock, poster eggs. Both may go away depending on which way bioblend goes w/ deps, but it keeps things working for now.
by commits-noreply＠bitbucket.org 23 Apr '14

23 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/51643642564f/ Changeset: 51643642564f User: dannon Date: 2014-04-23 23:07:39 Summary: Add mock, poster eggs. Both may go away depending on which way bioblend goes w/ deps, but it keeps things working for now. Affected #: 1 file diff -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f -r 51643642564f214f09c2eff32307360f5e09dfaf eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -46,6 +46,7 @@ kombu = 3.0.12 lrucache = 0.2 Mako = 0.4.1 +mock = 1.0.1 nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 @@ -54,6 +55,7 @@ Paste = 1.7.5.1 PasteDeploy = 1.5.0 pexpect = 2.4 +poster = 0.8.1 python_openid = 2.2.5 python_daemon = 1.5.5 pytz = 2013.9 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: davebgx: Twill test framework cleanup. Fix functional tests for history functions.
by commits-noreply＠bitbucket.org 23 Apr '14

23 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/299e9c8d29c5/ Changeset: 299e9c8d29c5 User: davebgx Date: 2014-04-23 22:46:14 Summary: Twill test framework cleanup. Fix functional tests for history functions. Affected #: 6 files diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -14,6 +14,7 @@ import urllib import zipfile +from urlparse import urlparse from galaxy.web import security from galaxy.web.framework.helpers import iff from galaxy.util.json import from_json_string @@ -63,7 +64,6 @@ os.makedirs(self.keepOutdir) except: pass - self.home() # Functions associated with files def files_diff( self, file1, file2, attributes=None ): @@ -232,7 +232,6 @@ tc.config("readonly_controls_writeable", 1) tc.fv( "tool_form", "NAME", name ) tc.submit( "runtool_btn" ) - self.home() except AssertionError, err: errmsg = "Uploading file resulted in the following exception. Make sure the file (%s) exists. " % filename errmsg += str( err ) @@ -251,13 +250,12 @@ def upload_url_paste( self, url_paste, ftype='auto', dbkey='unspecified (?)' ): """Pasted data in the upload utility""" - self.visit_page( "tool_runner/index?tool_id=upload1" ) + self.visit_url( "/tool_runner/index?tool_id=upload1" ) try: self.refresh_form( "file_type", ftype ) #Refresh, to support composite files tc.fv( "tool_form", "dbkey", dbkey ) tc.fv( "tool_form", "url_paste", url_paste ) tc.submit( "runtool_btn" ) - self.home() except Exception, e: errmsg = "Problem executing upload utility using url_paste: %s" % str( e ) raise AssertionError( errmsg ) @@ -271,8 +269,8 @@ # Wait for upload processing to finish (TODO: this should be done in each test case instead) self.wait() - def json_from_url( self, url ): - self.visit_url( url ) + def json_from_url( self, url, params={} ): + self.visit_url( url, params ) return from_json_string( self.last_page() ) # Functions associated with histories @@ -283,8 +281,8 @@ params = dict() if show_deleted is not None: params[ 'deleted' ] = show_deleted - api_url = '/api/histories/%s/contents?%s' % ( encoded_history_id, urllib.urlencode( params ) ) - json_data = self.json_from_url( api_url ) + api_url = '/api/histories/%s/contents' % encoded_history_id + json_data = self.json_from_url( api_url, params=params ) if show_deleted is not None: hdas = [] for hda in json_data: @@ -296,8 +294,8 @@ json_data = hdas if show_details: params[ 'details' ] = ','.join( [ hda[ 'id' ] for hda in json_data ] ) - api_url = '/api/histories/%s/contents?%s' % ( encoded_history_id, urllib.urlencode( params ) ) - json_data = self.json_from_url( api_url ) + api_url = '/api/histories/%s/contents' % encoded_history_id + json_data = self.json_from_url( api_url, params=params ) log.debug( 'detailed url: %s' % api_url ) log.debug( 'detailed json data: %s' % json_data ) return json_data @@ -314,19 +312,18 @@ def check_history_for_errors( self ): """Raises an exception if there are errors in a history""" - self.home() - self.visit_page( "history" ) + self.visit_url( "/history" ) page = self.last_page() if page.find( 'error' ) > -1: raise AssertionError( 'Errors in the history for user %s' % self.user ) def check_history_for_string( self, patt, show_deleted=False ): """Breaks patt on whitespace and searches for each element seperately in the history""" - self.home() if show_deleted: - self.visit_page( "history?show_deleted=True" ) + params = dict( show_deleted=True ) + self.visit_url( "/history", params ) else: - self.visit_page( "history" ) + self.visit_url( "/history" ) for subpatt in patt.split(): try: tc.find( subpatt ) @@ -334,22 +331,19 @@ fname = self.write_temp_file( tc.browser.get_html() ) errmsg = "no match to '%s'\npage content written to '%s'" % ( subpatt, fname ) raise AssertionError( errmsg ) - self.home() def check_history_for_exact_string( self, string, show_deleted=False ): """Looks for exact match to 'string' in history page""" - self.home() if show_deleted: - self.visit_page( "history?show_deleted=True" ) + self.visit_url( "/history?show_deleted=True" ) else: - self.visit_page( "history" ) + self.visit_url( "/history" ) try: tc.find( string ) except: fname = self.write_temp_file( tc.browser.get_html() ) errmsg = "no match to '%s'\npage content written to '%s'" % ( string, fname ) raise AssertionError( errmsg ) - self.home() def check_history_json( self, check_fn, show_deleted=None ): """ @@ -368,8 +362,6 @@ errmsg = ( "json could not be read\npage content written to '%s'" % ( fname ) ) raise AssertionError( errmsg ) - self.home() - def is_history_empty( self ): """ Uses history page JSON to determine whether this history is empty @@ -404,20 +396,15 @@ history_list = self.get_histories_as_data_list() self.assertTrue( history_list ) num_deleted = len( id.split( ',' ) ) - self.home() - self.visit_page( "history/list?operation=delete&id=%s" % ( id ) ) - + self.visit_url( "/history/list?operation=delete&id=%s" % ( id ) ) check_str = 'Deleted %d %s' % ( num_deleted, iff( num_deleted != 1, "histories", "history" ) ) self.check_page_for_string( check_str ) - self.home() def delete_current_history( self, strings_displayed=[] ): """Deletes the current history""" - self.home() - self.visit_page( "history/delete_current" ) + self.visit_url( "/history/delete_current" ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() def get_histories_as_data_list( self ): """Returns the data elements of all histories""" @@ -433,24 +420,21 @@ def history_as_xml_tree( self, show_deleted=False ): """Returns a parsed xml object of a history""" - self.home() - self.visit_page( 'history?as_xml=True&show_deleted=%s' % show_deleted ) + self.visit_url( '/history?as_xml=True&show_deleted=%s' % show_deleted ) xml = self.last_page() tree = ElementTree.fromstring(xml) return tree def histories_as_xml_tree( self ): """Returns a parsed xml object of all histories""" - self.home() - self.visit_page( 'history/list_as_xml' ) + self.visit_url( '/history/list_as_xml' ) xml = self.last_page() tree = ElementTree.fromstring(xml) return tree def history_options( self, user=False, active_datasets=False, activatable_datasets=False, histories_shared_by_others=False ): """Mimics user clicking on history options link""" - self.home() - self.visit_page( "root/history_options" ) + self.visit_url( "/root/history_options" ) if user: self.check_page_for_string( 'Previously</a> stored histories' ) if active_datasets: @@ -465,35 +449,28 @@ self.check_page_for_string( 'Show deleted</a> datasets in current history' ) self.check_page_for_string( 'Rename</a> current history' ) self.check_page_for_string( 'Delete</a> current history' ) - self.home() def new_history( self, name=None ): """Creates a new, empty history""" - self.home() if name: self.visit_url( "%s/history_new?name=%s" % ( self.url, name ) ) else: self.visit_url( "%s/history_new" % self.url ) self.check_page_for_string( 'New history created' ) assert self.is_history_empty(), 'Creating new history did not result in an empty history.' - self.home() def rename_history( self, id, old_name, new_name ): """Rename an existing history""" - self.home() - self.visit_page( "history/rename?id=%s&name=%s" % ( id, new_name ) ) + self.visit_url( "/history/rename", params=dict( id=id, name=new_name ) ) check_str = 'History: %s renamed to: %s' % ( old_name, urllib.unquote( new_name ) ) self.check_page_for_string( check_str ) - self.home() def set_history( self ): """Sets the history (stores the cookies for this run)""" if self.history_id: - self.home() - self.visit_page( "history?id=%s" % self.history_id ) + self.visit_url( "/history", params=dict( id=self.history_id ) ) else: self.new_history() - self.home() def share_current_history( self, email, strings_displayed=[], strings_displayed_after_submit=[], action='', action_strings_displayed=[], action_strings_displayed_after_submit=[] ): @@ -514,7 +491,6 @@ tc.submit( "share_restricted_button" ) for check_str in action_strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home() def share_histories_with_users( self, ids, emails, strings_displayed=[], strings_displayed_after_submit=[], action=None, action_strings_displayed=[] ): @@ -533,97 +509,70 @@ for check_str in action_strings_displayed: self.check_page_for_string( check_str ) - self.home() def unshare_history( self, history_id, user_id, strings_displayed=[] ): """Unshare a history that has been shared with another user""" - self.visit_url( "%s/history/list?id=%s&operation=share+or+publish" % ( self.url, history_id ) ) + self.visit_url( "/history/sharing", params=dict( id=history_id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.visit_url( "%s/history/sharing?unshare_user=%s&id=%s" % ( self.url, user_id, history_id ) ) - self.home() + self.visit_url( "/history/sharing", params=dict( unshare_user=user_id, id=history_id ) ) def switch_history( self, id='', name='' ): """Switches to a history in the current list of histories""" - self.visit_url( "%s/history/list?operation=switch&id=%s" % ( self.url, id ) ) + params = dict( operation='switch', id=id ) + self.visit_url( "/history/list", params ) if name: self.check_history_for_exact_string( name ) - self.home() def view_stored_active_histories( self, strings_displayed=[] ): - self.home() - self.visit_page( "history/list" ) + self.visit_url( "/history/list" ) self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( 'operation=Rename' ) self.check_page_for_string( 'operation=Switch' ) self.check_page_for_string( 'operation=Delete' ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() def view_stored_deleted_histories( self, strings_displayed=[] ): - self.home() - self.visit_page( "history/list?f-deleted=True" ) + self.visit_url( "/history/list?f-deleted=True" ) self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( 'operation=Undelete' ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() def view_shared_histories( self, strings_displayed=[] ): - self.home() - self.visit_page( "history/list_shared" ) + self.visit_url( "/history/list_shared" ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() def copy_history( self, history_id, copy_choice, strings_displayed=[], strings_displayed_after_submit=[] ): - self.home() - self.visit_page( "history/copy?id=%s" % history_id ) + self.visit_url( "/history/copy?id=%s" % history_id ) for check_str in strings_displayed: self.check_page_for_string( check_str ) tc.fv( '1', 'copy_choice', copy_choice ) tc.submit( 'copy_choice_button' ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home() def make_accessible_via_link( self, history_id, strings_displayed=[], strings_displayed_after_submit=[] ): - self.home() - self.visit_page( "history/list?operation=share+or+publish&id=%s" % history_id ) - for check_str in strings_displayed: - self.check_page_for_string( check_str ) # twill barfs on this form, possibly because it contains no fields, but not sure. # In any case, we have to mimic the form submission - self.home() - self.visit_page( 'history/sharing?id=%s&make_accessible_via_link=True' % history_id ) - for check_str in strings_displayed_after_submit: - self.check_page_for_string( check_str ) - self.home() + self.visit_url( '/history/sharing', dict( id=history_id, make_accessible_via_link=True ) ) + self.check_for_strings( strings_displayed=strings_displayed_after_submit ) def disable_access_via_link( self, history_id, strings_displayed=[], strings_displayed_after_submit=[] ): - self.home() - self.visit_page( "history/list?operation=share+or+publish&id=%s" % history_id ) - for check_str in strings_displayed: - self.check_page_for_string( check_str ) # twill barfs on this form, possibly because it contains no fields, but not sure. # In any case, we have to mimic the form submission - self.home() - self.visit_page( 'history/sharing?id=%s&disable_link_access=True' % history_id ) - for check_str in strings_displayed_after_submit: - self.check_page_for_string( check_str ) - self.home() + self.visit_url( '/history/sharing', dict( id=history_id, disable_link_access=True ) ) + self.check_for_strings( strings_displayed=strings_displayed_after_submit ) def import_history_via_url( self, history_id, email, strings_displayed_after_submit=[] ): - self.home() - self.visit_page( "history/imp?&id=%s" % history_id ) - for check_str in strings_displayed_after_submit: - self.check_page_for_string( check_str ) - self.home() + self.visit_url( "/history/imp", params=dict( id=history_id ) ) + self.check_for_strings( strings_displayed=strings_displayed_after_submit ) # Functions associated with datasets (history items) and meta data def _get_job_stream_output( self, hda_id, stream, format ): - self.visit_page( "datasets/%s/%s" % ( self.security.encode_id( hda_id ), stream ) ) + self.visit_url( "/datasets/%s/%s" % ( self.security.encode_id( hda_id ), stream ) ) output = self.last_page() return self._format_stream( output, stream, format ) @@ -657,7 +606,7 @@ elem = data_list[-1] hid = int( elem.get('hid') ) self.assertTrue( hid ) - self.visit_page( "dataset/edit?hid=%s" % hid ) + self.visit_url( "/dataset/edit?hid=%s" % hid ) for subpatt in patt.split(): tc.find(subpatt) @@ -686,19 +635,16 @@ self.visit_url( '%s/datasets/%s/display/' % ( self.url, self.security.encode_id( hda_id ) ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() def view_history( self, history_id, strings_displayed=[] ): """Displays a history for viewing""" self.visit_url( '%s/history/view?id=%s' % ( self.url, self.security.encode_id( history_id ) ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() def edit_hda_attribute_info( self, hda_id, new_name='', new_info='', new_dbkey='', new_startcol='', strings_displayed=[], strings_not_displayed=[] ): """Edit history_dataset_association attribute information""" - self.home() self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) ) submit_required = False self.check_page_for_string( 'Edit Attributes' ) @@ -725,7 +671,6 @@ raise AssertionError( "String (%s) incorrectly displayed on Edit Attributes page." % check_str ) except: pass - self.home() def check_hda_attribute_info( self, hda_id, strings_displayed=[] ): """Edit history_dataset_association attribute information""" @@ -734,7 +679,6 @@ def auto_detect_metadata( self, hda_id ): """Auto-detect history_dataset_association metadata""" - self.home() self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) ) self.check_page_for_string( 'This will inspect the dataset and attempt' ) tc.fv( 'auto_detect', 'detect', 'Auto-detect' ) @@ -745,28 +689,23 @@ except AssertionError: self.check_page_for_string( 'Attributes updated' ) #self.check_page_for_string( 'Attributes updated' ) - self.home() def convert_format( self, hda_id, target_type ): """Convert format of history_dataset_association""" - self.home() self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) ) self.check_page_for_string( 'This will inspect the dataset and attempt' ) tc.fv( 'convert_data', 'target_type', target_type ) tc.submit( 'convert_data' ) self.check_page_for_string( 'The file conversion of Convert BED to GFF on data' ) self.wait() # wait for the format convert tool to finish before returning - self.home() def change_datatype( self, hda_id, datatype ): """Change format of history_dataset_association""" - self.home() self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) ) self.check_page_for_string( 'This will change the datatype of the existing dataset but' ) tc.fv( 'change_datatype', 'datatype', datatype ) tc.submit( 'change' ) self.check_page_for_string( 'Changed the type of dataset' ) - self.home() def copy_history_item( self, source_dataset_id=None, target_history_id=None, all_target_history_ids=[], deleted_history_ids=[] ): @@ -774,7 +713,6 @@ Copy 1 history_dataset_association to 1 history (Limited by twill since it doesn't support multiple field names, such as checkboxes """ - self.home() self.visit_url( "%s/dataset/copy_datasets?source_dataset_ids=%s" % ( self.url, source_dataset_id ) ) self.check_page_for_string( 'Source History:' ) # Make sure all of users active histories are displayed @@ -792,7 +730,6 @@ tc.submit( 'do_copy' ) check_str = '1 dataset copied to 1 history' self.check_page_for_string( check_str ) - self.home() def get_hids_in_history( self ): """Returns the list of hid values for items in a history""" @@ -915,11 +852,10 @@ def __default_dataset_fetcher( self ): def fetcher( hda_id, filename=None ): if filename is None: - page_url = "display?encoded_id=%s" % hda_id - self.home() # I assume this is not needed. + page_url = "/display?encoded_id=%s" % hda_id else: - page_url = "datasets/%s/display/%s" % ( hda_id, filename ) - self.visit_page( page_url ) + page_url = "/datasets/%s/display/%s" % ( hda_id, filename ) + self.visit_url( page_url ) data = self.last_page() return data @@ -1019,7 +955,8 @@ def create( self, cntrller='user', email='test(a)bx.psu.edu', password='testuser', username='admin-user', redirect='' ): # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). - self.visit_url( "%s/user/create?cntrller=%s&use_panels=False" % ( self.url, cntrller ) ) + params = dict( cntrller=cntrller, use_panels=False ) + self.visit_url( "/user/create", params ) tc.fv( 'registration', 'email', email ) tc.fv( 'registration', 'redirect', redirect ) tc.fv( 'registration', 'password', password ) @@ -1095,7 +1032,6 @@ tc.submit( "edit_user_info_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home() def user_set_default_permissions( self, cntrller='user', permissions_out=[], permissions_in=[], role_id='2' ): # role.id = 2 is Private Role for test2(a)bx.psu.edu @@ -1112,7 +1048,6 @@ url = "%s&%s=%s" % ( url, key, str( role_id ) ) self.visit_url( "%s/%s" % ( self.url, url ) ) self.check_page_for_string( 'Default new history permissions have been changed.' ) - self.home() def history_set_default_permissions( self, permissions_out=[], permissions_in=[], role_id=3 ): # role.id = 3 is Private Role for test3(a)bx.psu.edu # NOTE: Twill has a bug that requires the ~/user/permissions page to contain at least 1 option value @@ -1126,10 +1061,8 @@ for pi in permissions_in: key = '%s_in' % pi url = "%s&%s=%s" % ( url, key, str( role_id ) ) - self.home() self.visit_url( "%s/%s" % ( self.url, url ) ) self.check_page_for_string( 'Default history permissions have been changed.' ) - self.home() def login( self, email='test(a)bx.psu.edu', password='testuser', username='admin-user', redirect='' ): # test(a)bx.psu.edu is configured as an admin user @@ -1139,14 +1072,12 @@ # The acount has previously been created, so just login. # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). - self.visit_url( "%s/user/login?use_panels=False" % self.url ) + self.visit_url( "/user/login?use_panels=False" ) self.submit_form( 1, 'login_button', email=email, redirect=redirect, password=password ) def logout( self ): - self.home() - self.visit_page( "user/logout" ) + self.visit_url( "%s/user/logout" % self.url ) self.check_page_for_string( "You have been logged out" ) - self.home() # Functions associated with browsers, cookies, HTML forms and page visits @@ -1208,9 +1139,6 @@ """Clears a form""" tc.formclear(str(form)) - def home( self ): - self.visit_url( self.url ) - def last_page( self ): return tc.browser.get_html() @@ -1383,16 +1311,30 @@ # Submit for refresh tc.submit( '___refresh_grouping___' ) - def visit_page( self, page ): - # tc.go("./%s" % page) - if not page.startswith( "/" ): - page = "/" + page - tc.go( self.url + page ) - tc.code( 200 ) - - def visit_url( self, url ): - tc.go("%s" % url) - tc.code( 200 ) + def visit_url( self, url, params=None, checkbox_params=None, allowed_codes=[ 200 ] ): + if params is None: + params = dict() + parsed_url = urlparse( url ) + if len( parsed_url.netloc ) == 0: + url = 'http://%s:%s%s' % ( self.host, self.port, parsed_url.path ) + else: + url = '%s://%s%s' % ( parsed_url.scheme, parsed_url.netloc, parsed_url.path ) + if parsed_url.query: + for query_parameter in parsed_url.query.split( '&' ): + key, value = query_parameter.split( '=' ) + params[ key ] = value + if params: + url += '?%s' % urllib.urlencode( params ) + if checkbox_params is not None: + if params or parsed_url.query: + url += '&%s&%s' % ( urllib.urlencode( checkbox_params ), urllib.urlencode( checkbox_params ) ) + else: + url += '?%s&%s' % ( urllib.urlencode( checkbox_params ), urllib.urlencode( checkbox_params ) ) + new_url = tc.go( url ) + return_code = tc.browser.get_code() + assert return_code in allowed_codes, 'Invalid HTTP return code %s, allowed codes: %s' % \ + ( return_code, ', '.join( str( code ) for code in allowed_codes ) ) + return new_url """Functions associated with Galaxy tools""" def run_tool( self, tool_id, repeat_name=None, **kwd ): @@ -1412,9 +1354,9 @@ def run_ucsc_main( self, track_params, output_params ): """Gets Data From UCSC""" tool_id = "ucsc_table_direct1" - track_string = urllib.urlencode( track_params ) galaxy_url = urllib.quote_plus( "%s/tool_runner/index?" % self.url ) - self.visit_url( "http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=%s&hgta_compressType=non…" % ( galaxy_url, tool_id, track_string ) ) + track_params.update( dict( GALAXY_URL=galaxy_url, hgta_compressType='none', tool_id=tool_id ) ) + self.visit_url( "http://genome.ucsc.edu/cgi-bin/hgTables", params=track_params ) tc.fv( "mainForm", "hgta_doTopSubmit", "get output" ) self.submit_form( button="get output" ) tc.fv( 2, "hgta_doGalaxyQuery", "Send query to Galaxy" ) @@ -1486,41 +1428,32 @@ def reset_password_as_admin( self, user_id, password='testreset' ): """Reset a user password""" - self.home() self.visit_url( "%s/admin/reset_user_password?id=%s" % ( self.url, user_id ) ) tc.fv( "1", "password", password ) tc.fv( "1", "confirm", password ) tc.submit( "reset_user_password_button" ) self.check_page_for_string( "Passwords reset for 1 user." ) - self.home() def mark_user_deleted( self, user_id, email='' ): """Mark a user as deleted""" - self.home() self.visit_url( "%s/admin/users?operation=delete&id=%s" % ( self.url, user_id ) ) check_str = "Deleted 1 users" self.check_page_for_string( check_str ) - self.home() def undelete_user( self, user_id, email='' ): """Undelete a user""" - self.home() self.visit_url( "%s/admin/users?operation=undelete&id=%s" % ( self.url, user_id ) ) check_str = "Undeleted 1 users" self.check_page_for_string( check_str ) - self.home() def purge_user( self, user_id, email ): """Purge a user account""" - self.home() self.visit_url( "%s/admin/users?operation=purge&id=%s" % ( self.url, user_id ) ) check_str = "Purged 1 users" self.check_page_for_string( check_str ) - self.home() def manage_roles_and_groups_for_user( self, user_id, in_role_ids=[], out_role_ids=[], in_group_ids=[], out_group_ids=[], strings_displayed=[] ): - self.home() url = "%s/admin/manage_roles_and_groups_for_user?id=%s" % ( self.url, user_id ) if in_role_ids: url += "&in_roles=%s" % ','.join( in_role_ids ) @@ -1535,7 +1468,6 @@ self.visit_url( url ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() # Tests associated with roles def browse_roles( self, strings_displayed=[] ): @@ -1552,16 +1484,17 @@ private_role='', strings_displayed=[] ): """Create a new role""" - url = "%s/admin/roles?operation=create&create_role_button=Save&name=%s&description=%s" % \ - ( self.url, name.replace( ' ', '+' ), description.replace( ' ', '+' ) ) + url = "/admin/roles" + url_params = dict( operation='create', create_role_button='Save', name=name, description=description ) if in_user_ids: - url += "&in_users=%s" % ','.join( in_user_ids ) + url_params[ 'in_users' ] = ','.join( in_user_ids ) if in_group_ids: - url += "&in_groups=%s" % ','.join( in_group_ids ) + url_params[ 'in_groups' ] = ','.join( in_group_ids ) if create_group_for_role == 'yes': - url += '&create_group_for_role=yes&create_group_for_role=yes' - self.home() - self.visit_url( url ) + checkbox_params = dict( create_group_for_role='yes' ) + else: + checkbox_params = None + self.visit_url( url, url_params, checkbox_params=checkbox_params ) for check_str in strings_displayed: self.check_page_for_string( check_str ) if private_role: @@ -1573,47 +1506,36 @@ except AssertionError: # Reaching here is the behavior we want since no private roles should be displayed pass - self.home() self.visit_url( "%s/admin/roles" % self.url ) self.check_page_for_string( name ) - self.home() def rename_role( self, role_id, name='Role One Renamed', description='This is Role One Re-described' ): """Rename a role""" - self.home() self.visit_url( "%s/admin/roles?operation=rename&id=%s" % ( self.url, role_id ) ) self.check_page_for_string( 'Change role name and description' ) tc.fv( "1", "name", name ) tc.fv( "1", "description", description ) tc.submit( "rename_role_button" ) - self.home() def mark_role_deleted( self, role_id, role_name ): """Mark a role as deleted""" - self.home() self.visit_url( "%s/admin/roles?operation=delete&id=%s" % ( self.url, role_id ) ) check_str = "Deleted 1 roles: %s" % role_name self.check_page_for_string( check_str ) - self.home() def undelete_role( self, role_id, role_name ): """Undelete an existing role""" - self.home() self.visit_url( "%s/admin/roles?operation=undelete&id=%s" % ( self.url, role_id ) ) check_str = "Undeleted 1 roles: %s" % role_name self.check_page_for_string( check_str ) - self.home() def purge_role( self, role_id, role_name ): """Purge an existing role""" - self.home() self.visit_url( "%s/admin/roles?operation=purge&id=%s" % ( self.url, role_id ) ) check_str = "Purged 1 roles: %s" % role_name self.check_page_for_string( check_str ) - self.home() def associate_users_and_groups_with_role( self, role_id, role_name, user_ids=[], group_ids=[] ): - self.home() url = "%s/admin/role?id=%s&role_members_edit_button=Save" % ( self.url, role_id ) if user_ids: url += "&in_users=%s" % ','.join( user_ids ) @@ -1622,26 +1544,25 @@ self.visit_url( url ) check_str = "Role '%s' has been updated with %d associated users and %d associated groups" % ( role_name, len( user_ids ), len( group_ids ) ) self.check_page_for_string( check_str ) - self.home() # Tests associated with groups def create_group( self, name='Group One', in_user_ids=[], in_role_ids=[], create_role_for_group='', strings_displayed=[] ): """Create a new group""" - url = "%s/admin/groups?operation=create&create_group_button=Save&name=%s" % ( self.url, name.replace( ' ', '+' ) ) + url = "/admin/groups" + params = dict( operation='create', create_group_button='Save', name=name ) if in_user_ids: - url += "&in_users=%s" % ','.join( in_user_ids ) + params [ 'in_users' ] = ','.join( in_user_ids ) if in_role_ids: - url += "&in_roles=%s" % ','.join( in_role_ids ) + params[ 'in_roles' ] = ','.join( in_role_ids ) if create_role_for_group == 'yes': - url += '&create_role_for_group=yes&create_role_for_group=yes' - self.home() - self.visit_url( url ) + checkbox_params = dict( create_role_for_group='yes' ) + else: + checkbox_params = None + self.visit_url( url, params=params, checkbox_params=checkbox_params ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() - self.visit_url( "%s/admin/groups" % self.url ) + self.visit_url( "/admin/groups" ) self.check_page_for_string( name ) - self.home() def browse_groups( self, strings_displayed=[] ): self.visit_url( '%s/admin/groups' % self.url ) @@ -1650,15 +1571,12 @@ def rename_group( self, group_id, name='Group One Renamed' ): """Rename a group""" - self.home() self.visit_url( "%s/admin/groups?operation=rename&id=%s" % ( self.url, group_id ) ) self.check_page_for_string( 'Change group name' ) tc.fv( "1", "name", name ) tc.submit( "rename_group_button" ) - self.home() def associate_users_and_roles_with_group( self, group_id, group_name, user_ids=[], role_ids=[] ): - self.home() url = "%s/admin/manage_users_and_roles_for_group?id=%s&group_roles_users_edit_button=Save" % ( self.url, group_id ) if user_ids: url += "&in_users=%s" % ','.join( user_ids ) @@ -1667,31 +1585,24 @@ self.visit_url( url ) check_str = "Group '%s' has been updated with %d associated roles and %d associated users" % ( group_name, len( role_ids ), len( user_ids ) ) self.check_page_for_string( check_str ) - self.home() def mark_group_deleted( self, group_id, group_name ): """Mark a group as deleted""" - self.home() self.visit_url( "%s/admin/groups?operation=delete&id=%s" % ( self.url, group_id ) ) check_str = "Deleted 1 groups: %s" % group_name self.check_page_for_string( check_str ) - self.home() def undelete_group( self, group_id, group_name ): """Undelete an existing group""" - self.home() self.visit_url( "%s/admin/groups?operation=undelete&id=%s" % ( self.url, group_id ) ) check_str = "Undeleted 1 groups: %s" % group_name self.check_page_for_string( check_str ) - self.home() def purge_group( self, group_id, group_name ): """Purge an existing group""" - self.home() self.visit_url( "%s/admin/groups?operation=purge&id=%s" % ( self.url, group_id ) ) check_str = "Purged 1 groups: %s" % group_name self.check_page_for_string( check_str ) - self.home() # Form stuff def create_form( self, name, description, form_type, field_type='TextField', form_layout_name='', @@ -1743,12 +1654,10 @@ tc.submit( "save_changes_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home() def edit_form( self, id, form_type='', new_form_name='', new_form_desc='', field_dicts=[], field_index=0, strings_displayed=[], strings_not_displayed=[], strings_displayed_after_submit=[] ): """Edit form details; name and description""" - self.home() self.visit_url( "%s/forms/edit_form_definition?id=%s" % ( self.url, id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) @@ -1784,10 +1693,9 @@ tc.submit( "save_changes_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home() + def view_form( self, id, form_type='', form_name='', form_desc='', form_layout_name='', field_dicts=[] ): '''View form details''' - self.home() self.visit_url( "%s/forms/view_latest_form_definition?id=%s" % ( self.url, id ) ) #self.check_page_for_string( form_type ) self.check_page_for_string( form_name ) @@ -1800,15 +1708,13 @@ if field_dict[ 'type' ].lower() == 'selectfield': for option_index, option in enumerate( field_dict[ 'selectlist' ] ): self.check_page_for_string( option ) - self.home() + def mark_form_deleted( self, form_id ): """Mark a form_definition as deleted""" - self.home() url = "%s/forms/delete_form_definition?id=%s" % ( self.url, form_id ) self.visit_url( url ) check_str = "1 forms have been deleted." self.check_page_for_string( check_str ) - self.home() # External services stuff def reload_external_service( self, external_service_type_id, strings_displayed=[], strings_displayed_after_submit=[] ): @@ -1819,6 +1725,7 @@ tc.submit( "reload_external_service_type_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) + def create_external_service( self, name, description, version, external_service_type_id, field_values={}, strings_displayed=[], strings_displayed_after_submit=[] ): self.visit_url( '%s/external_service/create_external_service' % self.url ) for check_str in strings_displayed: @@ -1832,10 +1739,12 @@ tc.submit( "create_external_service_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) + def view_external_service( self, external_service_id, strings_displayed=[] ): self.visit_url( '%s/external_service/view_external_service?id=%s' % ( self.url, external_service_id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) + def edit_external_service( self, external_service_id, field_values={}, strings_displayed=[], strings_displayed_after_submit=[] ): self.visit_url( '%s/external_service/edit_external_service?id=%s' % ( self.url, external_service_id ) ) for check_str in strings_displayed: @@ -1852,7 +1761,6 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) def create_request_type( self, name, desc, request_form_id, sample_form_id, states, strings_displayed=[], strings_displayed_after_submit=[] ): - self.home() self.visit_url( "%s/request_type/create_request_type" % self.url ) for check_str in strings_displayed: self.check_page_for_string( check_str ) @@ -1876,14 +1784,11 @@ for pi in permissions_in: key = '%s_in' % pi url = "%s&%s=%s" % ( url, key, role_ids_str ) - self.home() self.visit_url( "%s/%s" % ( self.url, url ) ) check_str = "Permissions updated for request type '%s'" % request_type_name self.check_page_for_string( check_str ) - self.home() def view_request_type( self, request_type_id, request_type_name, sample_states, strings_displayed=[] ): '''View request_type details''' - self.home() self.visit_url( "%s/request_type/view_request_type?id=%s" % ( self.url, request_type_id ) ) self.check_page_for_string( '"%s" request type' % request_type_name ) for name, desc in sample_states: @@ -1926,7 +1831,6 @@ tc.submit( "create_request_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home() def view_request( self, cntrller, request_id, strings_displayed=[], strings_displayed_count=[], strings_not_displayed=[] ): self.visit_url( "%s/%s/browse_requests?operation=view_request&id=%s" % ( self.url, cntrller, request_id ) ) self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) @@ -2121,7 +2025,6 @@ for check_str, count in strings_displayed_count: self.check_string_count_in_page( check_str, count ) def add_user_address( self, user_id, address_dict ): - self.home() self.visit_url( "%s/user/new_address?cntrller=user&user_id=%s" % ( self.url, user_id ) ) self.check_page_for_string( 'Add new address' ) for field_name, value in address_dict.items(): @@ -2137,7 +2040,6 @@ dis-inherit your template, call the manage_library_template_inheritance() below immediately after you call this method in your test code. Templates added to Requesttype objects are always inherited to samples. """ - self.home() if item_type == 'library': url = "%s/library_common/add_template?cntrller=%s&item_type=%s&form_type=%s&library_id=%s" % \ ( self.url, cntrller, item_type, form_type, library_id ) @@ -2155,10 +2057,9 @@ tc.fv( "select_template", "inheritable", '1' ) tc.submit( "add_template_button" ) self.check_page_for_string = 'A template based on the form "%s" has been added to this' % form_name - self.home() + def manage_library_template_inheritance( self, cntrller, item_type, library_id, folder_id=None, ldda_id=None, inheritable=True ): # If inheritable is True, the item is currently inheritable. - self.home() if item_type == 'library': url = "%s/library_common/manage_template_inheritance?cntrller=%s&item_type=%s&library_id=%s" % \ ( self.url, cntrller, item_type, library_id ) @@ -2173,7 +2074,7 @@ self.check_page_for_string = 'will no longer be inherited to contained folders and datasets' else: self.check_page_for_string = 'will now be inherited to contained folders and datasets' - self.home() + def browse_libraries_admin( self, deleted=False, strings_displayed=[], strings_not_displayed=[] ): self.visit_url( '%s/library_admin/browse_libraries?sort=name&f-description=All&f-name=All&f-deleted=%s' % ( self.url, str( deleted ) ) ) for check_str in strings_displayed: @@ -2214,7 +2115,7 @@ tc.submit( "create_library_button" ) check_str = "The new library named '%s' has been created" % name self.check_page_for_string( check_str ) - self.home() + def edit_template( self, cntrller, item_type, form_type, library_id, field_type, field_label_1, field_helptext_1, field_default_1, folder_id='', ldda_id='', action='add_field' ): """Edit the form fields defining a library template""" @@ -2251,7 +2152,7 @@ # Set the template field value tc.fv( "edit_info", field_name, field_value ) tc.submit( 'edit_info_button' ) - self.home() + def library_permissions( self, library_id, library_name, role_ids_str, permissions_in, permissions_out, cntrller='library_admin' ): # role_ids_str must be a comma-separated string of role ids url = "library_common/library_permissions?id=%s&cntrller=%s&update_roles_button=Save" % ( library_id, cntrller ) @@ -2261,11 +2162,10 @@ for pi in permissions_in: key = '%s_in' % pi url = "%s&%s=%s" % ( url, key, role_ids_str ) - self.home() self.visit_url( "%s/%s" % ( self.url, url ) ) check_str = "Permissions updated for library '%s'." % library_name self.check_page_for_string( check_str ) - self.home() + def make_library_item_public( self, library_id, id, cntrller='library_admin', item_type='library', contents=False, library_name='', folder_name='', ldda_name='' ): url = "%s/library_common/make_library_item_public?cntrller=%s&library_id=%s&item_type=%s&id=%s&contents=%s" % \ @@ -2293,7 +2193,7 @@ tc.submit( "new_folder_button" ) check_str = "The new folder named '%s' has been added to the data library." % name self.check_page_for_string( check_str ) - self.home() + def folder_info( self, cntrller, folder_id, library_id, name='', new_name='', description='', template_refresh_field_name='1_field_name', template_refresh_field_contents='', template_fields=[], strings_displayed=[], strings_not_displayed=[], strings_displayed_after_submit=[], strings_not_displayed_after_submit=[] ): @@ -2331,7 +2231,6 @@ raise AssertionError( "String (%s) incorrectly displayed." % check_str ) except: pass - self.home() # Library dataset stuff def upload_library_dataset( self, cntrller, library_id, folder_id, filename='', server_dir='', replace_id='', @@ -2342,29 +2241,29 @@ """Add datasets to library using any upload_option""" # NOTE: due to the library_wait() method call at the end of this method, no tests should be done # for strings_displayed_after_submit. - url = "%s/library_common/upload_library_dataset?cntrller=%s&library_id=%s&folder_id=%s" % \ - ( self.url, cntrller, library_id, folder_id ) + params = dict( cntrller=cntrller, library_id=library_id, folder_id=folder_id ) + url = "%s/library_common/upload_library_dataset" % self.url if replace_id: # If we're uploading a new version of a library dataset, we have to include the replace_id param in the # request because the form field named replace_id will not be displayed on the upload form if we dont. - url += "&replace_id=%s" % replace_id - self.visit_url( url ) + params[ 'replace_id' ] = replace_id + self.visit_url( url, params=params ) if template_refresh_field_contents: # A template containing an AddressField is displayed on the upload form, so we need to refresh the form # with the received template_refresh_field_contents. self.refresh_form( template_refresh_field_name, template_refresh_field_contents ) for tup in template_fields: tc.fv( "1", tup[0], tup[1] ) - tc.fv( "1", "library_id", library_id ) - tc.fv( "1", "folder_id", folder_id ) - tc.fv( "1", "show_deleted", show_deleted ) - tc.fv( "1", "ldda_message", ldda_message ) - tc.fv( "1", "file_type", file_type ) - tc.fv( "1", "dbkey", dbkey ) + tc.fv( "upload_library_dataset", "library_id", library_id ) + tc.fv( "upload_library_dataset", "folder_id", folder_id ) + tc.fv( "upload_library_dataset", "show_deleted", show_deleted ) + tc.fv( "upload_library_dataset", "ldda_message", ldda_message ) + tc.fv( "upload_library_dataset", "file_type", file_type ) + tc.fv( "upload_library_dataset", "dbkey", dbkey ) if space_to_tab: - tc.fv( "1", "space_to_tab", space_to_tab ) + tc.fv( "upload_library_dataset", "space_to_tab", space_to_tab ) for role_id in roles: - tc.fv( "1", "roles", role_id ) + tc.fv( "upload_library_dataset", "roles", role_id ) # Refresh the form by selecting the upload_option - we do this here to ensure # all previously entered form contents are retained. self.refresh_form( 'upload_option', upload_option ) @@ -2380,21 +2279,21 @@ tc.submit( 'add_history_datasets_to_library_button' ) else: if upload_option in [ 'upload_paths', 'upload_directory' ]: - tc.fv( "1", "link_data_only", link_data_only ) + tc.fv( "upload_library_dataset", "link_data_only", link_data_only ) if upload_option == 'upload_paths': - tc.fv( "1", "filesystem_paths", filesystem_paths ) + tc.fv( "upload_library_dataset", "filesystem_paths", filesystem_paths ) if upload_option == 'upload_directory' and server_dir: - tc.fv( "1", "server_dir", server_dir ) + tc.fv( "upload_library_dataset", "server_dir", server_dir ) if upload_option == 'upload_file': if filename: filename = self.get_filename( filename ) - tc.formfile( "1", "files_0|file_data", filename ) + tc.formfile( "upload_library_dataset", "files_0|file_data", filename ) for check_str in strings_displayed: self.check_page_for_string( check_str ) tc.submit( "runtool_btn" ) # Give the files some time to finish uploading self.library_wait( library_id ) - self.home() + def ldda_permissions( self, cntrller, library_id, folder_id, id, role_ids_str, permissions_in=[], permissions_out=[], strings_displayed=[], ldda_name='' ): # role_ids_str must be a comma-separated string of role ids @@ -2413,7 +2312,7 @@ strings_displayed = [ "Permissions updated for dataset '%s'." % ldda_name ] for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() + def ldda_info( self, cntrller, library_id, folder_id, ldda_id, strings_displayed=[], strings_not_displayed=[] ): """View library_dataset_dataset_association information""" self.visit_url( "%s/library_common/ldda_info?cntrller=%s&library_id=%s&folder_id=%s&id=%s" % \ @@ -2426,7 +2325,7 @@ raise AssertionError( "String (%s) should not have been displayed on ldda info page." % check_str ) except: pass - self.home() + def ldda_edit_info( self, cntrller, library_id, folder_id, ldda_id, ldda_name, new_ldda_name='', template_refresh_field_name='1_field_name', template_refresh_field_contents='', template_fields=[], strings_displayed=[], strings_not_displayed=[] ): """Edit library_dataset_dataset_association information, optionally template element information""" @@ -2458,7 +2357,7 @@ raise AssertionError( "String (%s) should not have been displayed on ldda Edit Attributes page." % check_str ) except: pass - self.home() + def act_on_multiple_datasets( self, cntrller, library_id, do_action, ldda_ids='', strings_displayed=[] ): # Can't use the ~/library_admin/libraries form as twill barfs on it so we'll simulate the form submission # by going directly to the form action @@ -2474,7 +2373,6 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) def download_archive_of_library_files( self, cntrller, library_id, ldda_ids, format ): - self.home() # Here it would be ideal to have twill set form values and submit the form, but # twill barfs on that due to the recently introduced page wrappers around the contents # of the browse_library.mako template which enable panel layout when visiting the @@ -2494,7 +2392,6 @@ self.visit_url( url ) tc.code( 200 ) archive = self.write_temp_file( self.last_page(), suffix='.' + format ) - self.home() return archive def check_archive_contents( self, archive, lddas ): def get_ldda_path( ldda ): @@ -2542,7 +2439,6 @@ def move_library_item( self, cntrller, item_type, item_id, source_library_id, make_target_current, target_library_id=None, target_folder_id=None, strings_displayed=[], strings_displayed_after_submit=[] ): - self.home() params = dict( cntrller=cntrller, item_type=item_type, item_id=item_id, @@ -2552,7 +2448,7 @@ params[ 'target_library_id' ] = target_library_id if target_folder_id is not None: params[ 'target_folder_id' ] = target_folder_id - self.visit_url( "%s/library_common/move_library_item?%s" % ( self.url, urllib.urlencode( params ) ) ) + self.visit_url( "%s/library_common/move_library_item" % self.url, params=params ) if target_library_id: self.refresh_form( 'target_library_id', target_library_id, form_name='move_library_item' ) if target_folder_id: @@ -2562,39 +2458,36 @@ tc.submit( 'move_library_item_button' ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home() def delete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ): """Mark a library item as deleted""" - self.home() - self.visit_url( "%s/library_common/delete_library_item?cntrller=%s&library_id=%s&item_id=%s&item_type=%s" \ - % ( self.url, cntrller, library_id, item_id, item_type ) ) + params = dict( cntrller=cntrller, library_id=library_id, item_id=item_id, item_type=item_type ) + self.visit_url( "/library_common/delete_library_item", params ) if item_type == 'library_dataset': item_desc = 'Dataset' else: item_desc = item_type.capitalize() check_str = "marked deleted" - self.check_page_for_string( check_str ) - self.home() + self.check_for_strings( strings_displayed=[ item_desc, check_str ] ) + def undelete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ): """Mark a library item as deleted""" - self.home() - self.visit_url( "%s/library_common/undelete_library_item?cntrller=%s&library_id=%s&item_id=%s&item_type=%s" \ - % ( self.url, cntrller, library_id, item_id, item_type ) ) + params = dict( cntrller=cntrller, library_id=library_id, item_id=item_id, item_type=item_type ) + self.visit_url( "/library_common/undelete_library_item", params ) if item_type == 'library_dataset': item_desc = 'Dataset' else: item_desc = item_type.capitalize() check_str = "marked undeleted" - self.check_page_for_string( check_str ) - self.home() + self.check_for_strings( strings_displayed=[ item_desc, check_str ] ) + def purge_library( self, library_id, library_name ): """Purge a library""" - self.home() - self.visit_url( "%s/library_admin/purge_library?id=%s" % ( self.url, library_id ) ) + params = dict( id=library_id ) + self.visit_url( "/library_admin/purge_library", params ) check_str = "Library '%s' and all of its contents have been purged" % library_name self.check_page_for_string( check_str ) - self.home() + def library_wait( self, library_id, cntrller='library_admin', maxiter=90 ): """Waits for the tools to finish""" count = 0 diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/functional/test_admin_features.py --- a/test/functional/test_admin_features.py +++ b/test/functional/test_admin_features.py @@ -232,7 +232,6 @@ # Rename the group rename = "Group One's been Renamed" self.rename_group( self.security.encode_id( group_one.id ), name=rename, ) - self.home() self.visit_url( '%s/admin/groups' % self.url ) self.check_page_for_string( rename ) # Reset the group back to the original name @@ -365,7 +364,6 @@ def test_065_mark_role_deleted( self ): """Testing marking a role as deleted""" # Logged in as admin_user - self.home() self.browse_roles( strings_displayed=[ role_two.name ] ) self.mark_role_deleted( self.security.encode_id( role_two.id ), role_two.name ) refresh( role_two ) diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -1,4 +1,3 @@ -import urllib import galaxy.model from galaxy.model.orm import * from base.test_db_util import sa_session @@ -109,7 +108,7 @@ .first() assert history1 is not None, "Problem retrieving history1 from database" self.upload_file( '1.bed', dbkey='hg18' ) - self.new_history( name=urllib.quote( 'history2' ) ) + self.new_history( name='history2' ) global history2 history2 = sa_session.query( galaxy.model.History ) \ .filter( and_( galaxy.model.History.table.c.deleted == False, @@ -158,7 +157,7 @@ assert history3 is not None, "Problem retrieving history3 from database" if history3.deleted: raise AssertionError( "History id %d deleted when it should not be" % latest_history.id ) - self.rename_history( self.security.encode_id( history3.id ), history3.name, new_name=urllib.quote( 'history 3' ) ) + self.rename_history( self.security.encode_id( history3.id ), history3.name, new_name='history 3' ) sa_session.refresh( history3 ) def test_015_history_list( self ): @@ -348,7 +347,7 @@ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history4 is not None, "Problem retrieving history4 from database" - self.rename_history( self.security.encode_id( history4.id ), history4.name, new_name=urllib.quote( 'history 4' ) ) + self.rename_history( self.security.encode_id( history4.id ), history4.name, new_name='history 4' ) sa_session.refresh( history4 ) # Galaxy's new history sharing code does not yet support sharing multiple histories; when support for sharing multiple histories is added, # this test will be uncommented and updated. @@ -383,7 +382,7 @@ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history5 is not None, "Problem retrieving history5 from database" - self.rename_history( self.security.encode_id( history5.id ), history5.name, new_name=urllib.quote( 'history 5' ) ) + self.rename_history( self.security.encode_id( history5.id ), history5.name, new_name='history 5' ) # Current history is history5 sa_session.refresh( history5 ) # Due to the limitations of twill ( not functional with the permissions forms ), we're forced @@ -547,7 +546,7 @@ # Make sure the history was unshared correctly self.logout() self.login( email=regular_user2.email ) - self.visit_page( "root/history_options" ) + self.visit_url( "/root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) raise AssertionError( "history5 still shared with regular_user2 after unsharing it with that user." ) @@ -695,7 +694,7 @@ # Make sure the histories were unshared correctly self.logout() self.login( email=regular_user2.email ) - self.visit_page( "root/history_options" ) + self.visit_url( "/root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) raise AssertionError( "history5 still shared with regular_user2 after unshaing it with that user." ) @@ -704,7 +703,7 @@ self.logout() self.login( email=regular_user3.email ) - self.visit_page( "root/history_options" ) + self.visit_url( "/root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) raise AssertionError( "history5 still shared with regular_user3 after unshaing it with that user." ) @@ -724,7 +723,7 @@ # Logged in as admin_user # create a new history and upload a new hda (1.bed) into it - self.new_history( name=urllib.quote( 'show hide deleted datasets' ) ) + self.new_history( name='show hide deleted datasets' ) latest_history = ( sa_session.query( galaxy.model.History ) .filter( and_( galaxy.model.History.table.c.deleted == False, @@ -739,7 +738,6 @@ .first() ) # delete that item and make sure the history is not empty - self.home() log.info( 'deleting last hda' ) self.delete_history_item( str( latest_hda.id ) ) # check the number of items returned from the api @@ -776,13 +774,12 @@ assert latest_history is not None, "Problem retrieving latest_history from database" self.rename_history( self.security.encode_id( latest_history.id ), - latest_history.name, new_name=urllib.quote( 'delete undelete history items' ) ) + latest_history.name, new_name='delete undelete history items' ) # Add a new history item self.upload_file( '1.bed', dbkey='hg15' ) latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ .first() - self.home() self.visit_url( "%s/history/?show_deleted=False" % self.url ) self.check_page_for_string( '1.bed' ) self.check_page_for_string( 'hg15' ) @@ -798,7 +795,6 @@ pass # Undelete the history item self.undelete_history_item( str( latest_hda.id ) ) - self.home() self.visit_url( "%s/history/?show_deleted=False" % self.url ) self.check_page_for_string( '1.bed' ) self.check_page_for_string( 'hg15' ) @@ -807,7 +803,7 @@ def test_080_copying_history_items_between_histories( self ): """Testing copying history items between histories""" # logged in as admin_user - self.new_history( name=urllib.quote( 'copy history items' ) ) + self.new_history( name='copy history items' ) history6 = sa_session.query( galaxy.model.History ) \ .filter( and_( galaxy.model.History.table.c.deleted == False, galaxy.model.History.table.c.user_id == admin_user.id ) ) \ @@ -836,7 +832,7 @@ if len( history6.datasets ) != 2: raise AssertionError( "Copying hda1 to the current history failed, history 6 has %d datasets, but should have 2" % len( history6.datasets ) ) # Test copying 1 hda to another history - self.new_history( name=urllib.quote( 'copy history items - 2' ) ) + self.new_history( name='copy history items - 2' ) history7 = sa_session.query( galaxy.model.History ) \ .filter( and_( galaxy.model.History.table.c.deleted == False, galaxy.model.History.table.c.user_id == admin_user.id ) ) \ diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/functional/test_metadata_editing.py --- a/test/functional/test_metadata_editing.py +++ b/test/functional/test_metadata_editing.py @@ -27,7 +27,6 @@ latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ .first() - self.home() # Due to twill not being able to handle the permissions forms, we'll eliminate # DefaultHistoryPermissions prior to uploading a dataset so that the permission # form will not be displayed on ted edit attributes page. diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -39,7 +39,6 @@ # TODO: Figure out a way to alter these attributes during tests. self.galaxy_tool_dependency_dir = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR' ) self.shed_tools_dict = {} - self.home() def initiate_installation_process( self, install_tool_dependencies=False, install_repository_dependencies=True, no_changes=True, new_tool_panel_section_label=None ): diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -61,7 +61,6 @@ # TODO: Figure out a way to alter these attributes during tests. self.galaxy_tool_dependency_dir = os.environ.get( 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ) self.shed_tools_dict = {} - self.home() def add_repository_review_component( self, **kwd ): url = '/repository_review/create_component?operation=create' @@ -597,10 +596,8 @@ self.submit_form( '1', 'login_button', email=email, redirect=redirect, password=password ) def galaxy_logout( self ): - self.home() self.visit_galaxy_url( "/user/logout" ) self.check_page_for_string( "You have been logged out" ) - self.home() def generate_complex_dependency_xml( self, filename, filepath, repository_tuples, package, version ): file_path = os.path.join( filepath, filename ) 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: Fix divide-by-0 resulting from mean depth of 0 in bai data provider.
by commits-noreply＠bitbucket.org 23 Apr '14

23 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0bc0fd94aaa4/ Changeset: 0bc0fd94aaa4 User: Jeremy Goecks Date: 2014-04-23 22:31:23 Summary: Fix divide-by-0 resulting from mean depth of 0 in bai data provider. Affected #: 1 file diff -r b2cf571d0b63948a7252fc703200b854f964bad6 -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -972,7 +972,7 @@ return { 'data': [], 'message': None, 'max_low': start, 'max_high': start } read_len = len( first_read.seq ) - num_reads = ( end - start ) * mean_depth / float ( read_len ) + num_reads = max( ( end - start ) * mean_depth / float ( read_len ), 1 ) threshold = float( max_vals )/ num_reads iterator = itertools.chain( iter( [ first_read ] ), iterator ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: UI, History: first pass at making display_structured a bit more useful and clean up the styling; CSS: move hda styling out of history scope
by commits-noreply＠bitbucket.org 23 Apr '14

23 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b2cf571d0b63/ Changeset: b2cf571d0b63 User: carlfeberhard Date: 2014-04-23 21:25:25 Summary: UI, History: first pass at making display_structured a bit more useful and clean up the styling; CSS: move hda styling out of history scope Affected #: 5 files diff -r 54695d3fa468250b1ee13a90facc753dc3d9831d -r b2cf571d0b63948a7252fc703200b854f964bad6 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -502,7 +502,7 @@ # Sort items by age items.sort( key=( lambda x: x[0].create_time ), reverse=True ) # - return trans.fill_template( "history/display_structured.mako", items=items ) + return trans.fill_template( "history/display_structured.mako", items=items, history=history ) @web.expose def delete_hidden_datasets( self, trans ): diff -r 54695d3fa468250b1ee13a90facc753dc3d9831d -r b2cf571d0b63948a7252fc703200b854f964bad6 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1621,50 +1621,50 @@ .search-input .search-clear,.search-input .search-loading{position:relative;display:inline-block;float:right;margin-top:-23px;margin-right:4px;font-size:1.4em;line-height:23px;color:grey} .search-input .search-clear:hover{color:#303030} #history-refresh-button,#history-options-button{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;padding:0px} -.history-panel .dataset{border:1px solid #bfbfbf}.history-panel .dataset .vertical-spacing{margin-bottom:8px} -.history-panel .dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} -.history-panel .dataset .dataset-padding{padding:6px 10px 6px 8px} -.history-panel .dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} -.history-panel .dataset .help-text{font-weight:normal;color:#555} -.history-panel .dataset .dataset-selector{float:left;display:none;width:32px;height:32px;margin:0 0 -6px 0;padding:8px 0 2px 7px;font-size:80%;color:#333;cursor:pointer;vertical-align:middle} -.history-panel .dataset .dataset-selector:hover{color:maroon} -.history-panel .dataset .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} -.history-panel .dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} -.history-panel .dataset .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.history-panel .dataset .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.history-panel .dataset .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.history-panel .dataset .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.history-panel .dataset .dataset-primary-actions .icon-btn:only-child{margin:0px;border-radius:3px} -.history-panel .dataset .dataset-primary-actions .icon-btn{margin-left:2px} -.history-panel .dataset .dataset-body{display:none;padding:0 10px 6px 8px}.history-panel .dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} -.history-panel .dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} -.history-panel .dataset .dataset-body .prompt{font-weight:normal;color:#555} -.history-panel .dataset .dataset-body .prompt:after{content:':';margin-right:4px} -.history-panel .dataset .dataset-body .dataset-summary{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} -.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} -.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555;margin-right:4px} -.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} -.history-panel .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto}.history-panel .dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} -.history-panel .dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} -.history-panel .dataset .dataset-body .dataset-actions .left{display:inline-block;float:left}.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:only-child{margin:0px;border-radius:3px} -.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} -.history-panel .dataset .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} -.history-panel .dataset .dataset-body .dataset-actions .right{display:inline-block;float:right}.history-panel .dataset .dataset-body .dataset-actions .right .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.history-panel .dataset .dataset-body .dataset-actions .right .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.history-panel .dataset .dataset-body .dataset-actions .right .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.history-panel .dataset .dataset-body .dataset-actions .right .icon-btn:only-child{margin:0px;border-radius:3px} -.history-panel .dataset .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} -.history-panel .dataset .dataset-body .tags-display{display:none;margin-bottom:8px}.history-panel .dataset .dataset-body .tags-display .select2-container{min-width:0px}.history-panel .dataset .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} -.history-panel .dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.history-panel .dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} -.history-panel .dataset .dataset-body .annotation-display .annotation:empty{height:22px} -.history-panel .dataset .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} -.history-panel .dataset .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} -.history-panel .dataset .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} -.history-panel .dataset .dataset-body .dataset-peek{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.history-panel .dataset .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} -.history-panel .dataset .dataset-body .dataset-peek pre.peek table,.history-panel .dataset .dataset-body .dataset-peek pre.peek th,.history-panel .dataset .dataset-body .dataset-peek pre.peek tr,.history-panel .dataset .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} -.history-panel .dataset .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;margin-right:4px;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} +.hda.dataset{border:1px solid #bfbfbf}.hda.dataset .vertical-spacing{margin-bottom:8px} +.hda.dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} +.hda.dataset .dataset-padding{padding:6px 10px 6px 8px} +.hda.dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} +.hda.dataset .help-text{font-weight:normal;color:#555} +.hda.dataset .dataset-selector{float:left;display:none;width:32px;height:32px;margin:0 0 -6px 0;padding:8px 0 2px 7px;font-size:80%;color:#333;cursor:pointer;vertical-align:middle} +.hda.dataset .dataset-selector:hover{color:maroon} +.hda.dataset .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} +.hda.dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} +.hda.dataset .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.hda.dataset .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.hda.dataset .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.hda.dataset .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.hda.dataset .dataset-primary-actions .icon-btn:only-child{margin:0px;border-radius:3px} +.hda.dataset .dataset-primary-actions .icon-btn{margin-left:2px} +.hda.dataset .dataset-body{display:none;padding:0 10px 6px 8px}.hda.dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} +.hda.dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} +.hda.dataset .dataset-body .prompt{font-weight:normal;color:#555} +.hda.dataset .dataset-body .prompt:after{content:':';margin-right:4px} +.hda.dataset .dataset-body .dataset-summary{margin-bottom:8px}.hda.dataset .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} +.hda.dataset .dataset-body .dataset-summary .dataset-datatype,.hda.dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.hda.dataset .dataset-body .dataset-summary .dataset-datatype .value,.hda.dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} +.hda.dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555;margin-right:4px} +.hda.dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} +.hda.dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto}.hda.dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} +.hda.dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} +.hda.dataset .dataset-body .dataset-actions .left{display:inline-block;float:left}.hda.dataset .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.hda.dataset .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.hda.dataset .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.hda.dataset .dataset-body .dataset-actions .left .icon-btn:only-child{margin:0px;border-radius:3px} +.hda.dataset .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} +.hda.dataset .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} +.hda.dataset .dataset-body .dataset-actions .right{display:inline-block;float:right}.hda.dataset .dataset-body .dataset-actions .right .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.hda.dataset .dataset-body .dataset-actions .right .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.hda.dataset .dataset-body .dataset-actions .right .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.hda.dataset .dataset-body .dataset-actions .right .icon-btn:only-child{margin:0px;border-radius:3px} +.hda.dataset .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} +.hda.dataset .dataset-body .tags-display{display:none;margin-bottom:8px}.hda.dataset .dataset-body .tags-display .select2-container{min-width:0px}.hda.dataset .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} +.hda.dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.hda.dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} +.hda.dataset .dataset-body .annotation-display .annotation:empty{height:22px} +.hda.dataset .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} +.hda.dataset .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} +.hda.dataset .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} +.hda.dataset .dataset-body .dataset-peek{margin-bottom:8px}.hda.dataset .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.hda.dataset .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} +.hda.dataset .dataset-body .dataset-peek pre.peek table,.hda.dataset .dataset-body .dataset-peek pre.peek th,.hda.dataset .dataset-body .dataset-peek pre.peek tr,.hda.dataset .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} +.hda.dataset .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;margin-right:4px;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} .state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .history-panel [class$="messagesmall"]{margin:0px} .history-panel .editable-text{border:solid transparent 1px} diff -r 54695d3fa468250b1ee13a90facc753dc3d9831d -r b2cf571d0b63948a7252fc703200b854f964bad6 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -125,254 +125,251 @@ // ---------------------------------------------------------------------------- datasets -//TODO: scope to history panels until embedded item .dataset is changed -.history-panel { - .dataset { - border: 1px solid @border-default-color; +.hda.dataset { + border: 1px solid @border-default-color; - // body mixins - @vertical-gap: 8px; - .vertical-spacing { - margin-bottom: @vertical-gap; + // body mixins + @vertical-gap: 8px; + .vertical-spacing { + margin-bottom: @vertical-gap; + } + .info-section { + border-radius: 3px; + border: 1px solid fadeout( @layout-border-color, 70% ); + //background-color: fadeout( white, 60% ); + padding: 4px; + } + @spacing-top : 6px; + @spacing-right : 10px; + @spacing-bottom : 6px; + @spacing-left : 8px; + .dataset-padding { + padding: @spacing-top @spacing-right @spacing-bottom @spacing-left; + } + + [class$=messagesmall] { + margin: @spacing-top @spacing-right ( @spacing-bottom - 4 ) @spacing-left; + font-size: 90%; + } + + .help-text { + font-weight: normal; + // font-style: italic; + // font-size: 90%; + color: #555; + } + + .dataset-selector { + float: left; + // always initially hidden and zero width + display: none; + width: 32px; + height: 32px; + //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish + margin: 0px 0px -( @spacing-bottom ) 0px; + padding: ( @spacing-top + 2 ) 0px 2px ( @spacing-left - 1 ); + font-size: 80%; + color: @btn-default-color; + cursor: pointer; + vertical-align: middle; + } + .dataset-selector:hover { + color: maroon; + } + + .dataset-title-bar { + cursor: pointer; + outline: none; + .dataset-padding; + + .dataset-state-icon { } - .info-section { - border-radius: 3px; - border: 1px solid fadeout( @layout-border-color, 70% ); - //background-color: fadeout( white, 60% ); - padding: 4px; + .dataset-title { + display: inline; + font-weight: bold; + text-decoration: underline; + word-wrap: break-word; + word-break: break-all; + line-height: 16px; } - @spacing-top : 6px; - @spacing-right : 10px; - @spacing-bottom : 6px; - @spacing-left : 8px; - .dataset-padding { - padding: @spacing-top @spacing-right @spacing-bottom @spacing-left; + } + + .dataset-primary-actions { + .icon-btn-group(); + float: right; + margin: @spacing-top @spacing-right 0; + .icon-btn { + margin-left: @icon-btn-margin; + } + } + + .dataset-body { + display: none; + // background-color: fadeout( white, 70% ); + //.dataset-padding; + padding: 0px @spacing-right @spacing-bottom @spacing-left; + + [class$=messagesmall] { + margin: 0px 0px 8px 0px; } - [class$=messagesmall] { - margin: @spacing-top @spacing-right ( @spacing-bottom - 4 ) @spacing-left; - font-size: 90%; + label { + margin: 0px; + padding: 0px; + font-weight: normal; + } + .prompt { + .help-text; + } + .prompt:after { + content: ':'; + margin-right: 4px; } - .help-text { - font-weight: normal; - // font-style: italic; - // font-size: 90%; - color: #555; - } - - .dataset-selector { - float: left; - // always initially hidden and zero width - display: none; - width: 32px; - height: 32px; - //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish - margin: 0px 0px -( @spacing-bottom ) 0px; - padding: ( @spacing-top + 2 ) 0px 2px ( @spacing-left - 1 ); - font-size: 80%; - color: @btn-default-color; - cursor: pointer; - vertical-align: middle; - } - .dataset-selector:hover { - color: maroon; - } - - .dataset-title-bar { - cursor: pointer; - outline: none; - .dataset-padding; - - .dataset-state-icon { + .dataset-summary { + .dataset-blurb { + margin-bottom: 2px; } - .dataset-title { + .dataset-datatype, .dataset-dbkey { display: inline; - font-weight: bold; - text-decoration: underline; - word-wrap: break-word; - word-break: break-all; - line-height: 16px; + .value { + font-weight: bold; + } } - } - - .dataset-primary-actions { - .icon-btn-group(); - float: right; - margin: @spacing-top @spacing-right 0; - .icon-btn { - margin-left: @icon-btn-margin; - } - } - - .dataset-body { - display: none; - // background-color: fadeout( white, 70% ); - //.dataset-padding; - padding: 0px @spacing-right @spacing-bottom @spacing-left; - - [class$=messagesmall] { - margin: 0px 0px 8px 0px; - } - - label { - margin: 0px; - padding: 0px; - font-weight: normal; - } - .prompt { + .dataset-datatype .value:after { + content: ','; .help-text; - } - .prompt:after { - content: ':'; margin-right: 4px; } - - .dataset-summary { - .dataset-blurb { - margin-bottom: 2px; - } - .dataset-datatype, .dataset-dbkey { - display: inline; - .value { - font-weight: bold; - } - } - .dataset-datatype .value:after { - content: ','; - .help-text; - margin-right: 4px; - } - .dataset-dbkey:after { - content: ' '; - display: block; - .vertical-spacing; - } - .dataset-info { - .info-section; - overflow: auto; - .value { - white-space: pre-line; - } - } - - .job-error-text { - .info-section; - overflow: auto; - white-space: pre; - } - - // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) + .dataset-dbkey:after { + content: ' '; + display: block; .vertical-spacing; } - - .dataset-actions { - .left { - .icon-btn-group(); - float: left; - .icon-btn { - margin-right: @icon-btn-margin; - } - //.icon-btn-group { - // margin-right: @icon-btn-margin; - // .icon-btn { - // margin-right: 0; - // } - //} - &:not(:empty) { - // can't use :empty on dataset-actions - will always have left & right, so - // add gap to left (more likely to have children) - .vertical-spacing; - } - } - .right { - .icon-btn-group(); - float: right; - .icon-btn { - margin-left: @icon-btn-margin; - } + .dataset-info { + .info-section; + overflow: auto; + .value { + white-space: pre-line; } } - //TODO: move these out - .tags-display { - display: none; - .vertical-spacing; - .select2-container { - min-width: 0px; - .select2-choices { - border-radius: 3px; - } - } - } - .annotation-display { - display: none; - .vertical-spacing; - .annotation { - .info-section; - white-space: pre-line; - } - .annotation:empty { - height: @icon-btn-size; - } - // fake placeholder for editable text annotation - .annotation:empty:after { - position: relative; - top: -4px; - font-size: 10px; - font-style: italic; - color: grey; - content : 'Click here to edit annotation'; - } - textarea { - margin: 0px 0px 2px 0px; - display: block; - border-radius: 3px; - width: 100%; - } + .job-error-text { + .info-section; + overflow: auto; + white-space: pre; } - .dataset-display-applications { - .display-application:last-child { + // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) + .vertical-spacing; + } + + .dataset-actions { + .left { + .icon-btn-group(); + float: left; + .icon-btn { + margin-right: @icon-btn-margin; + } + //.icon-btn-group { + // margin-right: @icon-btn-margin; + // .icon-btn { + // margin-right: 0; + // } + //} + &:not(:empty) { + // can't use :empty on dataset-actions - will always have left & right, so + // add gap to left (more likely to have children) .vertical-spacing; } } - - .dataset-peek { - .vertical-spacing; - pre.peek { - width: 100%; - margin: 0px; - border-radius: 3px; - background: white; - color: black; - font-size: 10px; - overflow: auto; - th { - color: white; - background: @panel-primary-heading-bg; - } - table, th, tr, td { - font-family: @font-family-monospace; - font-size: 10px; - } + .right { + .icon-btn-group(); + float: right; + .icon-btn { + margin-left: @icon-btn-margin; } } } + //TODO: move these out + .tags-display { + display: none; + .vertical-spacing; + .select2-container { + min-width: 0px; + .select2-choices { + border-radius: 3px; + } + } + } + .annotation-display { + display: none; + .vertical-spacing; + .annotation { + .info-section; + white-space: pre-line; + } + .annotation:empty { + height: @icon-btn-size; + } + // fake placeholder for editable text annotation + .annotation:empty:after { + position: relative; + top: -4px; + font-size: 10px; + font-style: italic; + color: grey; + content : 'Click here to edit annotation'; + } + textarea { + margin: 0px 0px 2px 0px; + display: block; + border-radius: 3px; + width: 100%; + } + } + + .dataset-display-applications { + .display-application:last-child { + .vertical-spacing; + } + } + + .dataset-peek { + .vertical-spacing; + pre.peek { + width: 100%; + margin: 0px; + border-radius: 3px; + background: white; + color: black; + font-size: 10px; + overflow: auto; + th { + color: white; + background: @panel-primary-heading-bg; + } + table, th, tr, td { + font-family: @font-family-monospace; + font-size: 10px; + } + } + } } - .dataset .state-icon { - .fa-icon; - display: inline-block; - margin-right: 4px; - vertical-align: middle; - width: 16px; - height: 16px; - line-height: 16px; - text-align: center; - font-size: 16px; - } +} + +.hda.dataset .state-icon { + .fa-icon; + display: inline-block; + margin-right: 4px; + vertical-align: middle; + width: 16px; + height: 16px; + line-height: 16px; + text-align: center; + font-size: 16px; } .state-icon-error { diff -r 54695d3fa468250b1ee13a90facc753dc3d9831d -r b2cf571d0b63948a7252fc703200b854f964bad6 templates/webapps/galaxy/history/display_structured.mako --- a/templates/webapps/galaxy/history/display_structured.mako +++ b/templates/webapps/galaxy/history/display_structured.mako @@ -1,83 +1,167 @@ <%inherit file="/base.mako"/> -<%namespace file="/root/history_common.mako" import="render_dataset" /> +<%namespace file="/show_params.mako" name="show_params" /> +## ---------------------------------------------------------------------------- +<%def name="title()">${ history.name } | ${ _( 'Structure' ) }</%def><%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css( "history" )} <style type="text/css"> body { - background: white; padding: 5px; } - + body > .workflow, body > .toolForm { + /*width : 80%;*/ + margin-bottom : 8px; + /*margin-left : auto;*/ + /*margin-right : auto;*/ + } + .bold { + font-weight: bold; + } + .light { + font-weight: lighter; + color: grey; + } + .right-aligned { + text-align: right; + } + .clickable { cursor: pointer; } - + .workflow { border: solid gray 1px; - margin: 5px 0; - border-left-width: 5px; } - .workflow > .header { background: lightgray; padding: 5px 10px; - - font-weight: bold; } - + .workflow > .light { + color: gray; + } .workflow > .body { border-top: solid gray 1px; - padding: 5px; } - + .workflow > .body > .toolForm { + border: 0px; + } + div.toolForm { - margin: 5px 0; - border-left-width: 5px; + border-width : 1px; + border-radius : 0px; } - div.toolFormBody { - padding: 5px 5px; + .toolForm > .header { + background-color: #EBD9B2; + padding: 5px 10px; } + .workflow div.toolForm:not(:first-child) .header { + border-top: 1px solid #D6B161; + } + div.toolFormTitle { + padding: 0px 0px 4px 0px; + margin: 0px 0px 4px 0px; + border: 0px; + background-color: transparent; + border-bottom: 1px solid #D6B161; + } + /* down from EBD9B2 --> 90743A */ + .toolFormTitle > .light { + color: #90743A; + } + .toolForm em { + color: #90743A; + } + + .job-inputs { + margin: 0px 6px 0px 6px; + text-align: left; + } + .job-inputs td:nth-child(1) { + text-align: right; + font-weight: lighter; + color: #90743A; + } + .job-inputs td:nth-child(1):after { + content : ':' + } + .job-inputs td:nth-child(2) { + padding-left: 4px; + } + .job-inputs em { + } + + .job-inputs-show { + float: right; + } + + .dataset.hda { + min-height : 37px; + border-width: 0px 0px 1px 0px; + } + .toolFormBody > .dataset.hda:last-child { + border-bottom-width: 0px; + } + .dataset.hda:first-child { + border-top: 1px solid #D6B161; + } + .dataset.hda .dataset-title-bar { + padding-top: 8px; + padding-left: 10px; + } + </style></%def><%def name="javascripts()"> +<% + self.js_app = 'display-structured' + + controller = trans.webapp.controllers[ 'history' ] + hda_dicts = [] + id_hda_dict_map = {} + for hda in history.active_datasets: + hda_dict = controller.get_hda_dict( trans, hda ) + id_hda_dict_map[ hda_dict[ 'id' ] ] = hda_dict + hda_dicts.append( hda_dict ) +%> ${parent.javascripts()} + + ## load edit views for each of the hdas <script type="text/javascript"> + define( 'display-structured', function(){ + require([ 'mvc/dataset/hda-edit' ], function( hdaEdit ){ + var hdaModel = require( 'mvc/dataset/hda-model' ), + hdaJSON = ${ h.to_json_string( hda_dicts, indent=( 2 if trans.debug else 0 ) ) }; + + window.hdas = hdaJSON.map( function( hda ){ + return new hdaEdit.HDAEditView({ + model : new hdaModel.HistoryDatasetAssociation( hda ), + el : $( '#hda-' + hda.id ), + linkTarget : '_self', + purgeAllowed : Galaxy.config.allow_user_dataset_purge, + logger : Galaxy.logger + }).render( false ); + }); + }); + }); + $(function(){ - - $(".workflow, .tool").each( function() { - var body = $(this).children( ".body" ); - $(this).children( ".header" ).click( function() { + $( ".workflow, .tool" ).each( function(){ + var body = $( this ).children( ".body" ); + $( this ).children( ".header" ).click( function(){ body.toggle(); }).addClass( "clickable" ); - // body.hide(); }); - - $(".historyItem").each( function() { - var id = this.id; - var body = $(this).children( "div.historyItemBody" ); - var peek = body.find( "pre.peek" ) - $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { - if ( body.is(":visible") ) { - // Hiding stuff here - if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } - body.slideUp( "fast" ); - } else { - // Showing stuff here - body.slideDown( "fast", function() { - if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } - }); - } - return false; - }); - body.hide(); - }); - }); + //$( ".job-inputs-show" ).click( function( ev ){ + // ev.stopPropagation(); + // $( this ).parent().siblings( '.job-inputs' ).toggle(); + //}); + }); </script></%def> +## ---------------------------------------------------------------------------- <%def name="render_item( entity, children )"><% entity_name = entity.__class__.__name__ @@ -91,42 +175,68 @@ </%def><%def name="render_item_hda( hda, children )"> - ${render_dataset( hda, hda.hid, display_structured=True )} +## render hdas as a id'd stub for js to fill later + <% id = trans.security.encode_id( hda.id ) %> + <div id="hda-${id}" class="dataset hda state-${hda.state}"></div></%def><%def name="render_item_job( job, children )"> - +## render a job (as a toolForm) and its children (hdas) <div class="tool toolForm"><% tool = trans.app.toolbox.get_tool( job.tool_id ) if tool: tool_name = tool.name + tool_desc = tool.description else: - tool_name = "Unknown tool with id '%s'" % job.tool_id + tool_name = "Unknown tool with id '%s'" % job.tool_id + tool_desc = '' + + params_object = None + try: + params_object = job.get_param_values( trans.app, ignore_errors=True ) + except Exception, exc: + pass %> - <div class="header toolFormTitle">Tool: ${tool_name}</div> + <div class="header"> + <div class="toolFormTitle"> + <span class="bold">${tool_name}</span> + <span class="light">- ${tool_desc}</span> + ##<a class="job-inputs-show" href="javascript:void(0)">${ _( "parameters" )}</a> + </div> + %if tool and params_object: + <table class="job-inputs"> + ${ show_params.inputs_recursive( tool.inputs, params_object, depth=1 ) } + </table> + %else: + <em>(${ _( 'No parameter data available' ) })</em> + %endif + </div><div class="body toolFormBody"> %for e, c in reversed( children ): ${render_item( e, c )} %endfor </div></div> - </%def><%def name="render_item_wf( wf, children )"> - +## render a workflow and its children (jobs/toolForms) <div class="workflow"> - <div class="header">Workflow: ${wf.workflow.name}</div> + <div class="header"> + <span class="bold">${wf.workflow.name}</span> + <span class="light">- Workflow</span> + </div><div class="body"> %for e, c in reversed( children ): ${render_item( e, c )} %endfor </div></div> - </%def> +## ---------------------------------------------------------------------------- +## render all items from a dictionary prov. by history/display_structured %for entity, children in items: ${render_item( entity, children )} -%endfor \ No newline at end of file +%endfor diff -r 54695d3fa468250b1ee13a90facc753dc3d9831d -r b2cf571d0b63948a7252fc703200b854f964bad6 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -18,9 +18,6 @@ %></%def> -<%def name="center_panel()"> -</%def> - ## ---------------------------------------------------------------------------- <%def name="body()"> ${center_panel()} @@ -70,12 +67,6 @@ <%def name="javascripts()"> ${parent.javascripts()} -%if not use_panels: -<script type="text/javascript"> -window.Galaxy = {}; -</script> -%endif - </%def> ## ---------------------------------------------------------------------------- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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