4272e1c7a2d10741a096eb7868c680bdb11e9895
braney
  Thu Mar 22 11:37:42 2018 -0700
changes in response to code review #21090

diff --git src/hg/js/hgCollection.js src/hg/js/hgCollection.js
index c2d05c2..4f3f48a 100644
--- src/hg/js/hgCollection.js
+++ src/hg/js/hgCollection.js
@@ -1,566 +1,567 @@
 // hgCollection.js - custom collection builder
 
 // Copyright (C) 2018 The Regents of the University of California
 
 var hgCollection = (function() {
     var selectedNode;
     var selectedTree;
     var $tracks;  // the #tracks object
     var trees = [];
     var isDirty = false;
     var goTracks = false;
     var loadFinished = false;
     var doAjaxAsync = true;
     var emptyCollectionText;
     var addWithoutCollectionText;
 
     function currentTrackItems(node) {
         // populate the menu for the currentCollection tree
         var items = {
             addItem: { // The "add" menu item
                 label: "Add",
                 action: function () {
                     if (selectedNode === undefined) {
                         alert(addWithoutCollectionText);
                         return;
                     }
                     var nodeIds = $("#tracks").jstree( "get_selected");
                     isDirty = true;
                     var nodes = [];
                     var node;
                     for(ii=0; ii < nodeIds.length; ii++) {
                         node = $("#tracks").jstree('get_node', nodeIds[ii]);
                         if (node.children.length === 0)
                             nodes.push(node);
                     }
                     var parentId = $(selectedNode).attr('id');
                     checkEmpty(parentId);
                     $(selectedTree).jstree("copy_node", nodes, parentId,'last');
                 }
             }
         };
 
         if ($(node).attr('children').length > 0)
             delete items.addItem;
 
         return items;
     }
 
     function currentCollectionItems(node) {
         // populate the menu for the currentCollection tree
         var items = {
             deleteItem: { // The "delete" menu item
                 label: "Delete",
                 action: function () {
                     var nodes = $(selectedTree).jstree( "get_selected");
                     var parentNode = $(selectedTree).jstree("get_node", node.parent);
                     isDirty = true;
                     if ((parentNode.id !== '#') && (parentNode.children.length === nodes.length) ){
                         $(selectedTree).jstree("create_node", node.parent, emptyCollectionText);
                         parentNode.li_attr.class = "folder empty";
                     }
                     $(selectedTree).jstree( "delete_node", nodes);
                     if (parentNode.id === '#') {
                         var firstChild = $(selectedTree).find("li").first();
                         $(selectedTree).jstree("select_node", $(firstChild).attr("id"));
                     } else {
                         $(selectedTree).jstree( "select_node", parentNode.id);
                     }
                 }
             }
         };
 
         return items;
         }
 
     function changeCollection() {
         var newName = $("#customName").val().trim();
         if (!validateLabel(newName))
             return;
 
         var newDescription = $("#customDescription").val().trim();
         if (!validateLabel(newDescription))
             return;
         $( "#newCollectionDialog" ).dialog("close");
         selectedNode.li_attr.class = "folder";
         selectedNode.li_attr.title = collectionTitle;
         selectedNode.li_attr.shortlabel = newName;
         selectedNode.li_attr.longlabel = newDescription;
         selectedNode.li_attr.visibility = $("#customVis").val();
         selectedNode.li_attr.color = $("#customColorInput").val();
         selectedNode.li_attr.missingmethod = $("input:radio[name ='missingData']:checked").val();
         selectedNode.li_attr.viewfunc = $("#viewFunc").val();
         rebuildLabel();
     }
 
     function doubleClickNode(tree) {
         var node = $(selectedTree).jstree("get_node", tree.id);
         var color = node.li_attr.color;
         var name =  node.li_attr.shortlabel;
         var description = node.li_attr.longlabel;
         var visibility = node.li_attr.visibility;
         var type = node.li_attr.viewtype;
         var viewFunc = node.li_attr.viewfunc;
 
         if (type == 'collection') 
             $("#viewFuncDiv").show();
         else
             $("#viewFuncDiv").hide();
 
         $("#CustomTrackOptions").show();
         $("#viewFunc").val(viewFunc);
         $("#customName").val(name);
         $("#customDescription").val(description);
         $("#customVis").val(visibility);
         $("#customColorInput").val(color);
         $("#customColorPicker").spectrum("set", color);
         if ( node.li_attr.missingmethod === 'zero') {
             $("input[name='missingData'][value='zero']").prop("checked",true);
             $("input[name='missingData'][value='missing']").prop("checked",false);
         } else {
             $("input[name='missingData'][value='zero']").prop("checked",false);
             $("input[name='missingData'][value='missing']").prop("checked",true);
         }
 
         $("#doNewCollection").off ( "click" );
         $("#doNewCollection").click ( changeCollection );
         if (type == 'collection')  {
             $( "#newCollectionDialog" ).dialog( 'option', 'title', 'Edit Collection');
             $('#collectionDialogHelp').show();
             $('#trackDialogHelp').hide();
         } else {
             $( "#newCollectionDialog" ).dialog( 'option', 'title', 'Edit Track');
             $('#collectionDialogHelp').hide();
             $('#trackDialogHelp').show();
         }
 
         $( "#newCollectionDialog" ).dialog("open");
     }
 
     function moveNode(evt, data) {
         // called when a node is moved
         checkEmpty(data.parent);
         var oldParentNode = $(selectedTree).jstree('get_node', data.old_parent);
         if (oldParentNode.children.length === 0) {
             oldParentNode.li_attr.class = "folder empty";
             $(selectedTree).jstree("create_node", data.old_parent, emptyCollectionText);
         }
     }
 
     function selectNode(tree, node) {
         // called when a node in the currentCollection tree is selected
         selectedNode = node;
         selectedTree = tree;
         $(selectedTree).jstree("open_node", selectedNode);
    }
 
     function doubleClickTreeNode(evt, data)             {
         doubleClickNode(evt.target);
     }
 
     function selectTreeNode(evt, data)             {
         selectNode(evt.target, data.node);
     }
 
     function checkCallback( operation, node, node_parent, node_position, more) {
         // called during a drag and drop action to see if the target is droppable
         if ((operation === "copy_node") ||  (operation === "move_node")) {
             if ((node.parent != '#') && (node_parent.parent === '#')) {
                 if (node.icon === true) // empty stub
                     return false;
                 return true;
             }
             return false;
         }
         return true;
     }
 
 
     function dialogCollection() {
         $("#doNewCollection").off ( "click" );
         $("#doNewCollection").click ( newCollection );
         $("#viewFuncDiv").show();
 
         var collectionLabel = getUniqueLabel();
         $("#customName").val(collectionLabel);
         $("#customDescription").val(collectionLabel + " description");
         $("#customVis").val("full");
         $("#customColorInput").val("#0");
         $("#customColorPicker").spectrum("set", "#0");
         $("#viewFunc").val("show all");
         $( "#customName" ).select();
         $('#collectionDialogHelp').show();
         $('#trackDialogHelp').hide();
         $( "#newCollectionDialog" ).dialog( 'option', 'title', 'Create New Collection');
         $( "#newCollectionDialog" ).dialog("open");
     } 
 
     function newCollection() {
         var newName = $("#customName").val().trim();
         if (!validateLabel(newName))
             return;
 
         var newDescription = $("#customDescription").val().trim();
         if (!validateLabel(newDescription))
             return;
         var ourCollectionName = getUniqueName();
         var parent = $(selectedTree).find("li").first();
         $( "#newCollectionDialog" ).dialog("close");
 
         var newId = $(selectedTree).jstree("create_node", "#", newName + " (" + newDescription + ")");
         var newId2 = $(selectedTree).jstree("create_node", newId, emptyCollectionText);
         var newNode = $(selectedTree).jstree("get_node", newId);
         isDirty = true;
         newNode.li_attr.class = "folder empty";
         newNode.li_attr.name = ourCollectionName;
         newNode.li_attr.shortlabel = newName;
         newNode.li_attr.longlabel = newDescription;
         newNode.li_attr.visibility = $("#customVis").val();
         newNode.li_attr.color = $("#customColorInput").val();
         newNode.li_attr.missingmethod = $("input:radio[name ='missingData']:checked").val();
         newNode.li_attr.viewfunc = $("#viewFunc").val();
         newNode.li_attr.viewtype = "collection";
         $(selectedTree).jstree("set_icon", newNode, '../images/folderC.png');
         $(selectedTree).jstree("deselect_node", selectedNode);
         $(selectedTree).jstree("select_node", newNode.id);
         $(selectedTree).on("move.jstree", moveNode);
         rebuildLabel();
     }
 
     function addCollection(trees, list) {
         // called when outputting JSON of all the collectionList
         var collectTree = trees[list.id];
         var v = collectTree.jstree(true).get_json('#', {flat:true, no_data:true, no_state:true, no_a_attr:true});
         var mytext = JSON.stringify(v);
         return mytext;
     }
 
     function finishSaving() {
         // save the collection tree to the server
        var json = "[";
         var v = $(selectedTree).jstree(true).get_json('#', {flat:true, no_data:true, no_state:true, no_a_attr:true});
         var children;
         var parents = {};
         for(ii=0; ii < v.length; ii++) {
             if (v[ii].parent === '#') {
                 parents[v[ii].id] = v[ii].text;
             }
         }
         for(ii=0; ii < v.length; ii++) { 
             if (v[ii].li_attr.name === undefined) {
                 alert(parents[v[ii].parent] + " does not have any wiggles.  Not saved.");
             }
         }
         json += JSON.stringify(v);
         json += ']';
         var requestData = 'jsonp=' + json;
         $.ajax({
             data:  requestData ,
             async: doAjaxAsync,
             dataType: "JSON",
             type: "PUT",
             url: "hgCollection?cmd=saveCollection",
             trueSuccess: updatePage,
             success: catchErrorOrDispatch,
             error: errorHandler,
         });
     }
 
     function saveCollections(trees) {
         // called when the "Save" button is pressed
         $("#workScreen").css("display","block");
         finishSaving();
     }
 
     function rebuildLabel() {
         // rebuild the label for tree item
         var newText = selectedNode.li_attr.shortlabel + "   (" + selectedNode.li_attr.longlabel + ")";
         $(selectedTree).jstree('rename_node', selectedNode, newText);
         isDirty = true;
     }
 
     function colorChange() {
         // change the color for a track
         isDirty = true;
         var color = $("#customColorPicker").spectrum("get"); 
         $('#customColorInput').val(color);
     }
 
     function isDraggable(nodes) {
         // only children can be dragged
         var ii;
         for (ii=0; ii < nodes.length; ii++)
             if (nodes[ii].children.length !== 0)
                 return false;
         return true;
     }
 
     function checkEmpty(parentId) {
         // add or remove the "empty collection" stub
         if ($('#'+parentId).hasClass('empty')) {
             var parentNode = $(selectedTree).jstree('get_node', parentId);
             var stub;
             for (i = 0; i < parentNode.children.length; i++) {
                 stub = $(selectedTree).jstree('get_node', parentNode.children[i]);
                 if (stub.icon === true)
                     break;
             }
 
             if (i === parentNode.children.length)
                 return;
 
             $(selectedTree).jstree('delete_node', stub);
             $('#'+parentId).removeClass('empty');
             parentNode.li_attr.class = 'folder';
         }
     }
 
     function findCollection(parentNode) {
         while(parentNode.parent !== '#') {
             parentNode = $(selectedTree).jstree("get_node", parentNode.parent);
         }
 
         return parentNode.id;
     }
     
     function plusHit(event, data) {
         // called with the plus icon is hit
         var treeObject = $(event.currentTarget).parent().parent();
         var id = treeObject.attr('id');
         var node = treeObject.jstree("get_node", id);
 
         if (node.icon !== 'fa fa-plus')  // if this isn't a leaf, then return
             return;
 
         if (selectedNode === undefined) {   // if there are no collections
             alert(addWithoutCollectionText);
             return;
         }
 
         var parentId = $(selectedNode).attr('id');
         parentId = findCollection(selectedNode);
         checkEmpty(parentId);
         isDirty = true;
         $(selectedTree).jstree("copy_node", node, parentId,'last');
     }
 
     function minusHit (event, data) {
         // called with the minus icon is hit
         var treeObject = $(event.currentTarget).parent().parent();
         var id = treeObject.attr('id');
         var node = treeObject.jstree("get_node", id);
         if (node.parent !== '#') {
             isDirty = true;
             var parentNode = treeObject.jstree("get_node", node.parent);
             if (parentNode.children.length === 1) {
                 treeObject.jstree("create_node", node.parent, emptyCollectionText);
                 parentNode.li_attr.class = "folder empty";
             }
             $(selectedTree).jstree( "delete_node", node);
         }
     }
 
     function buildCollections(node, cb) {
         // called when jstree wants data to open a node for the collection tree
         cb.call(this, collectionData[node.id]);
     }
 
     function buildTracks(node, cb) {
         // called when jstree wants data to open a node for the tracks tree
         cb.call(this, trackData[node.id]);
     }
 
     function trackTreeReady() {
         // called when the track tree has been loaded
         var firstChild = $(this).find("li").first();
         $(this).jstree("select_node", $(firstChild).attr("id"));
     }
 
     function collectionTreeReady() {
         // called when the collection tree has been loaded
         //$(selectedTree).on("load_all.jstree", collectionLoadFinished);
         var rootNode = $(selectedTree).jstree("get_node", '#');
         $(selectedTree).jstree('load_all', rootNode, collectionLoadFinished);
         var firstChild = $(this).find("li").first();
         $(this).jstree("select_node", $(firstChild).attr("id"));
     }
 
     function colorInputChange () {
         // called when the color text edit box changes
         $("#customColorPicker").spectrum("set",$("#customColorInput").val());
     }
 
     function collectionLoadFinished() {
         loadFinished = true;
         $("#workScreen").css("display","none");
     }
 
     function init() {
         // called at initialization time
         $body = $("body");
         $("#customColorInput").change(colorInputChange);
 
         emptyCollectionText = $('#emptyCollectionText').text();
         addWithoutCollectionText = $('#addWithoutCollectionText').text();
 
         // block user input when ajax is running
         $(document).on({
             ajaxStart: function() { $body.addClass("loading");    },
             ajaxStop: function() { $body.removeClass("loading"); }    
         });
 
         $('.gbButtonGoContainer').click(submitForm);
        
         window.addEventListener("beforeunload", function (e) {
             if (isDirty) {
                 doAjaxAsync = false;
                 if (loadFinished)
                     saveCollections(trees);
                 else
                     e.returnValue = "ask to leave";
             }
         });
 
         $("#saveCollections").click ( function() { saveCollections(trees); } );
         $("#discardChanges").click ( function () { isDirty = false; window.location.reload(); });
 
         $( "#newCollectionDialog" ).dialog({ modal: true, 
             width: "50%", 
             autoOpen: false,
             dialogClass: 'myTitleClass'
             });
         $("#newCollection").click ( dialogCollection );
         $("#doNewCollection").click ( newCollection );
 
         var trackOpt = {
             hideAfterPaletteSelect : true,
             color : $('#customColorInput').val(),
             showPalette: true,
             showInput: true,
             preferredFormat: "hex",
             change: colorChange,
         };
 
         $("#customColorPicker").spectrum(trackOpt);
         $.jstree.defaults.core.check_callback = checkCallback;
         $.jstree.defaults.core.themes.dots = true;
         $.jstree.defaults.contextmenu.show_at_node = false;
         var addedOne = false;
         if ( $("#currentCollection ul").length !== 0) {
             addedOne = true;
         }
 
         var newTree=$('#currentCollection');
         newTree.on("ready.jstree", collectionTreeReady);
         newTree.jstree({
            'plugins' : ['dnd', 'conditionalselect', 'contextmenu'],
            //'plugins' : [ 'conditionalselect', 'contextmenu'],
            'contextmenu': { "items" : currentCollectionItems},
            'core': {
                "data" : buildCollections,
                "dblclick_toggle" : false,
             },
            'dnd': {
                 "check_callback" : checkCallback,
             }
         });
         $(newTree).on("select_node.jstree", selectTreeNode);
         $(newTree).on("dblclick.jstree", doubleClickTreeNode);
         $(newTree).on("move_node.jstree", moveNode);
 
         $(newTree).on("copy_node.jstree", function (evt, data)  {
             $(evt.target).jstree("open_node", data.parent);
             $(evt.target).jstree("set_icon", data.node, 'fa fa-minus-square');
             data.node.li_attr.title = collectionTitle;
             $(evt.target).jstree("redraw", "true");
         });
         $(newTree).on('click', '.jstree-themeicon ', minusHit);
 
         selectedTree = newTree;
 
         treeDiv=$('#tracks');
         treeDiv.jstree({
                'plugins' : ['conditionalselect', 'contextmenu'],
                'contextmenu': { "items" : currentTrackItems},
                'dnd': {
                     "check_callback" : checkCallback,
                    'always_copy' : true,
                     is_draggable: isDraggable,
                },
                'core' :  {
                    "data" : buildTracks,
                    "check_callback" : checkCallback,
                    "dblclick_toggle" : false,
                 },
         });
         treeDiv.on("ready.jstree", trackTreeReady);
         treeDiv.on("select_node.jstree", function (evt, data)  {
             $(evt.target).jstree("open_node", data.node);
         });
         treeDiv.on('click', '.jstree-themeicon ', plusHit);
     }
 
    function submitForm() {
     // Submit the form (from GO button -- as in hgGateway.js)
     // Show a spinner -- sometimes it takes a while for hgTracks to start displaying.
         $('.gbIconGo').removeClass('fa-play').addClass('fa-spinner fa-spin');
         goTracks = true;
         saveCollections(trees);
     }
 
     function updatePage(responseJson) {
         // called after AJAX call
         isDirty = false;
         if (!responseJson) {
             return;
         }
 
         if (goTracks) {
             // we go straight to hgTracks after save
             $form = $('#redirectForm');
             $form.submit();
         }
     }
 
     function getUniqueLabel() {
         var root = "New Collection";
         if (!collectionLabels[root]) {
             collectionLabels[root] = 1;
             return root;
         } else {
             var counter = 1;
 
             for(; ; counter++) {
                 var label  = root + ' (' + counter + ')';
                 if (!collectionLabels[label]) {
                     collectionLabels[label] = 1;
                     return label;
                 }
             }
         }
     }
 
     function getUniqueName() {
         // make sure name is unique in track hub
-        var seconds =  Math.floor( Date.now() / 1000 ) - 1520631071;
+        var releaseDateInSeconds = 1520631071;
+        var seconds =  Math.floor( Date.now() / 1000 ) - releaseDateInSeconds;
         var root = "coll" + seconds;
         if (!collectionNames[root]) {
             collectionNames[root] = 1;
             return root;
         } else {
             var counter = 1;
 
             for(; ; counter++) {
                 var name  = root + counter;
                 if (!collectionNames[name]) {
                     collectionNames[name] = 1;
                     return name;
                 }
             }
         }
     }
 
     return {
         init: init
     };
 }());