f9c068638aaeddd15d998a5fa840e08898c6e83b
kate
  Tue Mar 20 22:55:59 2012 -0700
Changes responding to QA (redmine #5149, issues note 27).  1. Save user-selected search type in cookie so it persists across pages.  2. Include ChIP-seq in cell-based experiment table on data summary page.  3. encode URL passed to hgEncodeVocab so cells having terms with weird chars (e.g. +) will work.  Also, override extra search dropdowns (until figure out how to remove mdbVar cart vars by URL)
diff --git src/hg/js/encodeDataMatrix.js src/hg/js/encodeDataMatrix.js
index 731b423..6f47fc2 100644
--- src/hg/js/encodeDataMatrix.js
+++ src/hg/js/encodeDataMatrix.js
@@ -1,196 +1,199 @@
 /* encodeDataMatrix.js - ENCODE Data Matrix application
 
       Pulls experiment table and metadata from server 
       and displays in matrix of assay vs. cell type
 
  NOTE: $variables are jQuery objects
 
  Formatted: jsbeautify.py -j
  Syntax checked: jslint indent:4, plusplus: true, continue: true, unparam: true, sloppy: true, browser: true
 */
 /*global $, encodeProject */
 
 $(function () {
     var requests = [
     // requests to server API
         encodeProject.serverRequests.experiment, 
         encodeProject.serverRequests.dataType, 
         encodeProject.serverRequests.cellType,
         encodeProject.serverRequests.expId
         ];
 
     var $matrixTable = $('#matrixTable');
 
     function handleServerData(responses) {
         // Main actions, called when loading data from server is complete
 
         // NOTE: ordering of responses is based on request order
         var experiments = responses[0], 
                           dataTypes = responses[1], 
                           cellTypes = responses[2], 
                           expIds = responses[3];
 
         var dataGroups, cellTiers, expIdHash;
         var dataType, cellType;
         var matrix, dataTypeExps = {};
 
         // hide spinner and show table
         encodeMatrix.show($matrixTable);
 
         // set up structures for data types and their groups
         // data type labels tucked into their tiers
         dataGroups = encodeProject.getDataGroups(dataTypes);
 
         // set up structures for cell types and their tiers
         cellTiers = encodeProject.getCellTiers(cellTypes);
 
         // use to filter out experiments not in this assembly
         expIdHash = encodeProject.getExpIdHash(expIds);
 
         // gather experiments into matrix
         // NOTE: dataTypeExps is populated here
         matrix = makeExperimentMatrix(experiments, expIdHash, dataTypeExps);
 
         // fill in table using matrix
         encodeMatrix.tableOut($matrixTable, matrix, cellTiers, 
                     dataGroups, dataTypeExps, tableHeaderOut, rowAddCells);
     }
 
     function makeExperimentMatrix(experiments, expIdHash, dataTypeExps) {
         // Populate dataType vs. cellType array with counts of experiments
 
         var dataType, cellType;
         var matrix = {};
 
         $.each(experiments, function (i, exp) {
             // exclude ref genome annotations
             if (exp.cellType === 'None') {
                 return true;
             }
             // exclude experiments lacking an expID (not in this assembly)
             if (expIdHash[exp.ix] === undefined) {
                 return true;
             }
             // count experiments per dataType so we can prune those having none
             // (the matrix[cellType] indicates this for cell types 
             // so don't need hash for those
             dataType = exp.dataType;
             if (dataTypeExps[dataType] === undefined) {
                 dataTypeExps[dataType] = 0;
             }
             dataTypeExps[dataType]++;
 
             cellType = exp.cellType;
             if (!matrix[cellType]) {
                 matrix[cellType] = {};
             }
             if (!matrix[cellType][dataType]) {
                 matrix[cellType][dataType] = 0;
             }
             matrix[cellType][dataType]++;
         });
     return matrix;
     }
 
     function tableHeaderOut($table, dataGroups, dataTypeExps) {
         // Generate table header and add to document
         // NOTE: relies on hard-coded classes and ids
 
         var $tableHeader, $thead;
         var maxLen, dataType;
 
         // fill in column headers from dataTypes returned by server
         $tableHeader = $('#columnHeaders');
         $thead = $('thead');
 
         // 1st column is row headers
         // colgroups are needed to support cross-hair hover effect
         $thead.before('<colgroup></colgroup>');
 
         $.each(dataGroups, function (i, group) {
             $tableHeader.append('<th class="groupType"><div class="verticalText">' + 
                                 group.label + '</div></th>');
             maxLen = Math.max(maxLen, group.label.length);
             $thead.before('<colgroup></colgroup>');
             $.each(group.dataTypes, function (i, label) {
                 dataType = encodeProject.getDataTypeByLabel(label);
 
                 // prune out datatypes with no experiments
                 if (dataTypeExps[dataType.term] !== undefined) {
                     $tableHeader.append('<th class="elementType" title="' + 
                                         dataType.description + 
                                         '"><div class="verticalText">' + dataType.label + 
                                         '</div></th>');
                     // add colgroup element to support cross-hair hover effect
                     $thead.before('<colgroup class="experimentCol"></colgroup>');
                     maxLen = Math.max(maxLen, dataType.label.length);
                 }
             });
         });
         // adjust size of headers based on longest label length
         // empirically len/2 em's is right
         $('#columnHeaders th').css('height', (String((maxLen/2 + 2)).concat('em')));
         $('#columnHeaders th').css('width', '1em');
     }
 
     function rowAddCells($row, dataGroups, dataTypeExps, matrix, cellType) {
         // populate a row in the matrix with cells for data groups and data types
         // null cellType indicates this is a row for a cell group (tier)
 
         var $td;
 
         $.each(dataGroups, function (i, group) {
             // skip group header
             $td = $('<td></td>');
             $td.addClass('matrixCell');
             $row.append($td);
 
             $.each(group.dataTypes, function (i, dataTypeLabel) {
                 dataType = encodeProject.getDataTypeByLabel(dataTypeLabel).term;
                 // prune out datatypes with no experiments
                 if (dataTypeExps[dataType] === undefined) {
                     return true;
                 }
                 $td = $('<td></td>');
                 $td.addClass('matrixCell');
                 $row.append($td);
                 if (cellType === null) {
                     return true;
                 }
                 if (!matrix[cellType][dataType]) {
                     $td.addClass('todoExperiment');
                     return true;
                 }
                 // this cell represents experiments that
                 // fill in count, mouseover and selection by click
                 $td.addClass('experiment');
                 $td.text(matrix[cellType][dataType]);
                 $td.data({
                     'dataType' : dataType,
                     'cellType' : cellType
                 });
                 $td.mouseover(function() {
                     $(this).attr('title', 'Click to select: ' + 
                         encodeProject.getDataType($(this).data().dataType).label +
                             ' ' + ' in ' + $(this).data().cellType +' cells');
                 });
                 $td.click(function() {
                     var url = encodeMatrix.getSearchUrl(encodeProject.getAssembly());
                     // TODO: encapsulate var names
                     url +=
                        ('&hgt_mdbVar1=dataType&hgt_mdbVal1=' + $(this).data().dataType +
                        '&hgt_mdbVar2=cell&hgt_mdbVal2=' + $(this).data().cellType +
-                       '&hgt_mdbVar3=view&hgt_mdbVal3=Any');
+                       '&hgt_mdbVar3=view&hgt_mdbVal3=Any' +
+                       // TODO: figure out how to remove mdbVar4
+                       '&hgt_mdbVar4=view&hgt_mdbVal4=Any'
+                       );
                     // specifying window name limits open window glut
                     window.open(url, "searchWindow");
                 });
             });
         });
     }
 
     // initialize application
     encodeMatrix.start($matrixTable);
 
     // load data from server and do callback
     encodeProject.loadAllFromServer(requests, handleServerData);
 });