8398cecd1f2503d61a02f863c500d289b1bbdf52
kate
  Fri Mar 16 18:29:02 2012 -0700
1. Cleanup repetitive code   2. Exclude bogus Reference Genome experiments (currently 5C) that are actually supplemental files.  #5149-18.
diff --git src/hg/js/encodeDataSummary.js src/hg/js/encodeDataSummary.js
index 9cb787b..f590356 100644
--- src/hg/js/encodeDataSummary.js
+++ src/hg/js/encodeDataSummary.js
@@ -1,167 +1,182 @@
 /* encodeDataSummary.js - pull experiment table and metadata from server 
       and display in summary tables
 
  Formatted: jsbeautify.py -j -k
  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.antibody,
             encodeProject.serverRequests.expId
             ];
 
     var $summaryTables = $('.summaryTable');
 
+    function addDataType(dataTypeName, expList, isChip) {
+        // Helper function to fill datatype lists that are used to make tables
+
+        var dataType, dataTypeLabel;
+
+        if (!isChip) {
+            // get data type label
+            dataType = encodeProject.getDataType(dataTypeName);
+            if (dataType !== undefined) {
+                dataTypeLabel = dataType.label;
+            }
+        }
+        if (dataTypeLabel === undefined) {
+            // if there is a mismatch between experiment table and CV we might not
+            // find dataType for the experiment
+            dataTypeLabel = dataTypeName;
+        }
+        if (!expList[dataTypeLabel]) {
+            expList[dataTypeLabel] = 0;
+        }
+        expList[dataTypeLabel]++;
+    }
+
     function handleServerData(responses) {
         // Main actions, called when loading data from server is complete
         var experiments = responses[0], 
             dataTypes = responses[1], 
             antibodies = responses[2], 
             expIds = responses[3];
 
         var cellAssayExps = {}, tfbsExps = {},  refGenomeExps = {};
         var refGenomeTypes = [], elementTypes = [], tfbsTypes = [];
-        var dataType, antibody, target;
+        var antibody, dataType;
 
         encodeMatrix.show($summaryTables);
 
         antibodyGroups = encodeProject.getAntibodyGroups(antibodies);
         encodeProject.getDataGroups(dataTypes);
 
         // use to filter out experiments not in this assembly
         expIdHash = encodeProject.getExpIdHash(expIds);
 
         $.each(experiments, function (i, exp) {
-            // experiment not in this assembly
+            // exlude experiment not in this assembly
             if (expIdHash[exp.ix] === undefined) {
                 return true;
             }
-            antibody = encodeProject.antibodyFromExp(exp);
-            if (antibody) {
-                target = encodeProject.targetFromAntibody(antibody);
+            if (exp.dataType === undefined) {
+                return true;
             }
-            // add experiments into the appropriate table object
+            // add experiment into the appropriate list
             if (exp.cellType === 'None') {
-                dataType = encodeProject.getDataType(exp.dataType);
-                if (dataType !== undefined) {
-                    dataType = dataType.label;
-                } else {
-                    dataType = exp.dataType;
-                }
-                if (!refGenomeExps[dataType]) {
-                    refGenomeExps[dataType] = 0;
-                }
-                refGenomeExps[dataType]++;
+                addDataType(exp.dataType, refGenomeExps, false);
             } else if (exp.dataType === 'ChipSeq') {
-                if (!target) {
+                antibody = encodeProject.antibodyFromExp(exp);
+                if (!antibody) {
                     return true;
                 }
-                if (!tfbsExps[target]) {
-                    tfbsExps[target] = 0;
+                dataType = encodeProject.targetFromAntibody(antibody);
+                if (!dataType) {
+                    // this excludes controls
+                    return true;
                 }
-                tfbsExps[target]++;
-            } else {
-                dataType = encodeProject.getDataType(exp.dataType);
-                if (dataType !== undefined) {
-                    dataType = dataType.label;
+                addDataType(dataType, tfbsExps, true);
                 } else {
-                    dataType = exp.dataType;
+                addDataType(exp.dataType, cellAssayExps, false);
                 }
-                if (!cellAssayExps[dataType]) {
-                    cellAssayExps[dataType] = 0;
+        });
+        // work-around for some supplementary files being accessioned as experiments (5C)
+        // they show up in both reference genome and cell assay lists incorrectly
+        // remove them from refGenome list of they are in cellAssayExps
+        for (dataType in refGenomeExps) {
+            if (cellAssayExps[dataType] !== undefined) {
+                delete refGenomeExps[dataType];
                 }
-                cellAssayExps[dataType]++;
             }
-        });
         // fill in tables and activate buttons
         tableOut('#refGenomeTable', refGenomeTypes, refGenomeExps, false);
         tableOut('#elementTable', elementTypes, cellAssayExps, false);
         $('#buttonDataMatrix').click(function () {
             window.location = 'encodeDataMatrixHuman.html';
         });
         // TODO: enable selectable items in antibody table
         tableOut('#tfbsTable', tfbsTypes, tfbsExps, true);
         $('#buttonChipMatrix').click(function () {
             window.location = 'encodeChipMatrixHuman.html';
         });
 
         // add row highlight
         $('.summaryTable').delegate('.even, .odd', 'mouseover mouseleave', function (ev) {
             if (ev.type == 'mouseover') {
                 $(this).addClass('rowHighlight');
             } else {
                 $(this).removeClass('rowHighlight');
             }
         });
     }
 
     function tableOut(table, types, exps, isChipSeq) {
         // Helper function to output tables to document
         var total = 0, row = 0;
         var dataType, antibodyTarget;
 
         $.each(exps, function (key, value) {
             types.push(key);
             total += parseInt(value, 10);
         });
         types.sort(encodeProject.cmpNoCase);
 
         // lay out table
         $.each(types, function (i, value) {
             description = '';
             if (isChipSeq) {
                 antibodyTarget = encodeProject.getAntibodyTarget(value);
                 if (antibodyTarget !== undefined) {
                     description = antibodyTarget.description;
                 }
             } else {
                 dataType = encodeProject.getDataTypeByLabel(value);
                 if (dataType !== undefined) {
                     description = dataType.description;
                 }
             }
             // quote the end tags so HTML validator doesn't whine
             $(table).append("<tr class='" + (row % 2 === 0 ? "even" : "odd") + "'><td title='" + description + "'>" + value + "<\/td><td id='" + value + "' class='dataItem' title='Click to search for " + value + " data'>" + exps[value] + "<\/td><\/tr>");
             row++;
         });
 
         /* $(".dataItem").addClass("selectable"); */
         $(".even, .odd").click(function () {
             // TODO: base on preview ?
             var url = encodeMatrix.getSearchUrl(encodeProject.getAssembly());
             if (isChipSeq) {
                 target = $(this).children('.dataItem').attr("id");
                 url += '&hgt_mdbVar1=antibody';
                 antibodyTarget = encodeProject.getAntibodyTarget(target);
                 $.each(antibodyTarget.antibodies, function (i, antibody) {
                     url += '&hgt_mdbVal1=' + antibody;
                 });
             } else {
                 dataType = $(this).children('.dataItem').attr("id");
                 url += '&hgt_mdbVar1=dataType&hgt_mdbVal1=' + dataType;
             }
             url += '&hgt_mdbVar2=view&hgt_mdbVal2=Any';
             // TODO: open search window 
             window.open(url, "searchWindow");
             //window.location = url;
         });
 
         $(table).append("<tr><td class='totals'>Total: " + types.length + "<\/td><td class='totals'>" + total + "<\/td><\/tr>");
         if (total === 0) {
             $(table).remove();
         }
     }
 
     // initialize
 
     encodeMatrix.start($summaryTables);
 
     // load data from server
     encodeProject.loadAllFromServer(requests, handleServerData);
 });