a68ef370181a2876f6bbf788e72037779b11a60a kate Thu Oct 13 18:57:35 2011 -0700 Changes from code review: 1. Discover server 2. CLose html and body in single file 3. Replace hidden vars with js variables diff --git src/hg/js/encodeDataMatrix.js src/hg/js/encodeDataMatrix.js index ab6949d..855dee7 100644 --- src/hg/js/encodeDataMatrix.js +++ src/hg/js/encodeDataMatrix.js @@ -1,176 +1,175 @@ -// encodeDataMatrix.js - pull experiment table and metadata from server -// and display in data matrix -// Formatted: jsbeautify.py -j -// Syntax checked: jslint indent:4, plusplus: true, continue: true, unparam: true, sloppy: true, browser: true */ +/* encodeDataMatrix.js - pull experiment table and metadata from server + and display in data matrix + + 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 - ], dataType, organism, assembly; + ], + dataType, organism, assembly, server; function tableOut(matrix, cellTiers, cellTypeHash, dataGroups, dataTypeTermHash, dataTypeLabelHash) { // Create table where rows = cell types and columns are datatypes // create table and first row 2 rows (column title and column headers) var table, tableHeader, row, td; - table = $('<table>' + '<tr><td><td class="axisType" colspan=4>Element Types</td></tr>' + - '<tr id="columnHeaders"><td class="axisType" title="Click to view information about all cell types"><a href="/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&type=Cell+Line&organism=' + - organism + '">Cell Types</td></tr>'); + table = $('<table>' + '<tr><td><td class="axisType" colspan=4>Element Types</td></tr>' + '<tr id="columnHeaders"><td class="axisType" title="Click to view information about all cell types"><a href="/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&type=Cell+Line&organism=' + organism + '">Cell Types</td></tr>'); tableHeader = $('#columnHeaders', table); $.each(dataGroups, function (i, group) { tableHeader.append('<th class="groupType"><div class="verticalText">' + group.label + '</div></th>'); $.each(group.dataTypes, function (i, dataTypeLabel) { dataType = dataTypeLabelHash[dataTypeLabel].term; // prune out datatypes with no experiments if (dataTypeLabelHash[dataTypeLabel].count !== undefined) { - tableHeader.append('<th class="elementType" title="' + - dataTypeLabelHash[dataTypeLabel].description + - '"><div class="verticalText">' + dataTypeLabel + '</div></th>'); + tableHeader.append('<th class="elementType" title="' + dataTypeLabelHash[dataTypeLabel].description + '"><div class="verticalText">' + dataTypeLabel + '</div></th>'); } }); }); // add rows with cell type labels and matrix elements for indicating if // there's an experiment $.each(cellTiers, function (i, tier) { //skip bogus 4th tier (not my property ?) if (tier === undefined) { return true; } // td or th here ? table.append($('<tr class="matrix"><th class="groupType">' + "Tier " + tier.term + '</th></td></tr>')); $.each(tier.cellTypes, function (i, cellType) { if (!cellType) { return true; } if (!matrix[cellType]) { return true; } - row = $('<tr><th class="elementType" title="' + - cellTypeHash[cellType].description + - '"><a href="/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=' + - cellType + '">' + cellType + '</a><span title="karyotype: ' + - cellTypeHash[cellType].karyotype + '" class="' + - cellTypeHash[cellType].karyotype + '">•</span></th>'); + row = $('<tr><th class="elementType" title="' + cellTypeHash[cellType].description + '"><a href="/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=' + cellType + '">' + cellType + '</a><span title="karyotype: ' + cellTypeHash[cellType].karyotype + '" class="' + cellTypeHash[cellType].karyotype + '">•</span></th>'); $.each(dataGroups, function (i, group) { // skip group header row.append('<td></td>'); $.each(group.dataTypes, function (i, dataTypeLabel) { // TODO: change this class to matrixElementType //$(".cellType").click(matrixClickHandler); //"searchWindow"); - dataType = dataTypeLabelHash[dataTypeLabel].term; // prune out datatypes with no experiments if (dataTypeLabelHash[dataTypeLabel].count === undefined) { return true; } td = '<td class="cellType'; if (matrix[cellType][dataType]) { td += ' experiment'; } td += '">'; if (matrix[cellType][dataType]) { td += '<a target=_blank title="'; td += dataTypeLabel + ' in ' + cellType + ' cells "'; td += 'href="http://genome-preview.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&hgt_mdbVar1=cell&hgt_mdbVar2=dataType&hgt_mdbVal1='; td += cellType; td += '&hgt_mdbVal2='; td += dataType; //td += '"><font color=#00994D>'; td += '"><font>'; td += matrix[cellType][dataType]; //td += "....."; td += '</font></a>'; td += '</td>'; } row.append(td); }); table.append(row); }); table.append(row); }); }); $("body").append(table); } function handleServerData(responses) { // Main actions, called when loading data from server is complete var experiments = responses[0], dataTypes = responses[1], cellTypes = responses[2], dataTypeLabelHash = {}, dataTypeTermHash = {}, cellTypeHash = {}, dataType, cellType, matrix = {}, dataGroups = {}, cellTiers, header; - // variables passed in hidden fields - organism = $("#var_organism").val(); - assembly = $("#var_assembly").val(); - header = $("#var_pageHeader").val(); + // page-specific variables from calling page + organism = encodeDataMatrix_organism; + assembly = encodeDataMatrix_assembly; + header = encodeDataMatrix_pageHeader; $("#pageHeader").text(header); $("title").text('ENCODE ' + header); // set up structures for data types and their groups $.each(dataTypes, function (i, item) { dataTypeTermHash[item.term] = item; dataTypeLabelHash[item.label] = item; }); // data type labels tucked into their tiers dataGroups = encodeProject.getDataGroups(dataTypes); // set up structures for cell types and their tiers $.each(cellTypes, function (i, item) { cellTypeHash[item.term] = item; }); cellTiers = encodeProject.getCellTiers(cellTypes); // gather experiments into matrix $.each(experiments, function (i, exp) { // todo: filter out with arg to hgApi if (exp.organism !== organism) { return true; } // exclude ref genome annotations if (exp.cellType === 'None') { 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 (!dataTypeTermHash[dataType].count) { dataTypeTermHash[dataType].count = 0; } dataTypeTermHash[dataType].count++; cellType = exp.cellType; if (!matrix[cellType]) { matrix[cellType] = {}; } if (!matrix[cellType][dataType]) { matrix[cellType][dataType] = 0; } matrix[cellType][dataType]++; }); // fill in table tableOut(matrix, cellTiers, cellTypeHash, dataGroups, dataTypeTermHash, dataTypeLabelHash); } - // initialize + // initialize encodeProject + // get server from calling web page (intended for genome-preview) + if ('encodeDataMatrix_server' in window) { + server = encodeDataMatrix_server; + } else { + server = document.location.hostname; + // or document.domain ? + } + encodeProject.setup({ - // todo: add hidden page variable for server - server: "hgwdev.cse.ucsc.edu" - //server: "genome-preview.ucsc.edu" + server: server }); encodeProject.loadAllFromServer(requests, handleServerData); });