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/encodeChipMatrix.js src/hg/js/encodeChipMatrix.js index ebf22d9..4fd0990 100644 --- src/hg/js/encodeChipMatrix.js +++ src/hg/js/encodeChipMatrix.js @@ -1,178 +1,180 @@ // encodeChipMatrix.js - pull experiment table and metadata from server // and display ChIP antibodies vs. cell types in a matrix -// Formatted: jsbeautify.py -j -k +// Formatted: jsbeautify.py -j // Syntax checked: jslint indent:4, plusplus: true, continue: true, unparam: true, sloppy: true, browser: true */ /*global $, encodeProject */ $(function () { - var dataType; - var requests = + var dataType, server, requests = [ // Requests to server API - [ encodeProject.serverRequests.experiment, encodeProject.serverRequests.cellType, - encodeProject.serverRequests.antibody - ]; + encodeProject.serverRequests.antibody]; function tableOut(matrix, cellTiers, cellTypeHash, antibodyGroups, antibodyHash, targetHash) { // 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=6>Antibody Targets</td></tr>' + '<tr id="columnHeaders"><td class="axisType">Cell Types</td></tr>'); tableHeader = $('#columnHeaders', table); $.each(antibodyGroups, function (i, group) { tableHeader.append('<th class="groupType"><div class="verticalText">' + group.label + '</div></th>'); $.each(group.targets, function (i, target) { if (targetHash[target] === undefined) { return true; } // prune out targets with no experiments if (targetHash[target].count !== undefined) { tableHeader.append('<th class="elementType"><div class="verticalText">' + target + '</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">' + cellType + '</th>'); $.each(antibodyGroups, function (i, group) { // skip group header row.append('<td></td>'); $.each(group.targets, function (i, target) { // TODO: change this class to matrixElementType //$(".cellType").click(matrixClickHandler); //"searchWindow"); // prune out targets with no experiments if (targetHash[target] === undefined) { return true; } if (targetHash[target].count === undefined) { return true; } td = '<td class="cellType'; if (matrix[cellType][target]) { td += ' experiment'; } td += '">'; if (matrix[cellType][target]) { td += '<a target=_blank href="http://genome-preview.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&hgt_mdbVar1=cell&hgt_mdbVar2=target&hgt_mdbVal1='; td += cellType; td += '&hgt_mdbVal2='; // TODO: needs to be join of all antibodies for this target td += target; //td += '"><font color=#00994D>'; td += '"><font>'; td += matrix[cellType][target]; //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], cellTypes = responses[1], antibodies = responses[2], antibodyGroups, antibodyHash = {}, targetHash = {}, cellTypeHash = {}, antibody, target, cellTiers, cellType, matrix = {}, organism, assembly, header; // variables passed in hidden fields - organism = $("#var_organism").val(); - assembly = $("#var_assembly").val(); - header = $("#var_pageHeader").val(); + organism = encodeChipMatrix_organism; + assembly = encodeChipMatrix_assembly; + header = encodeChipMatrix_pageHeader; $("#pageHeader").text(header); $("title").text('ENCODE ' + header); // set up structures for antibodies and their groups $.each(antibodies, function (i, item) { antibodyHash[item.term] = item; }); antibodyGroups = encodeProject.getAntibodyGroups(antibodies); // 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; } // todo: filter out with arg to hgApi ? if (exp.dataType !== 'ChipSeq') { return true; } // count experiments per target so we can prune those having none // (the matrix[cellType] indicates this for cell types // so don't need hash for those antibody = encodeProject.antibodyFromExp(exp); target = encodeProject.targetFromAntibody(antibody, antibodyHash); if (!targetHash[target]) { targetHash[target] = { count: 0, antibodies: {} }; } if (!targetHash[target].antibodies[antibody]) { targetHash[target].antibodies[antibody] = antibody; } targetHash[target].count++; cellType = exp.cellType; if (!matrix[cellType]) { matrix[cellType] = {}; } if (!matrix[cellType][target]) { matrix[cellType][target] = 0; } matrix[cellType][target]++; }); // fill in table tableOut(matrix, cellTiers, cellTypeHash, antibodyGroups, antibodyHash, targetHash); } + // get server from calling web page (intended for genome-preview) + if ('encodeDataMatrix_server' in window) { + server = encodeDataMatrix_server; + } else { + server = document.location.hostname; + } + // initialize 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); });