d4623fb82603fb8e114e9ff8bfd41d717213909e kate Tue Apr 10 20:09:28 2012 -0700 Factor out ENCODE-specific API calls into separate CGI. Basic/rough cut diff --git src/hg/js/encodeProject.js src/hg/js/encodeProject.js index e75242a..d75e755 100644 --- src/hg/js/encodeProject.js +++ src/hg/js/encodeProject.js @@ -1,313 +1,313 @@ /* encodeProject - javascript utilities for ENCODE-specific things such as controlled vocabulary and experiment table Formatted: jsbeautify.py -j -k Syntax checked: jslint --indent=4 --plusplus=true --strict=false --browser=true */ /*global $ */ var encodeProject = (function () { // Configurable variables - change with setup function below var server = "genome.ucsc.edu", assembly = "hg19", - cgi = "/cgi-bin/hgApi?"; + cgi = "/cgi-bin/hgEncodeApi?"; var accessionPrefix = 'wgEncodeE?'; var dataTypeLabelHash = {}, dataTypeTermHash = {}; var cellTypeTermHash = {}; var antibodyHash = {}, antibodyTargetHash = {}; // Functions return { // Configuration setup: function (settings) { // Change defaults if (settings.server) { server = settings.server; } if (settings.assembly) { assembly = settings.assembly; } }, getAssembly: function () { // Get currently set assembly return assembly; }, getServer: function () { // Get currently set server return server; }, // Server interaction serverRequests: { // Requests for data from server API - experiment: "cmd=encodeExperiments", - expId: "cmd=encodeExpId", + experiment: "cmd=experiments", + expId: "cmd=experimentIds", dataType: "cmd=cv&type=dataType", cellType: "cmd=cv&type=cellType", antibody: "cmd=cv&type=antibody" }, loadAllFromServer: function (requests, handler) { // Execute requests to server via ajax var serverData = [], count = requests.length; $.each(requests, function (i, request) { $.getJSON("http://" + server + cgi + "db=" + assembly + "&" + request, function (data) { serverData[i] = data; if (--count === 0) { handler(serverData); } }); }); }, // Utility // Candidates for generic lib cmpNoCase: function (a, b) { // Case-insensitive sort. // Should be in a generic lib return a.toLowerCase().localeCompare(b.toLowerCase()); }, cmpCV: function (a, b) { // Case-insensitive sort of CV objects // Use label if any, otherwise the term return ((a.label !== undefined && b.label !== undefined) ? a.label.toLowerCase().localeCompare(b.label.toLowerCase()) : a.term.toLowerCase().localeCompare(b.term.toLowerCase())); }, isIE7: function() { // Detect IE version 7 return ($.browser.msie && parseInt($.browser.version, 10) === 7); }, isIE8: function() { // Detect IE version 8 return ($.browser.msie && parseInt($.browser.version, 10) === 8); }, getSearchType: function () { return $('input:radio[name=searchType]:checked').val(); }, // Experiments, data types and cell types expIdFromAccession: function(accession) { return accession.slice(accessionPrefix.length); }, getExpIdHash: function (ids) { // Return hash of experiment ID's var hash = {}; $.each(ids, function (i, id) { hash[id.expId] = true; }); return hash; }, getDataType: function (term) { // Return dataType object using term // Needs loader function (using getDataGroups below for now) if (dataTypeTermHash !== undefined) { return dataTypeTermHash[term]; } return undefined; }, getDataTypeByLabel: function (label) { // Return dataType object using label // Needs loader function (using getDataGroups below for now) if (dataTypeLabelHash !== undefined) { return dataTypeLabelHash[label]; } return undefined; }, getDataGroups: function (dataTypes) { // Unpack JSON list of dataTypes // Return sorted array of dataGroup objects each having a .label, // .dataTypes, // and an array of dataTypes, alphasorted, with 'Other' last // Also populates hashes for lookup by term or label (for now) var dataGroupHash = {}, dataGroups = [], otherGroup, group; $.each(dataTypes, function (i, dataType) { group = dataType.dataGroup; if (!group) { return true; } // stash hashes for lookup by utility functions dataTypeTermHash[dataType.term] = dataType; dataTypeLabelHash[dataType.label] = dataType; if (!dataGroupHash[group]) { dataGroupHash[group] = { label: group, dataTypes: [] }; } dataGroupHash[group].dataTypes.push(dataType.label); }); $.each(dataGroupHash, function (key, item) { if (key === "Other") { otherGroup = item; } else { dataGroups.push(item); } }); dataGroups.sort(encodeProject.cmpCV); dataGroups.push(otherGroup); $.each(dataGroups, function (i, group) { if (!dataGroups[i]) { // for some reason there's __ element here (not my property) return true; } dataGroups[i].dataTypes.sort(encodeProject.cmpNoCase); }); return dataGroups; }, getCellType: function (cellType) { // Return cellType object from term // Needs loader function (using getCellTiers below for now) if (cellTypeTermHash !== undefined) { return cellTypeTermHash[cellType]; } return undefined; }, getCellTiers: function (cellTypes) { // Unpack JSON list of cellTypes // Return sorted array of cellTier objects each having a .term, // with tier number, .celltypes, and an array of cell types, alphasorted // Also loads hash for lookup by term (for now) var cellTiers = [], tier; $.each(cellTypes, function (i, cellType) { tier = cellType.tier; // ignore untiered cell types (all human should have a tier) if (!tier) { return true; } cellTypeTermHash[cellType.term] = cellType; if (!cellTiers[tier]) { cellTiers[tier] = { term: tier, cellTypes: [] }; } cellTiers[tier].cellTypes.push(cellType.term); }); cellTiers.sort(encodeProject.cmpCV); $.each(cellTiers, function (i, tier) { if (!cellTiers[i]) { // for some reason there's __ element here (not my property) return true; } cellTiers[i].cellTypes.sort(encodeProject.cmpNoCase); }); return cellTiers; }, // Antibodies antibodyFromExp: function (experiment) { // Get antibody from expVars field of experiment var match = experiment.expVars.match(/antibody=(\S+)/); if (match) { return match[1]; } }, targetFromAntibody: function (antibody ) { // Get target for antibody // Needs loader function (using getAntibodyGroups below) if (antibodyHash !== undefined && antibodyHash[antibody] !== undefined) { return antibodyHash[antibody].target; } return undefined; }, getAntibodyTarget: function (target) { // Get target object by term if (antibodyTargetHash !== undefined) { return antibodyTargetHash[target]; } return undefined; }, isHistone: function (target) { // Helper function, returns true if antibody target histone modification if (target === undefined) { return false; } return target.match(/^H[234]/); }, getAntibodyGroups: function (antibodies) { // Return sorted array of antibodyGroup objects each having a .label // with group name (Histone Modification or Transcription Factor), // and an array of antibody targets, alphasorted var antibodyGroups = [], antibodyGroupHash = {}, group, target; $.each(antibodies, function (i, antibody) { // populate hashes to lookup antibodies by target and vice versa // organize into groups (histones vs TFs) antibodyHash[antibody.term] = antibody; target = antibody.target; // pull out of loop if needed to improve perf group = encodeProject.isHistone(target) ? "Histone Modification" : "Transcription Factor"; if (!antibodyGroupHash[group]) { antibodyGroupHash[group] = { label: group, targets: [] }; } if (antibodyTargetHash[target] === undefined) { antibodyTargetHash[target] = { description: antibody.targetDescription, antibodies: [] }; antibodyGroupHash[group].targets.push(target); } antibodyTargetHash[target].antibodies.push(antibody.term); }); // unpack temp stash into sorted array of groups containing // sorted array of antibody targets $.each(antibodyGroupHash, function (key, item) { antibodyGroups.push(item); }); antibodyGroups.sort(encodeProject.cmpCV); $.each(antibodyGroups, function (i, group) { if (!antibodyGroups[i]) { // for some reason there's __ element here (not my property) return true; } antibodyGroups[i].targets.sort(encodeProject.cmpNoCase); }); return antibodyGroups; } }; }());