basynthec-browser.js

Od600InspectorView.prototype.removeAll = function(duration) 
{
	var inspector = inspectors.selectAll("div.od600inspector").data([]);
	inspector.exit().transition()
		.duration(duration)
		.style("opacity", "0")
		.remove();
}

function od600DataForStrain(d) {
	if (null == d.dataSets) return [];
	
	var dataSets = d.dataSets.filter(function(ds) { return isOd600DataSet(ds) });
	var idx = -1;
	var data = [];
	dataSets.map(function(ds) { 
		if (null == ds.od600Map) return {};
		var strainData = ds.od600Map[d.name];
		if (null == strainData) return {};
		strainData.map(function(curve) {
			idx = idx + 1;
			data.push({ strain: d, index: idx, values: curve });
		});
	})
	return data;
}

function curveData(d, i)
{
	if (!d.values) return [];
	var color = curveColors(d.index);	
	// Don't normalize -- use 2 as the global max value
	// var maxValue = (0 == d.values.length) ? 0 : d3.max(d.values);
	return [{length : d.values.length, max : 2, values: d.values, color : color}]
}

function lineData(d)
{
	if (!d) return [];
	
	var data = d.values;
	// convert the data into pairs
	var pairs = data.reduce(function(sum, elt) {
		// initialization
		if (sum.length < 1) {
			sum.push([elt / d.max]);
			return sum;
		}
		
		// add the current elt as the second in the last pair and the first in the new pair
		sum[sum.length - 1].push(elt / d.max);
		// don't add the very last element
		if (sum.length < data.length - 1) sum.push([elt / d.max]);
		return sum;
	}, []);
	
	return pairs;
}

function dataSetLabel(d) { return d.bis.dataSetTypeCode + " registered on " + timeformat(new Date(d.bis.registrationDetails.registrationDate));  }

function downloadTableFile(d) { presenter.downloadTableFile(d) }

function filesForDataSet(d)
{
	if (d.loadingFiles) return [{ pathInListing : "Loading..." }];
	
	var fileFilter = function(file) {
		if (!file.isDirectory) {
			if (endsWith(file.pathInDataSet, "xls")) {
				return true;
			}
			if (endsWith(file.pathInDataSet, "xls.tsv")) {
				return true;
			}
		}
		return false;
	};
	
	return (d.files) ? d.files.filter(fileFilter) : [];
}


var model = new AppModel();
var presenter = new AppPresenter();

// The data set type visualization
var dataSetTypeVis, od600View, metabolomicsView, transcriptomicsView, proteomicsView, sequencesView;

// The strain visualization
var strainVis, strainView;

// The OD600 strain visualization
var od600StrainVis, od600StrainView;

var IGNORED_DATASET_TYPES = [ "EXCEL_ORIGINAL", "TSV_EXPORT", "TSV_MULTISTRAIN_EXPORT", "UNKNOWN" ];

//The inspected strains and data sets
var inspected = [];
var od600Inspected = [];

//The node inspectors
var inspectors, dataSetInspectorView, od600InspectorView;


function isOd600DataSet(d) { return "OD600" == d.bis.dataSetTypeCode }

function shouldRenderProperty(prop, value) {
	// strain properties are dealt with separately	
	if (prop == STRAIN_PROP_NAME) return false;

	// do not show properties with no values	
	if (!value) return false;
	return true;
}

/**
 * Convert properties to pairs
 */
function props_to_pairs(d)
{
	var pairs = [];
	
	var dataSetStrains = basynthec.getStrains({properties:d});
	dataSetStrains = dataSetStrains.map(function(strain){
		return { name : strain };
	});
	var strainGroups = createStrainGroups(dataSetStrains);
	
	strainGroups.forEach(function(group) {
		var shortedStrains = group.strains.map(function(elt) { return elt.label; });
		shortedStrains = uniqueElements(shortedStrains.sort())
		var pair = [ group.groupName, shortedStrains.join(" ") ];
		pairs.push(pair)
	});
	
	for (var prop in d) {
		if (shouldRenderProperty(prop, d[prop])) {
			var pair = [prop, d[prop]];
			pairs.push(pair);
	  }
	}
	pairs.sort(function(a, b) { 
		if (a[0] == b[0]) return 0;
		// Sort in reverse lexicographical
		return (a[0] < b[0]) ? -1 : 1;
	});
	return pairs;
}

function enterApp()
{
	$("#login-form-div").hide();
	$("#main").show();
	basynthec.listAllDataSets(function(data) { 
		presenter.showDataSets(data.result); 
	});
	
	$('#openbis-logo').height(50)
	
}