Adding review

views/review.html

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+<h3>Title</h3>
+
+
+<p id="participantCode">Loading1b</p>
+<p id="visitCode">Loading2</p>
+
+<div id="organ3">
+	<table>
+	<tr>
+		<td id="CT_organ3"></td>
+		<td id="PET_organ3"></td>
+		<td id="SUV_organ3"></td>
+	</tr>
+	<tr>
+		<td id="CT_organ4"></td>
+		<td id="PET_organ4"></td>
+		<td id="SUV_organ4"></td>
+	</tr>
+	<tr>
+		<td id="CT_organ5"></td>
+		<td id="PET_organ5"></td>
+		<td id="SUV_organ5"></td>
+	</tr>
+	</table>
+</div>
+<div id="debugDiv">
+	<textarea id="debugCode"></textarea>
+</div>
+
+<script type="text/javascript">
+
+let searchParams = new URLSearchParams(window.location.search);
+
+//update this to pick crfRef from url
+let participantCode=searchParams.get('participantCode');
+let visitCode=searchParams.get('visitCode');
+document.getElementById("participantCode").innerHTML=participantCode;
+document.getElementById("visitCode").innerHTML=visitCode;
+let project=LABKEY.ActionURL.getContainer();
+document.getElementById("debugCode").value+='\n'+project;
+
+let server="http://onko-nix.onko-i.si:8080/labkey";
+let basePath=server+"/_webdav/";
+basePath+=project;
+basePath+="/@files/preprocessedImages/";
+basePath+=participantCode+"/"+visitCode+"/";
+document.getElementById("debugCode").value+='\n'+basePath;
+let studyPath=server+project;
+
+//let divImg=document.getElementById("organ3_PET");
+
+let organs=["3","4","5"];
+let im=["PET","CT"];
+for (let i=0;i<organs.length;i++){
+	let organ=organs[i];
+	let type="PET";
+
+	let img=document.createElement('img');
+	let imgSrc=basePath+participantCode+"-"+visitCode+"_"+type+"_"+organ+"_v5.png";
+	img.src=imgSrc;
+	img.width="300";
+	document.getElementById(type+"_organ"+organ).appendChild(img);
+							
+
+	type="CT";
+	let img1=document.createElement('img');
+	let img1Src=basePath+participantCode+"-"+visitCode+"_"+type+"_"+organ+"_v5.png";
+	img1.src=img1Src;
+	img1.width="300";
+	document.getElementById(type+"_organ"+organ).appendChild(img1);
+}
+LABKEY.requiresScript('/vis/genericChart/genericChartHelper.js', 
+      function(){LABKEY.vis.GenericChartHelper.loadVisDependencies(dependencyCallback);});
+
+
+</script>

views/review.view.xml

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+<view xmlns="http://labkey.org/data/xml/view" title="Review">
+	<dependencies>
+			<dependency path="crf/crfReview.js"/>
+		</dependencies>
+	<permissions>
+		<permission name="login"/>
+	</permissions>
+
+</view>

web/crf/crfReview.js

@@ -0,0 +1,312 @@
+
+function renderMessages(id, messages) {
+	if (messages && messages.length > 0) {
+		let errorDiv = document.createElement('div');
+		let style='padding: 10px; background-color: #ffe5e5;' 
+		style+='color: #d83f48; font-weight: bold;';
+		errorDiv.setAttribute('style', style);
+		errorDiv.innerHTML = messages.join('<br/>');
+		document.getElementById(id).appendChild(errorDiv);
+	}
+};
+
+function validateChartConfig(chartConfig, aes, scales, measureStore) {
+	let hasNoDataMsg = LABKEY.vis.GenericChartHelper.validateResponseHasData(measureStore, false);
+	if (hasNoDataMsg != null)
+		return {"success": false, "messages": [hasNoDataMsg]};
+
+	let measureNames = Object.keys(chartConfig.measures);
+	for (let i = 0; i < measureNames.length; i++) {
+		let measureProps = chartConfig.measures[measureNames[i]];
+		if (measureProps && 
+			measureProps.name && 
+			measureStore.records()[0][measureProps.name] == undefined){
+					                    
+			let retVal=new Object();
+			retVal.success=false;
+			retVal.messages=['The measure, ' + 
+				measureProps.label + 
+				', is not available. It may have been renamed or removed.']
+			return retVal;
+		}
+	}
+
+	 let messages = [];
+	 let axisMeasureNames = ['x', 'xSub', 'y'];
+	 for (let i = 0; i < axisMeasureNames.length; i++) {
+		 if (measureNames.indexOf(axisMeasureNames[i]) > 0) {
+			let validation = LABKEY.vis.GenericChartHelper.validateAxisMeasure(
+				chartConfig.renderType, chartConfig, axisMeasureNames[i],
+				aes, scales, measureStore.records());
+			if (validation.message != null)
+				messages.push(validation.message);
+			if (!validation.success)
+				return {"success": false, "messages": messages};
+		 }
+	}
+
+	return {"success": true, "messages": messages};
+
+}
+function selectRowsCallback(renderConfig, measureStore) {
+	let responseMetaData = measureStore.getResponseMetadata();
+
+        // chartConfig is the saved information about the chart (labels, scales, etc.)
+
+	let chartConfig = new Object();
+	chartConfig.renderType="line_plot";
+
+	let mX=new Object();
+	mX.displayFieldJsonType="";
+        mX.hidden=false;
+        mX.fieldKey="percentile";
+        mX.label="Percentile";
+        mX.schemaName="study";
+        mX.type="float";
+        mX.normalizedType="float";
+        mX.measure=true;
+        mX.name="percentile";
+        mX.queryName="SUVQuantiles";
+        mX.alias="percentile";
+        mX.shortCaption="Percentile";
+        mX.dimension=false;
+
+	let mY=new Object();
+        mY.displayFieldJsonType="";
+        mY.hidden=false;
+        mY.fieldKey="value";
+        mY.label="Value";
+        mY.schemaName="study";
+        mY.type="float";
+        mY.normalizedType="float";
+        mY.measure=true;
+        mY.name="value";
+        mY.queryName="SUVQuantiles";
+        mY.alias="value";
+        mY.shortCaption="Value";
+        mY.dimension=false;
+
+
+	let mS=new Object();
+        mS.displayFieldJsonType="";
+        mS.hidden=false;
+        mS.fieldKey="ParticipantId";
+        mS.label="Participant ID";
+        mS.schemaName="study";
+        mS.type="string";
+        mS.normalizedType="string";
+        mS.measure=false;
+        mS.name="ParticipantId";
+        mS.queryName="SUVQuantiles";
+        mS.alias="ParticipantId";
+        mS.shortCaption="Participant ID";
+        mS.dimension=true;
+
+	chartConfig.measures=new Object();
+        chartConfig.measures.x=mX;
+        chartConfig.measures.y=mY;
+        chartConfig.measures.series=mS;
+        chartConfig.measures.pointClickFn=null;
+        chartConfig.scales=new Object();
+        chartConfig.scales.x=new Object();
+        chartConfig.scales.x.trans="linear";
+        chartConfig.scales.y=new Object();
+        chartConfig.scales.y.trans="linear";
+        chartConfig.labels=new Object();
+        chartConfig.labels.main="SUVQuantiles";
+        chartConfig.labels.subtitle="";
+        chartConfig.labels.x="Percentile";
+        chartConfig.labels.y="Value";
+ 	chartConfig.width=null;
+        chartConfig.height=null;
+        chartConfig.pointType="outliers";
+        chartConfig.geomOptions=new Object();
+        chartConfig.geomOptions.label="SUVQuantiles";
+        chartConfig.geomOptions.subtitle="";
+        chartConfig.geomOptions.width=null;
+        chartConfig.geomOptions.height=null;
+        chartConfig.geomOptions.pointType="outliers";
+        chartConfig.pointFillColor="3366FF";
+        chartConfig.lineWidth="3";
+        chartConfig.lineColor="000000";
+        chartConfig.boxFillColor="3366FF";
+        chartConfig.hideDataPoints=false;
+        chartConfig.colorPaletteScale="ColorDiscrete";
+        chartConfig.chartLayout="single";
+        chartConfig.chartSubjectSelection="subjects";
+        chartConfig.displayIndividual=true;
+        chartConfig.displayAggregate=false;
+        chartConfig.errorBars="None";
+        chartConfig.pieInnerRadius=0;
+	chartConfig.pieOuterRadius=80;
+        chartConfig.showPiePercentages=true;
+        chartConfig.pieHideWhenLessThanPercentage=5;
+        chartConfig.piePercentagesColor="333333";
+        chartConfig.gradientPercentage=95;
+        chartConfig.gradientColor="FFFFFF";
+        chartConfig.binThreshold=10000;
+        chartConfig.binShapeGroup="hex";
+        chartConfig.binColorGroup="BlueWhite";
+        chartConfig.binSingleColor="000000";
+        chartConfig.showOutliers=true;
+        chartConfig.binShape="hex";
+
+	if (!chartConfig.hasOwnProperty('width') || 
+		chartConfig.width == null) 
+		chartConfig.width = 1000;
+        if (!chartConfig.hasOwnProperty('height') || 
+		chartConfig.height == null) 
+		chartConfig.height = 600;
+	if (renderConfig.hasOwnProperty('width')){
+		chartConfig.width=renderConfig.width;
+		chartConfig.height=0.6*renderConfig.width;
+	}
+
+
+	let xAxisType = chartConfig.measures.x ? (
+		chartConfig.measures.x.normalizedType || 
+		chartConfig.measures.x.type) : null;
+        let chartType = LABKEY.vis.GenericChartHelper.getChartType(
+		chartConfig.renderType, xAxisType);
+        let aes = LABKEY.vis.GenericChartHelper.generateAes(
+                chartType, chartConfig.measures, 
+		responseMetaData.schemaName, responseMetaData.queryName);
+        let valueConversionResponse = 
+		LABKEY.vis.GenericChartHelper.doValueConversion(
+			chartConfig, aes, chartType, measureStore.records());
+     	if (!Ext4.Object.isEmpty(valueConversionResponse.processed)) {
+               Ext4.Object.merge(chartConfig.measures, 
+		       valueConversionResponse.processed);
+               aes = LABKEY.vis.GenericChartHelper.generateAes(
+                       chartType, chartConfig.measures, 
+		       responseMetaData.schemaName, responseMetaData.queryName);
+        }
+        let data = measureStore.records();
+        if (chartType == 'scatter_plot' && 
+		data.length > chartConfig.geomOptions.binThreshold) {
+               chartConfig.geomOptions.binned = true;
+        }
+        let scales = LABKEY.vis.GenericChartHelper.generateScales(
+		chartType, chartConfig.measures, chartConfig.scales, 
+		aes, measureStore);
+        let geom = LABKEY.vis.GenericChartHelper.generateGeom(
+		chartType, chartConfig.geomOptions);
+        let labels = LABKEY.vis.GenericChartHelper.generateLabels(
+		chartConfig.labels);
+
+	if (chartType == 'bar_chart' || chartType == 'pie_chart') {
+            	let dimName = null, subDimName = null; measureName = null,
+	               aggType = 'COUNT';
+
+        	if (chartConfig.measures.x) {
+			dimName = chartConfig.measures.x.converted ? 
+				chartConfig.measures.x.convertedName : 
+				chartConfig.measures.x.name;
+        	}
+        	if (chartConfig.measures.xSub) {
+	        	subDimName = chartConfig.measures.xSub.converted ? 
+				chartConfig.measures.xSub.convertedName : 
+				chartConfig.measures.xSub.name;
+		}
+	
+		if (chartConfig.measures.y) {
+			measureName = chartConfig.measures.y.converted ? 
+				chartConfig.measures.y.convertedName : 
+				chartConfig.measures.y.name;
+
+			if (Ext4.isDefined(chartConfig.measures.y.aggregate)) {
+				aggType = chartConfig.measures.y.aggregate;
+                	}
+                	else if (measureName != null) {
+				aggType = 'SUM';
+			}
+
+		}
+
+
+		data = LABKEY.vis.getAggregateData(data, dimName, subDimName, 
+			measureName, aggType, '[Blank]', false);
+        }
+
+	let plotConfig = LABKEY.vis.GenericChartHelper.generatePlotConfig(
+		renderConfig.chartId,chartConfig, labels, aes, scales, geom, data);
+
+        let validation = validateChartConfig(chartConfig, aes, scales, measureStore);
+        renderMessages(renderConfig.chartId, validation.messages);
+        if (!validation.success)
+            return;
+	
+	let plot;
+        if (chartType == 'pie_chart') {
+            new LABKEY.vis.PieChart(plotConfig);
+        }
+        else {
+            plot = new LABKEY.vis.Plot(plotConfig);
+            plot.render();
+        }
+	   
+
+
+
+}
+
+function dependencyCallback() {
+
+	let organs=["3","4","5"];
+		
+	for (let i=0;i < organs.length; i++){
+
+		let renderConfig=new Object();
+        	//all additional configuration stuff goes in here
+
+		renderConfig.chartId='SUV_organ'+organs[i];
+		renderConfig.width=500;
+		renderConfig.participantCode=document.getElementById("participantCode").innerHTML;
+		renderConfig.visitCode=document.getElementById("visitCode").innerHTML;
+
+		// When all the dependencies are loaded we then load the data via the MeasureStore selectRows API.
+		// The queryConfig object stores all the information needed to make a selectRows request
+		
+		let queryConfig = new Object;
+	        queryConfig.schemaName="study";
+        	queryConfig.queryName="SUVQuantiles";
+        	queryConfig.viewName=null;
+        	queryConfig.dataRegionName="Dataset";
+	        queryConfig.queryLabel="SUVQuantiles";
+        	queryConfig.parameters= new Object();
+		queryConfig.requiredVersion=13.2;
+	        queryConfig.maxRows=-1;
+        	queryConfig.sort="lsid";
+	        queryConfig.method="POST";
+        	queryConfig.columns=["percentile","value","ParticipantId"];
+	        queryConfig.filterArray=new Array();
+        	queryConfig.filterArray.push({
+			"name":"patientCode",
+			"value":renderConfig.participantCode,
+			"type":"eq"});
+	        queryConfig.filterArray.push({
+			"name":"visitCode",
+			"value":renderConfig.visitCode,
+			"type":"eq"});
+        	queryConfig.filterArray.push({
+			"name":"organ",
+			"value":organs[i],
+			"type":"eq"});
+
+		if (queryConfig.filterArray && 
+			queryConfig.filterArray.length > 0) {
+            		let filters = [];
+            		for (let i = 0; i < queryConfig.filterArray.length; i++) {
+                		let f = queryConfig.filterArray[i];
+                		filters.push(LABKEY.Filter.create(
+					f.name,  f.value, 
+					LABKEY.Filter.getFilterTypeForURLSuffix(f.type)));
+            		}
+            		queryConfig.filterArray = filters;
+        	}
+        	queryConfig.success = function(data){
+			selectRowsCallback(renderConfig,data);};
+        	queryConfig.containerPath = "/IPNUMMprospektiva/Study";
+        	LABKEY.Query.MeasureStore.selectRows(queryConfig);
+	}
+};