crf/web/crfTecant/crfReviewSection.js

//loadFile is in fileManager.js
var crfReviewSection={};

crfReviewSection.set=
function(parentClass){
   if ("parent" in this) 
      return;
   this.parent=parentClass;
}

crfReviewSection.generateErrorMessage=
function (id,listName,msg){
	this.parent.print('generateErrorMessage:');
	let eid=listName+"_errorMsg";
	let el=config.document.getElementById(eid);
	if (el===null){
		el=config.document.createElement("p");
		config.document.getElementById(id).appendChild(el);
	}
	el.innerHTML=msg;
}

crfReviewSection.clearErrorMessage=
function(listName){
	let eid=listName+"_errorMsg";
	let el=config.document.getElementById(eid);
	if (el===null) return;
	el.remove();
}




crfReviewSection.generateSection=
function(listName,id,callback){
   let that=this;
   let action=function(){that.fcontinue(listName,id,callback);};
   LABKEY.requiresScript(["crfTecant/fileManager.js"],action);
}

crfReviewSection.fcontinue=
function(listName,id,callback){
	//callback should be generateReviewSectionCB and it takes no arguments
	this.parent.print("generateReviewSection");
   let config=this.parent.config;
	//need base path


	config.loadFileConfig=new Object();
	
	
	config.loadFileConfig.cb=callback;
	config.loadFileConfig.id=id;
	config.loadFileConfig.url=fileManager.getBasePath()+'/@files/reportSetup/'+listName+'.json';
	fileManager.loadFile();
	//load file and continue in the next function
}

crfReviewSection.getParticipantCode=
function(pid){

	let filters=[LABKEY.Filter.create("crfRef",this.parent.getCRFref())];
   let config=this.parent.config;
	let mfId=config.formConfig.form['masterQuery'];
   let queryName=config.formConfig.queryMap[mfId];
   let that=this;
	pid.afterId=function(id){that.setParticipantCode(id);};
	pid.participantField=config.formConfig.studyData["SubjectColumnName"];
	let cb=function(data){that.afterRegistration(pid,data);}
   //untested
   this.parent.selectRows('lists',queryName,filters,cb,this.parent.getContainer('data'));
}

crfReviewSection.visitCodeFromVisitId=
function(visitId){
	if (visitId<0) return "NONE";
	let project=this.parent.getContainer('data');
this.parent.print('visitCodeFromVisitId: '+project.search('retro'));
	if (project.search('retro')>-1)
		visitId-=1;
	return 'VISIT_'+visitId.toString();
}

crfReviewSection.replaceSlash=
function(x){
	return x.replace(/\//,'_');
}

crfReviewSection.setParticipantCode=
function(pid){
	let fName='[setParticipantCode]';
	let rows=pid.registration.rows;
   let config=this.parent.config;
	//pick from study
	let participantField=config.formConfig.studyData["SubjectColumnName"];
	if (rows.length==1){
		this.parent.print(fName+': '+rows[0][participantField]+'/'+rows[0].visitId);
		let visitCode=this.visitCodeFromVisitId(rows[0].visitId);
		this.parent.print('setParticipantCode: '+pid.participantId+'/'+visitCode);
		pid.participantCode=this.replaceSlash(pid.participantId);
		pid.visitCode=visitCode;
	}
	this.generateReviewSection2(pid);
}

crfReviewSection.CB=
function(){
   let config=this.parent.config;
	let listName=config.loadFileConfig.listName;
	let id=config.loadFileConfig.id;

	this.parent.clearErrorMessage(listName);

	let pid=new Object();
	pid.participantCode="NONE";
	pid.visitCode="NONE";
	this.getParticipantCode(pid);
	this.parent.print('Get participant code sent');
	//involves database search, continue after callback
}

crfReviewSection.getValueFromElement=
function(id,defaultValue){
   let config=this.parent.config;
	let e=config.document.getElementById(id);
	if (e!=null){
		defaultValue=e.innerHTML;
	}
	return defaultValue;
}

crfReviewSection.pickParticipantCodeFromPage=
function(){
	let pid=new Object();
	pid.participantCode=this.getValueFromElement("participantCode","NIX-LJU-D2002-IRAE-A000");
	pid.visitCode=this.getValueFromElement("visitCode","VISIT_1");
	this.generateReviewSection2(pid);
}

crfReviewSection.patternReplace=
function(src,replacements,values){

	for (rep in replacements){
		let txt1=src.replace(new RegExp(rep),values[replacements[rep]]);
		src=txt1;
	}
	return src;

}

crfReviewSection.plotImage=
function(cell,k,row,rowVariable,obj,pid){
   let config=this.parent.config;
	let baseDir=this.patternReplace(obj.imageDir,obj.replacements,pid);
	this.parent.print('Base dir: '+pid.basePath);
	pid[obj.variable]=obj.values[k];
	cell.id=pid[obj.variable]+"_"+rowVariable+pid[rowVariable];
	let img=null;
	let imgId=cell.id+'_img_';
	img=config.document.getElementById(imgId);
	if (img===null){
		img=config.document.createElement('img');
		img.id=imgId;
		cell.appendChild(img);
	}
	let imgSrc=patternReplace(obj.file,obj.replacements,pid);
   this.parent.print('Image: '+imgSrc);
	let imagePath=pid.basePath+'/'+baseDir+'/'+imgSrc;
			
	img.src=imagePath;
	img.width="300";

	
}

crfReviewSection.showReport=
function(cell,k,row,rowVariable,obj,pid){

	cell.width="300px";
	cell.id='report_'+obj.values[k]+"_"+rowVariable+pid[rowVariable];
	let reportConfig=new Object();
	reportConfig.partName="Report";
	reportConfig.renderTo=cell.id;
	//reportConfig.showFrame=false;
	//reportConfig.width="300";
	reportConfig.frame="none";
	reportConfig.partConfig=new Object();
	reportConfig.partConfig.width="300";
	reportConfig.partConfig.title="R Report";
	reportConfig.partConfig.reportName=obj.values[k];
	for (f in obj.parameters){
		reportConfig.partConfig[f]=pid[f];
	}
	reportConfig.partConfig.showSection="myscatterplot";
	let reportWebPartRenderer = new LABKEY.WebPart(reportConfig);
   this.parent.print('Render to: '+reportConfig.renderTo);
	reportWebPartRenderer.render();
}

crfReviewSection.showProbability=
function(cell,k,row,rowSetup,j,obj,pid){
   this.parent.print('showProbability: '+rowSetup);
	let rowVariable=rowSetup.variable;	
	cell.id='prob_'+obj.values[k]+"_"+rowVariable+pid[rowVariable];

	let probDensity=new Object();
	probDensity.mean=rowSetup.mean[j];
	probDensity.sigma=rowSetup.sigma[j];

   this.parent.print('showProbability: mean '+probDensity.mean+' sigma '+probDensity.sigma);


	probDensity.func=obj.values[k];
	probDensity.organCode=pid.organCode;
	pid[obj.variable]=rowSetup[obj.variable][j];
	probDensity.percentile=pid.percentile;
	let selectRows=new Object();
	selectRows.queryName=obj.queryName;
	selectRows.schemaName="study";
	selectRows.filterArray=[];
	selectRows.containerPath=getContainer('data');
	for (let f in obj.filters){
		selectRows.filterArray.push(
				LABKEY.Filter.create(f,pid[obj.filters[f]]));
	   this.parent.print('Filter ['+f+']: '+pid[obj.filters[f]]);
	}
	selectRows.success=function(data){ 
		this.drawProbability(data,cell,obj,pid,probDensity);}
	LABKEY.Query.selectRows(selectRows);
}

crfReviewSection.erf=
function(x){
	let fx=[0,0.02,0.04,0.06,0.08,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,
		1,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,2,
		2.1,2.2,2.3,2.4,2.5,3,3.5];
	let fy=[0,0.222702589,0.328626759,0.428392355,0.520499878,
		0.603856091,0.677801194,0.742100965,0.796908212,
	 	0.842700793,0.880205070,0.910313978,0.934007945,
		0.952285120,0.966105146,0.976348383,
		0.983790459,0.989090502,0.992790429,0.995322265,
		0.997020533,0.998137154,0.998856823,0.999311486,
		0.999593048,0.999977910,0.999999257];
	let n=32;
	let i0=n-1;

	for (let i=1;i<n;i++){
		if (Math.abs(x)>fx[i]) continue;
		i0=i-1;
		break;
	}
	let fval=1;
	if (i0<n-1){
		//interpolate
		let y1=fy[i0+1];
		let y0=fy[i0];
		let x1=fx[i0+1];
		let x0=fx[i0];
		fval=y0+(y1-y0)/(x1-x0)*(Math.abs(x)-x0);
	}
   this.parent.print('Erf: '+fval);
	if (x<0) return -fval;
	return fval;
}

crfReviewSection.setLine=
function(fbox,name,value,fontSize){
	let fpId=fbox.id+name;
	let fp=config.document.getElementById(fpId);
	if (fp===null){
		fp=config.document.createElement("p");
		fp.id=fpId;
		fbox.appendChild(fp);
	}
	fp.classList.add("center");
	fp.style.textAlign="center";
	fp.style.fontSize=fontSize;
	fp.innerText=value;
}	

crfReviewSection.drawProbability=
function(data,cell,obj,pid,probDensity){
this.parent.print('drawProbability');
	if (data.rows.length!=1){
	   this.parent.print("drawProbability row length mismatch: "+data.rows.length);
		return;
	}
	//possible mismatch; I assume the dataset will have a field called value
	let val=data.rows[0].value;

	let prob=0;
	let fz=-100;

	if (probDensity.func=="gaus"){
		fz=(val-probDensity.mean)/probDensity.sigma/Math.sqrt(2);
		prob=0.5+0.5*erf(fz);
	}
	let color="red";
	let fzx=fz*Math.sqrt(2);
   this.parent.print('drawProbability '+fzx);

	for (let i=1;i<obj.intervals.n;i++){
		if (fzx>obj.intervals.zlimits[i]) continue;
		color=obj.intervals.colors[i-1];
		break;
	}
	
	let fboxId=cell.id+'_fbox_';
	let fbox=config.document.getElementById(fboxId);
	if (fbox===null){
		fbox=config.document.createElement("div");
		fbox.id=fboxId;
		cell.appendChild(fbox);
	}
	fbox.style.backgroundColor=color;
	fbox.style.width="180px";
	fbox.style.height="180px";
	

   this.parent.print('organCode '+probDensity.organCode);
	let organName="Lung";

	if (probDensity.organCode==4){
		organName="Thyroid";
	}
	if (probDensity.organCode==5){
		organName="Bowel";
	}

	this.setLine(fbox,'_fp4_',organName,"16px");
	this.setLine(fbox,'_fp_',val.toPrecision(3),"25px");
	this.setLine(fbox,'_fp1_',"SUV("+probDensity.percentile+"%)","16px");
	this.setLine(fbox,'_fp2_',fzx.toPrecision(3),"25px");
	this.setLine(fbox,'_fp3_',"z-value","16px");


}
crfReviewSection.generateReviewSection2=
function(pid){ 
	let config=this.parent.config;
	let listName=config.loadFileConfig.listName;
	let id=config.loadFileConfig.id;
	
   this.parent.print('generateReviewSection2: '+pid.participantCode+'/'+
		pid.visitCode);
	if (pid.participantCode=="NONE" || pid.visitCode=="NONE"){
		this.generateErrorMessage(id,listName,
			"ParticipantId/visitId not set");
		return;
	}
	

   this.parent.print('JSON: '+config.loadFileConfig.json);

	let json=config.loadFileConfig.json;
	let nrows=json.rows.values.length;
	let ncol=json.columns.length;

	pid.basePath=fileManager.getBasePath()+"/@files";
	
	
	let el=config.document.getElementById(id);
	let tableId=id+'_Table';
	let table=config.document.getElementById(tableId);
	if (table==null){
		table=config.document.createElement('table');
		table.id=tableId;
		el.appendChild(table);
	}
	table.style.tableLayout="fixed";
	table.style.columnWidth="300px";
	
	for (let i=0;i<nrows;i++){
		pid[json.rows.variable]=json.rows.values[i];
		//let organ=organs[i];
		let row=null;
		if (i<table.rows.length)
			row=table.rows[i];
		else
			row=table.insertRow();

		let ic=0;
		for (let j=0;j<ncol;j++){
			let obj=json.columns[j];
			let nv=obj.values.length;
			for (let k=0;k<nv;k++){
				let cell=null;
				if (ic<row.cells.length)
					cell=row.cells[ic];
				else
					cell=row.insertCell();
				if (obj.display=="image") 
					this.plotImage(cell,k,row,json.rows.variable,obj,pid);
				if (obj.display=="report") 
					this.showReport(cell,k,row,json.rows.variable,obj,pid);
				if (obj.display=="probability"){ 
					this.showProbability(cell,k,row,json.rows,i,obj,pid);
				}	
				ic++;
			}


		}
		

	}
}

///>>>>>>>>>>>>>>end of reviewSection(REPORT)

crfReviewSection.afterRegistration=
function(data,fc){
	let fName='[afterRegistration/'+data.queryName+']';
   this.parent.print(fName+": rows:"+data.rows.length);
	fc.registration=data;
	let registrationData=fc.registration;
	this.parent.clearErr();
	if (registrationData.rows.length!=1){
		let msg=fName+": ERROR: Found "+registrationData.rows.length;
		msg+=" registration entries for crfrefid "+this.parent.getCRFref();
	   this.parent.print(msg);
		fc.afterId(fc);
		return;
	}
   this.parent.print(fName+'registration participant field: '+fc.participantField);
	fc.participantId=registrationData.rows[0][fc.participantField];
	//could be a lookup field (particularly for studies)
   this.parent.print('ID: '+fc.participantId);	
	let fields=registrationData.metaData.fields;
	let field="NONE";
	for (f in fields){
		if (fields[f]["name"]==fc.participantField)
			field=fields[f];
	}
	if ("lookup" in field){
		let pid=fc.participantId;
	   this.parent.print("Using lookup for participantId: "+pid);
		let lookup=field["lookup"];
   	this.parent.print("Lookup: ["+lookup.schemaName+','+lookup.queryName+']');

      //load lookup
      let that=this;
		let cb=function(data){that.afterRegistrationLookup(data,lookup.displayColumn,fc)};
		let filters=[LABKEY.Filter.create(lookup.keyColumn,pid)];
      this.parent.selectRows(lookup.schemaName,lookup.queryName,filters,cb,lookup.containerPath);

	}
	else{
		//afterParticipantId(configUpload);
		fc.afterId(fc);
	}
}

crfReviewSection.afterRegistrationLookup=
function(data,displayColumn,fc){
   this.parent.print("afterRegistrationLookup");
	let entry=data.rows[0];
	fc.participantId=entry[displayColumn];
   this.parent.print('Setting to '+fc.participantId);
	fc.afterId(fc);
	//afterParticipantId(configUpload);
}