crf/web/crf/crfData.js

//not tested yet.
//to use, add crfTecant/crfData.js to requiresScript and in the call-back, run init
//will work with crfSetup as setup object

var crfData={};

crfData.init=
function(cb=null){
   this.print('[crfData:init]');
   let that=this;
   let action=function(){that.afterScripts(cb);};
   LABKEY.requiresScript(["crf/runQuery.js","crf/variableList.js"],action);
}

crfData.afterScripts=
function(cb=null){
   if (cb) cb();
}

crfData.setSetup=
function(setup){
   this.setup=setup;
}

crfData.getContainer=
function(label){
   return this.setup.getContainer(label);
}

crfData.print=
function(msg){
   console.log(msg);
}

//getters
crfData.getSnapshotObject=
function(){
   if (!("dataQueriesSnapshot" in this))
      this.dataQueriesSnapshot=new Object();
   return this.dataQueriesSnapshot;
}


crfData.getQuerySnapshot=
function(queryName){
   //check whether queryName is in snapshotObject?
   return this.getSnapshotObject()[queryName];
}

crfData.getLayoutObject=
function(){
   if (!("dataQueriesLayout" in this))
      this.dataQueriesLayout=new Object();
   return this.dataQueriesLayout;
}

crfData.getQueryLayout=
function(queryName){
   //check whether queryName is in snapshotObject?
   return this.getLayoutObject()[queryName];
}

crfData.getLookupObject=
function(){
   if (!("lookup" in this))
      this.lookup=new Object();
   return this.lookup;
}

crfData.getLookup=
function(queryName){
   let x=this.getLookupObject();
   if (queryName in x) return x[queryName];
   return null;
}

crfData.getRegistration=
function(){
   let fName='[getRegistration]';
   let regQueryPars=variableList.parseVariables(this.setup.getSettings('registrationQuery'));
   let query=regQueryPars['query'];
   this.print(fName+' query '+query);
   return this.getQuerySnapshot(query).rows;
}

crfData.getCrfEntry=
function(){
   return this.getQuerySnapshot('crfEntry').rows[0];
}

crfData.getActiveQueries=
function(){
   if (!("activeQueries" in this))
      this.activeQueries=new Object();
   return this.activeQueries;
}

crfData.getActiveQuery=
function(queryName){
   let aq=this.getActiveQueries();
   if (queryName in aq) return aq[queryName];
   return null;
}

crfData.getRegistrationMap=
function(value=null){
   let rows=this.getRegistration();
   let qMap=new Object();
   let key='Key';
   if (!value) value='participantStudyId';
   for (let i=0;i<rows.length;i++){
      qMap[rows[i][key]]=rows[i][value];
   }
   return qMap;
}

crfData.getRegistrationEntryMap=
function(key=null){
   let rows=this.getRegistration();
   let qMap=new Object();
   if (!key) key='Key';
   for (let i=0;i<rows.length;i++){
      qMap[rows[i][key]]=rows[i];
   }
   return qMap;
}

crfData.getCrfRefForData=
function(){
   let parentCrf=this.getCrfEntry()['parentCrf'];
   if (!parentCrf) return this.getCrfEntry()['entryId'];
   return parentCrf;
}


crfData.setDataLayout=
function(formId,role,cb){
   let fName='[setDataLayout]';
   this.print(fName);
	let rowsSetup=this.setup.selectFormSetupRows(formId);
   let queryArray=new Array();
	let dS=this.getLayoutObject();//reference only
	let qMap=this.setup.getMap('inputLists');
   let qMapInverse=this.setup.invertMap(qMap);
   this.clearActiveQueries();
	//config.formConfig.lookup=new Object();
	for (let i=0;i<rowsSetup.length;i++){
		let entry=rowsSetup[i];
		//skip review rows
		if (entry['showFlag']=='REVIEW')
			continue;
      let accessMode=role+'Mode';
		//skipField
		if (entry[accessMode]=="NONE") continue;

		let queryId=entry['queryName'];
		let q=qMap[queryId];
		queryArray.push(runQuery.makeQuery(dS,'data',q,q,[]));
      this.addActiveQuery(crfSetup.getEntryMap('inputLists')[queryId]);
      this.print(fName+' adding '+q);
		if (entry['showQuery']!="NONE"){
			let sq=entry['showQuery'];
		   queryArray.push(runQuery.makeQuery(dS,'data',sq,sq,[]));
         //need inverse of qMap
         let sQueryId=qMapInverse[sq];
         this.addActiveQuery(crfSetup.getEntryMap('inputLists')[sQueryId]);
         this.print(fName+' adding '+sq);
			
		}
   }
	//always add reviews
   let q='reviewComments';
   queryArray.push(runQuery.makeQuery(dS,'data',q,q,[]));
   let rQueryId=qMapInverse[q];
   if (!rQueryId){
      this.print(fName+' missing query '+q+' in inputLists');
      return
   }
   this.addActiveQuery(crfSetup.getEntryMap('inputLists')[rQueryId]);
	
   //debug
   this.print("List of datasets in form : ");
	for (f in this.getActiveQueries()){
      let entry=this.getActiveQuery(f);
      this.print("\t"+f+" ID: "+entry['Key']+' title '+entry['title']);
   }

   let that=this;
   let action=function(){that.processLayout(cb);};
   runQuery.getDataFromQueries(this,queryArray,action);
}

//this happens after the for loop, so all dataQueries objects are set
crfData.processLayout=
function(cb=null){
   let fName='[processLayout]';
   let qList=this.getActiveQueries();
   //for layouts
   let queryArray=new Array();
   let targetObject=this.getLookupObject();
   let lookupSet=new Object();
   for (let qId in qList){
      let entry=this.getActiveQuery(qId);
      let q=entry['queryName'];
      let qobject=this.getQueryLayout(q);
	   this.print(fName+" inspecting layout for "+q+" "+qobject);
	   qobject.fields=qobject.metaData.fields;
	   qobject.title=entry['title'];

      //check for lookups
	   for (let f in qobject.fields){
		   //anything else is simple but lookup
		   let field=qobject.fields[f];
		   if (!("lookup" in field)) continue;
         let lookup=field.lookup;
         let qObject=this.getLookup(lookup.queryName);
         if (qObject) continue;
         //add to list
         let qName=lookup.queryName;
         let qCode=qName+':'+lookup.keyColumn+':'+lookup.displayColumn;
         let e=runQuery.makeQuery(targetObject,'data',qName,qCode,[]);
         //adjust minor settings
         if (lookup.containerPath) e.containerPath=lookup.containerPath;
         e.schemaName=lookup.schemaName;
         e.columns=lookup.keyColumn+','+lookup.displayColumn;
         lookupSet[qCode]=e;
         this.print(fName+' inserting '+qCode);
      }
   }
   for (let x in lookupSet){
      queryArray.push(lookupSet[x]);
      this.print(fName+' adding '+x);
      for (let v in lookupSet[x]){
         this.print(fName+' value ['+v+'] '+lookupSet[x][v]);
      }
   }
   //this.print(fName+' print '+targetObject.print);
   let that=this;
   let action=function(){that.processLookup(cb);};
   this.print(fName+' getDataFromQueries');
   runQuery.getDataFromQueries(this,queryArray,action);
   this.print(fName+' getDataFromQueries done');
}

crfData.processLookup=
function(cb=null){
   let fName="[processLookup]";

   let obj=this.getLookupObject();
   for (let q in obj){
	   this.print(fName+" "+q);
      let a=q.split(':');
      if (a.length<3) continue;
      let lookupName=a[0];
      let key=a[1];
      let val=a[2];
      obj[lookupName]=new Object();
      this.print(fName+' adding ['+lookupName+'] '+key+'/'+val);
      let lObject=obj[lookupName];

	   lObject.LUT=new Array();//key to value
	   lObject.ValToKey=new Array();//value to key
	   lObject.keyColumn=key
	   lObject.displayColumn=val;
      
      let qRows=obj[q].rows;
	   for (let i=0;i<qRows.length;i++){
         let r=qRows[i];
         this.print(fName+' LUT ['+r[key]+'] '+r[val]);
		   lObject.LUT[r[key]]=r[val];
		   lObject.ValToKey[r[val]]=r[key];
	   }
   }
	if (cb) cb();
}

crfData.setData=
function(crfRef,cb=null, schemaName=null){
	fName='[setData]';
	//let crfMatch=this.getCRFref();
	//let parentCrf=config.formConfig.crfEntry['parentCrf'];
	//if (parentCrf!=undefined) crfMatch=parentCrf;

	this.print(fName+' form crf ['+crfRef+'] ');

   let queryArray=new Array();
   let targetObject=this.getSnapshotObject();
	//collect data and execute callback cb for queries in cb.queryList
   let qList=this.getActiveQueries();
	for (let qId in qList){
      let entry=qList[qId];
      let q=entry['queryName'];
		let filters=[LABKEY.Filter.create("crfRef",crfRef)];
      let fieldName=q;
      if (schemaName=='study') fieldName=q+'Study';
      queryArray.push(runQuery.makeQuery(targetObject,'data',q,fieldName,filters,schemaName));

	}
   runQuery.getDataFromQueries(this,queryArray,cb);
}

crfData.setDataForQuery=
function(queryName,crfRef=null,cb=null,schemaName='lists',crfField='crfRef'){
   let queryArray=new Array();
   let targetObject=this.getSnapshotObject();
	
   let filters=[LABKEY.Filter.create(crfField,crfRef)];
   let fieldName=q;
   if (schemaName=='study') fieldName=q+'Study';
   queryArray.push(runQuery.makeQuery(targetObject,'data',q,fieldName,filters,schemaName));
   runQuery.getDataFromQueries(this,queryArray,cb);
}

crfData.uploadData=
function(id,crfRef,cb=null){
   let fName='[uploadData['+id+']'+crfRef+']';
   this.print(fName);
   let qList=this.getActiveQueries();
   let modArray=new Array();
   let schemaName='study';
   let containerName='data';
   for (let qId in qList){

      let entry=qList[qId];
      let q=entry['queryName'];

      this.print(fName+' working on '+q);
      
      //determine rows that need to be updated form querySnapshot
      let studyRows=this.getQuerySnapshot(q+'Study').rows;
      let listRows=this.getQuerySnapshot(q).rows;
      this.print(fName+' studies '+studyRows.length+' lists '+listRows.length);
      //rows to be UPDATED (already in dataset)
      let modRows=new Array();
      for (let i=0;i<studyRows.length;i++){
         let entry=studyRows[i];
         //
         if (! (i<listRows.length) ) continue;
         let entryList=listRows[i];
		   //keeps study only variables (ParticipantId, SequenceNum)
		   for (let f in entryList) {
			   entry[f]=entryList[f];
			   this.print(fName+" copying ["+f+"]: "+entry[f]+"/"+entryList[f]);
		   }
         modRows.push(entry);
      }

      //rows to be INSERTED 
      let insRows=new Array();
      let participantField=crfSetup.getRows('studyData')[0]["SubjectColumnName"];
      for (let i=studyRows.length;i<listRows.length;i++){
         let entry=listRows[i];
         //make sure you have the participantField right
         //
         entry[participantField]=id;
         entry.crfRef=crfRef;;
         entry.SequenceNum=crfRef;
         entry.SequenceNum=entry.SequenceNum % 1000000000;
		
         if (listRows.length>1){
            entry.SequenceNum+=i/100;
         }
         this.print( "Adding sequence number "+entry.SequenceNum);
         insRows.push(entry);
      }

      if (modRows.length>0)
         modArray.push(runQuery.makeModification('update',containerName,schemaName,q,modRows));
      //determine rows that need to be inserted from querySnapshot
      if (insRows.length>0)
         modArray.push(runQuery.makeModification('insert',containerName,schemaName,q,insRows));

   }
   //do the whole batch
   runQuery.modifyDataFromQueries(this,modArray,cb);
}

crfData.removeData=
function(cb=null){
   let qList=this.getActiveQueries();
   let modArray=new Array();
   for (let qId in qList){
      let entry=qList[qId];
      let q=entry['queryName'];
      
      //determine rows that need to be updated form querySnapshot
      let studyRows=this.getQuerySnapshot(q+'Study').rows;
      if (studyRows.length>0)
         modArray.push(runQuery.makeModification('delete','data','study',q,studyRows));

      let listRows=this.getQuerySnapshot(q).rows;
      if (listRows.length>0)
         modArray.push(runQuery.makeModification('delete','data','lists',q,listRows));
   }
   //do the whole batch
   runQuery.modifyDataFromQueries(this,modArray,cb);
}



crfData.setRegistration=
function(cb=null){
   let regQueryPars=variableList.parseVariables(this.setup.getSettings('registrationQuery'));
   let q=regQueryPars['query'];
   let queryArray=new Array();   
   let targetObject=this.getSnapshotObject();
   let filters=[];
   queryArray.push(runQuery.makeQuery(targetObject,'data',q,q,filters));
   runQuery.getDataFromQueries(this,queryArray,cb);
}

crfData.setCrfEntry=
function(crfRef,cb=null){
   let q='crfEntry';
   let queryArray=new Array();   
   let targetObject=this.getSnapshotObject();
	let filters=[LABKEY.Filter.create('entryId',crfRef)];
   queryArray.push(runQuery.makeQuery(targetObject,'data',q,q,filters));
   runQuery.getDataFromQueries(this,queryArray,cb);
}

crfData.createCrfStatus=
function(crfEntry){
   let crfStatus=new Object();
   crfStatus.entryId=crfEntry.entryId;
   crfStatus.submissionDate=new Date();
   crfStatus.FormStatus=crfEntry.FormStatus;
   crfStatus.User=crfEntry.UserId;
   crfStatus.Form=crfEntry.Form;
   return crfStatus;
}

crfData.addActiveQuery=
function(entry){
   let aq=this.getActiveQueries();
   let qName=entry['queryName'];
   if (qName in aq) return;
   aq[qName]=entry;
   return;
}

crfData.clearActiveQueries=
function(){
   let aq=this.getActiveQueries();
   for (q in aq){
      delete aq[q];
   }
}