Does what I'm trying to do here make sense?

example ruby

var patList = {};

var fs = require('fs');
function saveFile(patId, obj) {
fs.writeFile(patId+".json", JSON.stringify(obj), function(err) {
    if(err) {
        return console.log(err);
    }

     //console.log("The file was saved: %s" , patId+".json");
}); 

}


function writeFiles() {
        for (var key in patList) {
                //console.log(JSON.stringify(patList[key]))
                saveFile(key,patList[key]);
        }
}

function updateTumor() {

                const csvTumor=require('csvtojson')

                csvTumor()
                        .fromFile('tumor_properties_1523643565883.csv')
                        .on('json',(jsonTumor)=>{
                        // combine csv header row and csv line to a json object
                        pat = patList[jsonTumor['Patient ID']];
                        if (pat != undefined ) {
				console.log("Tumor Pat: %s", pat.patId);
                                var dx =  {
                                                "tumorCode": jsonTumor['Tumor Property Code'] ,
                                                "description": jsonTumor['Tumor Property Description'] ,
                                                "date": jsonTumor['Observation Date'] ,
                                                "docId": jsonTumor['Document ID'] ,
                                                "negated": jsonTumor['Negated'] ,
                                                };
                                pat.info.tumor.push(dx);
                        }
                }).on('done',(error)=>{ 
		updateOncology()
		 } );
}


function updateOncology() {
  console.log("starting oncology")
  const csvOnc=require('csvtojson')

  csvOnc()
     .fromFile('oncology_1523643565883.csv')
     .on('json',(jsonOnc)=>{
        // combine csv header row and csv line to a json object
	console.log("Checking pat: %s", jsonOnc['Patient ID']);
        pat = patList[jsonOnc['Patient ID']];
        if (pat != undefined ) {
	    console.log("Oncology Pat: %s", pat.patId);
            var dx =  {
                "tumorSiteCode": jsonOnc['Tumor Site Code'] ,
                "morphologyCode": jsonOnc['Morphology Code'] ,
                "date": jsonOnc['Observation Date'] ,
                "docId": jsonOnc['Document ID'] ,
                "grade": jsonOnc['Grade Code'] ,
                "stage": jsonOnc['Stage Code'] ,
                "T": jsonOnc['T'] ,
                "N": jsonOnc['N'] ,
                "M": jsonOnc['M'] ,
                "negated": jsonOnc['Negated'] ,
                };
            pat.info.oncology.push(dx);
         }
    }).on('done',(error)=>{ writeFiles()  } );
}

const idMRNList = 'ID_MRN_List.csv';
const idMap=require('csvtojson')
idMap().fromFile(idMRNList)
        .on('json',(jsonObj)=>{
    // combine csv header row and csv line to a json object
    
   var patient =  {"dx" : [] ,  "tumor" : [] , "oncology": [] };
   patList[""+jsonObj.patient_ir_id] =  { "patId": jsonObj.patient_ir_id, "patmrn": jsonObj.PAT_MRN_ID, "info": patient };
})
.on('done',(error)=>{

	const csvFilePath='diagnosis_1523643565883.csv'
	const csv=require('csvtojson')
	csv()
        	.fromFile(csvFilePath)
        	.on('json',(json)=>{
    	// combine csv header row and csv line to a json object
	pat = patList[json['Patient ID']];
	if (pat != undefined ) {
		var dx =  { 
				"icd10": json['Diagnosis Code'] ,
				"description": json['Diagnosis Description'] ,
				"date": json['Diagnosis Date'] ,
				"docId": json['Document ID'] ,
				"negated": json['Negated'] ,
				}; 
	        pat.info.dx.push(dx);
		//console.log(patList[json['Patient ID']].patId + ": " + pat.info.dx) ;
	}
	})
        .on('done',(error) => {
		 updateTumor();
	})
 
	.on('done',(error1) => {
	//writeFiles(); 
	} )

    console.log('end')
})

I think so, but I'm not sure why you have my_hash & ids ...

my_hash = {}
#first loop
my_hash.put(row[0], {:dx => empty, :tumor => empty})
#second loop
my_hash.has_key? row[0]

Depending on how big these files are you might also want lazy
http://blog.honeybadger.io/using-lazy-enumerators-to-work-with-large-files-in-ruby/