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openHealth.js
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openHealth.js
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console.log("openHealth loaded")
openHealth=function(){}
openHealth.ini=function(){
this.buildUI=function(){};
this.getScript=function(src,fun){
if(Array.isArray(src)){ // multiple scripts are being loaded
if(src.length==1){
openHealth.getScript(src[0],fun);
}else{
openHealth.getScript(src[0],function(){
src.shift(); // remove [0]
openHealth.getScript(src,fun);
});
}
} else {
// check for the possibility that this is a css sheet
if(src.match(/\.css/)){
var lk = document.createElement('link');
lk.rel='stylesheet';
lk.href = src;
if(!!fun){lk.onload=fun} // if there is a callback run it
document.head.appendChild(lk);
return src
} else { // it's javascript
var s = document.createElement('script');
s.src = src;
if(!!fun){s.onload=fun} // if there is a callback run it
document.head.appendChild(s);
return src; // I never know what to do about returns in asynchronous calls ...
}
}
};
this.xhr=function(url,meth,fun){ // XMLHttpRequest
if(typeof(meth)=="function"){fun=meth;meth="GET"} // in case this is a regular GET call
var r = new XMLHttpRequest();
if(!!fun){r.onload=fun}; // calback
r.open(meth,url,true);
r.send();
return r
}
this.getJSON=function(url,fun){
if(!this.getJSON.cache){ // if caching not enabled
this.xhr(url,function(x){fun(JSON.parse(x.target.responseText))});
} else {
var key = encodeURIComponent(url);
localforage.getItem(key,function(x){
if(!x){ // if item not found
var moreFun = function(x){
var y = JSON.parse(x.target.responseText);
fun(y);
localforage.setItem(key,y);
//console.log('seting '+key);
}
openHealth.xhr(url,moreFun);
} else {
fun(x);
//console.log('got '+key);
}
})
}
}
this.getJSON.cache=true
this.sodaData={ // some reference SODA data links
"NY Medicare Inpatient":"http://health.data.ny.gov/resource/2yck-xisk.json",
// DSRIP NY
// Hospital Inpatient Prevention Quality Indicators
"DSRIP Hospital Inpatient Prevention Quality Indicators (PQI) for Adult Discharges by Zip Code (SPARCS): Beginning 2009":"https://health.data.ny.gov/resource/5q8c-d6xq.json",
"DSRIP Hospital Inpatient Prevention Quality Indicators (PQI) for Adult Discharges by County (SPARCS): Beginning 2009":"https://health.data.ny.gov/resource/iqp6-vdi4.json",
"DSRIP Medicaid Inpatient Prevention Quality Indicators (PQI) for Adult Discharges by Patient Zip Code: Beginning 2011":"https://health.data.ny.gov/resource/izyt-3msa.json",
"DSRIP Medicaid Inpatient Prevention Quality Indicators (PQI) for Adult Discharges by Patient County: Beginning 2011":"https://health.data.ny.gov/resource/6kjt-7svn.json",
"DSRIP Medicaid Beneficiaries, Inpatient Admissions and Emergency Room Visits by Zip Code: Beginning 2012":"https://health.data.ny.gov/resource/m2wt-pje4.json",
"DSRIP Medicaid Chronic Conditions, Inpatient Admissions and Emergency Room Visits by County: Beginning 2012":"https://health.data.ny.gov/resource/wybq-m39t.json",
"DSRIP Medicaid Chronic Conditions, Inpatient Admissions and Emergency Room Visits by Zip Code: Beginning 2012":"https://health.data.ny.gov/resource/2yck-xisk.json",
"DSRIP Medicaid Hospital Inpatient Potentially Preventable Readmission (PPR) Rates by Hospital: Beginning 2011":"https://health.data.ny.gov/resource/ckvf-rbyn.json",
// Medicaid Inpatient Admissions and Emergency Room Visits
// "NY DSRIP Medicaid Beneficiaries, Inpatient Admissions, and Emergency Room Visits by Zip Code: Beginning 2012":"http://health.data.ny.gov/resource/m2wt-pje4.json",
// "NY DSRIP Medicaid Chronic Conditions, Inpatient Admissions and Emergency Room Visits by Zip Code: Beginning 2012":"http://health.data.ny.gov/resource/2yck-xisk.json",
//"NY DSRIP Medicaid Chronic Conditions, Inpatient Admissions and Emergency Room Visits by County: Beginning 2012":"http://health.data.ny.gov/resource/wybq-m39t.json",
"DSRIP Medicaid Potentially Preventable Emergency Visit (PPV) Rates by Patient County: Beginning 2011":"https://health.data.ny.gov/resource/cr7a-34ka.json",
"DSRIP Medicaid Potentially Preventable Emergency Visits (PPV) by Patient Zip Code: Beginning 2011":"https://health.data.ny.gov/resource/khkm-zkp2.json",
"DSRIP Medicaid Inpatient Prevention Quality Indicators (PDI) for Pediatric Discharges by Patient County: Beginning 2011":"https://health.data.ny.gov/resource/64yg-akce.json",
"DSRIP Medicaid Program Enrollment by Month: Beginning 2009":"https://health.data.ny.gov/resource/m4hz-kzn3.json",
"DSRIP Hospital Inpatient Discharges (SPARCS De-Identified): 2012":"https://health.data.ny.gov/resource/u4ud-w55t.json"
//"Medicaid Inpatient Prevention Quality Indicators (PDI) for Pediatric Discharges by Patient County: Beginning 2011":"http://health.data.ny.gov/resource/64yg-akce.json",
// MIS
// "NY DSRIP Discharge":"http://health.data.ny.gov/resource/ckvf-rbyn.json"
}
this.soda=function(url,q,fun){ // operate Socrata Open Data API (SODA), http://dev.socrata.com/docs/endpoints.html
if(!url.match("http[s]{0,1}://")){ // if url is not a URL then assume it is an entry of openHealth.sodaData
url=this.sodaData[url];
}
if(!q){q=""}
if(typeof(q)=="function"){fun=q;q=""}
if(!fun){fun=function(x){console.log(x)}}
this.getJSON(url+q,fun);
return this
}
this.soda2=function(url,q,fun){ // operate SODA2 services
if(!url.match("http[s]{0,1}://")){ // if url is not a URL then assume it is an entry of openHealth.sodaData
url=this.sodaData[url];
}
if(typeof(q)=="object"){
if(url.match(/\?/)){var qq="&"}
else{var qq="?"}
var F = Object.getOwnPropertyNames(q);
F.forEach(function(fi){
qq+='$'+fi+'='+q[fi]+'&';
})
q=qq.slice(0,qq.length-1); // remove the last &
}
return this.soda(url,q,fun)
}
this.sodaAll=function(url,q,fun,xx,fun0){ // version of soda2 that keeps reading reccords untill all are retrieved
// for example: openHealth.sodaAll("https://health.data.ny.gov/resource/u4ud-w55t.json?hospital_county=Suffolk",false,function(x){y=x;console.log("done")})
if(!q){q={}};
if(!q.limit){q.limit=10000};
if(typeof(q.offset)=="undefined"){q.offset=0}else{q.offset+=q.limit};
if(!xx){xx=[]} // the array being assembled throughout multiple calls
if(!fun0){fun0=fun} // to carry original fun all eh way to the end
var moreFun = function(x){
xx=xx.concat(x);
console.log([xx.length,x.length,q.limit,q.offset,url])
//console.log(xx);
//if(lala){
if(x.length<q.limit){fun0(xx)} // reached the end of the line, just have the original fun and be done with it
else{openHealth.sodaAll(url,q,moreFun,xx,fun0)}
//lala=false
//}
}
return this.soda2(url,q,moreFun)
}
this.sodas=function(urls,q,fun,xx){ // version of sodaAll with multiple urls, for example, to load from a list of zip codes
//console.log(urls[0]);
//var urlsi = urls;
if(typeof(urls)=="string"){urls=[urls]} // so it can handle a single url too
if(!xx){xx=[]}
if(urls.length>0){ // keep going
var funLater=function(x){
openHealth.sodas(urls.slice(1),q,fun,x)
}
this.sodaAll(urls[0],q,funLater,xx)
}else{
fun(xx);
}
}
this.txt2docs=function(txt){
if (txt[0]=='['){ // txt is json
var docs = JSON.parse(txt);
} else { //txt should be tab delimited text
var y = txt.split(/[\n\r]/).map(function(xi){return xi.split(/\t/).map(function(c){return c.replace(/["\,]/g,'')})});
var docs=[];
var parms = y[0];
for(var i=1;i<y.length-1;i++){
docs[i-1]={};
parms.map(function(p,j){
docs[i-1][p]=y[i][j];
})
}
}
return docs
}
this.docs2tab=function(docs){ // convert array of docs into table
var F = Object.getOwnPropertyNames(docs[0]);
var m = F.length; // number of fields
var n = docs.length; // number of docs
var tab = {};
for(j=0;j<m;j++){
var Fj=F[j];
tab[Fj]=[]; // initialize array for jth field
for(i=0;i<n;i++){
tab[Fj][i]=docs[i][Fj];
}
// recognize numeric types
if(!tab[Fj].join('').match(/[^\d\.\s]/g)){
tab[Fj] = tab[Fj].map(function(xi){
return parseFloat(xi);
})
}
}
return tab
}
this.tab2docs=function(tab){
var docs=[];
var F = Object.getOwnPropertyNames(tab);
var n = tab[F[0]].length; // # rows
var m = F.length; // # fields
for(var i=0 ; i<n ; i++){
docs[i]={};
for(var j=0 ; j<m ; j++){
docs[i][F[j]]=tab[F[j]][i];
}
}
return docs
}
this.docs2docs=function(docs){ // recognize numerical types
return this.tab2docs(this.docs2tab(docs))
}
this.unique=function (x){ // x should be an Array
if(typeof(x)=='string'){x=x.split('')}; // if it is a string, break it into an array of its characters
var u = []; // store unique here
u[0]=x[0];
for (var i=1; i<x.length; i++){
// check if x[i] is new
if (u.map(function(ui){return ui===x[i]}).reduce(function(a,b){return a+b})==0){
u[u.length]=x[i];
}
}
return u;
}
this.avgKeyValue=function(tab,key,val,x){ // find avverage value of a key value pair
// i.e. openHealth.avgKeyValue(paintSuffolk.tab,"Disease state","Septicemia","Rate per 1000")
var tabKey = tab[key];
tabKeyVal=[];
tabKey.map(function(k,i){
if(k===val){tabKeyVal.push(tab[x][i])}
})
return this.sum(tabKeyVal)/tabKeyVal.length
}
this.avgKeyValues=function(tab,key,vals,x){ // aplies .avgKeyValue to all values
var y={}
vals.map(function(v){
y[v]=openHealth.avgKeyValue(tab,key,v,x)
})
return y
}
this.countKeyValue=function(tab,key,val,x){ // count entries of a key value pair
// i.e. openHealth.countKeyValue(paintSuffolk.tab,"Disease state","Septicemia","Rate per 1000")
var tabKey = tab[key];
tabKeyVal=[];
i=0;
tabKey.map(function(k,i){
if(k===val){i++}
})
return i
}
this.countKeyValues=function(tab,key,vals,x){ // aplies .avgKeyValue to all values
var y={}
vals.map(function(v){
y[v]=openHealth.countKeyValue(tab,key,v,x)
})
return y
}
this.list=function(x){
for(var i=0;i<x.length;i++){
console.log(i+1,x[i])
}
}
this.saveFile=function(x,fileName) { // x is the content of the file
// var bb = new Blob([x], {type: 'application/octet-binary'});
// see also https://github.com/eligrey/FileSaver.js
var bb = new Blob([x]);
var url = URL.createObjectURL(bb);
var a = document.createElement('a');
a.href=url;
if (fileName){
if(typeof(fileName)=="string"){ // otherwise this is just a boolean toggle or something of the sort
a.download=fileName;
}
a.click() // then download it automatically
}
return a
}
this.countUnique=function(x){ // creates object with unique counts for each attribute fount in array x
var u = this.unique(x);
var c = {};
u.map(function(ui){c[ui]=0});
x.map(function(xi){c[xi]++});
return c
}
this.transpose=function (x){ // transposes 2D array
if(!Array.isArray(x[0])){y=[x]} // in case x is a 1D Array
else{
var y=[],n=x.length,m=x[0].length;
for(var j=0;j<m;j++){
y[j]=[];
for(var i=0;i<n;i++){
y[j][i]=x[i][j];
}
}
}
return y
}
this.max=function(x){ //return maximum value of array
return x.reduce(function(a,b){if(a>b){return a}else{return b}})
}
this.min=function(x){ //return maximum value of array
return x.reduce(function(a,b){if(a<b){return a}else{return b}})
}
this.sum=function(x){
if(Array.isArray(x[0])){return x.map(function(xi){return openHealth.sum(xi)})}
else{return x.reduce(function(a,b){return a+b})};
}
this.sort=function(x){ // [y,I]=sort(x), where y is the sorted array and I contains the indexes
x=x.map(function(xi,i){return [xi,i]});
x.sort(function(a,b){return a[0]-b[0]});
return this.transpose(x)
}
this.interp1=function(X,Y,XI){ // linear interpolation, remember X is supposed to be sorted
var n = X.length;
var YI = XI.map(function(XIi){
var i=openHealth.sum(X.map(function(Xi){if (Xi<XIi){return 1}else{return 0}}));
if (i==0){return Y[0]} // lower bound
else if (i==n){return Y[n-1]} // upper bound
else{return (Y[i-1]+(XIi-X[i-1])*(Y[i]-Y[i-1])/(X[i]-X[i-1]))}
});
return YI
}
this.memb=function(x,dst){ // builds membership function
var n = x.length-1;
if(!dst){
dst = this.sort(x);
Ind=dst[1];
dst[1]=dst[1].map(function(z,i){return i/(n)});
var y = x.map(function(z,i){return dst[1][Ind[i]]});
return dst;
}
else{ // interpolate y from distributions, dst
var y = this.interp1(dst[0],dst[1],x);
return y;
}
}
this.tabulateCount=function(tab,p1,p2,Up1,Up2){//tabulate parameter p1 against p2, optional: arrays with unique values
if(Array.isArray(tab)){tab=this.tab2docs(tab)} // in case an array of docs is being submitted
if(!Up1){Up1 = this.unique(tab[p1])}
if(!Up2){Up2 = this.unique(tab[p2])}
var tabcount={}
// prepare table structure
Up1.map(function(p1){
tabcount[p1]={}
Up2.map(function(p2){
tabcount[p1][p2]=0
})
})
var j=0
for(var i=0;i<tab[p1].length;i++){
tabcount[tab[p1][i]][tab[p2][i]]+=1
j++
}
console.log(j+' counted')
return tabcount
}
this.crossdoc2csv=function(d,title){
if(!title){title=Date()+'.csv'}
var csv=title;
// header
var rr=Object.getOwnPropertyNames(d).sort(); //rows
var cc=Object.getOwnPropertyNames(d[rr[0]]).sort() //columns
cc.map(function(p2){
csv+=','+p2.replace(/[;,]/g,' ')
})
csv+='\n'
// body
rr.map(function(p1){
csv+=p1.replace(/[;,]/g,' ');
cc.map(function(p2){
csv+=','+d[p1][p2];
})
csv+='\n'
})
return csv
}
this.crossdoc2html=function(d,title){ // create table from cross-document
if(!title){title=Date()+'.csv'}
var html = '<table border=1>';
var rows = Object.getOwnPropertyNames(d);
var cols = [""].concat(Object.getOwnPropertyNames(d[rows[0]]));
// header
html +='<tr>';
for(j=0;j<cols.length;j++){html+='<th style="text-align:right">'+cols[j]+'</th>'};
html +='</tr>';
// body
for(i=0;i<rows.length;i++){
html +='<tr>';
html +='<th>'+rows[i]+'</th>'; // row label
for(j=1;j<cols.length;j++){html+='<td style="text-align:right">'+d[rows[i]][cols[j]]+'</td>'}
html +='</tr>';
}
html += '</table>';
// download button
var div = document.createElement('div');
div.innerHTML=html;
var bt = document.createElement('input');
bt.type = "button";
bt.value = "download"
//lala = bt;
bt.d=d;// the data
bt.onclick=function(){
openHealth.saveFile(openHealth.crossdoc2csv(this.d,title),title)
//console.log(this)
}
div.appendChild(bt)
return div;
}
this.markdown=function(x){ // basic markdown2html
x = x.replace(/\[([^\]]+)\]\(([^\)]+)\)/g,'<a href="$2" target=_blank>$1</a>'); // links
x = x.replace(/\n/g,'<br>'); // new lines
return x;
}
this.log=function(x){
var div = document.getElementById("openHealthJob")
if(div){
var p = document.createElement('p');
p.innerHTML=openHealth.markdown(x);
div.appendChild(p);
} else{
console.log(x);
}
}
this.createLog=function(h){ // create log div, if posiible, within an existing openHealth div
var div0 = document.getElementById("openHealth");
if(!div0){
div0 = document.createElement('div');
document.body.appendChild(div0);
}
var divLog = document.createElement('div');
divLog.id="openHealthJob";
if(h){divLog.innerHTML=h};
div0.appendChild(divLog);
return divLog;
}
this.startJobMsgURL=function(){ // post URL of job into the div.id="msg" if it exists
var divMsg=document.getElementById("msg")
if(divMsg){
divMsg.innerHTML='Processing ... : <a href="'+window.location.search.slice(1)+'" target=_blank>'+window.location.search.slice(1)+'</a>';
divMsg.style.color="red";
}
this.createLog('<p style="color:red">Executing job, please wait ...</p>')
}
this.endJobMsgURL=function(){ // post URL of job into the div.id="msg" if it exists
var divMsg=document.getElementById("msg")
if(divMsg){
//document.getElementById("openHealthJob").innerHTML="";
divMsg.style.color="blue";
divMsg.innerHTML='Processing ... done : <a href="'+window.location.search.slice(1)+'" target=_blank>'+window.location.search.slice(1)+'</a>';
setTimeout(function(){
divMsg.innerHTML='Script (<a href="'+window.location.search.slice(1)+'" target=_blank>'+window.location.search.slice(1)+'</a>) processed <i>'+new Date(Date.now())+'</i>:';
divMsg.style.color="green";
},1000)
}
}
}
// initiatize openHealth object
openHealth.ini();
// run external analysis if called with a search argument
window.onload=function(){
if(window.location.search.length>0){
console.log("window loaded");
openHealth.startJobMsgURL();
openHealth.getScript(window.location.search.slice(1),function(){
openHealth.endJobMsgURL();
});
}
}