// import entire SDK
const HealthLytix = require('hytx-sdk-js');

// all methods return either a promise or callback if no promise provided
// it works with async/await
const HealthLytix = require('hytx-sdk-js');
const hytx = new HealthLytix('ApiID', 'ApiSecret');

(async function() {
    try {
        const hello = await hytx.ping();

        // upload a file
        // inputFile is the location of the file to upload
        // inputContent is the content-type of the file
        const inputFile = "./my-file";
        const inputContent = "text/plain";
        let requestId = await hytx.uploadFile(inputFile, inputContent);

        // run one of our apps... Alzheimers PHS
        // report will have the results
        const subjectAge = 70;
        const report = await hytx.runAlzheimersPHS(requestId, subjectAge)

        // check if report returned
        // check out https://developer.healthlytix.com/#alzheimers-phs
        // for details on the report Object structure
        if (report.requestId)
            console.log("Yay! ran the Alzheimer's App!");


        // retrieve some old results...sometime later
        const oldReport = await hytx.getAlzheimersPHS(requestId);
        if (oldReport.requestId)
            console.log("Ohh yeah! got the Alzhiemer's results report!");

        // lets upload the file again and run the
        // prostate PHS app
        requestId = await hytx.uploadFile(inputFile, inputContent);
        const prostateReport = await hytx.runProstatePHS(requestId, subjectAge)
        if(prostateReport.requestId)
            console.log("Yay! ran the Prostate's App!");

        // retrieve some old results...sometime later
        const oldProstateReport = await hytx.getProstatePHS(requestId);
        if (oldProstateReport.requestId)
            console.log("Ohh yeah! got the Prostate report!");

    } catch (e) {
        console.error(e);
    }
})();

// path to my VCF file
const myVCFfile = 'path-to-my-vcf-file';

// where should we store the converted VCF file
const vcfOutput = 'file-to-write-new-VCF-file-to';

// convert it with our helper function
// only variants with PASS on the FILTER column will be kept
await hytx.convertVCF(myVCFfile, vcfOutput);

// (optional) to specify a threshold on the Qual field, use 
// convertVCFwithThreshold(vcfFile, vcfOutput, threshold, callback)
// instead of convertVCF()

// upload a file
const inputContent = "text/plain";
const requestId = await hytx.uploadFile(vcfOutput, inputContent);

// request the Prostate PHS Processing
const subjectAge = 70;
const response = await hytx.runProstatePHS(requestId, subjectAge);

// ...wait for about 2 minutes before proceeding

// get the results using the query method
// report will be an object with the API response.
// the structure of this object can be found on https://developer.healthlytix.com
// use the requestId from uploadFile()
const report = await hytx.getProstatePHS(requestId);

// vcfFile = file path to your VCF file
// outputFile = file to create with new HealthLytix format

convertVCF(vcfFile, outputFile, (err) => {

})

// vcfFile = file path to your VCF file
// outputFile = file to create with new HealthLytix format
// qualityThres = number to act as threshold to filter out variants 

convertVCFwithThreshold(vcfFile, outputFile, qualityThres, (err) => {

})

// file = path to file to upload
// contentType = the MIME type of file to be uploaded. 

uploadFile(file, contentType, (err, requestId) => {
    // use requestId for some other algorithm
})

ping((err, response) => {
    console.log(response)
})

// requestId = requestId from uploadFile
// age = age of the subject as a number

runAlzheimersPHS(requestId, age, (err, report) => {
    // report has the results
})

// requestId = requestId used when running runAlzheimersPHS

getAlzheimersPHS(requestId, (err, report) => {
    // report has the results
})

// requestId = requestId from uploadFile
// age = age of the subject as a number

runProstatePHS(requestId, age, (err, response) => {
    // response indicates whether the request was succesful
    // it will not have the results of the algorithm...
})

// requestId = requestId used when running runProstatePHS

getProstatePHS(requestId, (err, report) => {
    // report has the results
})