hytx-sdk-js

HealthLytix NodeJS SDK

Showing:

Popularity

Downloads/wk

0

GitHub Stars

0

Maintenance

Last Commit

7mos ago

Contributors

2

Package

Dependencies

5

License

MIT

Type Definitions

Tree-Shakeable

No?

Categories

Readme

HealthLytix SDK for NodeJS

NPM

Version

The official HealthLytix SDK for Node.js

Installing

In Node.js

The preferred way to install the HealthLytix SDK for Node.js is to use the npm package manager for Node.js. Simply type the following into a terminal window:

npm install hytx-sdk-js

Usage and Getting Started

You can find the RESTful API documenation here:

https://developer.healthlytix.com

More documenation for SDK coming soon...

In Node.js

In a JavaScript file:

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

Example


// 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);
    }
})();

Prostate Cancer PHS Example

To process a VCF/23andMe, or Ancestry.com genetic file with our Prostate Cancer PHS Algorithm, the workflow is the following:

  1. If using VCF file, preprocess the file before uploading with the helper function convertVCF(vcfFile, vcfOutputFile, qualityThresholdNumber)
  2. Upload the file
  3. Invoke the processing using the requestId from step 2. You get immediately a response, but without the results. The results will be processed in 1 to 2 minutes. To get the results, proceed to step 4 after a minute or so.
  4. Retrieve the results using the getProstatePHS(requestId) method and the requestId from step 2 and 3.

Here is an example with code when using VCF files:

// 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);

API

All methods that provide a callback will return a promise if no callback supplied

This SDK has the following API methods:

convertVCF

Convert VCF file to a special HealthLytix format that speeds the upload, and improves the efficiency when processing them with algorithms such as runProstatePHS. Note: Only variants with PASS on the FILTER column will be kept. Others are filtered out. We accept VCF files that conform to the standards found: IGSR, SamTools

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

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

})

convertVCFwithThreshold

Same as convertVCF except that it allows to specify an additional threshold to further filter out variants. The threshold adds a constraint to filter out variants that are lower than then value specified when compared to the QUAL field of the VCF file.

// 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) => {

})

uploadFile

Upload a file to our cloud in order to use it with some other algorithm/api. It returns a requestId, which is needed by some other API calls. This call requires to specify the type of content being uploaded (MIME). This conforms to the IANA Standards.

Sample MIME types:

  • application/gzip
  • application/octet-stream
  • application/zip
  • text/plain
// 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

Pings the API. Used for testing authentication.

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

runAlzheimersPHS

Run the Alzheimer's PHS Algorithm. Make sure to upload the file before executing this call using the uploadFile. File can be uploaded as a text, zip, or tar file. If using a zip/tar/gzip file, make sure to only include the file with the genetics inside the compressed file. Additional files inside the compressed file are not allowed.

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

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

getAlzheimersPHS

Retrieve some previously calculated results from runAlzheimersPHS

// requestId = requestId used when running runAlzheimersPHS

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

runProstatePHS

Run the Prostate Cancer PHS Algorithm. Make sure to upload the file before executing this call using the uploadFile. Note Unlike runAlzheimersPHS, this call does not return the report. This is so because the ProstatePHS algorithm takes longer than 30 seconds and an HTTP request is not kept open waiting for the algorithm to finish. To retrieve the results, use getProstatePHS.

// 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...
})

getProstatePHS

Retrieve some previously calculated results from runProstatePHS

// requestId = requestId used when running runProstatePHS

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

Getting Help

Please use these community resources for getting help. We use the GitHub issues for tracking bugs and feature requests and have limited bandwidth to address them.

Opening Issues

If you encounter a bug with the HealthLytix SDK for NodeJS we would like to hear about it. Search the existing issues and try to make sure your problem doesn’t already exist before opening a new issue. Please include a stack trace and reduced repro case when appropriate, too.

The GitHub issues are intended for bug reports and feature requests. For help and questions with using the HealthLytix SDK for NodeJS please make use of the resources listed in the Getting Help section. There are limited resources available for handling issues and by keeping the list of open issues lean we can respond in a timely manner.

License

This SDK is distributed under the MIT License.

Rate & Review

Great Documentation0
Easy to Use0
Performant0
Highly Customizable0
Bleeding Edge0
Responsive Maintainers0
Poor Documentation0
Hard to Use0
Slow0
Buggy0
Abandoned0
Unwelcoming Community0
100
No reviews found
Be the first to rate

Alternatives

No alternatives found

Tutorials

No tutorials found
Add a tutorial