Use Node.js to consume Europe PMC SOAP web service

Question

Any example of using JavaScript in the Node.js environment to consume the Europe PMC SOAP web service?

Answer 1

This is an example of Node.js using the SOAP web service from Europe PMC to get the reference list of an article.

const XMLHttpRequest = require("xmlhttprequest").XMLHttpRequest;
const DOMParser = require('xmldom').DOMParser;

function parseXml(text) {
    let parser = new DOMParser();
    let xmlDoc = parser.parseFromString(text, "text/xml");
    Array.from(xmlDoc.getElementsByTagName("reference")).forEach(function (item) {
        console.log('Title: ', item.childNodes[3].childNodes[0].nodeValue);
    });

}

function soapRequest(url, payload) {
    let xmlhttp = new XMLHttpRequest();
    xmlhttp.open('POST', url, true);

    // build SOAP request
    xmlhttp.onreadystatechange = function () {
        if (xmlhttp.readyState == 4) {
            if (xmlhttp.status == 200) {
                parseXml(xmlhttp.responseText);
            }
        }
    }

    // Send the POST request
    xmlhttp.setRequestHeader('Content-Type', 'text/xml');
    xmlhttp.send(payload);
}

soapRequest('https://www.ebi.ac.uk/europepmc/webservices/soap', 
    `<?xml version="1.0" encoding="UTF-8"?>
    <S:Envelope xmlns:S="http://schemas.xmlsoap.org/soap/envelope/">
    <S:Header />
    <S:Body>
        <ns4:getReferences xmlns:ns4="http://webservice.cdb.ebi.ac.uk/"
            xmlns:ns2="http://www.scholix.org"
            xmlns:ns3="https://www.europepmc.org/data">
            <id>C7886</id>
            <source>CTX</source>
            <offSet>0</offSet>
            <pageSize>25</pageSize>
            <email>[email protected]</email>
        </ns4:getReferences>
    </S:Body>
    </S:Envelope>`);

Before running the code, you need to install two packages xmlhttprequest and xmldom:

npm install xmlhttprequest
npm install xmldom

Now you can run the code:

node soap-node.js

And you'll see the output as below:

Title:  Perspective: Sustaining the big-data ecosystem.
Title:  Making proteomics data accessible and reusable: current state of proteomics databases and repositories.
Title:  ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
Title:  Toward effective software solutions for big biology.
Title:  The NIH Big Data to Knowledge (BD2K) initiative.
Title:  Database resources of the National Center for Biotechnology Information.
Title:  Europe PMC: a full-text literature database for the life sciences and platform for innovation.
Title:  Bio-ontologies-fast and furious.
Title:  BioPortal: ontologies and integrated data resources at the click of a mouse.
Title:  PubMed related articles: a probabilistic topic-based model for content similarity.
Title:  High-Impact Articles-Citations, Downloads, and Altmetric Score.