ncbiParse/workers/esearch.ts

import axios from 'axios'
import genbankParser from 'genbank-parser'
import { XMLParser } from 'fast-xml-parser'
import jsonata from "jsonata"

const getEsearch = async (
    params: any
) => {
    const endpoint = params?.endpoint ? params.endpoint : 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'
    const query = params?.query || ''
    const allowedParams = ['id', 'db', 'retmode', 'rettype']
    
    // console.log('query :', `${endpoint}?${Object.keys(params).flatMap(k => allowedParams.includes(k) ? k + '=' + params[k] : []).join('&')}`);
    const response = await axios.get(`${endpoint}?${Object.keys(params).flatMap(k => allowedParams.includes(k) ? k + '=' + params[k] : []).join('&')}`)
    
    let results = Array.isArray(response.data) ? response.data.join('') : response.data
    if (params?.retmode) {
        switch (params.retmode) {
            case 'xml':
                const parser = new XMLParser({
                    ignoreAttributes : false, alwaysCreateTextNode: false, attributeNamePrefix : "attr-", allowBooleanAttributes: true
            })
                results = parser.parse(results)
                break;
            case 'gb':
                results = genbankParser(results)
                break;
            default:
                break;
        }
    }

    if (query !== '') results = jsonata(query).evaluate(results)

    return results
}

module.exports = async (params:any) => await getEsearch(params)