ncbiParse/workers/esearch.ts

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

const simpleJSON = (json:any):any => {
    if (Array.isArray(json)) {
        if (json.length === 1) { return simpleJSON(json[0]) }
        else { return json }
    } else if (typeof json === 'object') {
        if (Object.keys(json).length === 1 && typeof json[Object.keys(json)[0]] === 'object') { return simpleJSON(json[Object.keys(json)[0]]) }
        else { return json }
    } else {
        return json
    }
}

const renameKeys = (json:any):any => {
    if(Array.isArray(json)) {
        return json.map(e => renameKeys(e))
    } else if (typeof json === 'object') {
        const newObj:any = {}
        Object.keys(json).map(key => {
            let tmp
            if(typeof json[key] === 'object') {
                tmp = renameKeys(json[key])
            } else {
                tmp = json[key]
            }
            newObj[key.replace(/-/g,"_")] = tmp
        })
        return newObj
    } else {
        return json
    }
}

const getEsearch = async (params: any) => {
    const endpoint = params?.endpoint ? params.endpoint : 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'
    const queries = Array.isArray(params?.query) ? params?.query : [params?.query] 
    params.id = Array.isArray(params?.id) ? params.id.join(',') : params.id
   
    let allowedParams: string[]
    let connType: string = 'get'
    if (endpoint.match('esearch')) {
        allowedParams = ['db', 'term', 'retmax', 'retstart', 'api_key']
        params = {...params, retmax: 100000, retmode: 'xml'}
    } else if (endpoint.match('efetch')) {
        connType = 'get'
        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retmax', 'api_key']
        const retmode = params?.rettype === 'fasta' || params?.rettype === 'gb'? 'txt' : 'xml'
        params = {...params, retmax: 10000, retmode}
    } else if (endpoint.match('esummary')) {
        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retstart', 'version', 'api_key']
        params = {...params, retmax: 10000, retmode: 'xml', version: '2.0'}
    }

    let response:any = ''
    switch (connType) {
        case 'post':
            let postParam:any = {}
            Object.keys(params).flatMap(k => allowedParams.includes(k) ? postParam[k] = params[k] : [])
            response = await axios.post(endpoint, postParam)
            break;
        case 'get':
            const q = `${endpoint}?${Object.keys(params).flatMap(k => allowedParams.includes(k) ? k + '=' + params[k] : []).join('&')}`
            console.log(q);
            let block = 0
            let ctrl = true
            while(ctrl && block <= 5) {
                try {
                    response = await axios.get(q)
                    ctrl = false
                } catch (error) {}
                block++
                if(block === 6) {
                    console.log("Dropping !!! ", q);
                }
            }
        default:
            break;
    }
    
    let json = 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: "",
                    textNodeName: "value",
                    allowBooleanAttributes: true,
                })
                json = parser.parse(json)
                break;
            case 'gb':
                json = genbankParser(json)
                break;
            default:
                break;
        }
    }
    
    json = renameKeys(json)
    const results = []
    
    for (const query of queries) {
        let result:any
        if (query !== '') {
            result = {query, value: jsonata(query).evaluate(json)/*simpleJSON(JSONPath({path: query, json})) */}
        } else {
            result = ''
        }
        results.push(result)
    }
    
    return simpleJSON(results)
}

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