ncbiParse/workers/esearch.js

"use strict";
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
    return new (P || (P = Promise))(function (resolve, reject) {
        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
        step((generator = generator.apply(thisArg, _arguments || [])).next());
    });
};
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const axios_1 = __importDefault(require("axios"));
const genbank_parser_1 = __importDefault(require("genbank-parser"));
const fast_xml_parser_1 = require("fast-xml-parser");
const jsonata_1 = __importDefault(require("jsonata"));
const simpleJSON = (json) => {
    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) => {
    if (Array.isArray(json)) {
        return json.map(e => renameKeys(e));
    }
    else if (typeof json === 'object') {
        const newObj = {};
        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 = (params) => __awaiter(void 0, void 0, void 0, function* () {
    const endpoint = (params === null || params === void 0 ? void 0 : params.endpoint) ? params.endpoint : 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi';
    const queries = Array.isArray(params === null || params === void 0 ? void 0 : params.query) ? params === null || params === void 0 ? void 0 : params.query : [params === null || params === void 0 ? void 0 : params.query];
    params.id = Array.isArray(params === null || params === void 0 ? void 0 : params.id) ? params.id.join(',') : params.id;
    let allowedParams;
    let connType = 'get';
    if (endpoint.match('esearch')) {
        allowedParams = ['db', 'term', 'retmax', 'retstart', 'api_key'];
        params = Object.assign(Object.assign({}, params), { retmax: 100000, retmode: 'xml' });
    }
    else if (endpoint.match('efetch')) {
        connType = 'get';
        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retmax', 'api_key'];
        const retmode = (params === null || params === void 0 ? void 0 : params.rettype) === 'fasta' || (params === null || params === void 0 ? void 0 : params.rettype) === 'gb' ? 'txt' : 'xml';
        params = Object.assign(Object.assign({}, params), { retmax: 10000, retmode });
    }
    else if (endpoint.match('esummary')) {
        allowedParams = ['id', 'db', 'retmode', 'rettype', 'retstart', 'version', 'api_key'];
        params = Object.assign(Object.assign({}, params), { retmax: 10000, retmode: 'xml', version: '2.0' });
    }
    let response = '';
    switch (connType) {
        case 'post':
            let postParam = {};
            Object.keys(params).flatMap(k => allowedParams.includes(k) ? postParam[k] = params[k] : []);
            response = yield axios_1.default.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 = yield axios_1.default.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 === null || params === void 0 ? void 0 : params.retmode) {
        switch (params.retmode) {
            case 'xml':
                const parser = new fast_xml_parser_1.XMLParser({
                    ignoreAttributes: false,
                    alwaysCreateTextNode: false,
                    attributeNamePrefix: "",
                    textNodeName: "value",
                    allowBooleanAttributes: true,
                });
                json = parser.parse(json);
                break;
            case 'gb':
                json = (0, genbank_parser_1.default)(json);
                break;
            default:
                break;
        }
    }
    json = renameKeys(json);
    const results = [];
    for (const query of queries) {
        let result;
        if (query !== '') {
            result = { query, value: (0, jsonata_1.default)(query).evaluate(json) /*simpleJSON(JSONPath({path: query, json})) */ };
        }
        else {
            result = '';
        }
        results.push(result);
    }
    return simpleJSON(results);
});
module.exports = (params) => __awaiter(void 0, void 0, void 0, function* () { return yield getEsearch(params); });