molstar/lib/commonjs/servers/model/query.js

A comprehensive macromolecular library.

#!/usr/bin/env node
"use strict";
/**
 * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 */
Object.defineProperty(exports, "__esModule", { value: true });
const tslib_1 = require("tslib");
const fs = tslib_1.__importStar(require("fs"));
const version_1 = require("./version");
const api_local_1 = require("./server/api-local");
console.log(`Mol* ModelServer (${version_1.VERSION}), (c) 2018-2020 Mol* authors`);
console.log(``);
const exampleWorkload = [{
        output: 'c:/test/quick/localapi/1tqn_full.cif',
        queries: [{
                input: 'c:/test/quick/1tqn.cif',
                query: 'full', // same as defined in Api/Queries
            }]
    }, {
        output: 'c:/test/quick/localapi/1tqn_full.bcif',
        queries: [{
                input: 'c:/test/quick/1tqn.cif',
                query: 'full'
            }]
    }, {
        output: 'c:/test/quick/localapi/1cbs_ligint.cif',
        queries: [{
                input: 'c:/test/quick/1cbs_updated.cif',
                query: 'residueInteraction', // action is case sensitive
                params: { atom_site: { label_comp_id: 'REA' }, radius: 5 }
            }]
    }, {
        output: 'c:/test/quick/localapi/1cbs_ligint.bcif',
        queries: [{
                input: 'c:/test/quick/1cbs_updated.cif', // multiple files that are repeated will only be parsed once
                query: 'residueInteraction',
                params: { atom_site: [{ label_comp_id: 'REA' }], radius: 5 } // parameters are just a JSON version of the query string
            }]
    }, {
        output: 'c:/test/quick/localapi/multiple.tar.gz',
        queries: [{
                input: 'c:/test/quick/1cbs_updated.cif',
                query: 'residueInteraction', // action is case sensitive
                params: { atom_site: { label_comp_id: 'REA' }, radius: 5 }
            }, {
                input: 'c:/test/quick/1tqn.cif',
                query: 'full', // same as defined in Api/Queries
            }],
        asTarGz: true,
        gzipLevel: 6
    }];
if (process.argv.length !== 3) {
    const help = [
        `Usage: `,
        ``,
        `   node local jobs.json`,
        ``,
        `jobs.json is a JSON version of the WebAPI. Query names are case sensitive.`,
        `The jobs are automatically sorted by inputFilenama and the given file is only loaded once.`,
        `All processing errors are sent to stderr.`,
        ``,
        `Jobs example:`,
        ``,
        JSON.stringify(exampleWorkload, null, 2)
    ];
    console.log(help.join('\n'));
}
else {
    try {
        const input = JSON.parse(fs.readFileSync(process.argv[2], 'utf8'));
        (0, api_local_1.runLocal)(input);
    }
    catch (e) {
        console.error(e);
    }
}
// TODO: write utility that splits jobs into multiple chunks?