load.js

const { runLoader } = require('../src');
const { createOptionsMenu, fileExists } = require('../src/cli');

const civic = require('../src/civic');
const dgidb = require('../src/dgidb');
const docm = require('../src/docm');
const oncotree = require('../src/oncotree');
const fdaApprovals = require('../src/fdaApprovals');

const cancerhotspots = require('../src/cancerhotspots');
const cgi = require('../src/cancergenomeinterpreter');
const cgl = require('../src/cgl');
const diseaseOntology = require('../src/diseaseOntology');
const drugbank = require('../src/drugbank');
const ensembl = require('../src/ensembl');
const fdaSrs = require('../src/fdaSrs');
const gscTherapeuticOntology = require('../src/gscTherapeuticOntology');
const ncit = require('../src/ncit');
const ncitFdaXref = require('../src/ncit/ncitFdaXref');
const ontology = require('../src/ontology');
const refseq = require('../src/refseq');
const PMC4468049 = require('../src/PMC4468049');
const PMC4232638 = require('../src/PMC4232638');
const sources = require('../src/all_sources');
const uberon = require('../src/uberon');
const variants = require('../src/variants');
const asco = require('../src/asco');
const moa = require('../src/moa');

const clinicaltrialsgov = require('../src/clinicaltrialsgov');

const cosmicResistance = require('../src/cosmic/resistance');
const cosmicFusions = require('../src/cosmic/fusions');

const API_MODULES = {
    asco,
    dgidb,
    docm,
    fdaApprovals,
    moa,
    oncotree,
};

const FILE_MODULES = {
    PMC4232638,
    PMC4468049,
    cancerhotspots,
    cgi,
    cgl,
    diseaseOntology,
    drugbank,
    ensembl,
    fdaSrs,
    gscTherapeuticOntology,
    ncit,
    ncitFdaXref,
    ontology,
    refseq,
    sources,
    uberon,
    variants,
};

const COSMIC_MODULES = {
    fusions: cosmicFusions,
    resistance: cosmicResistance,
};

const ALL_MODULES = {
    ...API_MODULES,
    ...FILE_MODULES,
    ...COSMIC_MODULES,
    civic,
    clinicaltrialsgov,
};

const parser = createOptionsMenu();

const subparsers = parser.add_subparsers({ dest: 'subparser_name', help: 'Sub-command help', required: true });
const apiParser = subparsers.add_parser('api');
apiParser.add_argument('module', {
    choices: Object.keys(API_MODULES),
    help: 'module to run',
});

const fileParser = subparsers.add_parser('file');
fileParser.add_argument('module', {
    choices: Object.keys(FILE_MODULES),
    help: 'module to run',
});
fileParser.add_argument('input', {
    help: 'path to the file/dir to be loaded',
    type: fileExists,
});
fileParser.add_argument('--ignoreCache', {
    action: 'store_true',
    default: false,
    help: 'Load the full content, to not check for previously loaded records already in the GraphKB instance',
});

const civicParser = subparsers.add_parser('civic');
civicParser.add_argument('--trustedCurators', {
    default: [],
    help: 'CIViC User IDs of curators whose statements should be imported even if they have not yet been reviewed (evidence is submitted but not accepted)',
    nargs: '+',
});
civicParser.add_argument('--noUpdate', {
    action: 'store_true',
    default: false,
    help: 'Will not check for updating content of existing GraphKB Statements',
});
civicParser.add_argument('--noDeleteOnUnmatched', {
    action: 'store_true',
    default: false,
    help: 'Will not delete GraphKB Statements from valid sourceID but not matching a combination',
});
civicParser.add_argument('--deleteDeprecated', {
    action: 'store_true',
    default: false,
    help: 'Will delete GraphKB Statements from deprecated sourceID',
});

const clinicaltrialsgovParser = subparsers.add_parser('clinicaltrialsgov');
clinicaltrialsgovParser.add_argument('--days', {
    help: 'Load new and existing studies added or modified (last update posted) in the last # of days',
    type: Number,
});

const cosmicParser = subparsers.add_parser('cosmic');
cosmicParser.add_argument('module', {
    choices: Object.keys(COSMIC_MODULES),
    help: 'module to run',
});
cosmicParser.add_argument('input', {
    help: 'path to the file to be loaded',
    type: fileExists,
});
cosmicParser.add_argument('classification', {
    help: 'path to the cosmic classification file',
    type: fileExists,
});

const {
    subparser_name, module: moduleName, input, ...options
} = parser.parse_args();

let loaderFunction;

if (input) {
    loaderFunction = ALL_MODULES[moduleName || subparser_name].uploadFile;
} else {
    loaderFunction = ALL_MODULES[moduleName || subparser_name].upload;
}

const loaderOptions = { ...options };

if (input) {
    loaderOptions.filename = input;
}

runLoader(options, loaderFunction, loaderOptions)
    .catch((err) => {
        console.error(err);
        process.exit(1);
    });