@lifeomic/cli/lib/cmds/tasks_cmds/create-ashion-task.js

CLI for interacting with the LifeOmic PHC API.

'use strict';

const { post } = require('../../api');
const print = require('../../print');
const { convertToISODateString } = require('../../dateConversion');

exports.command = 'create-ashion-import <datasetId>';
exports.desc = 'Create a task to ingest a Ashion TAR file';
exports.builder = yargs => {
  yargs.positional('datasetId', {
    describe: 'The dataset Id.',
    type: 'string'
  }).option('tar-file-id', {
    describe: 'The ID of the uploaded Ashion TAR file',
    alias: 'f',
    type: 'string',
    demandOption: true
  }).option('subject-id', {
    describe: 'The ID of the subject to associated the report with',
    alias: 's',
    type: 'string',
    demandOption: true
  }).option('indexed-date', {
    describe: 'The indexed date.',
    type: 'string'
  }).option('performer-id', {
    describe: 'The ID of the FHIR Organization resource that performed the sequencing.',
    type: 'string'
  }).option('output-prefix', {
    describe: 'A prefix to put at the front of the output file names.',
    type: 'string',
    demandOption: false
  }).option('body-site', {
    describe: 'The body site of the specimen.',
    type: 'string',
    demandOption: false
  }).option('body-site-display', {
    describe: 'The display field for the body-site.',
    type: 'string',
    demandOption: false
  }).option('body-site-system', {
    describe: 'The defining system of the provided body site.',
    type: 'string',
    demandOption: false
  }).option('re-ingest-file', {
    describe: 'Force a re-ingestion of a file that has already been ingested.',
    type: 'Boolean',
    default: false,
    demandOption: false
  }).option('send-failed-to', {
    describe: 'An optional email address for sending failed task notifications.',
    type: 'string',
    demandOption: false
  });
};

exports.handler = async argv => {
  const response = await post(argv, `/v1/tasks/system/ashion-import`, {
    tarFileId: argv.tarFileId,
    datasetId: argv.datasetId,
    subjectId: argv.subjectId,
    indexedDate: convertToISODateString(argv.indexedDate),
    performerId: argv.performerId,
    outputFilePrefix: argv.outputPrefix,
    bodySite: argv.bodySite,
    bodySiteSystem: argv.bodySiteSystem,
    bodySiteDisplay: argv.bodySiteDisplay,
    reIngestFile: argv.reIngestFile,
    sendFailedTo: argv.sendFailedTo
  });
  print(response.data, argv);
};