initRegistry.js

/**
 * File used to init a raw copy of InterMine Registry on a new DB environment.
 *
 */

const request = require('request');
const asyncLoop = require('node-async-loop');

mines = [
  ["FlyMine", 'http://www.flymine.org/query', "flymine"],
  ["HumanMine", 'http://www.humanmine.org/humanmine', "humanmine"],
  ["MouseMine", 'http://www.mousemine.org/mousemine', "mousemine"],
  ["YeastMine", 'https://yeastmine.yeastgenome.org/yeastmine', "yeastmine"],
  ["ZebrafishMine", 'http://www.zebrafishmine.org/', "zebrafishmine"],
  ["WormMine", 'http://intermine.wormbase.org/tools/wormmine', "wormmine"],
  ["SoyMine", 'https://mines.legumeinfo.org/soymine', "soymine"],
  ["BeanMine", 'https://mines.legumeinfo.org/beanmine', "beanmine"],
  ["MedicMine", 'http://medicmine.jcvi.org/medicmine', "medicmine"],
  ["PeanutMine", 'https://mines.legumeinfo.org/peanutmine', "peanutmine"],
  ["ChickpeaMine", 'https://mines.legumeinfo.org/chickpeamine', "chickpeamine"],
  ["LegumeMine", 'https://intermine.legumefederation.org/legumemine', "legumemine"],
  ["RatMine", 'http://ratmine.mcw.edu/ratmine', "ratmine"],
  ["WheatMine", 'http://urgi.versailles.inra.fr/WheatMine', "wheatmine"],
  ["RepetDB", 'http://urgi.versailles.inra.fr/repetdb', "repetdb"],
  ["ThaleMine", 'https://apps.araport.org/thalemine', "thalemine"],
  ["BovineMine", 'http://128.206.116.12:8080/bovinemine/begin.do', "bovinemine"],
  ["PhytoMine", 'https://phytozome.jgi.doe.gov/phytomine', "phytomine"],
  ["HymenopteraMine", 'http://hymenopteragenome.org/hymenopteramine', "hymenopteramine"],
  ["Mitominer", 'http://mitominer.mrc-mbu.cam.ac.uk/release-4.0', "mitominer"],
  ["TargetMine", 'http://targetmine.mizuguchilab.org/targetmine', "targetmine"],
  ["INDIGO", "http://www.cbrc.kaust.edu.sa/indigo", "indigo"],
  ["Shaare", "http://www.shaare.org.uk/release-1.0", "shaare"],
  ["XenMine", "http://www.xenmine.org/xenmine", "xenmine"],
  ["GrapeMine", "http://urgi.versailles.inra.fr/GrapeMine", "grapemine"],
  ["PlanMine", "http://planmine.mpi-cbg.de/planmine", "planmine"],
  ["TetraMine", "http://adenine.bradley.edu/tetramine", "tetramine"],
  ["modMine", "http://intermine.modencode.org/release-33", "modmine"],
  ["CHOmine", "https://chomine.boku.ac.at/chomine", "chomine", ]
]

const host = 'http://localhost:3000'; // Host where InterMine registry is running
const username = '';
const password = '';

//check host is set correctly & error if not.

request.get(host, function(err, res, body) {

  if (err) {
    console.error("No registry server found at ", host, " check the server is running and the url is set correctly");
  }
  asyncLoop(mines, function(mine, next) {
    var mineName = mine[0];
    var mineURL = mine[1];
    var mineNamespace = mine[2];
    var req = {
      "name": mineName,
      "url": mineURL,
      "namespace": mineNamespace
    };
    request.post({
      json: true,
      url: host + "/service/instances",
      body: req,
      auth: {
        "user": username,
        "pass": password
      },
    }, function(err, res, body) {
      if (!err) {
        console.log(mineName, " ==> ", res.statusCode,  body.friendlyMessage);
        // forgot to create a user and/or put the password in the script?
        // we'll remind you.
        if (res.statusCode === 401) {
          console.error("Auth error. Please check your username and password are correct.");
        }
      } else {
        //catchall for bad errors
        console.error(err)
      }
      next();
    });
  });

});