auspice/cli/view.js

Web app for visualizing pathogen evolution

/* eslint no-console: off */
/* eslint global-require: off */

const path = require("path");
const fs = require("fs");
const express = require("express");
const expressStaticGzip = require("express-static-gzip");
const compression = require('compression');
const nakedRedirect = require('express-naked-redirect');
const utils = require("./utils");
const version = require('../src/version').version;
const chalk = require('chalk');
const SUPPRESS = require('argparse').Const.SUPPRESS;


const addParser = (parser) => {
  const description = `Launch a local server to view locally available datasets & narratives.
  The handlers for (auspice) client requests can be overridden here (see documentation for more details).
  If you want to serve a customised auspice client then you must have run "auspice build" in the same directory
  as you run "auspice view" from.
  `;
  const subparser = parser.addParser('view', {addHelp: true, description});
  subparser.addArgument('--verbose', {action: "storeTrue", help: "Print more verbose logging messages."});
  subparser.addArgument('--handlers', {action: "store", metavar: "JS", help: "Overwrite the provided server handlers for client requests. See documentation for more details."});
  subparser.addArgument('--datasetDir', {metavar: "PATH", help: "Directory where datasets (JSONs) are sourced. This is ignored if you define custom handlers."});
  subparser.addArgument('--narrativeDir', {metavar: "PATH", help: "Directory where narratives (Markdown files) are sourced. This is ignored if you define custom handlers."});
  /* there are some options which we deliberately do not document via `--help`. */
  subparser.addArgument('--customBuild', {action: "storeTrue", help: SUPPRESS}); /* see printed warning in the code below */
  subparser.addArgument('--gh-pages', {action: "store", help: SUPPRESS}); /* related to the "static-site-generation" or "github-pages" */
};

const serveRelativeFilepaths = ({app, dir}) => {
  app.get("*.json", (req, res) => {
    const filePath = path.join(dir, req.originalUrl);
    utils.log(`${req.originalUrl} -> ${filePath}`);
    res.sendFile(filePath);
  });
  return `JSON requests will be served relative to ${dir}.`;
};

const loadAndAddHandlers = ({app, handlersArg, datasetDir, narrativeDir}) => {
  /* load server handlers, either from provided path or the defaults */
  const handlers = {};
  let datasetsPath, narrativesPath;
  if (handlersArg) {
    const handlersPath = path.resolve(handlersArg);
    utils.verbose(`Loading handlers from ${handlersPath}`);
    const inject = require(handlersPath); // eslint-disable-line
    handlers.getAvailable = inject.getAvailable;
    handlers.getDataset = inject.getDataset;
    handlers.getNarrative = inject.getNarrative;
  } else {
    datasetsPath = utils.resolveLocalDirectory(datasetDir, false);
    narrativesPath = utils.resolveLocalDirectory(narrativeDir, true);
    handlers.getAvailable = require("./server/getAvailable")
      .setUpGetAvailableHandler({datasetsPath, narrativesPath});
    handlers.getDataset = require("./server/getDataset")
      .setUpGetDatasetHandler({datasetsPath});
    handlers.getNarrative = require("./server/getNarrative")
      .setUpGetNarrativeHandler({narrativesPath});
  }

  /* apply handlers */
  app.get("/charon/getAvailable", handlers.getAvailable);
  app.get("/charon/getDataset", handlers.getDataset);
  app.get("/charon/getNarrative", handlers.getNarrative);
  app.get("/charon*", (req, res) => {
    res.statusMessage = "Query unhandled -- " + req.originalUrl;
    utils.warn(res.statusMessage);
    return res.status(500).end();
  });

  return handlersArg ?
    `Custom server handlers provided.` :
    `Looking for datasets in ${datasetsPath}\nLooking for narratives in ${narrativesPath}`;
};

const getAuspiceBuild = () => {
  const cwd = path.resolve(process.cwd());
  const sourceDir = path.resolve(__dirname, "..");
  if (
    cwd !== sourceDir &&
    fs.existsSync(path.join(cwd, "index.html")) &&
    fs.existsSync(path.join(cwd, "dist")) &&
    fs.existsSync(path.join(cwd, "dist", "auspice.bundle.js"))
  ) {
    return {
      message: "Serving the auspice build which exists in this directory.",
      baseDir: cwd,
      distDir: path.join(cwd, "dist")
    };
  }
  return {
    message: `Serving auspice version ${version}`,
    baseDir: sourceDir,
    distDir: path.join(sourceDir, "dist")
  };
};

const run = (args) => {
  /* Basic server set up */
  const app = express();
  app.set('port', process.env.PORT || 4000);
  app.set('host', process.env.HOST || "localhost");
  app.use(compression());
  app.use(nakedRedirect({reverse: true})); /* redirect www.name.org to name.org */

  if (args.customBuild) {
    utils.warn("--customBuild is no longer used and will be removed in a future version. We now serve a custom auspice build if one exists in the directory `auspice view` is run from");
  }

  const auspiceBuild = getAuspiceBuild();
  utils.verbose(`Serving index / favicon etc from  "${auspiceBuild.baseDir}"`);
  utils.verbose(`Serving built javascript from     "${auspiceBuild.distDir}"`);
  app.get("/favicon.png", (req, res) => {res.sendFile(path.join(auspiceBuild.baseDir, "favicon.png"));});
  app.use("/dist", expressStaticGzip(auspiceBuild.distDir));
  app.use(express.static(auspiceBuild.distDir));

  let handlerMsg = "";
  if (args.gh_pages) {
    handlerMsg = serveRelativeFilepaths({app, dir: path.resolve(args.gh_pages)});
  } else {
    handlerMsg = loadAndAddHandlers({app, handlersArg: args.handlers, datasetDir: args.datasetDir, narrativeDir: args.narrativeDir});
  }

  /* this must be the last "get" handler, else the "*" swallows all other requests */
  app.get("*", (req, res) => {
    res.sendFile(path.join(auspiceBuild.baseDir, "index.html"));
  });

  const server = app.listen(app.get('port'), app.get('host'), () => {
    utils.log("\n\n---------------------------------------------------");
    const host = app.get('host');
    const {port} = server.address();
    console.log(chalk.blueBright("Auspice server now running at ") + chalk.blueBright.underline.bold(`http://${host}:${port}`));
    utils.log(auspiceBuild.message);
    utils.log(handlerMsg);
    utils.log("---------------------------------------------------\n\n");
  }).on('error', (err) => {
    if (err.code === 'EADDRINUSE') {
      utils.error(`Port ${app.get('port')} is currently in use by another program. 
      You must either close that program or specify a different port by setting the shell variable
      "$PORT". Note that on MacOS / Linux, "lsof -n -i :${app.get('port')} | grep LISTEN" should
      identify the process currently using the port.`);
    }
    utils.error(`Uncaught error in app.listen(). Code: ${err.code}`);
  });

};

module.exports = {
  addParser,
  run,
  loadAndAddHandlers,
  serveRelativeFilepaths
};