visualise.js

const git = require('isomorphic-git')
const fs = require('fs');
const fspromises = require('fs').promises;
const http = require('isomorphic-git/http/node')
const got = require('got');
const logger = require('../config/winston');
const config = require('config');
const yaml = require('yaml');

class Visualise {

  static async commitPushWorkflowRepo(id, timestamp, name, workflow, steps) {

    const GIT_SERVER_URL = config.get("gitserver.PREFIX") + config.get("gitserver.HOST") + config.get("gitserver.PORT");
    let workflowRepo = "output/" + id;

    try {
      await fspromises.mkdir(workflowRepo, {recursive:true});
    } catch(error) {
      logger.error("Error creating repo dir: " + workflowRepo + " " + JSON.stringify(error));
      return false;
    }

    const yamlWorkflow = yaml.parse(workflow);
    if(!yamlWorkflow.steps) {
      logger.debug("Error creating visualisation: no steps passed: " + JSON.stringify(workflow));
      return false;
    }
    let lastStepName;
    for(let step in yamlWorkflow.steps) {
      if(lastStepName) yamlWorkflow.steps[step].in.potentialCases.source = yamlWorkflow.steps[step].in.potentialCases.source.replace(/([0-9])+/, lastStepName);
      lastStepName = step + "-" + yamlWorkflow.steps[step].run.replace(".cwl", "");
      yamlWorkflow.steps[lastStepName] = yamlWorkflow.steps[step];
      delete yamlWorkflow.steps[step];
    }
    if(yamlWorkflow.outputs&&yamlWorkflow.outputs.cases) {
      yamlWorkflow.outputs.cases.outputSource = yamlWorkflow.outputs.cases.outputSource.replace(/([0-9])+/, lastStepName);
    } else {
      logger.error("Error adding outputSource: " + JSON.stringify(yamlWorkflow.outputs?yamlWorkflow.outputs:"") + " " + JSON.stringify(workflow));
      return false;
    }
    await fspromises.writeFile(workflowRepo + "/" + name + ".cwl", yaml.stringify(yamlWorkflow));
    for(let step of steps) await fspromises.writeFile(workflowRepo + "/" + step.name + ".cwl", step.content);
    await git.init({fs, dir: workflowRepo})
    await git.add({fs, dir: workflowRepo, filepath: '.'})
    let sha = await git.commit({
      fs,
      dir: workflowRepo,
      author: {
        name: "martinchapman",
        email: "contact@martinchapman.co.uk",
      },
      message: "visualisation"
    });
    logger.debug("SHA: " + sha);

    try {
      let addRemoteResult = await git.addRemote({
        fs,
        dir: workflowRepo,
        remote: "workflow" + id + timestamp,
        url: GIT_SERVER_URL + "/workflow" + id + timestamp + ".git"
      });
    } catch(error) {
      logger.error("Cannot add remote (" + workflow + id + timestamp + "): " + error);
      return false;
    }

    try {
      let pushResult = await git.push({
        fs,
        http,
        dir: workflowRepo,
        remote: "workflow" + id + timestamp,
        ref: "master"
      });
      logger.debug("Pushed to: " + id + timestamp);
    } catch(error) {
      logger.error("Cannot push to remote (" + id + timestamp + "): " + error);
      return false;
    }

    return true;

  }

  static async getWorkflowPNGFromViewer(id, file) {

    const urlSuffix = config.get("gitserver.CONTAINER_HOST") + config.get("gitserver.PORT") + "/workflow" + id + ".git/master/" + file + ".cwl"

    try {
      const pngPromise = got.get(config.get("visualiser.URL") + "/graph/png/" + urlSuffix, {timeout: 120000, followRedirect: false});
	    const pngBufferPromise = pngPromise.buffer();
      var [png, pngBuffer] = await Promise.all([pngPromise, pngBufferPromise]);
    } catch (error) {
      logger.debug("Failed to get PNG: " + urlSuffix + " " + error);
      return null;
    }

    logger.debug("Response from get workflow png from viewer: " + png.statusCode);

    if(png.statusCode==200 && pngBuffer) {
      return pngBuffer;
    } else {
      return null;
    }

  }

  static async addWorkflowToViewer(id, file) {

    const GIT_CONTAINER_URL = config.get("gitserver.PREFIX") + config.get("gitserver.CONTAINER_HOST") + config.get("gitserver.PORT");

    try {
      var generate = await got.post(config.get("visualiser.URL") + "/workflows", {
        headers: {'user-agent': 'pf/0.0.1', 'accept':'application/json'},
        form: {
          url: GIT_CONTAINER_URL + "/workflow" + id + ".git",
          branch: "master",
          path: file + ".cwl"
        },
        timeout: 120000
      });
    } catch (error) {
      logger.debug("Failed to add workflow to viewer: " + id + " " + file + " " + error);
      return null;
    }

    logger.debug("Response from add workflow to viewer: " + JSON.stringify(generate.headers) + " " + JSON.stringify(generate.body));

    if(generate && generate.headers && generate.headers.location) {
      return generate.headers.location;
    } else if(generate && generate.body && JSON.parse(generate.body).visualisationPng) {
      return await Utils.getWorkflowPNGFromViewer(id, file);
    } else {
      return null;
    }

  }

  static async getWorkflowFromViewer(id, file, queueLocation, remainingTries=10) {

    if(!queueLocation || (queueLocation && queueLocation.indexOf("queue")==-1)) {
      logger.debug("No queue location specified");
      return null;
    }

    let options = {headers: {'user-agent': 'pf/0.0.1', 'accept':'application/json'}, timeout: 120000, followRedirect: false};

    try {
      var queue = await got.get(config.get("visualiser.URL") + queueLocation, options);
    } catch (error) {
      logger.debug("Failed to get queue information: " + error);
      return null;
    }

    logger.debug("Response from get workflow from viewer: " + queue.statusCode + " " + JSON.stringify(queue.body));

    if(queue && queue.statusCode==200 && queue.body && JSON.parse(queue.body).cwltoolStatus=="RUNNING" && remainingTries>0) {
      logger.debug("Visualisation still processing, trying again.");
      await new Promise(resolve=>setTimeout(resolve, 1000));
      return await Visualise.getWorkflowFromViewer(id, file, queueLocation, remainingTries-1);
    } else if(queue && queue.statusCode==303 && queue.body && JSON.parse(queue.body).cwltoolStatus=="SUCCESS") {
      logger.debug("Visualisation processed, getting PNG.");
      return await Visualise.getWorkflowPNGFromViewer(id, file);
    } else {
      return null;
    }

  }

}

module.exports = Visualise;