MZmineModuleStarter.java

/*
 * Copyright 2006-2016 The MZmine 3 Development Team
 * 
 * This file is part of MZmine 3.
 * 
 * MZmine 3 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 * 
 * MZmine 3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with MZmine 3; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package io.github.mzmine.main;

import java.io.File;
import java.util.Collections;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;

import com.google.common.collect.ImmutableList;

import io.github.mzmine.modules.MZmineModule;
import io.github.mzmine.parameters.ParameterSet;

/**
 * MZmine modules support class
 */
public final class MZmineModuleStarter implements Runnable {

  private static final File MODULES_FILE = new File("conf/Modules.xml");

  private final Logger logger = LoggerFactory.getLogger(this.getClass());

  private static Map<Class<? extends MZmineModule>, MZmineModule> initializedModules =
      Collections.synchronizedMap(new Hashtable<>());

  @Override
  public void run() {

    logger.info("Loading modules");

    try {
      DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
      Document modulesDocument = null;
      DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
      modulesDocument = dBuilder.parse(MODULES_FILE);
      Element rootElement = modulesDocument.getDocumentElement();
      NodeList moduleNodes = rootElement.getChildNodes();
      for (int i = 0; i < moduleNodes.getLength(); i++) {
        Node moduleNode = moduleNodes.item(i);
        if (moduleNode.getNodeName() != "module")
          continue;
        String moduleClassName = moduleNode.getTextContent();
        try {

          // Start up the module
          startModule(moduleClassName);

        } catch (Exception e) {
          logger.warn("Failed to initialize module class " + moduleClassName + ": " + e);
          e.printStackTrace();
        }
      }

    } catch (Exception e) {
      logger.error("Could not load modules from " + MODULES_FILE);
      System.exit(1);
    }

    try {
      logger.info("Loading configuration");
      MZmineCore.getConfiguration().loadConfiguration(MZmineConfiguration.CONFIG_FILE);
    } catch (Exception e) {
      logger.error("Could not load configuration from " + MZmineConfiguration.CONFIG_FILE);
    }

  }

  private void startModule(final String moduleClassName)
      throws ClassNotFoundException, InstantiationException, IllegalAccessException {

    logger.info("Starting module class " + moduleClassName);

    // Create an instance of the module
    @SuppressWarnings("unchecked")
    Class<? extends MZmineModule> moduleClass =
        (Class<? extends MZmineModule>) Class.forName(moduleClassName);
    MZmineModule newModule = moduleClass.newInstance();
    initializedModules.put(moduleClass, newModule);

    // Create a parameter set
    Class<? extends ParameterSet> parameterSetClass = newModule.getParameterSetClass();
    ParameterSet newParameterSet = parameterSetClass.newInstance();
    MZmineCore.getConfiguration().setModuleParameters(moduleClass, newParameterSet);
  }

  static List<MZmineModule> getAllModules() {
    List<MZmineModule> list = ImmutableList.copyOf(initializedModules.values());
    return list;
  }

  /**
   * Returns the instance of a module of given class
   */
  @SuppressWarnings("unchecked")
  static <ModuleType extends MZmineModule> ModuleType getModuleInstance(
      Class<ModuleType> moduleClass) {
    return (ModuleType) initializedModules.get(moduleClass);
  }

}