/******************************************************************************* * Copyright (C) 2017 Philipp Spohr * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE * SOFTWARE. ******************************************************************************/ package de.hhu.ba.yoshikoWrapper; import java.util.Properties; import org.cytoscape.application.CyApplicationManager; import org.cytoscape.application.swing.CySwingApplication; import org.cytoscape.application.swing.CytoPanelComponent; import org.cytoscape.command.CommandExecutorTaskFactory; import org.cytoscape.model.CyNetworkFactory; import org.cytoscape.model.CyNetworkManager; import org.cytoscape.model.subnetwork.CyRootNetworkManager; import org.cytoscape.service.util.AbstractCyActivator; import org.cytoscape.service.util.CyServiceRegistrar; import org.cytoscape.task.create.CloneNetworkTaskFactory; import org.cytoscape.view.model.CyNetworkViewFactory; import org.cytoscape.view.layout.CyLayoutAlgorithmManager; import org.cytoscape.view.model.CyNetworkViewManager; import org.cytoscape.view.presentation.RenderingEngineFactory; import org.cytoscape.view.vizmap.VisualMappingFunctionFactory; import org.cytoscape.view.vizmap.VisualMappingManager; import org.cytoscape.view.vizmap.VisualStyleFactory; import org.cytoscape.work.TaskFactory; import org.cytoscape.work.swing.DialogTaskManager; import org.osgi.framework.BundleContext; import static org.cytoscape.work.ServiceProperties.COMMAND; import static org.cytoscape.work.ServiceProperties.COMMAND_DESCRIPTION; import static org.cytoscape.work.ServiceProperties.COMMAND_NAMESPACE; import de.hhu.ba.yoshikoWrapper.core.ConfigurationManager; import de.hhu.ba.yoshikoWrapper.core.CyCore; import de.hhu.ba.yoshikoWrapper.core.LocalizationManager; import de.hhu.ba.yoshikoWrapper.core.YoshUtil; import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader; import de.hhu.ba.yoshikoWrapper.swing.components.MainPanel; import de.hhu.ba.yoshikoWrapper.taskFactories.CommandTaskFactory; import de.hhu.ba.yoshikoWrapper.taskFactories.YoshikoCommand; /** * Entry point for the application as required by the Cytoscape API * Registers services and sets up resources for Yoshiko */ public class CyActivator extends AbstractCyActivator { public CyActivator() { super(); } @Override public void start(BundleContext context) throws Exception { //Initialize Cytoscape configuration system //This is responsible for saving/loading configuration ConfigurationManager cm = new ConfigurationManager("yoshikoWrapper", "yoshiko.props"); Properties propsReaderServiceProps = new Properties(); propsReaderServiceProps.setProperty("cyPropertyName", "yoshiko.props"); registerAllServices(context,cm,propsReaderServiceProps); //Create symbolic links to give other classes access to Cytoscape Services CyCore.cy = getService(context, CyApplicationManager.class); CyCore.dialogTaskManager = getService(context, DialogTaskManager.class); CyCore.registrar = getService(context, CyServiceRegistrar.class); CyCore.cm = cm; CyCore.networkViewFactory = getService(context, CyNetworkViewFactory.class); CyCore.networkFactory = getService(context, CyNetworkFactory.class); CyCore.swing = getService(context, CySwingApplication.class); CyCore.networkViewManager = getService(context,CyNetworkViewManager.class); CyCore.networkManager = getService(context,CyNetworkManager.class); CyCore.layoutAlgorithmManager = getService(context,CyLayoutAlgorithmManager.class); CyCore.visualMappingManager = getService(context,VisualMappingManager.class); CyCore.visualStyleFactory = getService(context,VisualStyleFactory.class); CyCore.continuousMappingFactory = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=continuous)"); CyCore.rootNetworkManager = getService(context,CyRootNetworkManager.class); //TODO: Not sure how to correctly infer arguments here CyCore.renderingEngineFactory = getService(context,RenderingEngineFactory.class); CyCore.cloneNetworkTaskFactory = getService(context,CloneNetworkTaskFactory.class); CyCore.commandExecutorTaskFactory = getService(context,CommandExecutorTaskFactory.class); //Store a reference to the Version for easier access YoshUtil.version = context.getBundle().getVersion(); //Set language according to settings -> Default to enUS LocalizationManager.switchLanguage(cm.getProperties().getProperty("locale", "enUS")); //Attempt to find the Yoshiko lib in a previously stored location and load it //TODO: Move into a separate handler to keep CyActivator clean if (!YoshikoLoader.isLibraryLoaded()){ String pathToYosh = cm.getProperties().getProperty("pathToYoshiko"); if (pathToYosh != null && pathToYosh != "null") { YoshikoLoader.loadLibrary(pathToYosh); } } //Register commands / CyRest TaskFactory commandTaskFactory = new CommandTaskFactory(YoshikoCommand.PERFORM_ALGORITHM); Properties props = new Properties(); props.setProperty(COMMAND_NAMESPACE, "yoshiko"); props.setProperty(COMMAND, YoshikoCommand.PERFORM_ALGORITHM.toString()); props.setProperty(COMMAND_DESCRIPTION,"Cluster a network with the Yoshiko algorithm"); registerService(context, commandTaskFactory, TaskFactory.class, props); //Initialize and register main panel MainPanel mainPanel = new MainPanel(); registerService(context,mainPanel,CytoPanelComponent.class, new Properties()); } }