diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index 080eb6a453f4ad873556e1fe8ad92b1e50e07d0a..feb666df60918d5d31bf6c2400222f75655ce008 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -39,15 +39,22 @@ 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 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
@@ -55,13 +62,15 @@ import de.hhu.ba.yoshikoWrapper.swing.components.MainPanel;
*/
public class CyActivator extends AbstractCyActivator {
+ private static final String COMMAND_NAMESPACE = "yoshiko";
+
public CyActivator() {
super();
}
@Override
public void start(BundleContext context) throws Exception {
- //Initialize cytoscape configuration system
+ //Initialize Cytoscape configuration system
//This is responsible for saving/loading configuration
ConfigurationManager cm = new ConfigurationManager("yoshikoWrapper", "yoshiko.props");
Properties propsReaderServiceProps = new Properties();
@@ -83,17 +92,18 @@ public class CyActivator extends AbstractCyActivator {
CyCore.visualStyleFactory = getService(context,VisualStyleFactory.class);
CyCore.continuousMappingFactory = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
CyCore.rootNetworkManager = getService(context,CyRootNetworkManager.class);
- //Not sure how to correctly infer arguments here
+ //TODO: Not sure how to correctly infer arguments here
CyCore.renderingEngineFactory = getService(context,RenderingEngineFactory.class);
CyCore.cloneNetworkTaskFactory = getService(context,CloneNetworkTaskFactory.class);
- //Store a reference to the Version
+ //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
+ //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") {
@@ -101,12 +111,20 @@ public class CyActivator extends AbstractCyActivator {
}
}
+ //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,"TEST PERFORM ALGORITHM");
+ registerService(context, commandTaskFactory, TaskFactory.class, props);
+
+
//Initialize and register main panel
MainPanel mainPanel = new MainPanel();
registerService(context,mainPanel,CytoPanelComponent.class, new Properties());
-
}
-
-}
+}
\ No newline at end of file
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanelFactory.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanel.java
similarity index 81%
rename from src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanelFactory.java
rename to src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanel.java
index 0d408884c60bdd98e28eb9a5f0046d3931a530ab..1b175e4f3eaf153c37fb3700e858bfe7eeab9aa7 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanelFactory.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/LanguageSwitcherPanel.java
@@ -1,16 +1,16 @@
/*******************************************************************************
* 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
@@ -29,19 +29,21 @@ import org.cytoscape.util.swing.BasicCollapsiblePanel;
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.swing.components.LanguageSwitcher;
-public class LanguageSwitcherPanelFactory{
-
- public static BasicCollapsiblePanel createLanguageSwitcherPanel() {
+@SuppressWarnings("serial")
+public class LanguageSwitcherPanel extends BasicCollapsiblePanel{
+
+
+ public LanguageSwitcherPanel() {
+ super(LocalizationManager.get("switchLanguage"));
final LanguageSwitcher switcher;
- final BasicCollapsiblePanel ret = new BasicCollapsiblePanel(LocalizationManager.get("switchLanguage"));
- ret.getContentPane().setLayout(new BoxLayout(ret.getContentPane(),BoxLayout.X_AXIS));
+ //final BasicCollapsiblePanel ret = new BasicCollapsiblePanel();
+ getContentPane().setLayout(new BoxLayout(getContentPane(),BoxLayout.X_AXIS));
//SWING COMPONENTS INIT
switcher = new LanguageSwitcher();
-
- SwingUtil.addAll(ret,
+
+ SwingUtil.addAll(this,
switcher
);
- return ret;
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java
index 859de27bf79a3fa30253e804ec57cf5999439131..ada41217a66d5f9c8265426c933e1cbb47e5997e 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ColumnMapper.java
@@ -44,6 +44,11 @@ import de.hhu.ba.yoshikoWrapper.core.CyCore;
import de.hhu.ba.yoshikoWrapper.swing.EnableWhenSelectedListener;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
+/**
+ *
+ * @author Philipp Spohr, Nov 30, 2017
+ *
+ */
@SuppressWarnings("serial") //will never be serialized
public class ColumnMapper extends JPanel
implements //everything
@@ -208,24 +213,36 @@ SetCurrentNetworkListener
@Override
public void handleEvent(ColumnDeletedEvent e) {
- if (
- e.getSource() == CyCore.cy.getCurrentNetwork().getDefaultEdgeTable() ||
- e.getSource() == CyCore.cy.getCurrentNetwork().getDefaultNetworkTable()
- )
- {
- updateValues();
+ try {
+ if (
+ e.getSource() == CyCore.cy.getCurrentNetwork().getDefaultEdgeTable() ||
+ e.getSource() == CyCore.cy.getCurrentNetwork().getDefaultNetworkTable()
+ )
+ {
+ updateValues();
+ }
+ }
+ catch (Exception ex) {
+ //TODO:
}
+
}
@Override
public void handleEvent(ColumnCreatedEvent e) {
- if (
- e.getSource() == CyCore.cy.getCurrentNetwork().getDefaultEdgeTable() ||
- e.getSource() == CyCore.cy.getCurrentNetwork().getDefaultNetworkTable()
- )
- {
- updateValues();
+ try {
+ if (
+ e.getSource() == CyCore.cy.getCurrentNetwork().getDefaultEdgeTable() ||
+ e.getSource() == CyCore.cy.getCurrentNetwork().getDefaultNetworkTable()
+ )
+ {
+ updateValues();
+ }
+ }
+ catch (Exception ex) {
+ //TODO:
}
+
}
public CyColumn getEditingCostColumn() {
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
index 54063d36c3689abec64f5158236e10d21667b806..5a5289a1e143f89a8ff491cec91f943bed282ef8 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/MainPanel.java
@@ -59,7 +59,7 @@ import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
import de.hhu.ba.yoshikoWrapper.swing.AboutDialogFactory;
import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
-import de.hhu.ba.yoshikoWrapper.swing.LanguageSwitcherPanelFactory;
+import de.hhu.ba.yoshikoWrapper.swing.LanguageSwitcherPanel;
import de.hhu.ba.yoshikoWrapper.swing.LibraryPanelFactory;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
@@ -125,7 +125,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
scrollPane.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
scrollPane.setBorder(BorderFactory.createEmptyBorder());
- langPanel = LanguageSwitcherPanelFactory.createLanguageSwitcherPanel();
+ langPanel = new LanguageSwitcherPanel();
libraryPanel = LibraryPanelFactory.createLibraryPanel();
//If no library is loaded yet the obvious panel should be showing up
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..8d17d1bb0ff85c60a6d059de43180ac2ef2210f4
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
@@ -0,0 +1,43 @@
+package de.hhu.ba.yoshikoWrapper.taskFactories;
+
+import org.cytoscape.work.AbstractTaskFactory;
+import org.cytoscape.work.TaskIterator;
+
+import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
+
+public class CommandTaskFactory extends AbstractTaskFactory{
+
+ private final YoshikoCommand command;
+
+ /**
+ * Default constructor
+ */
+ public CommandTaskFactory(YoshikoCommand command) {
+ super();
+ this.command = command;
+ }
+
+ @Override
+ public TaskIterator createTaskIterator() {
+ //We simply switch between the possible commands
+ if (command == YoshikoCommand.CREATE_CLUSTER_VIEW) {
+ return null;
+ }
+ else if (command == YoshikoCommand.CREATE_META_GRAPH) {
+ return null;
+ }
+ else if (command == YoshikoCommand.PERFORM_ALGORITHM) {
+ return new TaskIterator(
+ new AlgorithmTask(
+ null,
+ null,
+ null
+ )
+ );
+ }
+ else return null; //TODO: Might be useful to generate an error/ throw an exception here as this should never be invoked
+ }
+
+
+ public boolean isReady () { return true; } //TODO: Think about when that would actually make sense / prevent launching of multiple tasks
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java
new file mode 100644
index 0000000000000000000000000000000000000000..0a964ecd2d1a98ee7f11490def7ea976b7a41ad7
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java
@@ -0,0 +1,15 @@
+package de.hhu.ba.yoshikoWrapper.taskFactories;
+
+/**
+ * Describes commands for the Yoshiko App that can be invoked via REST/CyREST
+ * @author Philipp Spohr, Nov 30, 2017
+ *
+ */
+public enum YoshikoCommand {
+ /**
+ * Creates a CV for a given Cluster found in a result
+ */
+ CREATE_CLUSTER_VIEW,
+ CREATE_META_GRAPH,
+ PERFORM_ALGORITHM
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/package-info.java b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/package-info.java
new file mode 100644
index 0000000000000000000000000000000000000000..2058a2032e2915e38793c91ab64dfd263e7af57a
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/package-info.java
@@ -0,0 +1,8 @@
+/**
+ *
+ */
+/**
+ * @author Philipp Spohr, Nov 30, 2017
+ *
+ */
+package de.hhu.ba.yoshikoWrapper.taskFactories;
\ No newline at end of file
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
index fbe450f777d3eb576cdf6c36fe80bc9417b6a007..70568cf9914887ce8537afca0e515923153f85e2 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java
@@ -32,6 +32,7 @@ import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
import org.slf4j.Logger;
import de.hhu.ba.yoshikoWrapper.core.CyCore;
@@ -54,17 +55,23 @@ import de.hhu.ba.yoshikoWrapper.swing.components.ResultPanel;
public class AlgorithmTask extends AbstractTask {
- private String SOLUTION_COLUMN_PREFIX = "yoshikoSolution_";
+ //Constants
+ private static final String SOLUTION_COLUMN_PREFIX = "yoshikoSolution_"; //TODO: Make customizable?
//Symbolic links
private static Logger logger = YoshikoLogger.getInstance().getLogger();
- private Window statusWindow;
+
+
+ private final Window statusWindow; //TODO: Make tunable?
//Parameters
+ @Tunable(description="Parameter Set determining the operation mode for Yoshiko", context="nogui")
private final ParameterSet parameterSet;
+
+ @Tunable(description="Network to analyze for clusters", context="nogui")
private final CyNetwork net;
- //Temps, need to be freed in C++
+ //Temps, pointing to and need to be freed in C++
private LibraryInput input;
private ClusterEditingSolutions result;
private CoreAlgorithm ca;
diff --git a/src/main/resources/yoshiko b/src/main/resources/yoshiko.props
similarity index 100%
rename from src/main/resources/yoshiko
rename to src/main/resources/yoshiko.props