From 147092efd55111453183edfd438cf5db0dd72e5b Mon Sep 17 00:00:00 2001
From: Philipp Spohr <spohr.philipp@web.de>
Date: Mon, 11 Dec 2017 08:11:24 +0100
Subject: [PATCH] -Hotfix: Prevented using forbidden and permanent for the same
edge -Work on CyRest support
---
pom.xml | 5 ++
.../de/hhu/ba/yoshikoWrapper/CyActivator.java | 2 +
.../de/hhu/ba/yoshikoWrapper/core/CyCore.java | 2 +
.../ba/yoshikoWrapper/core/NetworkParser.java | 31 +++++----
.../core/NetworkParsingException.java | 17 +++++
.../hhu/ba/yoshikoWrapper/core/YoshUtil.java | 2 +
.../cytoUtil/CommandExecutor.java | 20 ++++++
.../hhu/ba/yoshikoWrapper/help/HelpLinks.java | 68 +------------------
.../swing/AboutDialogFactory.java | 57 ----------------
.../swing/components/HelpButton.java | 26 ++++---
.../swing/components/MainPanel.java | 3 +-
src/main/resources/YoshikoStrings.properties | 6 ++
12 files changed, 91 insertions(+), 148 deletions(-)
create mode 100644 src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java
create mode 100644 src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/CommandExecutor.java
delete mode 100644 src/main/java/de/hhu/ba/yoshikoWrapper/swing/AboutDialogFactory.java
diff --git a/pom.xml b/pom.xml
index 453fd7a..83bdc3b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -162,6 +162,11 @@
<artifactId>group-api</artifactId>
<version>${cytoscape.api.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>command-executor-api</artifactId>
+ <version>${cytoscape.api.version}</version>
+ </dependency>
</dependencies>
<description>A Cytoscape plugin for graph-based clustering that wraps the yoshiko algorithm.</description>
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index 1652fed..a228110 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -26,6 +26,7 @@ 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;
@@ -94,6 +95,7 @@ public class CyActivator extends AbstractCyActivator {
//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();
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
index e51449e..0707782 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java
@@ -25,6 +25,7 @@ import java.util.concurrent.CountDownLatch;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.command.CommandExecutorTaskFactory;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
@@ -68,6 +69,7 @@ public class CyCore {
public static CyRootNetworkManager rootNetworkManager;
public static RenderingEngineFactory<CyNetwork> renderingEngineFactory;
public static CloneNetworkTaskFactory cloneNetworkTaskFactory;
+ public static CommandExecutorTaskFactory commandExecutorTaskFactory;
//
//Convenience
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
index eed69b6..64d16b7 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.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
@@ -34,18 +34,18 @@ import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
import de.hhu.ba.yoshikoWrapper.swig.LibraryInput;
public class NetworkParser {
-
+
//Symbolic Links
private static Logger logger = YoshikoLogger.getInstance().getLogger();
- public static LibraryInput parseNetwork(
+ public static LibraryInput parseNetwork (
CyNetwork net,
NodeMap nodeMap,
CyColumn weightColumn,
CyColumn permanentColumn,
CyColumn forbiddenColumn,
double deletionCostDefault
- )
+ ) throws NetworkParsingException
{
//Create an empty instance / fetch C++ object pointer
LibraryInput generatedInput = new LibraryInput();
@@ -54,18 +54,16 @@ public class NetworkParser {
generatedInput.setSize(net.getNodeCount());
//Fetch edges
List<CyEdge> edges = net.getEdgeList();
-
-
//Loop over edges
for (CyEdge e : edges) {
-
+
//Parse editing costs
double weight = deletionCostDefault;
-
+
//Fetch entry and check if it exists
CyRow edgeEntry = net.getRow(e);
-
+
//Check if there is a weight column defined, else skip
if (weightColumn != null){
//Check if the column contains an entry for the respective edge
@@ -83,7 +81,7 @@ public class NetworkParser {
//Parse Forbidden/Permanent markers
boolean forbidden = false;
boolean permanent = false;
-
+
if (permanentColumn != null) {
//Additional check as it is not required to have a value in every row
if (edgeEntry.get(permanentColumn.getName(), Boolean.class) != null) {
@@ -97,8 +95,13 @@ public class NetworkParser {
}
}
+ //Check for edges that are forbidden AND permanent -> Throw exception
+ if (forbidden && permanent) {
+ throw new NetworkParsingException(LocalizationManager.get("dualInfinityError"));
+ }
+
logger.debug("Found Edge: "+edgeEntry.get("name", String.class)+ " with weight:"+weight);
-
+
generatedInput.addEdge(
nodeMap.get(e.getSource()),
nodeMap.get(e.getTarget()),
@@ -106,7 +109,7 @@ public class NetworkParser {
permanent,
forbidden
);
-
+
}
}
return generatedInput;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java
new file mode 100644
index 0000000..65b9c43
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParsingException.java
@@ -0,0 +1,17 @@
+package de.hhu.ba.yoshikoWrapper.core;
+
+@SuppressWarnings("serial")
+public class NetworkParsingException extends Exception {
+
+ private String msg;
+
+ public NetworkParsingException(String msg) {
+ this.msg = msg;
+ }
+
+ @Override
+ public String getMessage() {
+ return LocalizationManager.get("networkParsingException")+" "+msg;
+ }
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshUtil.java b/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshUtil.java
index b85271e..9580bd5 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshUtil.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshUtil.java
@@ -5,4 +5,6 @@ import org.osgi.framework.Version;
public class YoshUtil {
public static Version version;
+
+ public static final String ABOUT_LINK = "https://spqrph.github.io/cytoscape-tutorials/presentations/yoshiko/yoshiko.html#/title";
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/CommandExecutor.java b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/CommandExecutor.java
new file mode 100644
index 0000000..382678f
--- /dev/null
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/CommandExecutor.java
@@ -0,0 +1,20 @@
+package de.hhu.ba.yoshikoWrapper.cytoUtil;
+
+import java.util.Map;
+
+import org.cytoscape.work.TaskObserver;
+
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
+
+public class CommandExecutor{
+
+ public static void executeCommand(String namespace, String command,
+ Map<String, Object> args, TaskObserver observer) {
+ ;
+ CyCore.dialogTaskManager.execute(
+ CyCore.commandExecutorTaskFactory.createTaskIterator(namespace, command, args, observer)
+ );
+
+ }
+
+}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java b/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
index 3c77e1c..597eca4 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java
@@ -21,75 +21,13 @@
******************************************************************************/
package de.hhu.ba.yoshikoWrapper.help;
-import java.awt.Container;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.util.WeakHashMap;
+import java.util.HashMap;
-import org.slf4j.Logger;
-
-import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
-import de.hhu.ba.yoshikoWrapper.swing.components.EditCostPanel;
-
-/**
- * Helper class that provides URIs to access the Bachelor Thesis paper sections that can be used as a manual
- *
- */
public final class HelpLinks {
- //SYMBOLIC LINKS
-
- /**
- * Convenience function for better code readability
- */
- private static final Logger logger = YoshikoLogger.getInstance().getLogger();
-
- //
-
- /**
- * The base location of the bachelor thesis paper
- */
- //TODO: Add final location when published
- private static final String docLocation = "https://gitlab.cs.uni-duesseldorf.de/spohr/YoshikoWrapper/tree/master";
-
- /**
- * A HashMap linking Classes to a link, pointing to a specific subsection of the BachelorThesis paper that is relevant for understanding the Class
- */
- private static final WeakHashMap <Class<? extends Container>,URI> helpLinks;
-
- /**
- * Initialization for the HashMap
- */
+ public static final HashMap<String,Object> mainInfo = new HashMap<String,Object>();
static {
- helpLinks = new WeakHashMap<Class<? extends Container>,URI>();
- try {
- helpLinks.put(EditCostPanel.class, (buildURI("subsubsection.2.2.1")));
- } catch (URISyntaxException e) {
- logger.error("Error initializing URI for help file:\n"+e.getMessage());
- }
- }
-
-
- /**
- * Returns the URI that leads to the relevant help section for the class provided
- * @param c The Container class for which the help link should be fetched
- * @return The help link as URI
- */
- public static URI getHelpLink(Class<? extends Container> c) {
- if (helpLinks.containsKey(c)) {
- return helpLinks.get(c);
- }
- return null;
- }
-
- /**
- * Internal helper function that builds a valid URI from the base address and the fragment denoting the relevant section
- * @param fragment The fragment naming the nameddest in the pdf file
- * @return The compound URI made from base address and fragment
- * @throws URISyntaxException If invalid -> Should never be called during runtime in a stable version
- */
- private static URI buildURI(String fragment) throws URISyntaxException {
- return new URI(null,docLocation,"nameddest="+fragment);
+ mainInfo.put("url", "https://spqrph.github.io/cytoscape-tutorials/presentations/yoshiko/yoshiko.html#/title");
}
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/AboutDialogFactory.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/AboutDialogFactory.java
deleted file mode 100644
index 915093c..0000000
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/AboutDialogFactory.java
+++ /dev/null
@@ -1,57 +0,0 @@
-package de.hhu.ba.yoshikoWrapper.swing;
-
-import javax.swing.GroupLayout;
-import javax.swing.GroupLayout.Alignment;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-
-import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
-import de.hhu.ba.yoshikoWrapper.core.YoshUtil;
-import de.hhu.ba.yoshikoWrapper.swing.components.YoshikoHeader;
-
-/**Factory for a simple About-Dialog that provides some basic info about the software
- *
- */
-public class AboutDialogFactory{
-
- private static JPanel getDialogPanel() {
-
- JPanel ret = new JPanel();
-
- final YoshikoHeader header;
- final JLabel version;
- final JLabel text;
-
- header = new YoshikoHeader();
- version = new JLabel(LocalizationManager.get("wrapperVersion")+": "+YoshUtil.version);
- text = new JLabel(LocalizationManager.get("about"));
-
- SwingUtil.addAll(ret, header,version,text);
-
- GroupLayout layout = new GroupLayout(ret);
- layout.setAutoCreateGaps(true);
- layout.setHorizontalGroup(layout.createParallelGroup(Alignment.CENTER)
- .addComponent(header)
- .addComponent(version)
- .addComponent(text)
- );
- layout.setVerticalGroup(layout.createSequentialGroup()
- .addComponent(header)
- .addComponent(version)
- .addComponent(text)
- );
-
- ret.setLayout(layout);
-
- return ret;
- }
-
- public static void showDialog() {
- JOptionPane.showMessageDialog(
- null,
- getDialogPanel(),
- LocalizationManager.get("aboutTitle"),
- JOptionPane.PLAIN_MESSAGE);
- }
-}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/HelpButton.java b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/HelpButton.java
index f4bdbc1..bb7a004 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/HelpButton.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/HelpButton.java
@@ -6,13 +6,17 @@ import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.io.IOException;
import java.net.URI;
+import java.util.HashMap;
import javax.swing.BorderFactory;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JOptionPane;
+import org.cytoscape.command.CommandExecutorTaskFactory;
+
import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.CommandExecutor;
import de.hhu.ba.yoshikoWrapper.help.HelpLinks;
import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
@@ -28,31 +32,33 @@ public class HelpButton extends JButton{
* The default icon for the help button that should be shown if the button is not highlighted
*/
private static final ImageIcon defaultIcon = GraphicsLoader.getInfoIcon(SIZE);
+
/**
- * The icon tor the help button that should be shown if the button is highlighted
+ * The icon for the help button that should be shown if the button is highlighted
*/
private static final ImageIcon hlIcon = GraphicsLoader.getInfoIconHL(SIZE);
+
+
public HelpButton() {
+
super(defaultIcon);
+
+ //Design/Style
setToolTipText(LocalizationManager.get("tooltip_helpButton"));
setBorder(BorderFactory.createEmptyBorder());
+
+ //Add main functionality
addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
- URI uri = HelpLinks.getHelpLink(getParent().getClass());
- if (uri != null) {
- try {
- java.awt.Desktop.getDesktop().browse(uri);
- } catch (IOException ex) {
- JOptionPane.showMessageDialog(null, "DEBUG: Thesis is currently not online! Works only on my pc!");
- ex.printStackTrace();
- }
- }
+
+ CommandExecutor.executeCommand("cybrowser", "show",HelpLinks.mainInfo , null);
}
}
);
+
//Add mouse listener (cosmetic only)
addMouseListener(new MouseListener() {
@Override
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 0b60b3c..5c521c5 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 +59,6 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
import de.hhu.ba.yoshikoWrapper.cytoUtil.GraphAnalyzer;
-import de.hhu.ba.yoshikoWrapper.swing.AboutDialogFactory;
import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
import de.hhu.ba.yoshikoWrapper.swing.LibraryPanelFactory;
import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@@ -118,7 +117,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
@Override
public void actionPerformed(ActionEvent e) {
- AboutDialogFactory.showDialog();
+ //CommandExecutorTaskFactory fac;
}
});
diff --git a/src/main/resources/YoshikoStrings.properties b/src/main/resources/YoshikoStrings.properties
index 085bc84..69c2d91 100644
--- a/src/main/resources/YoshikoStrings.properties
+++ b/src/main/resources/YoshikoStrings.properties
@@ -34,12 +34,15 @@ cost = Editing Cost:
createMetaGraph = Create Meta-Graph
createClusterView = Create Cluster Views
currentGap = [ILP] Current Instance Gap
+
defaultDeletion = Default deletion cost:
defaultInsertion = Default insertion cost:
deleteSolution = Do you really want to delete this solution?
directedGraphWarning = This algorithm works on undirected graphs. Directed edges are \n treated as undirected edges.
disableMultiThreading = Disable Multithreading
discardSolution = Discard
+dualInfinityError = An edge was marked as forbidden and permanent.
+
editingCostPanel = Editing Costs
exportSelectedClusters = Export selected clusters
firstStart = Thanks for using the Yoshiko Clustering Tool!\nIt appears, that this is your first time using this tool.\nIf you want an in-depth explanation of the algorithm please refer to: [INSERT COOL LINK HERE]
@@ -57,11 +60,14 @@ metaGraph = Meta Graph
metaGraph_edges = Fetching edges and calculating edge strengths
multFactor = Multiplicative Factor for SNR:
multiGraphWarning = This graph is a multigraph. This algorithms behavior on multigraphs is not yet researched.
+
+networkParsingException: An error occured while parsing the network:
noFeasible = No feasible solution found!
noLibMessage = There is no Yoshiko Library currently loaded! You might have to specify its location.
noLibTitle = Library not loaded!
noMappingHint = You haven't mapped the cost value to a column in your edge table.\nYoshiko runs significantly faster and generates better solutions if you map values.
nodes = Nodes
+
optionpane_title = Yoshiko Info
noClustersSelected = You have not selected any clusters
notOptimal = Optimality not guaranteed
--
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