From 8b49e01e4ed5a0fa69fc44df8030a5f10d5a4302 Mon Sep 17 00:00:00 2001
From: Philipp Spohr <spohr.philipp@web.de>
Date: Mon, 11 Dec 2017 12:11:29 +0100
Subject: [PATCH] Support for retrieving clusters via CyRest
---
.../de/hhu/ba/yoshikoWrapper/CyActivator.java | 7 +++++++
.../yoshikoWrapper/graphModel/YoshikoResult.java | 4 ++++
.../graphModel/YoshikoSolution.java | 1 -
.../taskFactories/CommandTaskFactory.java | 10 ++++++----
.../taskFactories/YoshikoCommand.java | 6 +++++-
.../ba/yoshikoWrapper/tasks/GetClustersTask.java | 15 ++++++++++-----
6 files changed, 32 insertions(+), 11 deletions(-)
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
index ee46985..15bcfce 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java
@@ -127,6 +127,13 @@ public class CyActivator extends AbstractCyActivator {
props_GET_SOLUTIONS.setProperty(COMMAND_DESCRIPTION,"Retrieve solutions associated with a result");
registerService(context, commandTaskFactory_GET_SOLUTIONS, TaskFactory.class, props_GET_SOLUTIONS);
+ TaskFactory commandTaskFactory_GET_CLUSTERS = new CommandTaskFactory(YoshikoCommand.GET_CLUSTERS);
+ Properties props_GET_CLUSTERS = new Properties();
+ props_GET_CLUSTERS.setProperty(COMMAND_NAMESPACE, "yoshiko");
+ props_GET_CLUSTERS.setProperty(COMMAND, YoshikoCommand.GET_CLUSTERS.toString());
+ props_GET_CLUSTERS.setProperty(COMMAND_DESCRIPTION,"Retrieve clusters associated with a solution");
+ registerService(context, commandTaskFactory_GET_CLUSTERS, TaskFactory.class, props_GET_CLUSTERS);
+
//Initialize and register main panel
MainPanel mainPanel = new MainPanel();
registerService(context,mainPanel,CytoPanelComponent.class, new Properties());
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
index 47f1c4d..0a4ea3b 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.java
@@ -88,4 +88,8 @@ public class YoshikoResult{
return id;
}
+ public YoshikoSolution getSolution(long solutionID) {
+ return solutions.get(solutionID);
+ }
+
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
index bf8eb5e..1a20245 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java
@@ -22,7 +22,6 @@
package de.hhu.ba.yoshikoWrapper.graphModel;
import java.util.Collection;
-import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
index 53e7fbb..dc9e5cc 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java
@@ -4,9 +4,7 @@ import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
-import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
-import de.hhu.ba.yoshikoWrapper.tasks.CreateClusterViewsTask;
-import de.hhu.ba.yoshikoWrapper.tasks.GetSolutionsTask;
+import de.hhu.ba.yoshikoWrapper.tasks.*;
public class CommandTaskFactory implements TaskFactory{
@@ -39,7 +37,11 @@ public class CommandTaskFactory implements TaskFactory{
new GetSolutionsTask()
);
}
-
+ else if (command == YoshikoCommand.GET_CLUSTERS) {
+ return new TaskIterator(
+ new GetClustersTask()
+ );
+ }
else if (command == YoshikoCommand.PERFORM_ALGORITHM) {
return new TaskIterator(
new AlgorithmTask(
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java
index 25ead63..3f4913c 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java
@@ -12,7 +12,8 @@ public enum YoshikoCommand {
CREATE_CLUSTER_VIEW,
CREATE_META_GRAPH,
PERFORM_ALGORITHM,
- GET_SOLUTIONS;
+ GET_SOLUTIONS,
+ GET_CLUSTERS;
@Override
public String toString() {
@@ -22,6 +23,9 @@ public enum YoshikoCommand {
else if (this==CREATE_CLUSTER_VIEW) {
return "createcvs";
}
+ else if (this==GET_CLUSTERS) {
+ return "clusters"; //TODO: maybe smarter names for the commands
+ }
else if (this==GET_SOLUTIONS) {
return "solutions";
}
diff --git a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java
index 78888ae..9975bba 100644
--- a/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java
+++ b/src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java
@@ -1,6 +1,6 @@
package de.hhu.ba.yoshikoWrapper.tasks;
-import java.util.ArrayList;
+import java.util.Collection;
import org.cytoscape.work.ObservableTask;
import org.cytoscape.work.TaskMonitor;
@@ -17,9 +17,9 @@ public class GetClustersTask implements ObservableTask {
public int resultID = -1;
@Tunable(description="The solution ID for which the solutions should be displayed", context="nogui")
- public int solutionID = -1;
+ public long solutionID = -1;
- private ArrayList<YoshikoCluster> clusters;
+ private Collection<YoshikoCluster> clusters;
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
@@ -27,11 +27,14 @@ public class GetClustersTask implements ObservableTask {
if (result == null) {
throw new Exception("No result with ID: "+resultID+" was found!"); //TODO: Localization
}
+ if (result.getSolution(solutionID)== null) {
+ throw new Exception("No solution with ID: "+solutionID+" was found!"); //TODO: Localization
+ }
+ clusters = result.getSolution(solutionID).getClusters();
}
@Override
public void cancel() {
- // TODO Auto-generated method stub
}
@@ -40,7 +43,9 @@ public class GetClustersTask implements ObservableTask {
public <R> R getResults(Class<? extends R> type) {
if (type.equals(String.class)) {
String ret = "";
-
+ for (YoshikoCluster c: clusters) {
+ ret+="Cluster[ID="+c.getID()+"]: "+c.getSize()+" nodes\n";
+ }
return (R) ret;
}
return null;
--
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