Loading example data from the wizard

cas-bioinf · Jan 9, 2017 · b3d636f · b3d636f
1 parent 66f66e2
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diff --git a/cy-genexpi/sampleData/B.subtilis-germination (GSE6865) - used only.tsv b/cy-genexpi/sampleData/B.subtilis-germination (GSE6865) - used only.tsv
@@ -0,0 +1,8 @@
+ID_REF	0	5	10	15	20	25	30	40	50	60	70	80	90	100
+sigA	65.02848915	126.4129103	4272.900479	5841.001338	3827.004813	4214.074196	3655.872395	3023.491903	2252.013874	771.2207189	1624.747711	1463.289999	2063.674901	1638.318343
+sigB	61.94860972	37.89669158	668.1369332	862.2724645	701.8407961	1585.805369	2365.615687	3475.488365	11206.12601	3856.295791	3227.049517	2245.778613	2055.110141	1884.544308
+dnaA	141.1416529	599.6596128	14776.3262	10631.07598	9554.734037	4408.279551	3439.540195	4630.653203	2886.288907	6463.05252	6051.176708	5845.051415	3942.786839	4463.624652
+glnR	102.1821935	982.2864582	4617.832088	5992.73972	5341.391812	6472.018427	6774.975434	2661.456	3676.201168	2281.868597	3877.739034	4261.069892	3850.953533	2900.327297
+tnrA	39.89123822	77.17170097	412.7144097	335.2282683	522.7582084	452.8847029	289.6165025	470.4833963	213.4863472	400.3172573	441.7235684	374.0273609	398.1035704	320.6820963
+bmrR	76.79816847	49.45347518	357.1781456	286.0255073	385.0761604	302.9634616	187.1433534	398.1035704	276.0909905	232.3249038	155.9565138	124.4998333	154.9866347	190.282622
+ctsR	77.54705027	382.9467541	2772.554299	1288.074211	827.1470363	933.8195615	922.8804737	1986.481992	2904.350793	2065.105828	1555.32461	1150.463901	1326.124031	1375.747508
diff --git a/cy-genexpi/src/main/java/cz/cas/mbu/cygenexpi/internal/tasks/LoadExampleDataTask.java b/cy-genexpi/src/main/java/cz/cas/mbu/cygenexpi/internal/tasks/LoadExampleDataTask.java
@@ -0,0 +1,72 @@
+package cz.cas.mbu.cygenexpi.internal.tasks;
+
+import java.io.File;
+import java.io.InputStream;
+import java.nio.file.CopyOption;
+import java.nio.file.Files;
+import java.nio.file.StandardCopyOption;
+
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.io.read.CySessionReader;
+import org.cytoscape.io.read.CySessionReaderManager;
+import org.cytoscape.service.util.CyServiceRegistrar;
+import org.cytoscape.session.CySession;
+import org.cytoscape.session.CySessionManager;
+import org.cytoscape.session.events.SessionAboutToBeLoadedEvent;
+import org.cytoscape.session.events.SessionLoadCancelledEvent;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+
+public class LoadExampleDataTask extends AbstractTask {
+	@Tunable(description="<html>Current session (all networks and tables) will be lost.<br />Do you want to continue?</html>",
+			 params="ForceSetDirectly=true;ForceSetTitle=Open Session")
+	public boolean approve;
+
+	private final CyServiceRegistrar registrar;		
+
+	public LoadExampleDataTask(CyServiceRegistrar registrar) {
+		super();
+		this.registrar = registrar;
+	}
+
+	@Override
+	public void run(TaskMonitor taskMonitor) throws Exception {
+		if(approve)
+		{
+			CyEventHelper eventHelper = registrar.getService(CyEventHelper.class);
+			eventHelper.fireEvent(new SessionAboutToBeLoadedEvent(this));
+			try {
+				InputStream is = getClass().getResourceAsStream("/cz/cas/mbu/genexpi/example1_ds.cys");
+				File tempFile = File.createTempFile("cygenexpi_example", ".cys");
+				tempFile.deleteOnExit();
+				Files.copy(is, tempFile.toPath(),StandardCopyOption.REPLACE_EXISTING);
+
+				CySessionReader reader = registrar.getService(CySessionReaderManager.class).getReader(tempFile.toURI(), tempFile.getName());
+
+				if (reader == null)
+				{
+					throw new NullPointerException("Failed to find appropriate reader for example data.");
+				}
+				reader.run(taskMonitor);
+
+				final CySession newSession = reader.getSession();
+
+				if (newSession == null)
+					throw new NullPointerException("Example session could not be read.");
+
+				CySessionManager sessionMgr = registrar.getService(CySessionManager.class);
+				sessionMgr.setCurrentSession(newSession, "CyGenexpi example");
+
+			}
+			catch(Exception ex)
+			{
+				eventHelper.fireEvent(new SessionLoadCancelledEvent(this));
+				throw ex;
+			}
+		}
+
+	}
+
+
+}
diff --git a/cy-genexpi/src/main/java/cz/cas/mbu/cygenexpi/internal/tasks/StartWizardTask.java b/cy-genexpi/src/main/java/cz/cas/mbu/cygenexpi/internal/tasks/StartWizardTask.java
@@ -40,6 +40,7 @@ public void run(TaskMonitor taskMonitor) throws Exception {
 		data.selectedNetwork = registrar.getService(CyApplicationManager.class).getCurrentNetwork();
 
 		WizardPanel<GNWizardData> panel = new WizardPanel<>(registrar, InferenceWizard.getSteps(), InferenceWizard.TITLE, data);
+		data.wizardPanel = panel;
 		registrar.registerService(panel, CytoPanelComponent.class, new Properties());
 
 		UIUtils.ensurePanelVisible(registrar, panel);		

diff --git a/cy-genexpi/src/main/java/cz/cas/mbu/cygenexpi/internal/ui/wizard/GNWizardData.java b/cy-genexpi/src/main/java/cz/cas/mbu/cygenexpi/internal/ui/wizard/GNWizardData.java
@@ -14,6 +14,9 @@ public class GNWizardData {
 	@RememberValue(type=Type.NEVER)
 	public CyNetwork selectedNetwork;
 
+	@RememberValue(type=Type.NEVER)
+	public WizardPanel<GNWizardData> wizardPanel;
+
 	public String expressionMappingColumn = "";
 
 	@RememberValueRecursive

diff --git a/cy-genexpi/src/main/java/cz/cas/mbu/cygenexpi/internal/ui/wizard/SelectTimeSeriesStep.java b/cy-genexpi/src/main/java/cz/cas/mbu/cygenexpi/internal/ui/wizard/SelectTimeSeriesStep.java
@@ -37,6 +37,7 @@
 import cz.cas.mbu.cydataseries.TimeSeries;
 import cz.cas.mbu.cygenexpi.PredictionService;
 import cz.cas.mbu.cygenexpi.internal.tasks.CheckConfigurationTask;
+import cz.cas.mbu.cygenexpi.internal.tasks.LoadExampleDataTask;
 
 import com.jgoodies.forms.layout.FormSpecs;
 import javax.swing.JLabel;
@@ -103,6 +104,12 @@ public SelectTimeSeriesStep() {
 				FormSpecs.RELATED_GAP_ROWSPEC,
 				FormSpecs.DEFAULT_ROWSPEC,
 				FormSpecs.RELATED_GAP_ROWSPEC,
+				FormSpecs.DEFAULT_ROWSPEC,
+				FormSpecs.RELATED_GAP_ROWSPEC,
+				FormSpecs.DEFAULT_ROWSPEC,
+				FormSpecs.RELATED_GAP_ROWSPEC,
+				FormSpecs.DEFAULT_ROWSPEC,
+				FormSpecs.RELATED_GAP_ROWSPEC,
 				FormSpecs.DEFAULT_ROWSPEC,}));
 
 		JLabel lblDescription = new JLabel("<html>First we need a time series for the expression data. The time series needs to be mapped to nodes in the network.\r\n</html>");
@@ -154,6 +161,16 @@ public SelectTimeSeriesStep() {
 		btnSmoothTimeSeries = new JButton("Smooth a Time Series");
 		add(btnSmoothTimeSeries, "2, 28, 3, 1");
 		btnSmoothTimeSeries.addActionListener(evt -> smoothTimeSeries());
+
+		JSeparator separator_3 = new JSeparator();
+		add(separator_3, "2, 30, 3, 1");
+
+		JLabel lblAlternativelyYouCan = new JLabel("Alternatively you can load example data directly:");
+		add(lblAlternativelyYouCan, "2, 32, 3, 1");
+
+		JButton btnLoadExampleData = new JButton("Load example data");
+		add(btnLoadExampleData, "2, 34, 3, 1");
+		btnLoadExampleData.addActionListener(evt -> loadExampleData());
 
 	}
 
@@ -293,6 +310,27 @@ private void smoothTimeSeries()
 		registrar.getService(DialogTaskManager.class).execute(smoothTaskIterator);		
 	}
 
+	private void loadExampleData()
+	{
+		registrar.getService(DialogTaskManager.class).execute(new TaskIterator(
+				new LoadExampleDataTask(registrar)
+				, new AbstractTask(){
+
+					@Override
+					public void run(TaskMonitor taskMonitor) throws Exception {
+						SwingUtilities.invokeLater(() -> {
+							CyNetwork exampleNetwork = registrar.getService(CyNetworkManager.class).getNetworkSet().iterator().next();
+							data.selectedNetwork = exampleNetwork;
+							data.expressionMappingColumn = "Expression_smooth";
+							refreshUI();
+							data.wizardPanel.nextStep();							
+						});
+					}
+
+				}
+				));		
+
+	}
 
 
 	@Override

diff --git a/cy-genexpi/src/main/java/cz/cas/mbu/cygenexpi/internal/ui/wizard/WizardPanel.java b/cy-genexpi/src/main/java/cz/cas/mbu/cygenexpi/internal/ui/wizard/WizardPanel.java
@@ -195,15 +195,15 @@ public void run(TaskMonitor taskMonitor) throws Exception {
 		}
 	}
 
-	protected void previousStep()
+	public void previousStep()
 	{
 		if(shownStepIndex > 0)
 		{
 			setShownStepIndex(shownStepIndex - 1, false); 
 		}
 	}
 
-	protected void nextStep()
+	public void nextStep()
 	{
 		registrar.getService(RememberValueService.class).saveProperties(data);
 

diff --git a/cy-genexpi/src/main/resources/cz/cas/mbu/genexpi/example1_ds.cys b/cy-genexpi/src/main/resources/cz/cas/mbu/genexpi/example1_ds.cys