Bug Fixed

cannin · Oct 18, 2021 · fa003d4 · fa003d4
1 parent 3fdebb5
commit fa003d4
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Showing 29 changed files with 225 additions and 128 deletions.
diff --git a/causalpath-cytoscape-app/pom.xml b/causalpath-cytoscape-app/pom.xml
@@ -3,20 +3,21 @@
     <modelVersion>4.0.0</modelVersion>
 
     <properties>
-        <bundle.symbolicName>CausalpathCytoscapeApp</bundle.symbolicName>
-        <bundle.namespace>org.biopax.cytoscape.causalpath_cytoscape_app</bundle.namespace>
+        <bundle.symbolicName>causalpath</bundle.symbolicName>
+        <bundle.namespace>org.biopax.cytoscape.causalpath</bundle.namespace>
         <cytoscape.api.version>3.7.0</cytoscape.api.version>
-
         <maven-bundle-plugin.version>3.5.0</maven-bundle-plugin.version>
         <osgi.api.version>4.2.0</osgi.api.version>
     </properties>
 
     <groupId>org.biopax.cytoscape</groupId>
-    <artifactId>causalpath-cytoscape-app</artifactId>
+    <artifactId>causalpath</artifactId>
     <packaging>bundle</packaging>
-    <version>0.99.1</version>
+    <version>1.0.1</version>
+
+    <name>causalpath</name>
+
 
-    <name>causalpath-cytoscape-app</name>
 
 
     <build>
@@ -235,6 +236,5 @@
             <artifactId>jackson-databind</artifactId>
             <version>2.9.6</version>
         </dependency>
-
     </dependencies>
 </project>
diff --git a/causalpath-cytoscape-app/src/main/java/org/biopax/cytoscape/causalpath/CyActivator.java b/causalpath-cytoscape-app/src/main/java/org/biopax/cytoscape/causalpath/CyActivator.java
@@ -10,17 +10,20 @@
 import org.biopax.cytoscape.causalpath.Panel.CreateLegendAction;
 import org.biopax.cytoscape.causalpath.Panel.ResultPanel;
 import org.cytoscape.service.util.CyServiceRegistrar;
+import org.cytoscape.work.SynchronousTaskManager;
+import org.cytoscape.work.Tunable;
 import org.osgi.framework.BundleContext;
 
 import org.cytoscape.service.util.AbstractCyActivator;
 
 import java.util.Properties;
 
 
+
 public class CyActivator extends AbstractCyActivator {
 
     public static CyServiceRegistrar cyServiceRegistrar;
-
+    SynchronousTaskManager synchronousTaskManager;
     public static ResultPanel resultPanel;
 
     public CyActivator() {
@@ -30,20 +33,24 @@ public CyActivator() {
 
     public void start(BundleContext bc) {
         CySwingApplication cytoscapeDesktopService = getService(bc, CySwingApplication.class);
-
+       // synchronousTaskManager = getService(bc,SynchronousTaskManager.class);
 
         cyServiceRegistrar = getService(bc, CyServiceRegistrar.class);
         resultPanel = new ResultPanel(cyServiceRegistrar);
         registerService(bc, resultPanel, CytoPanelComponent.class, new Properties());
-        LegendPanel controlpanel = new LegendPanel(cyServiceRegistrar, resultPanel);
+        synchronousTaskManager  = getService(bc,SynchronousTaskManager.class);
+        LegendPanel controlpanel = new LegendPanel(cyServiceRegistrar, resultPanel,synchronousTaskManager);
         CreateLegendAction controlPanelAction = new CreateLegendAction(cytoscapeDesktopService, controlpanel, cyServiceRegistrar);
         registerService(bc, controlpanel, CytoPanelComponent.class, new Properties());
 
         registerService(bc, controlPanelAction, CyAction.class, new Properties());
+       // registerService(bc,synchronousTaskManager,SynchronousTaskManager.class,new Properties());
 
+        System.out.println("CausalPath started");
 
-        System.out.println("CausalPath App started");
-
+    }
+    public SynchronousTaskManager getSynchronousTaskManager(){
+        return synchronousTaskManager;
     }
 
 

diff --git a/...app/src/main/java/org/biopax/cytoscape/causalpath/ImportandExecutor/tasks/JsonImport.java b/...app/src/main/java/org/biopax/cytoscape/causalpath/ImportandExecutor/tasks/JsonImport.java
@@ -78,7 +78,7 @@ public void writeJSON(File Jsonfile, String jsonpath, LegendPanel legendPanel) t
             } else name = jsonpath.substring(jsonpath.lastIndexOf("/") + 1, jsonpath.length());
             String modelID = name;
 
-            cyNetwork = CyNetworkUtils.readCyNetworkFromFile(cyServiceRegistrar, temp);
+            //cyNetwork = CyNetworkUtils.readCyNetworkFromFile(cyServiceRegistrar, temp);
             cyNetwork.getRow(cyNetwork).set(CyNetwork.NAME, modelID);
             JProgressBar jProgressBar = legendPanel.getStatusBar();
             jProgressBar.setValue(50);

diff --git a/...-app/src/main/java/org/biopax/cytoscape/causalpath/ImportandExecutor/tasks/SIFImport.java b/...-app/src/main/java/org/biopax/cytoscape/causalpath/ImportandExecutor/tasks/SIFImport.java
@@ -7,20 +7,25 @@
 
 import java.awt.*;
 import java.io.*;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Scanner;
+import java.util.*;
 
 import javax.swing.*;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
+import org.biopax.cytoscape.causalpath.CyActivator;
+import org.biopax.cytoscape.causalpath.ImportandExecutor.utils.CommandExecutor;
 import org.biopax.cytoscape.causalpath.Panel.LegendPanel;
+import org.cytoscape.io.read.CyNetworkReader;
+import org.cytoscape.io.read.CyNetworkReaderManager;
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyTable;
 import org.cytoscape.service.util.CyServiceRegistrar;
+import org.cytoscape.work.SynchronousTaskManager;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskManager;
+import org.cytoscape.work.Tunable;
 import org.xml.sax.SAXException;
 import org.biopax.cytoscape.causalpath.utils.CyNetworkUtils;
 
@@ -35,21 +40,26 @@ public class SIFImport {
     private String fXmlFile;
     private File Siffile;
     private LegendPanel legendPanel;
-    public CyNetwork SIFCyNetwork;
+
     public static String Edge_Info_col_Name = "CausalPath_Edge_Information";
     public File temp = File.createTempFile("tempSIF", ".sif");
     public HashMap<String, String> edgeinformation = new HashMap<>();
 
-    public SIFImport(File siffile, String fXmlFile, CyServiceRegistrar cyServiceRegistrar, LegendPanel legendPanel) throws ParserConfigurationException, SAXException, IOException, TransformerException {
+    public CyNetwork SIFCyNetwork;
 
+   public  SynchronousTaskManager synchronousTaskManager;
+    @Tunable(description = "networkName", context = "nogui")
+    public String networkName = "";
+    public SIFImport(File siffile, String fXmlFile, CyServiceRegistrar cyServiceRegistrar, LegendPanel legendPanel, SynchronousTaskManager synchronousTaskManager, boolean flag) throws ParserConfigurationException, SAXException, IOException, TransformerException {
+        this.synchronousTaskManager =synchronousTaskManager;
         this.cyServiceRegistrar = cyServiceRegistrar;
         this.fXmlFile = fXmlFile;
         this.Siffile = siffile;
         this.legendPanel = legendPanel;
-        writeSIF(siffile, fXmlFile);
+        writeSIF(siffile, fXmlFile,flag);
     }
 
-    public void writeSIF(File siffile, String fXmlFile) throws ParserConfigurationException, SAXException, IOException, TransformerException {
+    public void writeSIF(File siffile, String fXmlFile, boolean flag) throws ParserConfigurationException, SAXException, IOException, TransformerException {
 
 
         try {
@@ -67,6 +77,7 @@ public void writeSIF(File siffile, String fXmlFile) throws ParserConfigurationEx
                 if (splited.length >= 3) {
 
                     bw.write(splited[0] + "\t" + splited[1] + "\t" + splited[2]);
+                    //System.out.println(splited[0] + "\t" + splited[1] + "\t" + splited[2]);
                     bw.write("\n");
 
                     if (splited.length == 5) {
@@ -75,19 +86,27 @@ public void writeSIF(File siffile, String fXmlFile) throws ParserConfigurationEx
 
                 }
             }
+
             sc.close();     //closes the scanner
             bw.close();
             String OS = System.getProperty("os.name").toLowerCase();
+            System.out.println("OS"+OS);
             String name = "";
             if (OS.indexOf("win") >= 0) {
                 name = fXmlFile.substring(fXmlFile.lastIndexOf("\\") + 1, fXmlFile.length());
             } else name = fXmlFile.substring(fXmlFile.lastIndexOf("/") + 1, fXmlFile.length());
             String[] arr;
 
-            String modelID = name;
 
-            SIFCyNetwork = CyNetworkUtils.readCyNetworkFromFile(cyServiceRegistrar, temp);
-            SIFCyNetwork.getRow(SIFCyNetwork).set(CyNetwork.NAME, modelID);
+
+            networkName = name;
+
+            // setting up the tunable here
+            if(flag)
+             CommandExecutor.execute("network set current network=" + networkName, cyServiceRegistrar);
+            SIFCyNetwork = CyNetworkUtils.readCyNetworkFromFile(cyServiceRegistrar, temp,synchronousTaskManager);
+
+            SIFCyNetwork.getRow(SIFCyNetwork).set(CyNetwork.NAME, networkName);
             CyTable edgetable = SIFCyNetwork.getDefaultEdgeTable();
             Collection<CyEdge> edgelist = SIFCyNetwork.getEdgeList();
             edgetable.createColumn(Edge_Info_col_Name, String.class, false);
@@ -113,6 +132,8 @@ public void writeSIF(File siffile, String fXmlFile) throws ParserConfigurationEx
             JButton submitbutton = legendPanel.getSubmitbutton();
             submitbutton.setEnabled(false);
         } catch (NullPointerException ignored) {
+            ignored.printStackTrace();
+
             JOptionPane optionPane = new JOptionPane("File Open Failed", JOptionPane.ERROR_MESSAGE);
             JDialog dialog = optionPane.createDialog("Failure");
             dialog.setAlwaysOnTop(true);
@@ -121,6 +142,7 @@ public void writeSIF(File siffile, String fXmlFile) throws ParserConfigurationEx
             legendPanel.getStatusLabel().setForeground(Color.RED);
 
         } catch (FileNotFoundException e) {
+            e.printStackTrace();
             JOptionPane optionPane = new JOptionPane("File Not Found", JOptionPane.ERROR_MESSAGE);
             JDialog dialog = optionPane.createDialog("Failure");
             dialog.setAlwaysOnTop(true);

diff --git a/...rc/main/java/org/biopax/cytoscape/causalpath/ImportandExecutor/utils/CommandExecutor.java b/...rc/main/java/org/biopax/cytoscape/causalpath/ImportandExecutor/utils/CommandExecutor.java
@@ -3,32 +3,64 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.poi.ss.formula.functions.T;
+import org.biopax.cytoscape.causalpath.CyActivator;
 import org.biopax.cytoscape.causalpath.Panel.LegendPanel;
 import org.cytoscape.command.CommandExecutorTaskFactory;
 import org.cytoscape.service.util.CyServiceRegistrar;
-import org.cytoscape.work.SynchronousTaskManager;
-import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.*;
+import org.cytoscape.work.swing.DialogTaskManager;
 
 public class CommandExecutor {
 
-    public static void execute(String command, CyServiceRegistrar cyServiceRegistrar, LegendPanel legendPanel, int flag) {
+    public static void execute(String command, CyServiceRegistrar cyServiceRegistrar, LegendPanel legendPanel) {
         CommandExecutorTaskFactory executor = cyServiceRegistrar.getService(CommandExecutorTaskFactory.class);
 
         List<String> commands = new ArrayList<String>();
         commands.add(command);
 
         TaskIterator task = executor.createTaskIterator(commands, null);
         SynchronousTaskManager manager = cyServiceRegistrar.getService(SynchronousTaskManager.class);
-        manager.execute(task);
+
         legendPanel.getStatusBar().setValue(100);
         legendPanel.getStatusLabel().setText("Success!");
+        manager.execute(task);
+
         legendPanel.getSubmitbutton().setEnabled(false);
         legendPanel.getFormatfileuploadbutton().setEnabled(false);
+        try{
+            Thread.sleep(3000);
+
+        } catch (InterruptedException e) {
+            System.out.println("Sleep for User's Understanding");
+            e.printStackTrace();
+        }
+
+        legendPanel.getStatusBar().setValue(0);
 
 
     }
+    public static void execute(String command, CyServiceRegistrar cyServiceRegistrar) {
+        CommandExecutorTaskFactory executor = cyServiceRegistrar.getService(CommandExecutorTaskFactory.class);
+
+        List<String> commands = new ArrayList<String>();
+        commands.add(command);
+
+        TaskIterator task = executor.createTaskIterator(commands, null);
+        SynchronousTaskManager manager = cyServiceRegistrar.getService(SynchronousTaskManager.class);
+
+        manager.execute(task);
+
+    }
+
+    public static void execute(TaskIterator commandTask, CyServiceRegistrar cyServiceRegistrar) {
+        CyActivator cyActivator = cyServiceRegistrar.getService(CyActivator.class);
+        cyActivator.getSynchronousTaskManager().execute(commandTask);
 
-    public static void execute(TaskIterator commandTask, CyServiceRegistrar cyServiceRegistrar, int flag) {
-        cyServiceRegistrar.getService(SynchronousTaskManager.class).execute(commandTask);
     }
+    public static void execute(TaskIterator commandTask, CyServiceRegistrar cyServiceRegistrar,SynchronousTaskManager synchronousTaskManager) {
+
+        synchronousTaskManager.execute(commandTask);
+    }
+
 }
diff --git a/...cytoscape-app/src/main/java/org/biopax/cytoscape/causalpath/Panel/CreateLegendAction.java b/...cytoscape-app/src/main/java/org/biopax/cytoscape/causalpath/Panel/CreateLegendAction.java
@@ -8,6 +8,7 @@
 import org.cytoscape.application.swing.CytoPanelName;
 import org.cytoscape.application.swing.CytoPanelState;
 import org.cytoscape.service.util.CyServiceRegistrar;
+import org.cytoscape.work.Tunable;
 
 
 public class CreateLegendAction extends AbstractCyAction {
@@ -21,7 +22,7 @@ public class CreateLegendAction extends AbstractCyAction {
     public CreateLegendAction(CySwingApplication desktopApp,
                               LegendPanel myCytoPanel, CyServiceRegistrar cyServiceRegistrar) {
 
-        super("CausalPath");
+        super("CausalPath ");
         setPreferredMenu("Apps");
 
         this.desktopApp = desktopApp;