fix the multi user logging out problem

pom.xml

@@ -11,7 +11,7 @@
 	</parent>
 	<groupId>com.gw</groupId>
 	<artifactId>geoweaver</artifactId>
-	<version>1.2.0</version>
+	<version>1.2.1</version>
 	<name>geoweaver</name>
 	<description>A lightweight workflow management software for organizing data analysis workflows, 
 	preserving history of every workflow run, and improving scientist producitvity and workflow FAIRness,

src/main/java/com/gw/GeoweaverApplication.java

@@ -188,8 +188,6 @@ public static void addDefaultPublicUser(){
 
         }
 
-        logger.debug("test what is going on");
-
         //set everything that doesn't have an owner to this user
         ut.belongToPublicUser();
 

src/main/java/com/gw/local/LocalSessionNixImpl.java

@@ -28,6 +28,7 @@
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Scope;
 import org.springframework.stereotype.Service;
 
@@ -93,6 +94,7 @@ public class LocalSessionNixImpl implements LocalSession {
     public LocalSessionNixImpl() {
 
     	//this is for spring
+		log.info("localsessionniximpl object is created for " + token); 
 
     }
 
@@ -112,10 +114,10 @@ public void initHistory(String history_id, String script, String processid, bool
 		this.isClose = false;
 
 		history = history_tool.initProcessHistory(history_id, processid, script);
+
+		// this.sender = createLocalSessionOutput(); 
 
 	}
-
-
 
 	/**
 	 * If the process ends with error

src/main/java/com/gw/local/LocalSessionOutput.java

@@ -1,6 +1,7 @@
 package com.gw.local;
 
 import java.io.BufferedReader;
+import java.io.IOException;
 
 import javax.websocket.Session;
 
@@ -73,7 +74,7 @@ public LocalSessionOutput() {
      * @param jupyterfilepath The Jupyter file path, if applicable.
      */
     public void init(BufferedReader in, String token, String history_id, String lang, String jupyterfilepath) {
-        log.info("LocalSessionOutput created");
+        log.info("LocalSessionOutput created for token "+ token);
         this.in = in;
         this.token = token;
         this.run = true;
@@ -96,21 +97,19 @@ public void stop() {
      * @param msg The message to be sent to the WebSocket.
      */
     public void sendMessage2WebSocket(String msg) {
-        if (!BaseTool.isNull(wsout)) {
-            synchronized (wsout) {
-                try {
-                    if (wsout.isOpen()) {
-                        wsout.getBasicRemote().sendText(msg);
-                    } else {
-                        log.debug("WebSocket is closed, message didn't send: " + msg);
-                    }
-                } catch (Exception e) {
-                    e.printStackTrace();
-                    log.debug("Exception happens, message didn't send: " + msg);
+        try {
+            this.wsout = CommandServlet.findSessionById(token);
+            if (!BaseTool.isNull(wsout)){
+                if(wsout.isOpen()) {
+                    wsout.getBasicRemote().sendText(msg);
+                }else{
+                    CommandServlet.removeSessionById(token);
                 }
+            }else{
+                log.warn(String.format("cannot find websocket for token %s", token));
             }
-        } else {
-            log.debug("WebSocket is null, message didn't send: " + msg);
+        } catch (IOException e1) {
+            e1.printStackTrace();
         }
     }
 
@@ -162,7 +161,7 @@ public void endWithCode(String token, int exitvalue) {
 
 		ht.saveHistory(h);
 
-		CommandServlet.sendMessageToSocket(token, "Exit Code: " + exitvalue);
+		this.sendMessage2WebSocket("Exit Code: " + exitvalue);
 	}
 
 	/**
@@ -248,7 +247,7 @@ public void run() {
 			this.updateStatus("Running", "Running");
 
 			// Send a message to the WebSocket indicating that the process has started
-			CommandServlet.sendMessageToSocket(token, "Process " + this.history_id + " Started");
+			this.sendMessage2WebSocket("Process " + this.history_id + " Started");
 
 			String line = null; // Initialize a variable to store each line of output
 
@@ -265,7 +264,7 @@ public void run() {
 					}
 
 					linenumber++; // Increment the line number
-					
+
 					if(linenumber%1==0){
 						this.updateStatus(logs.toString(), "Running");
 					}
@@ -297,16 +296,15 @@ public void run() {
 					} else if (line.contains("==== Geoweaver Bash Output Finished ====")) {
 						// Handle specific marker lines if present
 					} else {
-						log.info("Local thread output >> " + line); // Log each line of output
+						log.info("Local thread output >> " + line + " - token: " + token); // Log each line of output
 						logs.append(line).append("\n"); // Append the line to the logs
 
 						if (!BaseTool.isNull(wsout) && wsout.isOpen()) {
 							if (prelog.toString() != null) {
 								line = prelog.toString() + line;
 								prelog = new StringBuffer();
 							}
-							//this.sendMessage2WebSocket(line); // Send the line to the WebSocket
-							CommandServlet.sendMessageToSocket(token, line);
+							this.sendMessage2WebSocket(line);
 						} else {
 							prelog.append(line).append("\n"); // Append to the prelog if WebSocket isn't available
 						}
@@ -344,7 +342,7 @@ public void run() {
 			}
 
 			// Send a message to the WebSocket indicating that the process has finished
-			CommandServlet.sendMessageToSocket(token, "The process " + history_id + " is finished.");
+			this.sendMessage2WebSocket("The process " + history_id + " is finished.");
 
 			// This thread will end by itself when the task is finished; you don't have to close it manually
 			GeoweaverController.sessionManager.closeByToken(token); // Close the session by token
@@ -355,7 +353,7 @@ public void run() {
 			// Depending on the language, update the status to "Failed"
 			this.updateStatus(logs.toString() + "\n" + e.getLocalizedMessage(), "Failed");
 		} finally {
-			CommandServlet.sendMessageToSocket(token, "======= Process " + this.history_id + " ended");
+			this.sendMessage2WebSocket("======= Process " + this.history_id + " ended");
 		}
 	}
 

src/main/java/com/gw/server/CommandServlet.java

@@ -241,7 +241,7 @@ public static javax.websocket.Session findSessionById(String token) {
      * @param token   The token of the target WebSocket session.
      * @param message The message to be sent.
      */
-    public static void sendMessageToSocket(String token, String message) {
+    public static Session sendMessageToSocket(String token, String message) {
         try {
             Session wsout = CommandServlet.findSessionById(token);
             if (!BaseTool.isNull(wsout)){
@@ -253,9 +253,11 @@ public static void sendMessageToSocket(String token, String message) {
             }else{
                 logger.warn(String.format("cannot find websocket for token %s", token));
             }
+            return wsout;
         } catch (IOException e1) {
             e1.printStackTrace();
         }
+        return null;
     }
 
     /**

src/main/java/com/gw/tools/ExecutionTool.java

@@ -1,9 +1,11 @@
 package com.gw.tools;
 
 import com.gw.utils.BaseTool;
+import com.gw.utils.BeanTool;
 
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Scope;
 import org.springframework.stereotype.Service;
 
@@ -14,20 +16,8 @@
 @Scope("prototype")
 public class ExecutionTool {
 
-    @Autowired
-    ProcessTool pt;
-
-	@Autowired
-	LocalhostTool lt;
-
-	@Autowired
-	RemotehostTool rt;
-
     @Autowired
     BaseTool bt;
-
-	@Autowired
-	EnvironmentTool envt;
 
 	@Autowired
 	TaskManager tm;
@@ -51,6 +41,8 @@ public String executeProcess(String history_id, String id, String hid, String ps
 
 		String bin = null, pyenv = null, basedir = null;
 
+		EnvironmentTool envt = BeanTool.getBean(EnvironmentTool.class);
+
 		Environment envobj = envt.getEnvironmentById(envid);
 
 		if(!BaseTool.isNull(envobj)){
@@ -85,6 +77,7 @@ public String executeProcess(String history_id, String id, String hid, String ps
 	public String executeProcess(String history_id, String id, String hid, String pswd, String httpsessionid, 
     boolean isjoin, String bin, String pyenv, String basedir) {
 
+		ProcessTool pt = BeanTool.getBean(ProcessTool.class);
 
         String category = pt.getTypeById(id);
 
@@ -95,6 +88,8 @@ public String executeProcess(String history_id, String id, String hid, String ps
         if(BaseTool.isNull(basedir)) basedir = "~";
 
         if(bt.islocal(hid)) {
+
+			LocalhostTool lt = BeanTool.getBean(LocalhostTool.class);
 
             //localhost
             if("shell".equals(category)) {
@@ -123,6 +118,7 @@ public String executeProcess(String history_id, String id, String hid, String ps
         }else {
 
             //non-local remote server
+			RemotehostTool rt = BeanTool.getBean(RemotehostTool.class);
 
             if("shell".equals(category)) {
 
@@ -166,10 +162,14 @@ public String readEnvironment(String hid, String password){
 
 		if(bt.islocal(hid)){
 
+			LocalhostTool lt = BeanTool.getBean(LocalhostTool.class);
+
 			resp = lt.readPythonEnvironment(hid, password);
 
 		}else{
 
+			RemotehostTool rt = BeanTool.getBean(RemotehostTool.class);
+
 			resp = rt.readPythonEnvironment(hid, password);
 
 		}

src/main/java/com/gw/tools/LocalhostTool.java

@@ -13,6 +13,7 @@
 import com.gw.tasks.GeoweaverProcessTask;
 import com.gw.tasks.TaskManager;
 import com.gw.utils.BaseTool;
+import com.gw.utils.BeanTool;
 import com.gw.utils.OSValidator;
 import com.gw.web.GeoweaverController;
 
@@ -62,12 +63,6 @@ public class LocalhostTool {
 	@Autowired
 	ProcessRepository processrepository;
 
-	@Autowired
-	LocalSessionNixImpl nixsession;
-
-	@Autowired
-	LocalSessionWinImpl winsession;
-
 	public void saveHistory(String processid, String script, String history_id){
 
 		History history = histool.getHistoryById(history_id);
@@ -182,11 +177,11 @@ public LocalSession getLocalSession() {
 
 		if(OSValidator.isWindows()) {
 
-			session = winsession;
+			session = BeanTool.getBean(LocalSessionWinImpl.class);
 
 		}else if(OSValidator.isMac() || OSValidator.isUnix()) {
 
-			session = nixsession;
+			session = BeanTool.getBean(LocalSessionNixImpl.class);
 
 		}else {
 

src/main/java/com/gw/tools/WorkflowTool.java

@@ -340,7 +340,7 @@ public String execute(String history_id, String wid, String mode,
 		try {
 
 			task.initialize(history_id, wid, mode, hosts, pswds, envs, token);
-
+			
 			task.execute();
 
 			resp = "{\"history_id\": \""+task.getHistory_id()+

src/main/java/com/gw/utils/BeanTool.java

@@ -5,26 +5,45 @@
 import org.springframework.context.ApplicationContextAware;
 import org.springframework.stereotype.Component;
 
+/**
+ * BeanTool is a utility class designed to interact with Spring Application Context for bean management.
+ * It provides methods to access beans and the application context within a Spring application.
+ */
 @Component
 public class BeanTool implements ApplicationContextAware {
-
-	private static ApplicationContext context;
+
+    // The application context is set by Spring when this class is ApplicationContextAware.
+    private static ApplicationContext context;
 
-	@Override
-	public void setApplicationContext(ApplicationContext applicationContext) throws BeansException {
-
-		context = applicationContext;
-
-	}
-
-	public static ApplicationContext getApplicationContext() {
-		return context;
- 	}
-
-	public static <T extends Object> T getBean(Class<T> beanClass) {
-
-        return context.getBean(beanClass);
+    /**
+     * Called by Spring to set the application context for this class.
+     *
+     * @param applicationContext The Spring application context.
+     * @throws BeansException If an error occurs while setting the application context.
+     */
+    @Override
+    public void setApplicationContext(ApplicationContext applicationContext) throws BeansException {
+        context = applicationContext;
     }
-
 
+    /**
+     * Get the current Spring Application Context.
+     *
+     * @return The Spring Application Context.
+     */
+    public static ApplicationContext getApplicationContext() {
+        return context;
+    }
+
+    /**
+     * Get a bean of the specified class from the Spring Application Context.
+     *
+     * @param <T>       The type of the bean to retrieve.
+     * @param beanClass The class of the bean to retrieve.
+     * @return An instance of the specified bean class.
+     */
+    public static <T extends Object> T getBean(Class<T> beanClass) {
+        return context.getBean(beanClass);
+    }
 }
+

src/main/resources/static/js/gw.js

@@ -9,7 +9,7 @@ edu = {
 
 					sponsor: "ESIPLab incubator project, NASA ACCESS project, NSF Geoinformatics project, NSF Cybertraining project",
 
-					version: "1.2.0",
+					version: "1.2.1",
 
 					author: "open source contributors",