Added StackTraceUtils (renaming misnamed StackTraceUtilsTest in the p…

…rocess)

vcell-core/src/main/java/cbit/vcell/resource/ErrorUtils.java

@@ -16,7 +16,7 @@
 import org.apache.http.ssl.SSLContextBuilder;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.vcell.util.BeanUtils;
+import org.vcell.util.StackTraceUtils;
 import org.vcell.util.document.UserLoginInfo;
 import org.vcell.util.document.VCellSoftwareVersion;
 
@@ -71,7 +71,7 @@ public ErrorReport(String username, String message, String exceptionMessage, Str
 	public static void sendErrorReport(Throwable exception, String message) throws RuntimeException {
 		String softwareVersion = PropertyLoader.getRequiredProperty(PropertyLoader.vcellSoftwareVersion);
 		String exceptionMessage = exception!=null ? exception.getMessage() : "null";
-		String stackTrace = exception!=null ? BeanUtils.getStackTrace(exception) : "null";
+		String stackTrace = exception!=null ? StackTraceUtils.getStackTrace(exception) : "null";
 		String platform = "Running under Java "+(System.getProperty("java.version"))+
 			", published by "+(System.getProperty("java.vendor"))+", on the "+ (System.getProperty("os.arch"))+" architecture running version "+(System.getProperty("os.version"))+
 			" of the "+(System.getProperty("os.name"))+" operating system";

vcell-core/src/main/java/cbit/vcell/resource/LibraryLoaderThread.java

@@ -4,7 +4,7 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.vcell.util.BeanUtils;
+import org.vcell.util.StackTraceUtils;
 
 /**
  * Start and monitor Monitor library loading in thread, show error message when done
@@ -47,7 +47,7 @@ public void run() {
 				}
 				sb.append(librarySet);
 				sb.append(":  ");
-				sb.append(BeanUtils.getMessageRecursive(e));
+				sb.append(StackTraceUtils.getMessageRecursive(e));
 				sb.append(newline);
 				if (isGui){
 					ErrorUtils.sendErrorReport(e, sb.toString());

vcell-util/src/main/java/org/vcell/util/BeanUtils.java

@@ -16,9 +16,7 @@
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
-import java.io.PrintWriter;
 import java.io.Serializable;
-import java.io.StringWriter;
 import java.math.BigDecimal;
 import java.net.InetSocketAddress;
 import java.net.URL;
@@ -30,7 +28,6 @@
 import javax.mail.MessagingException;
 import javax.mail.Session;
 import javax.mail.Transport;
-import javax.mail.internet.AddressException;
 import javax.mail.internet.InternetAddress;
 import javax.mail.internet.MimeMessage;
 import javax.net.ssl.HttpsURLConnection;
@@ -49,7 +46,6 @@
 import org.jboss.netty.handler.codec.http.HttpRequest;
 import org.jboss.netty.handler.codec.http.HttpVersion;
 
-import edu.uchc.connjur.wb.ExecutionTrace;
 /**
  * Insert the type's description here.
  * Creation date: (8/18/2000 2:29:31 AM)
@@ -206,47 +202,6 @@ public static boolean triggersPropertyChangeEvent(Object a, Object b) {
 		return (a == null || !a.equals(b));
 	}
 
-	public static String getStackTrace(Throwable throwable) {
-		StringWriter out = new StringWriter();
-		PrintWriter pw = new PrintWriter(out);
-		Throwable t = throwable;
-		while (t != null) {
-			t.printStackTrace(pw);
-			t = t.getCause( );
-		}
-		pw.close();
-		return out.getBuffer().toString();
-	}
-
-	/**
-	 * @return String for current stack trace
-	 */
-	public static String getStackTrace() {
-		StackTraceElement[] stackTraceArray = Thread.currentThread().getStackTrace();
-		StringBuilder sb = new StringBuilder();
-		//0 and 1 are "getStackTrace" -- start with callers invocation
-		for (int i = 2; i < stackTraceArray.length; i++) {
-			sb.append(stackTraceArray[i]);
-			sb.append('\n');
-		}
-		return sb.toString();
-	}
-	/**
-	 * recursive assemble exception message
-	 * @param throwable exception / error to recursively get the message from
-	 * @return {@link Throwable#getMessage()}, recursively
-	 */
-	public static String getMessageRecursive(Throwable throwable) {
-		StringBuilder rval = new StringBuilder(throwable.getMessage());
-		Throwable cause = throwable.getCause();
-		while (cause != null) {
-			rval.append(" caused by ").append(cause.getMessage());
-			cause = cause.getCause();
-		}
-
-		return rval.toString();
-	}
-
 
 	public static void sendSMTP(String smtpHost, int smtpPort,String from, String to,String subject, String content)
 			throws MessagingException {

vcell-util/src/main/java/org/vcell/util/StackTraceUtils.java

@@ -0,0 +1,48 @@
+package org.vcell.util;
+
+import java.io.PrintWriter;
+import java.io.StringWriter;
+
+public class StackTraceUtils {
+    public static String getStackTrace(Throwable throwable) {
+        StringWriter out = new StringWriter();
+        PrintWriter pw = new PrintWriter(out);
+        Throwable t = throwable;
+        while (t != null) {
+            t.printStackTrace(pw);
+            t = t.getCause( );
+        }
+        pw.close();
+        return out.getBuffer().toString();
+    }
+
+    /**
+     * @return String for current stack trace
+     */
+    public static String getStackTrace() {
+        StackTraceElement[] stackTraceArray = Thread.currentThread().getStackTrace();
+        StringBuilder sb = new StringBuilder();
+        //0 and 1 are "getStackTrace" -- start with callers invocation
+        for (int i = 2; i < stackTraceArray.length; i++) {
+            sb.append(stackTraceArray[i]);
+            sb.append('\n');
+        }
+        return sb.toString();
+    }
+
+    /**
+     * recursive assemble exception message
+     * @param throwable exception / error to recursively get the message from
+     * @return {@link Throwable#getMessage()}, recursively
+     */
+    public static String getMessageRecursive(Throwable throwable) {
+        StringBuilder rval = new StringBuilder(throwable.getMessage());
+        Throwable cause = throwable.getCause();
+        while (cause != null) {
+            rval.append(" caused by ").append(cause.getMessage());
+            cause = cause.getCause();
+        }
+
+        return rval.toString();
+    }
+}

vcell-util/src/test/java/org/vcell/util/BeanUtilsTest.java

@@ -2,16 +2,12 @@
 
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.concurrent.TimeUnit;
 
-import org.junit.Assert;
 import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.vcell.test.Fast;
 
-import static org.junit.Assert.*;
-
 @Category(Fast.class)
 public class BeanUtilsTest {
 
@@ -22,7 +18,7 @@ public class BeanUtilsTest {
 	private void miney() {mo();}
 
 	private void mo( ) {
-		System.out.println(BeanUtils.getStackTrace());
+		System.out.println(StackTraceUtils.getStackTrace());
 	}
 
 	@Ignore

vcell-util/src/test/java/org/vcell/util/StackTraceUtilsTest.java

@@ -0,0 +1,4 @@
+package org.vcell.util;
+
+public class StackTraceUtilsTest {
+}