more class loading issues CompEvol#834

rbouckaert · Apr 5, 2022 · bb5bccf · bb5bccf
1 parent efd769c
commit bb5bccf
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Showing 5 changed files with 65 additions and 8 deletions.
diff --git a/beast.base/version.xml b/beast.base/version.xml
@@ -69,6 +69,26 @@
                 <provider classname="beast.base.evolution.operator.kernel.BactrianScaleOperator"/>
                 <provider classname="beast.base.evolution.operator.kernel.BactrianSubtreeSlide"/>
                 <provider classname="beast.base.evolution.operator.kernel.BactrianTipDatesRandomWalker"/>
+
+                <provider classname="beast.base.inference.operator.kernel.Transform$Array"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$Collection"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$Compose"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$ComposeMultivariable"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$FisherZTransform"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$Inverse"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$InverseMultivariate"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$LogConstrainedSumTransform"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$LogTransform"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$LogitTransform"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$MultivariableTransformWithParameter"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$MultivariateTransform"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$NegateTransform"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$NoTransform"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$NoTransformMultivariable"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$ParsedTransform"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$PositiveOrdered"/>
+                <provider classname="beast.base.inference.operator.kernel.Transform$PowerTransform"/>
+
                 <provider classname="beast.base.evolution.sitemodel.SiteModel"/>
                 <provider classname="beast.base.evolution.speciation.BirthDeathGernhard08Model"/>
                 <provider classname="beast.base.evolution.speciation.CalibratedBirthDeathModel"/>

diff --git a/beast.pkgmgmt/src/beast/pkgmgmt/BEASTClassLoader.java b/beast.pkgmgmt/src/beast/pkgmgmt/BEASTClassLoader.java
@@ -75,7 +75,7 @@ public void addParent(String packageName, String parentPackage) {
     		}
 	    	MultiParentURLClassLoader loader = getClassLoader(packageName);
 	    	MultiParentURLClassLoader parentLoader = getClassLoader(parentPackage);
-	    	loader.addParentLoader(parentLoader);
+	    	loader.addParentLoader(parentLoader);	    	
 	    }
 
 	    /** dynamically load jars **/
@@ -106,12 +106,15 @@ public void addJar(String jarFile, String packageName) {
 	     *  The latter won't work for loading classes from packages from BEAST v2.6.0 onwards. 
 	     * **/
 		public static Class<?> forName(String className) throws ClassNotFoundException {
+			// System.err.println("forName: " + className);
+
 			if (class2loaderMap.containsKey(className)) {
 				ClassLoader loader = class2loaderMap.get(className);
+				// System.err.println("class2loaderMap " + loader.toString());
 				return Class.forName(className, false, loader);
 			}
 
-//			System.err.println("Loading non-service: " + className);
+			// System.err.println("Loading non-service: " + className);
 			for (MultiParentURLClassLoader loader : package2classLoaderMap.values()) {
 				try { 
 					// System.err.println("Trying to load "+className+" using " + loader.name);
@@ -123,13 +126,17 @@ public static Class<?> forName(String className) throws ClassNotFoundException {
 
 			try { 
 				// System.err.println("Trying to load using BEASTClassLoader.classLoader");
-				return Class.forName(className, false, BEASTClassLoader.classLoader);
+				Class<?> c = Class.forName(className, false, BEASTClassLoader.classLoader);
+				// System.err.println("Loading from " + c.getProtectionDomain().getCodeSource().getLocation());
+				return c;
 			} catch (NoClassDefFoundError e) {
 				throw new ClassNotFoundException(e.getMessage());
 			}
 		}	
 
 		public static Class<?> forName(String className, String service) throws ClassNotFoundException {
+			// System.err.println("forName: " + className + " " + service);
+
 			if (!services.containsKey(service)) {
 				if (services.size() == 0) {
 					services.put(service, new HashSet<>());

diff --git a/beast.pkgmgmt/src/beast/pkgmgmt/MultiParentURLClassLoader.java b/beast.pkgmgmt/src/beast/pkgmgmt/MultiParentURLClassLoader.java
@@ -99,6 +99,32 @@ public Class<?> forName(String className) throws ClassNotFoundException {
 		}
 	}
 
+    @Override
+    public Class<?> loadClass(String name) throws ClassNotFoundException {
+    	System.err.println("MPCL: load class " + name + " " + this.name);
+		try {
+			return loadClass(name, false);
+		} catch (NoClassDefFoundError | ClassNotFoundException e) {
+			// ignore -- try the next class loader instead
+		}
+
+		// no luck trying the parents
+		for (ClassLoader parentLoader : parentLoaders) {			
+			try {
+				Class<?> c =  parentLoader.loadClass(name);
+				if (c != null) {
+					return c;
+				}
+			} catch (NoClassDefFoundError e) {
+				// ignore -- try the next class loader instead
+			}			
+		}
+
+		System.err.println("MPCL: giving up " + name + " " + this.name);
+
+		throw new NoClassDefFoundError(name);
+    }
+
     @Override
     public String toString() {
     	return super.toString() +"["+ name + "]";

diff --git a/beast.pkgmgmt/src/beast/pkgmgmt/PackageManager.java b/beast.pkgmgmt/src/beast/pkgmgmt/PackageManager.java
@@ -763,13 +763,13 @@ public static String getPackageSystemDir() {
 
     /**
      * Returns directory where BEAST installation resides, based on the location of the jar containing the
-     * BeastMain class file.  This assumes that the parent directory of the beast.jar is the base install
+     * beast.pkgmgmt.PackageManager class file.  This assumes that the parent directory of the launcher.jar is the base install
      * directory.
      *
      * @return string representation of BEAST install directory or null if this directory cannot be identified.
      */
     public static String getBEASTInstallDir() {
-    	return getInstallDir(BEAST_PACKAGE_NAME, "beast.app.beastapp.BeastMain");
+    	return getInstallDir(BEAST_PACKAGE_NAME, "beast.pkgmgmt.PackageManager");
 
     }
 

diff --git a/beast.pkgmgmt/src/beast/pkgmgmt/launcher/BeastLauncher.java b/beast.pkgmgmt/src/beast/pkgmgmt/launcher/BeastLauncher.java
@@ -675,14 +675,18 @@ public static void run(String classPath, String main, String[] args) {
 	        		System.err.println("WARNING: arg1 the first argument, arg2, the second, etc.");
 	        	}
 	        }            
-           	        	     
+
 			for (String jarFileName : classPath.substring(1, classPath.length() - 1).split(File.pathSeparator)) {
-				if (jarFileName.toLowerCase().endsWith("jar")) {
+				if (jarFileName.toLowerCase().endsWith("base.jar")) {
 					File jarFile = new File(jarFileName);
 					BEASTClassLoader.classLoader.addURL(jarFile.toURI().toURL(), "BEAST.base", null);
 				}
+				if (jarFileName.toLowerCase().endsWith("app.jar")) {
+					File jarFile = new File(jarFileName);
+					BEASTClassLoader.classLoader.addURL(jarFile.toURI().toURL(), "BEAST.app", null);
+				}
 			}
-
+			BEASTClassLoader.classLoader.addParent("BEAST.app", "BEAST.base");
 			BEASTClassLoader.initServices(classPath);
 
 			Class<?> mainClass = BEASTClassLoader.forName(main);