fix some code to make unit tests pass CompEvol#834

rbouckaert · Apr 4, 2022 · 7aa04ed · 7aa04ed
1 parent cc12546
commit 7aa04ed
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Showing 10 changed files with 29 additions and 12 deletions.
diff --git a/beast.app/src/beast/app/draw/Document.java b/beast.app/src/beast/app/draw/Document.java
@@ -105,7 +105,7 @@ boolean sanitiseIDs() {
 
     public Document() {
         // load all parsers
-        Set<String> plugInNames = BEASTClassLoader.listServices("beast.base.core.BEASTInterface");
+        Set<String> plugInNames = PackageManager.listServices("beast.base.core.BEASTInterface");
         m_sPlugInNames = plugInNames.toArray(new String[0]);
         tabulist = new HashSet<>();
         Properties properties = new Properties();

diff --git a/beast.app/src/beast/app/tools/DocMaker.java b/beast.app/src/beast/app/tools/DocMaker.java
@@ -95,7 +95,7 @@ public DocMaker(String[] args) {
 
     public DocMaker() {
         // find plug ins to document
-        m_beastObjectNames = BEASTClassLoader.listServices("beast.base.core.BEASTInterface");
+        m_beastObjectNames = PackageManager.listServices("beast.base.core.BEASTInterface");
         /** determine hierarchical relation between plug-ins **/
         m_isa = new HashMap<>();
         m_ancestors = new HashMap<>();

diff --git a/beast.app/test/test/beast/integration/DocumentationTest.java b/beast.app/test/test/beast/integration/DocumentationTest.java
@@ -29,7 +29,7 @@ public class DocumentationTest extends TestCase {
      */
     @Test
     public void testDescriptions() {
-        final Set<String> pluginNames = BEASTClassLoader.listServices("beast.base.core.BEASTInterface");
+        final Set<String> pluginNames = PackageManager.listServices("beast.base.core.BEASTInterface");
         final List<String> undocumentedPlugins = new ArrayList<String>();
         for (final String beastObjectName : pluginNames) {
             try {
@@ -60,7 +60,7 @@ public void testDescriptions() {
      */
     @Test
     public void testInputTipText() {
-        final Set<String> pluginNames = BEASTClassLoader.listServices("beast.base.core.BEASTInterface");
+        final Set<String> pluginNames = PackageManager.listServices("beast.base.core.BEASTInterface");
         final List<String> undocumentedInputs = new ArrayList<String>();
         for (final String beastObjectName : pluginNames) {
             try {

diff --git a/beast.app/test/test/beast/integration/InputTypeTest.java b/beast.app/test/test/beast/integration/InputTypeTest.java
@@ -32,7 +32,7 @@ public class InputTypeTest extends TestCase {
 	 */
 	@Test
 	public void testInputTypeCanBeSet() throws Exception {
-		final Set<String> beastObjectNames = BEASTClassLoader.listServices("beast.base.core.BEASTInterface");
+		final Set<String> beastObjectNames = PackageManager.listServices("beast.base.core.BEASTInterface");
 		List<String> failingInputs = new ArrayList<String>();
 		for (String beastObjectName : beastObjectNames) {
 			try {
@@ -63,7 +63,7 @@ public void testInputTypeCanBeSet() throws Exception {
 
 	@Test
 	public void testAnnotatedInputHasGetters() throws Exception {
-		final Set<String> beastObjectNames = BEASTClassLoader.listServices("beast.base.core.BEASTInterface");
+		final Set<String> beastObjectNames = PackageManager.listServices("beast.base.core.BEASTInterface");
 		System.err.println("Testing " + beastObjectNames.size() + " classes");
 		List<String> failingInputs = new ArrayList<String>();
 		for (String beastObject : beastObjectNames) {

diff --git a/beast.app/test/test/beast/integration/XMLElementNameTest.java b/beast.app/test/test/beast/integration/XMLElementNameTest.java
@@ -23,7 +23,7 @@ public class XMLElementNameTest extends TestCase {
      */
     @Test
     public void test_NameUniqueness() {
-		final Set<String> pluginNames = BEASTClassLoader.listServices("beast.base.core.BEASTInterface");
+		final Set<String> pluginNames = PackageManager.listServices("beast.base.core.BEASTInterface");
         List<String> improperInputs = new ArrayList<String>();
         for (String beastObjectName : pluginNames) {
             try {
@@ -67,7 +67,7 @@ public void test_ReservedElementNames() {
         element2ClassMap.put("parameter", "beast.core.parameter.Parameter");
 
         // check each beastObject
-		final Set<String> pluginNames = BEASTClassLoader.listServices("beast.base.core.BEASTInterface");
+		final Set<String> pluginNames = PackageManager.listServices("beast.base.core.BEASTInterface");
         List<String> improperInputs = new ArrayList<String>();
         for (String beastObjectName : pluginNames) {
             try {

diff --git a/beast.app/test/test/beast/util/XMLParserTest.java b/beast.app/test/test/beast/util/XMLParserTest.java
@@ -46,7 +46,7 @@ public void testClassMap() throws IOException {
 
     	// create new version.xml
     	PrintStream out = new PrintStream(new File(versionFile));
-    	out.println("<package name='BEAST' version='" + new BEASTVersion().getVersion() + "'>");
+    	out.println("<package name='BEAST.base' version='" + new BEASTVersion().getVersion() + "'>");
     	out.println("<map from='beast.base.evolution.substitutionmodel.JoMamma' to='beast.base.evolution.substitutionmodel.JukesCantor'/>");
     	out.println("</package>");
     	out.close();

diff --git a/beast.base/src/beast/base/parser/XMLParser.java b/beast.base/src/beast/base/parser/XMLParser.java
@@ -941,6 +941,9 @@ BEASTInterface createObject(final Node node, final String classname) throws XMLP
 
 		// sanity check		
 		try {
+        	if (oldClass2ClassMap.containsKey(clazzName)) {
+        		clazzName = oldClass2ClassMap.get(clazzName);
+        	}
 			Class<?> clazz = BEASTClassLoader.forName(clazzName, BEASTInterface.class.getName());
 			if (!BEASTInterface.class.isAssignableFrom(clazz)) {
 				// throw new XMLParserException(node, "Expected object to be instance of BEASTObject", 108);

diff --git a/beast.base/src/beast/base/parser/XMLParserUtils.java b/beast.base/src/beast/base/parser/XMLParserUtils.java
@@ -40,7 +40,7 @@
  */
 public class XMLParserUtils {
 
-	final static public Set<String> beastObjectNames = BEASTClassLoader.listServices("beast.base.core.BEASTInterface");
+	final static public Set<String> beastObjectNames = PackageManager.listServices("beast.base.core.BEASTInterface");
 
     /**
      * Expand plates in XML by duplicating the containing XML and replacing

diff --git a/beast.pkgmgmt/src/beast/pkgmgmt/BEASTClassLoader.java b/beast.pkgmgmt/src/beast/pkgmgmt/BEASTClassLoader.java
@@ -225,8 +225,8 @@ private static void addServices(String versionFile) {
 			}
 		}	
 
-		public static Set<String> listServices(String service) {
-			return BEASTClassLoader.services.get(service);
+		public static Map<String, Set<String>> getServices() {			
+			return services;
 		}
 
 		public void addServices(String packageName, Map<String, Set<String>> services) {

diff --git a/beast.pkgmgmt/src/beast/pkgmgmt/PackageManager.java b/beast.pkgmgmt/src/beast/pkgmgmt/PackageManager.java
@@ -1300,6 +1300,20 @@ public static Map<String, Set<String>> parseServices(Document doc) {
 		return serviceMap;
 	}
 
+
+	public static Set<String> listServices(String service) {
+		Set<String> services = BEASTClassLoader.getServices().get(service);
+		if (services == null) {
+			try {
+				loadExternalJars();
+			} catch (IOException e) {
+				// ignore
+			}
+		}
+		services = BEASTClassLoader.getServices().get(service);
+		return services;
+	}
+
 	/**
      * Populate given map with versions of packages to install which satisfy dependencies
      * of those already present.