fix ExtManager after merging SPI and loaders #400

LinguaPhylo · Dec 8, 2023 · a78e6af · a78e6af
1 parent 59fe48d
commit a78e6af
Show file tree

Hide file tree

Showing 11 changed files with 51 additions and 30 deletions.
diff --git a/lphy-studio/src/main/java/lphystudio/app/ExtManagerApp.java b/lphy-studio/src/main/java/lphystudio/app/ExtManagerApp.java
@@ -11,7 +11,7 @@
  */
 public class ExtManagerApp extends JFrame {
 
-    public static final String APP_NAME = "Extension Manager";
+    public static final String APP_NAME = "LPhyExtension Manager";
     static {
         LPhyAppConfig.setupEcoSys(APP_NAME);
     }

diff --git a/lphy-studio/src/main/java/lphystudio/app/docgenerator/GenerateDocs.java b/lphy-studio/src/main/java/lphystudio/app/docgenerator/GenerateDocs.java
@@ -59,7 +59,7 @@ public static void main(String[] args) throws IOException {
         // Do not change default
         String extName = LPHY_DOC_TITLE;
         // for extension only, e.g.
-        // args = 0.0.5 "LPhy Extension Phylonco" phylonco.lphy.spi.Phylonco
+        // args = 0.0.5 "LPhy LPhyExtension Phylonco" phylonco.lphy.spi.Phylonco
         // set WD = ~/WorkSpace/beast-phylonco/PhyloncoL/doc
         if (args.length > 2)  {
             extName = args[1];

diff --git a/lphy-studio/src/main/java/lphystudio/app/manager/Dependency.java b/lphy-studio/src/main/java/lphystudio/app/manager/Dependency.java
@@ -6,7 +6,7 @@
  * Data class maps to pom.xml {@code <dependency>}.
  * @author Walter Xie
  */
-public class Dependency {
+public class Dependency implements Comparable<Dependency> {
 
     private String groupId;
     private String artifactId;
@@ -51,6 +51,26 @@ public String toString() {
         return groupId + ':' + artifactId + ':' + version;
     }
 
+    @Override
+    public int compareTo(Dependency other) {
+        // Handle null cases to avoid NullPointerException
+        if (other == null) {
+            return 1; // Consider non-null greater than null
+        }
+
+        // Concatenate the fields for comparison
+        String thisKey = getDependencyId().toLowerCase();
+        String otherKey = other.getDependencyId().toLowerCase();
+
+        // Compare the concatenated strings
+        return thisKey.compareTo(otherKey);
+    }
+
+    public String getDependencyId() {
+        return groupId + artifactId + version;
+    }
+
+
     //    public String getScope() {
 //        return scope;
 //    }

diff --git a/lphy-studio/src/main/java/lphystudio/app/manager/DependencyUtils.java b/lphy-studio/src/main/java/lphystudio/app/manager/DependencyUtils.java
@@ -65,7 +65,7 @@ public static String getVersion(Class<?> cls, String propertyKey) { // TODO retu
             // if not, then try pom.xml
             if (version == null) {
                 try {
-                    Extension lphyExt = getExtensionFrom(module);
+                    LPhyExtension lphyExt = getExtensionFrom(module);
                     if (lphyExt != null) {
                         version = lphyExt.getVersion();
                     }
@@ -89,10 +89,12 @@ public static String getVersion(Class<?> cls, String propertyKey) { // TODO retu
     }
 
     /**
-     * @param module  the Java {@link Module} contains the classes of the {@link Extension}.
-     * @return  an {@link Extension} created from pom.xml, or from MANIFEST.MF, or from source
+     * This could extract the same LPhyExtension multiple times,
+     * because the Extension SPI can be multiple in the same LPhyExtension.
+     * @param module  the Java {@link Module} contains the classes of the {@link LPhyExtension}.
+     * @return  an {@link LPhyExtension} created from pom.xml, or from MANIFEST.MF, or from source
      */
-    public static Extension getExtensionFrom(Module module)
+    public static LPhyExtension getExtensionFrom(Module module)
             throws IOException, ParserConfigurationException, SAXException {
         // 1. first look for pom.xml in jar
         InputStream in = module.getResourceAsStream(POM_XML_LOCATION);
@@ -110,7 +112,7 @@ public static Extension getExtensionFrom(Module module)
                 String version = attr.getValue("Implementation-Version");
                 System.out.println(", extract meta-data from MANIFEST.MF");
 
-                return new Extension("", name, version);
+                return new LPhyExtension("", name, version);
             }
         }
 
@@ -141,7 +143,7 @@ public static Extension getExtensionFrom(Module module)
         // 4. unknown
         if (in == null) {
             System.err.println("Warning : cannot find extension information from module " + module.getName() + " !");
-            return new Extension("", module.getName(), "unknown");
+            return new LPhyExtension("", module.getName(), "unknown");
         }
 //               String pom = new String(in.readAllBytes(), StandardCharsets.UTF_8);
 //               System.out.println(pom);

diff --git a/lphy-studio/src/main/java/lphystudio/app/manager/ExtManager.java b/lphy-studio/src/main/java/lphystudio/app/manager/ExtManager.java
@@ -37,10 +37,10 @@ public ExtManager()  {
 
     /**
      * Find loaded LPhy extensions from loaded modular jars.
-     * @return  a list of {@link Extension}
+     * @return  a list of {@link LPhyExtension}
      */
-    public List<Extension> getLoadedLPhyExts() {
-        List<Extension> extList = new ArrayList<>();
+    public List<LPhyExtension> getLPhyExtensions() {
+        Set<LPhyExtension> extSet = new TreeSet<>();
 
         // find all loaded lphy exts
         for (lphy.core.spi.Extension ext : extensions) {
@@ -57,26 +57,25 @@ public List<Extension> getLoadedLPhyExts() {
             // use module path
             if (module != null) {
                 try {
-                    Extension lphyExt = DependencyUtils.getExtensionFrom(module);
-                    extList.add(lphyExt);
+                    LPhyExtension lphyExt = DependencyUtils.getExtensionFrom(module);
+                    extSet.add(lphyExt);
                 } catch (ParserConfigurationException | SAXException | IOException e) {
                     e.printStackTrace();
                 }
             } else { // use class path
 //                URL jarURL = cls.getResource(pkgNm);
 //                jarURL = cls.getResource(pkgNm);
-//                Extension lphyExt = new Extension(jarURL);
+//                LPhyExtension lphyExt = new LPhyExtension(jarURL);
 //                extList.add(lphyExt);
                 throw new UnsupportedOperationException("Do not support class path ! Please use module path.");
             }
 
         }
 
-        // sort by ext artifactId
-        extList.sort(Comparator.comparing(Extension::getArtifactId));
+        List<LPhyExtension> extList = new ArrayList<>(extSet);
         // pin lphy on the top
         for (int i = 0; i < extList.size(); i++) {
-            Extension ext = extList.get(i);
+            LPhyExtension ext = extList.get(i);
             if (LPHY_ID.equalsIgnoreCase(ext.getArtifactId())) {
                 extList.add(0, extList.remove(i));
             }

diff --git a/lphy-studio/src/main/java/lphystudio/app/manager/ExtManagerPanel.java b/lphy-studio/src/main/java/lphystudio/app/manager/ExtManagerPanel.java
@@ -16,7 +16,7 @@ public class ExtManagerPanel extends JPanel {
     public ExtManagerPanel(ExtManager manager) {
         this.manager = manager;
 
-        final List<Extension> extList = manager.getLoadedLPhyExts();
+        final List<LPhyExtension> extList = manager.getLPhyExtensions();
         String dirStr = manager.getJarDirStr();
         if (dirStr.trim().isEmpty())
             System.err.println("Warning: no directory is found to store lphy extensions " + dirStr);

diff --git a/lphy-studio/src/main/java/lphystudio/app/manager/ExtManagerTableModel.java b/lphy-studio/src/main/java/lphystudio/app/manager/ExtManagerTableModel.java
@@ -9,13 +9,13 @@
  */
 public class ExtManagerTableModel extends EasyTableModel {
 
-    public ExtManagerTableModel(List<Extension> extList) {
+    public ExtManagerTableModel(List<LPhyExtension> extList) {
         super(new String[]{"ID", "GroupID", "Installed", "Dependencies", "Description"}, extList);
     }
 
     @Override
     public Object getValueAt(int row, int col) {
-        Extension ext = (Extension) dataList.get(row);
+        LPhyExtension ext = (LPhyExtension) dataList.get(row);
         return switch (col) {
             case 0 -> ext.getArtifactId();
             case 1 -> ext.getGroupId();

diff --git a/...ava/lphystudio/app/manager/Extension.java → ...lphystudio/app/manager/LPhyExtension.java b/...ava/lphystudio/app/manager/Extension.java → ...lphystudio/app/manager/LPhyExtension.java
@@ -9,19 +9,19 @@
  * metadata only for the extension.
  * @author Walter Xie
  */
-public class Extension extends Dependency {
+public class LPhyExtension extends Dependency {
 
     private String name; // may be diff to artifactId
     private String desc;
     private String website;
 
     private List<Dependency> dependencies = new ArrayList<>();
 
-    public Extension() {
+    public LPhyExtension() {
         super();
     }
 
-    public Extension(String groupId, String artifactId, String version) {
+    public LPhyExtension(String groupId, String artifactId, String version) {
         super(groupId, artifactId, version);
 
     }
@@ -67,7 +67,7 @@ public void setWebsite(String website) {
      //     * @param jarURL
      * @throws FileNotFoundException
      @Deprecated
-     public Extension(URL jarURL) throws FileNotFoundException {
+     public LPhyExtension(URL jarURL) throws FileNotFoundException {
      String jarLoc = Objects.requireNonNull(jarURL).toString();
 
      if (!jarLoc.startsWith("jar:file:") || !jarLoc.contains(".jar"))

diff --git a/lphy-studio/src/main/java/lphystudio/app/manager/POMXMLHandler.java b/lphy-studio/src/main/java/lphystudio/app/manager/POMXMLHandler.java
@@ -20,7 +20,7 @@ public class POMXMLHandler extends DefaultHandler {
     public static final String DEPD_LIST = "dependencies";
     public static final String SCOPE = "scope";
 
-    private Extension extension;
+    private LPhyExtension extension;
     private StringBuffer currVal = new StringBuffer();
 
     // same tags (e.g. groupId, artifactId) in dependencies
@@ -30,14 +30,14 @@ public class POMXMLHandler extends DefaultHandler {
     private Dependency currDepd;
 
 
-    public Extension getExtension() {
+    public LPhyExtension getExtension() {
 //        System.out.println(extension.getArtifactId());
         return extension;
     }
 
     @Override
     public void startDocument() {
-        extension = new Extension();
+        extension = new LPhyExtension();
         // extension artifactId in the beginning of XML
         isDependency = false;
         dependencies = new ArrayList<>();

diff --git a/lphy-studio/src/main/java/lphystudio/spi/LPhyStudioImpl.java b/lphy-studio/src/main/java/lphystudio/spi/LPhyStudioImpl.java
@@ -9,7 +9,7 @@
 
 /**
  * TODO: it is unused now, overwrite the register() when any new classes being to add.
- * Empty class to show studio ext in the Extension Manager.
+ * Empty class to show studio ext in the LPhyExtension Manager.
  * @author Walter Xie
  */
 public class LPhyStudioImpl extends LPhyCoreImpl { //} implements LPhyExtension {

diff --git a/lphy-studio/src/main/java/module-info.java b/lphy-studio/src/main/java/module-info.java
@@ -21,7 +21,7 @@
     exports lphystudio.core.valueeditor;
     exports lphystudio.core.theme;
 
-    // Both are empty now, but must be declared in order to show studio ext in the Extension Manager.
+    // Both are empty now, but must be declared in order to show studio ext in the LPhyExtension Manager.
     // LPhy extensions
     uses lphy.core.spi.Extension;
     // declare what service interface the provider intends to use