Specify search depth

build.gradle

@@ -1 +1 @@
-version = "0.1.3"
+version = "0.1.4"

javadocviewer-app/src/main/java/qupath/ui/javadocviewer/app/JavadocViewerApp.java

@@ -39,12 +39,14 @@ public void start(Stage stage) throws IOException {
                             try {
                                 return new URI(param);
                             } catch (URISyntaxException e) {
-                                logger.warn(String.format("Couldn't convert URI %s", param), e);
+                                logger.warn("Couldn't convert URI {}", param, e);
+
                                 return null;
                             }
                         })
                         .filter(Objects::nonNull)
-                        .toArray(URI[]::new)
+                        .toList(),
+                7
         );
 
         Scene scene = new Scene(javadocViewer);

javadocviewer/src/main/java/qupath/ui/javadocviewer/UriUtils.java

@@ -7,9 +7,11 @@
 import java.io.InputStream;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.net.URLDecoder;
 import java.net.http.HttpClient;
 import java.net.http.HttpRequest;
 import java.net.http.HttpResponse;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.time.Duration;
@@ -101,10 +103,14 @@ private static CompletableFuture<String> getContentOfHttpUri(URI uri) {
     }
 
     private static String getContentOfJarUri(URI uri) {
-        // The provided URI is expected to be like: jar:file:/path/to/some-javadoc.jar!/index.html#someParameters
-        String jarUri = uri.toString().substring(
-                uri.toString().indexOf('/'),
-                uri.toString().lastIndexOf('!')
+        // The provided URI is expected to be like: jar:file:/path/to/some-javadoc.jar!/index.html#someParameters with some
+        // HTML encoding for special characters
+        String jarUri = URLDecoder.decode(
+                uri.toString().substring(
+                        uri.toString().indexOf('/'),
+                        uri.toString().lastIndexOf('!')
+                ),
+                StandardCharsets.UTF_8
         );
         logger.debug("Opening {} jar file to read the content of {}...", jarUri, uri);
 

javadocviewer/src/main/java/qupath/ui/javadocviewer/core/JavadocsFinder.java

@@ -11,7 +11,6 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.Arrays;
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
@@ -28,7 +27,6 @@ public class JavadocsFinder {
     private static final Logger logger = LoggerFactory.getLogger(JavadocsFinder.class);
     private static final String JAVADOC_INDEX_FILE = "index.html";
     private static final List<String> ARCHIVE_EXTENSIONS = List.of(".jar", ".zip");
-    private static final int SEARCH_DEPTH = 4;
 
     private JavadocsFinder() {
         throw new AssertionError("This class is not instantiable.");
@@ -37,13 +35,14 @@ private JavadocsFinder() {
     /**
      * Asynchronously search for Javadocs in the specified URIs.
      *
-     * @param urisToSearch URIs to search for Javadocs. It can be a directory, an HTTP link,
-     *                     a link to a jar file...
+     * @param urisToSearch URIs to search for Javadocs. It can be a directory, an HTTP link, a link to a jar file...
+     * @param searchDepth if one of the provided URI points to a local directory, indicate how deep to search for Javadocs
+     *                    inside that directory
      * @return a CompletableFuture with the list of Javadocs found
      */
-    public static CompletableFuture<List<Javadoc>> findJavadocs(URI... urisToSearch) {
-        return CompletableFuture.supplyAsync(() -> Arrays.stream(urisToSearch)
-                .map(JavadocsFinder::findJavadocUrisFromUri)
+    public static CompletableFuture<List<Javadoc>> findJavadocs(List<URI> urisToSearch, int searchDepth) {
+        return CompletableFuture.supplyAsync(() -> urisToSearch.stream()
+                .map(uri -> findJavadocUrisFromUri(uri, searchDepth))
                 .flatMap(List::stream)
                 .map(uri -> {
                     try {
@@ -63,32 +62,32 @@ public static CompletableFuture<List<Javadoc>> findJavadocs(URI... urisToSearch)
         );
     }
 
-    private static List<URI> findJavadocUrisFromUri(URI uri) {
+    private static List<URI> findJavadocUrisFromUri(URI uri, int searchDepth) {
         if (UriUtils.doesUriLinkToWebsite(uri)) {
             logger.debug("URI {} retrieved", uri);
             return List.of(uri);
         } else {
             try {
-                return findJavadocUrisFromPath(Paths.get(uri));
+                return findJavadocUrisFromPath(Paths.get(uri), searchDepth);
             } catch (Exception e) {
                 logger.debug("Could not convert URI {} to path", uri, e);
                 return List.of();
             }
         }
     }
 
-    private static List<URI> findJavadocUrisFromPath(Path path) {
+    private static List<URI> findJavadocUrisFromPath(Path path, int searchDepth) {
         if (Files.isDirectory(path)) {
-            return findJavadocUrisFromDirectory(path);
+            return findJavadocUrisFromDirectory(path, searchDepth);
         } else {
             return findJavadocUrisFromFile(path).map(List::of).orElse(List.of());
         }
     }
 
-    private static List<URI> findJavadocUrisFromDirectory(Path directory) {
-        logger.debug("Searching for javadocs in {} directory with depth {}", directory, SEARCH_DEPTH);
+    private static List<URI> findJavadocUrisFromDirectory(Path directory, int searchDepth) {
+        logger.debug("Searching for javadocs in {} directory with depth {}", directory, searchDepth);
 
-        try (Stream<Path> walk = Files.walk(directory, JavadocsFinder.SEARCH_DEPTH)) {
+        try (Stream<Path> walk = Files.walk(directory, searchDepth)) {
             return walk
                     .map(JavadocsFinder::findJavadocUrisFromFile)
                     .flatMap(Optional::stream)

javadocviewer/src/main/java/qupath/ui/javadocviewer/gui/viewer/JavadocViewer.java

@@ -24,7 +24,6 @@
 import java.net.URI;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.Arrays;
 import java.util.Comparator;
 import java.util.List;
 import java.util.Optional;
@@ -58,11 +57,13 @@ public class JavadocViewer extends BorderPane {
      *
      * @param stylesheet a property containing a link to a stylesheet which should
      *                   be applied to this viewer. Can be null
-     * @param urisToSearch URIs to search for Javadocs. See {@link JavadocsFinder#findJavadocs(URI...)}
+     * @param urisToSearch URIs to search for Javadocs. See {@link JavadocsFinder#findJavadocs(List, int)}
+     * @param searchDepth if one of the provided URI points to a local directory, indicate how deep to search for Javadocs
+     *                    inside that directory
      * @throws IOException if the window creation fails
      */
-    public JavadocViewer(ReadOnlyStringProperty stylesheet, URI... urisToSearch) throws IOException {
-        initUI(stylesheet, Arrays.stream(urisToSearch).toList());
+    public JavadocViewer(ReadOnlyStringProperty stylesheet, List<URI> urisToSearch, int searchDepth) throws IOException {
+        initUI(stylesheet, urisToSearch, searchDepth);
         setUpListeners();
     }
 
@@ -85,7 +86,7 @@ private void onForwardClicked(ActionEvent ignoredEvent) {
         offset(1);
     }
 
-    private void initUI(ReadOnlyStringProperty stylesheet, List<URI> urisToSearch) throws IOException {
+    private void initUI(ReadOnlyStringProperty stylesheet, List<URI> urisToSearch, int searchDepth) throws IOException {
         FXMLLoader loader = new FXMLLoader(JavadocViewer.class.getResource("javadoc_viewer.fxml"), resources);
         loader.setRoot(this);
         loader.setController(this);
@@ -123,7 +124,7 @@ protected void updateItem(URI item, boolean empty) {
         }
 
         webView.getEngine().loadContent(resources.getString("JavadocViewer.findingJavadocs"));
-        JavadocsFinder.findJavadocs(urisToSearch.toArray(new URI[0])).thenAccept(javadocs -> Platform.runLater(() -> {
+        JavadocsFinder.findJavadocs(urisToSearch, searchDepth).thenAccept(javadocs -> Platform.runLater(() -> {
             this.uris.getItems().setAll(javadocs.stream()
                     .map(Javadoc::uri)
                     .sorted(Comparator.comparing(JavadocViewer::getName))

javadocviewer/src/main/java/qupath/ui/javadocviewer/gui/viewer/JavadocViewerCommand.java

@@ -6,7 +6,6 @@
 
 import java.io.IOException;
 import java.net.URI;
-import java.util.Arrays;
 import java.util.List;
 import java.util.ResourceBundle;
 
@@ -20,21 +19,25 @@ public class JavadocViewerCommand implements Runnable {
     private final Stage owner;
     private final ReadOnlyStringProperty stylesheet;
     private final List<URI> urisToSearch;
+    private final int searchDepth;
     private Stage stage;
     private JavadocViewer javadocViewer;
 
     /**
-     * Create the command. This will not create the viewer until either the command is run or {@link #getJavadocViewer()} is called.
+     * Create the command. This will not create the viewer until either the command is run or {@link #getJavadocViewer()}
+     * is called.
      *
      * @param owner the stage that should own the viewer window. Can be null
-     * @param stylesheet a property containing a link to a stylesheet which should
-     *                   be applied to the viewer. Can be null
-     * @param urisToSearch URIs to search for Javadocs. See {@link JavadocViewer#JavadocViewer(ReadOnlyStringProperty, URI...)}
+     * @param stylesheet a property containing a link to a stylesheet which should be applied to the viewer. Can be null
+     * @param urisToSearch URIs to search for Javadocs. See {@link JavadocViewer#JavadocViewer(ReadOnlyStringProperty, List, int)}
+     * @param searchDepth if one of the provided URI points to a local directory, indicate how deep to search for Javadocs
+     *                    inside that directory
      */
-    public JavadocViewerCommand(Stage owner, ReadOnlyStringProperty stylesheet, URI... urisToSearch) {
+    public JavadocViewerCommand(Stage owner, ReadOnlyStringProperty stylesheet, List<URI> urisToSearch, int searchDepth) {
         this.owner = owner;
         this.stylesheet = stylesheet;
-        this.urisToSearch = Arrays.stream(urisToSearch).toList();
+        this.urisToSearch = List.copyOf(urisToSearch);
+        this.searchDepth = searchDepth;
     }
 
     /**
@@ -46,7 +49,7 @@ public JavadocViewerCommand(Stage owner, ReadOnlyStringProperty stylesheet, URI.
     public JavadocViewer getJavadocViewer() {
         if (javadocViewer == null) {
             try {
-                javadocViewer = new JavadocViewer(stylesheet, urisToSearch.toArray(new URI[0]));
+                javadocViewer = new JavadocViewer(stylesheet, urisToSearch, searchDepth);
             } catch (IOException e) {
                 throw new RuntimeException(e);
             }