Switch to stream-based loading

src/main/java/org/jabref/architecture/AllowedToUseClassGetResource.java

@@ -0,0 +1,11 @@
+package org.jabref.architecture;
+
+/**
+ * Annotation to indicate that this logic class can use class.getResource().
+ * Mostly, because {@link java.nio.file.Path} is not used.
+ * See <a href="graal#7682">https://github.com/oracle/graal/issues/7682</a> for a longer discussion.
+ */
+public @interface AllowedToUseClassGetResource {
+    // The rationale
+    String value();
+}

src/main/java/org/jabref/architecture/AllowedToUseSwing.java

@@ -4,7 +4,6 @@
  * Annotation to indicate that this logic class can access swing
  */
 public @interface AllowedToUseSwing {
-
     // The rationale
     String value();
 }

src/main/java/org/jabref/gui/fieldeditors/journalinfo/JournalInfoView.java

@@ -8,10 +8,12 @@
 import javafx.scene.control.Label;
 import javafx.scene.layout.VBox;
 
+import org.jabref.architecture.AllowedToUseClassGetResource;
 import org.jabref.logic.importer.FetcherException;
 
 import com.airhacks.afterburner.views.ViewLoader;
 
+@AllowedToUseClassGetResource("JavaFX internally handles the passed URLs properly.")
 public class JournalInfoView extends VBox {
     @FXML private Label title;
     @FXML private Label categories;

src/main/java/org/jabref/gui/groups/GroupTreeView.java

@@ -43,6 +43,7 @@
 import javafx.scene.layout.StackPane;
 import javafx.scene.text.Text;
 
+import org.jabref.architecture.AllowedToUseClassGetResource;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.DragAndDropDataFormats;
 import org.jabref.gui.StateManager;
@@ -70,6 +71,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@AllowedToUseClassGetResource("JavaFX internally handles the passed URLs properly.")
 public class GroupTreeView extends BorderPane {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(GroupTreeView.class);

src/main/java/org/jabref/gui/icon/IconTheme.java

@@ -22,6 +22,8 @@
 import javafx.scene.image.Image;
 import javafx.scene.paint.Color;
 
+import org.jabref.architecture.AllowedToUseClassGetResource;
+
 import org.kordamp.ikonli.Ikon;
 import org.kordamp.ikonli.IkonProvider;
 import org.kordamp.ikonli.materialdesign2.MaterialDesignA;
@@ -50,6 +52,7 @@
 
 import static java.util.EnumSet.allOf;
 
+@AllowedToUseClassGetResource("JavaFX internally handles the passed URLs properly.")
 public class IconTheme {
 
     public static final Color DEFAULT_DISABLED_COLOR = Color.web("#c8c8c8");

src/main/java/org/jabref/gui/icon/JabRefIkonHandler.java

@@ -3,9 +3,12 @@
 import java.io.InputStream;
 import java.net.URL;
 
+import org.jabref.architecture.AllowedToUseClassGetResource;
+
 import org.kordamp.ikonli.AbstractIkonHandler;
 import org.kordamp.ikonli.Ikon;
 
+@AllowedToUseClassGetResource("JavaFX internally handles the passed URLs properly.")
 public class JabRefIkonHandler extends AbstractIkonHandler {
 
     private static String FONT_RESOURCE = "/fonts/JabRefMaterialDesign.ttf";

src/main/java/org/jabref/gui/maintable/MainTable.java

@@ -24,6 +24,7 @@
 import javafx.scene.input.MouseEvent;
 import javafx.scene.input.TransferMode;
 
+import org.jabref.architecture.AllowedToUseClassGetResource;
 import org.jabref.gui.ClipBoardManager;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.DragAndDropDataFormats;
@@ -60,6 +61,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@AllowedToUseClassGetResource("JavaFX internally handles the passed URLs properly.")
 public class MainTable extends TableView<BibEntryTableViewModel> {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(MainTable.class);

src/main/java/org/jabref/gui/mergeentries/newmergedialog/ThreeWayMergeView.java

@@ -11,6 +11,7 @@
 import javafx.scene.layout.VBox;
 import javafx.stage.Screen;
 
+import org.jabref.architecture.AllowedToUseClassGetResource;
 import org.jabref.gui.mergeentries.newmergedialog.fieldsmerger.FieldMergerFactory;
 import org.jabref.gui.mergeentries.newmergedialog.toolbar.ThreeWayMergeToolbar;
 import org.jabref.logic.l10n.Localization;
@@ -19,6 +20,7 @@
 import org.jabref.model.entry.field.FieldProperty;
 import org.jabref.preferences.PreferencesService;
 
+@AllowedToUseClassGetResource("JavaFX internally handles the passed URLs properly.")
 public class ThreeWayMergeView extends VBox {
     public static final int GRID_COLUMN_MIN_WIDTH = 250;
 

src/main/java/org/jabref/gui/search/GlobalSearchBar.java

@@ -40,6 +40,7 @@
 import javafx.scene.text.Text;
 import javafx.scene.text.TextFlow;
 
+import org.jabref.architecture.AllowedToUseClassGetResource;
 import org.jabref.gui.ClipBoardManager;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.LibraryTabContainer;
@@ -445,6 +446,7 @@ public void setSearchTerm(String searchTerm) {
         UiTaskExecutor.runInJavaFXThread(() -> searchField.setText(searchTerm));
     }
 
+    @AllowedToUseClassGetResource("JavaFX internally handles the passed URLs properly.")
     private static class SearchPopupSkin<T> implements Skin<AutoCompletePopup<T>> {
 
         private final AutoCompletePopup<T> control;

src/main/java/org/jabref/gui/search/SearchResultsTable.java

@@ -8,6 +8,7 @@
 import javafx.scene.control.TableColumn;
 import javafx.scene.control.TableView;
 
+import org.jabref.architecture.AllowedToUseClassGetResource;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.maintable.BibEntryTableViewModel;
@@ -22,6 +23,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.preferences.PreferencesService;
 
+@AllowedToUseClassGetResource("JavaFX internally handles the passed URLs properly.")
 public class SearchResultsTable extends TableView<BibEntryTableViewModel> {
 
     public SearchResultsTable(SearchResultsTableDataModel model,

src/main/java/org/jabref/gui/theme/StyleSheet.java

@@ -9,11 +9,13 @@
 import java.nio.file.Path;
 import java.util.Optional;
 
+import org.jabref.architecture.AllowedToUseClassGetResource;
 import org.jabref.gui.JabRefGUI;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@AllowedToUseClassGetResource("JavaFX internally handles the passed URLs properly.")
 abstract class StyleSheet {
 
     static final String DATA_URL_PREFIX = "data:text/css;charset=utf-8;base64,";

src/main/java/org/jabref/gui/theme/StyleSheetFile.java

@@ -87,7 +87,7 @@ public URL getSceneStylesheet() {
      * This method allows callers to obtain the theme's additional stylesheet.
      *
      * @return the stylesheet location if there is an additional stylesheet present and available. The
-     * location will be a local URL. Typically it will be a {@code 'data:'} URL where the CSS is embedded. However for
+     * location will be a local URL. Typically, it will be a {@code 'data:'} URL where the CSS is embedded. However, for
      * large themes it can be {@code 'file:'}.
      */
     @Override

src/main/java/org/jabref/logic/citationstyle/CitationStyle.java

@@ -1,11 +1,11 @@
 package org.jabref.logic.citationstyle;
 
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.StringReader;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
@@ -22,7 +22,6 @@
 
 import org.jabref.logic.util.StandardFileType;
 
-import de.undercouch.citeproc.helper.CSLUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.CharacterData;
@@ -57,31 +56,41 @@ private CitationStyle(final String filename, final String title, final String so
     /**
      * Creates an CitationStyle instance out of the style string
      */
-    private static Optional<CitationStyle> createCitationStyleFromSource(final String source, final String filename) {
-        if ((filename != null) && !filename.isEmpty() && (source != null) && !source.isEmpty()) {
-            try {
-                InputSource inputSource = new InputSource();
-                inputSource.setCharacterStream(new StringReader(stripInvalidProlog(source)));
-
-                Document doc = FACTORY.newDocumentBuilder().parse(inputSource);
-
-                // See CSL#canFormatBibliographies, checks if the tag exists
-                NodeList bibs = doc.getElementsByTagName("bibliography");
-                if (bibs.getLength() <= 0) {
-                    LOGGER.debug("no bibliography element for file {} ", filename);
-                    return Optional.empty();
-                }
-
-                NodeList nodes = doc.getElementsByTagName("info");
-                NodeList titleNode = ((Element) nodes.item(0)).getElementsByTagName("title");
-                String title = ((CharacterData) titleNode.item(0).getFirstChild()).getData();
-
-                return Optional.of(new CitationStyle(filename, title, source));
-            } catch (ParserConfigurationException | SAXException | IOException e) {
-                LOGGER.error("Error while parsing source", e);
+    private static Optional<CitationStyle> createCitationStyleFromSource(final InputStream source, final String filename) {
+        try {
+            // We need the content twice:
+            //   First, for parsing it here for the name
+            //   Second for the CSL library to parse it
+            String content = new String(source.readAllBytes());
+
+            Optional<String> title = getTitle(filename, content);
+            if (title.isEmpty()) {
+                return Optional.empty();
             }
+
+            return Optional.of(new CitationStyle(filename, title.get(), content));
+        } catch (ParserConfigurationException | SAXException | IOException e) {
+            LOGGER.error("Error while parsing source", e);
+            return Optional.empty();
         }
-        return Optional.empty();
+    }
+
+    private static Optional<String> getTitle(String filename, String content) throws SAXException, IOException, ParserConfigurationException {
+        // TODO: Switch to StAX parsing (to speed up - we need only the title)
+        InputSource inputSource = new InputSource(new StringReader(content));
+        Document doc = FACTORY.newDocumentBuilder().parse(inputSource);
+
+        // See CSL#canFormatBibliographies, checks if the tag exists
+        NodeList bibs = doc.getElementsByTagName("bibliography");
+        if (bibs.getLength() <= 0) {
+            LOGGER.debug("no bibliography element for file {} ", filename);
+            return Optional.empty();
+        }
+
+        NodeList nodes = doc.getElementsByTagName("info");
+        NodeList titleNode = ((Element) nodes.item(0)).getElementsByTagName("title");
+        String title = ((CharacterData) titleNode.item(0).getFirstChild()).getData();
+        return Optional.of(title);
     }
 
     private static String stripInvalidProlog(String source) {
@@ -102,18 +111,11 @@ public static Optional<CitationStyle> createCitationStyleFromFile(final String s
             return Optional.empty();
         }
 
-        try {
-            String text;
-            String internalFile = STYLES_ROOT + (styleFile.startsWith("/") ? "" : "/") + styleFile;
-            URL url = CitationStyle.class.getResource(internalFile);
-
-            if (url != null) {
-                text = CSLUtils.readURLToString(url, StandardCharsets.UTF_8.toString());
-            } else {
-                // if the url is null then the style is located outside the classpath
-                text = Files.readString(Path.of(styleFile));
-            }
-            return createCitationStyleFromSource(text, styleFile);
+        String internalFile = STYLES_ROOT + (styleFile.startsWith("/") ? "" : "/") + styleFile;
+        Path internalFilePath = Path.of(internalFile);
+        boolean isExternalFile = Files.exists(internalFilePath);
+        try (InputStream inputStream = isExternalFile ? Files.newInputStream(internalFilePath) : CitationStyle.class.getResourceAsStream(internalFile)) {
+            return createCitationStyleFromSource(inputStream, styleFile);
         } catch (NoSuchFileException e) {
             LOGGER.error("Could not find file: {}", styleFile, e);
         } catch (IOException e) {

src/main/java/org/jabref/logic/citationstyle/JabRefLocaleProvider.java

@@ -1,13 +1,14 @@
 package org.jabref.logic.citationstyle;
 
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.UncheckedIOException;
-import java.net.URL;
+import java.nio.charset.StandardCharsets;
 import java.util.HashMap;
 import java.util.Map;
 
 import de.undercouch.citeproc.LocaleProvider;
-import de.undercouch.citeproc.helper.CSLUtils;
+import org.slf4j.Logger;
 
 /**
  * A {@link LocaleProvider} that loads locales from a directory in the current module.
@@ -16,20 +17,22 @@
  */
 public class JabRefLocaleProvider implements LocaleProvider {
 
+    private static final Logger LOGGER = org.slf4j.LoggerFactory.getLogger(JabRefLocaleProvider.class);
+
     private static final String LOCALES_ROOT = "/csl-locales";
 
     private final Map<String, String> locales = new HashMap<>();
 
     @Override
     public String retrieveLocale(String lang) {
         return locales.computeIfAbsent(lang, locale -> {
-            try {
-                URL url = getClass().getResource(LOCALES_ROOT + "/locales-" + locale + ".xml");
-                if (url == null) {
+            try (InputStream inputStream = getClass().getResourceAsStream(LOCALES_ROOT + "/locales-" + locale + ".xml")) {
+                if (inputStream == null) {
                     throw new IllegalArgumentException("Unable to load locale " + locale);
                 }
-                return CSLUtils.readURLToString(url, "UTF-8");
+                return new String(inputStream.readAllBytes(), StandardCharsets.UTF_8);
             } catch (IOException e) {
+                LOGGER.error("failed to read locale {}", locale, e);
                 throw new UncheckedIOException("failed to read locale " + locale, e);
             }
         });

src/main/java/org/jabref/logic/exporter/OpenDocumentSpreadsheetCreator.java

@@ -10,7 +10,6 @@
 import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.io.Writer;
-import java.net.URL;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -129,18 +128,8 @@ private static void addResourceFile(String name, String resource, ZipOutputStrea
     }
 
     private static void addFromResource(String resource, OutputStream out) {
-        URL url = OpenDocumentSpreadsheetCreator.class.getResource(resource);
-        try (InputStream in = url.openStream()) {
-            byte[] buffer = new byte[256];
-            synchronized (out) {
-                while (true) {
-                    int bytesRead = in.read(buffer);
-                    if (bytesRead == -1) {
-                        break;
-                    }
-                    out.write(buffer, 0, bytesRead);
-                }
-            }
+        try (InputStream in = OpenDocumentSpreadsheetCreator.class.getResourceAsStream(resource)) {
+            in.transferTo(out);
         } catch (IOException e) {
             LOGGER.warn("Cannot get resource", e);
         }

src/main/java/org/jabref/logic/exporter/OpenOfficeDocumentCreator.java

@@ -10,7 +10,6 @@
 import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.io.Writer;
-import java.net.URL;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -111,18 +110,8 @@ private static void addResourceFile(String name, String resource, ZipOutputStrea
     }
 
     private static void addFromResource(String resource, OutputStream out) {
-        URL url = OpenOfficeDocumentCreator.class.getResource(resource);
-        try (InputStream in = url.openStream()) {
-            byte[] buffer = new byte[256];
-            synchronized (out) {
-                while (true) {
-                    int bytesRead = in.read(buffer);
-                    if (bytesRead == -1) {
-                        break;
-                    }
-                    out.write(buffer, 0, bytesRead);
-                }
-            }
+        try (InputStream in = OpenOfficeDocumentCreator.class.getResourceAsStream(resource)) {
+            in.transferTo(out);
         } catch (IOException e) {
             LOGGER.warn("Cannot get resource", e);
         }