Change lucene index path to have sub directories

CHANGELOG.md

@@ -113,7 +113,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where entering a date in the format "YYYY/MM" in the entry editor date field caused an exception. [#9492](https://github.com/JabRef/jabref/issues/9492)
 - For portable versions, the `.deb` file now works on plain debian again. [#9472](https://github.com/JabRef/jabref/issues/9472)
 - We fixed an issue where the download of linked online files failed after an import of entries for certain urls. [#9518](https://github.com/JabRef/jabref/issues/9518)
-- We fixed an issue where an exception occured when manually downloading a file from an URL in the entry editor. [#9521](https://github.com/JabRef/jabref/issues/9521)
+- We fixed an issue where an exception occurred when manually downloading a file from an URL in the entry editor. [#9521](https://github.com/JabRef/jabref/issues/9521)
 - We fixed an issue with open office csv file formatting where commas in the abstract field where not escaped. [#9087][https://github.com/JabRef/jabref/issues/9087]
 - We fixed an issue with deleting groups where subgroups different from the selected group were deleted. [#9281][https://github.com/JabRef/jabref/issues/9281]
 
@@ -412,7 +412,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ### Fixed
 
 - We fixed an issue where an exception occurred when pasting an entry with a publication date-range of the form 1910/1917 [#7864](https://github.com/JabRef/jabref/issues/7864)
-- We fixed an issue where an exception occured when a preview style was edited and afterwards another preview style selected. [#8280](https://github.com/JabRef/jabref/issues/8280)
+- We fixed an issue where an exception occurred when a preview style was edited and afterwards another preview style selected. [#8280](https://github.com/JabRef/jabref/issues/8280)
 - We fixed an issue where the actions to move a file to a directory were incorrectly disabled. [#7908](https://github.com/JabRef/jabref/issues/7908)
 - We fixed an issue where an exception occurred when a linked online file was edited in the entry editor [#8008](https://github.com/JabRef/jabref/issues/8008)
 - We fixed an issue when checking for a new version when JabRef is used behind a corporate proxy. [#7884](https://github.com/JabRef/jabref/issues/7884)
@@ -496,11 +496,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
-- We fixed an isuse where some texts (e.g. descriptionss) in dialogs could not be translated [#7854](https://github.com/JabRef/jabref/issues/7854)
+- We fixed an issue where some texts (e.g. descriptions) in dialogs could not be translated [#7854](https://github.com/JabRef/jabref/issues/7854)
 - We fixed an issue where import hangs for ris files with "ER - " [#7737](https://github.com/JabRef/jabref/issues/7737)
 - We fixed an issue where getting bibliograhpic data from DOI or another identifer did not respect the library mode (BibTeX/biblatex)[#1018](https://github.com/JabRef/jabref/issues/6267)
 - We fixed an issue where importing entries would not respect the library mode (BibTeX/biblatex)[#1018](https://github.com/JabRef/jabref/issues/1018)
-- We fixed an issue where an exception occured when importing entries from a web search [#7606](https://github.com/JabRef/jabref/issues/7606)
+- We fixed an issue where an exception occurred when importing entries from a web search [#7606](https://github.com/JabRef/jabref/issues/7606)
 - We fixed an issue where the table column sort order was not properly stored and resulted in unsorted eports [#7524](https://github.com/JabRef/jabref/issues/7524)
 - We fixed an issue where the value of the field `school` or `institution` would be printed twice in the HTML Export [forum#2634](https://discourse.jabref.org/t/problem-with-exporting-techreport-phdthesis-mastersthesis-to-html/2634)
 - We fixed an issue preventing to connect to a shared database. [#7570](https://github.com/JabRef/jabref/pull/7570)
@@ -725,11 +725,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where long directory names created from patterns could create an exception. [#3915](https://github.com/JabRef/jabref/issues/3915)
 - We fixed an issue where sort on numeric cases was broken. [#6349](https://github.com/JabRef/jabref/issues/6349)
 - We fixed an issue where year and month fields were not cleared when converting to biblatex [#6224](https://github.com/JabRef/jabref/issues/6224)
-- We fixed an issue where an "Not on FX thread" exception occured when saving on linux [#6453](https://github.com/JabRef/jabref/issues/6453)
+- We fixed an issue where an "Not on FX thread" exception occurred when saving on linux [#6453](https://github.com/JabRef/jabref/issues/6453)
 - We fixed an issue where the library sort order was lost. [#6091](https://github.com/JabRef/jabref/issues/6091)
 - We fixed an issue where brackets in regular expressions were not working. [6469](https://github.com/JabRef/jabref/pull/6469)
 - We fixed an issue where multiple background task popups stacked over each other.. [#6472](https://github.com/JabRef/jabref/issues/6472)
-- We fixed an issue where LaTeX citations for specific commands (\autocites) of biblatex-mla were not recognized. [#6476](https://github.com/JabRef/jabref/issues/6476)
+- We fixed an issue where LaTeX citations for specific commands (`\autocite`s) of biblatex-mla were not recognized. [#6476](https://github.com/JabRef/jabref/issues/6476)
 - We fixed an issue where drag and drop was not working on empty database. [#6487](https://github.com/JabRef/jabref/issues/6487)
 - We fixed an issue where the name fields were not updated after the preferences changed. [#6515](https://github.com/JabRef/jabref/issues/6515)
 - We fixed an issue where "null" appeared in generated BibTeX keys. [#6459](https://github.com/JabRef/jabref/issues/6459)

src/main/java/org/jabref/cli/Launcher.java

@@ -21,14 +21,11 @@
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.logic.remote.RemotePreferences;
 import org.jabref.logic.remote.client.RemoteClient;
-import org.jabref.logic.util.BuildInfo;
 import org.jabref.logic.util.OS;
 import org.jabref.migrations.PreferencesMigrations;
-import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.PreferencesService;
 
-import net.harawata.appdirs.AppDirsFactory;
 import org.apache.commons.cli.ParseException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -90,12 +87,7 @@ public static void main(String[] args) {
      * the log configuration programmatically anymore.
      */
     private static void addLogToDisk() {
-        Path directory = Path.of(AppDirsFactory.getInstance()
-                                               .getUserDataDir(
-                OS.APP_DIR_APP_NAME,
-                "logs",
-                OS.APP_DIR_APP_AUTHOR))
-                .resolve(new BuildInfo().version.toString());
+        Path directory = OS.getNativeDesktop().getLogDirectory();
         try {
             Files.createDirectories(directory);
         } catch (IOException e) {
@@ -168,7 +160,7 @@ private static void configureSSL(SSLPreferences sslPreferences) {
     }
 
     private static void clearOldSearchIndices() {
-        Path currentIndexPath = BibDatabaseContext.getFulltextIndexBasePath();
+        Path currentIndexPath = OS.getNativeDesktop().getFulltextIndexBaseDirectory();
         Path appData = currentIndexPath.getParent();
 
         try {

src/main/java/org/jabref/gui/OpenConsoleAction.java

@@ -47,7 +47,7 @@ public OpenConsoleAction(StateManager stateManager, PreferencesService preferenc
     public void execute() {
         Optional.ofNullable(databaseContext.get()).or(stateManager::getActiveDatabase).flatMap(BibDatabaseContext::getDatabasePath).ifPresent(path -> {
             try {
-                JabRefDesktop.openConsole(path.toFile(), preferencesService, dialogService);
+                JabRefDesktop.openConsole(path, preferencesService, dialogService);
             } catch (IOException e) {
                 LOGGER.info("Could not open console", e);
             }

src/main/java/org/jabref/gui/desktop/JabRefDesktop.java

@@ -1,6 +1,5 @@
 package org.jabref.gui.desktop;
 
-import java.io.File;
 import java.io.IOException;
 import java.net.URI;
 import java.nio.file.Files;
@@ -13,11 +12,7 @@
 
 import org.jabref.gui.DialogService;
 import org.jabref.gui.Globals;
-import org.jabref.gui.desktop.os.DefaultDesktop;
-import org.jabref.gui.desktop.os.Linux;
 import org.jabref.gui.desktop.os.NativeDesktop;
-import org.jabref.gui.desktop.os.OSX;
-import org.jabref.gui.desktop.os.Windows;
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.logic.importer.util.IdentifierParser;
@@ -36,14 +31,14 @@
 import org.slf4j.LoggerFactory;
 
 /**
- * TODO: Replace by http://docs.oracle.com/javase/7/docs/api/java/awt/Desktop.html
- * http://stackoverflow.com/questions/18004150/desktop-api-is-not-supported-on-the-current-platform
+ * See http://stackoverflow.com/questions/18004150/desktop-api-is-not-supported-on-the-current-platform for more implementation hints.
+ * http://docs.oracle.com/javase/7/docs/api/java/awt/Desktop.html cannot be used as we don't want to rely on AWT
  */
 public class JabRefDesktop {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(JabRefDesktop.class);
 
-    private static final NativeDesktop NATIVE_DESKTOP = getNativeDesktop();
+    private static final NativeDesktop NATIVE_DESKTOP = OS.getNativeDesktop();
     private static final Pattern REMOTE_LINK_PATTERN = Pattern.compile("[a-z]+://.*");
 
     private JabRefDesktop() {
@@ -61,7 +56,7 @@ public static void openExternalViewer(BibDatabaseContext databaseContext,
             throws IOException {
         String link = initialLink;
         Field field = initialField;
-        if (StandardField.PS == field || StandardField.PDF == field) {
+        if ((StandardField.PS == field) || (StandardField.PDF == field)) {
             // Find the default directory for this field type:
             List<Path> directories = databaseContext.getFileDirectories(preferencesService.getFilePreferences());
 
@@ -202,25 +197,64 @@ public static void openFolderAndSelectFile(Path fileLink, PreferencesService pre
         boolean useCustomFileBrowser = preferencesService.getExternalApplicationsPreferences().useCustomFileBrowser();
         if (!useCustomFileBrowser) {
             NATIVE_DESKTOP.openFolderAndSelectFile(fileLink);
-        } else {
-            String absolutePath = fileLink.toAbsolutePath().getParent().toString();
-            String command = preferencesService.getExternalApplicationsPreferences().getCustomFileBrowserCommand();
-            if (!command.isEmpty()) {
-                command = command.replaceAll("\\s+", " "); // normalize white spaces
-
-                // replace the placeholder if used
-                command = command.replace("%DIR", absolutePath);
-                String[] subcommands = command.split(" ");
-
-                LOGGER.info("Executing command \"" + command + "\"...");
-
-                try {
-                    new ProcessBuilder(subcommands).start();
-                } catch (IOException exception) {
-                    LOGGER.error("Open File Browser", exception);
-                    dialogService.notify(Localization.lang("Error occured while executing the command \"%0\".", command));
-                }
-            }
+            return;
+        }
+        String absolutePath = fileLink.toAbsolutePath().getParent().toString();
+        String command = preferencesService.getExternalApplicationsPreferences().getCustomFileBrowserCommand();
+        if (command.isEmpty()) {
+            LOGGER.info("No custom file browser command defined");
+            NATIVE_DESKTOP.openFolderAndSelectFile(fileLink);
+            return;
+        }
+        executeCommand(command, absolutePath, dialogService);
+    }
+
+    /**
+     * Opens a new console starting on the given file location
+     * <p>
+     * If no command is specified in {@link Globals}, the default system console will be executed.
+     *
+     * @param file Location the console should be opened at.
+     *
+     */
+    public static void openConsole(Path file, PreferencesService preferencesService, DialogService dialogService) throws IOException {
+        if (file == null) {
+            return;
+        }
+
+        String absolutePath = file.toAbsolutePath().getParent().toString();
+
+        boolean useCustomTerminal = preferencesService.getExternalApplicationsPreferences().useCustomTerminal();
+        if (!useCustomTerminal) {
+            NATIVE_DESKTOP.openConsole(absolutePath, dialogService);
+            return;
+        }
+        String command = preferencesService.getExternalApplicationsPreferences().getCustomTerminalCommand();
+        command = command.trim();
+        if (command.isEmpty()) {
+            NATIVE_DESKTOP.openConsole(absolutePath, dialogService);
+            LOGGER.info("Preference for custom terminal is empty. Using default terminal.");
+            return;
+        }
+        executeCommand(command, absolutePath, dialogService);
+    }
+
+    private static void executeCommand(String command, String absolutePath, DialogService dialogService) {
+        // normalize white spaces
+        command = command.replaceAll("\\s+", " ");
+
+        // replace the placeholder if used
+        command = command.replace("%DIR", absolutePath);
+
+        LOGGER.info("Executing command \"{}\"...", command);
+        dialogService.notify(Localization.lang("Executing command \"%0\"...", command));
+
+        String[] subcommands = command.split(" ");
+        try {
+            new ProcessBuilder(subcommands).start();
+        } catch (IOException exception) {
+            LOGGER.error("Error during command execution", exception);
+            dialogService.notify(Localization.lang("Error occurred while executing the command \"%0\".", command));
         }
     }
 
@@ -256,58 +290,4 @@ public static void openBrowserShowPopup(String url, DialogService dialogService)
             dialogService.showErrorDialogAndWait(couldNotOpenBrowser, couldNotOpenBrowser + "\n" + openManually + "\n" + copiedToClipboard);
         }
     }
-
-    /**
-     * Opens a new console starting on the given file location
-     * <p>
-     * If no command is specified in {@link Globals}, the default system console will be executed.
-     *
-     * @param file Location the console should be opened at.
-     *
-     */
-    public static void openConsole(File file, PreferencesService preferencesService, DialogService dialogService) throws IOException {
-        if (file == null) {
-            return;
-        }
-
-        String absolutePath = file.toPath().toAbsolutePath().getParent().toString();
-
-        boolean useCustomTerminal = preferencesService.getExternalApplicationsPreferences().useCustomTerminal();
-        if (!useCustomTerminal) {
-            NATIVE_DESKTOP.openConsole(absolutePath, dialogService);
-        } else {
-            String command = preferencesService.getExternalApplicationsPreferences().getCustomTerminalCommand();
-            command = command.trim();
-
-            if (!command.isEmpty()) {
-                command = command.replaceAll("\\s+", " "); // normalize white spaces
-                command = command.replace("%DIR", absolutePath); // replace the placeholder if used
-
-                String[] subcommands = command.split(" ");
-
-                LOGGER.info("Executing command \"" + command + "\"...");
-                dialogService.notify(Localization.lang("Executing command \"%0\"...", command));
-
-                try {
-                    new ProcessBuilder(subcommands).start();
-                } catch (IOException exception) {
-                    LOGGER.error("Open console", exception);
-
-                   dialogService.notify(Localization.lang("Error occured while executing the command \"%0\".", command));
-                }
-            }
-        }
-    }
-
-    // TODO: Move to OS.java
-    public static NativeDesktop getNativeDesktop() {
-        if (OS.WINDOWS) {
-            return new Windows();
-        } else if (OS.OS_X) {
-            return new OSX();
-        } else if (OS.LINUX) {
-            return new Linux();
-        }
-        return new DefaultDesktop();
-    }
 }

src/main/java/org/jabref/gui/desktop/os/NativeDesktop.java

@@ -1,9 +1,15 @@
 package org.jabref.gui.desktop.os;
 
+import java.io.File;
 import java.io.IOException;
 import java.nio.file.Path;
 
 import org.jabref.gui.DialogService;
+import org.jabref.logic.util.BuildInfo;
+import org.jabref.logic.util.OS;
+import org.jabref.model.pdf.search.SearchFieldConstants;
+
+import net.harawata.appdirs.AppDirsFactory;
 
 public interface NativeDesktop {
 
@@ -45,4 +51,35 @@ public interface NativeDesktop {
     default Path getUserDirectory() {
         return Path.of(System.getProperty("user.home"));
     }
+
+    default Path getLogDirectory() {
+        return Path.of(AppDirsFactory.getInstance()
+                                     .getUserDataDir(
+                                             OS.APP_DIR_APP_NAME,
+                                             "logs",
+                                             OS.APP_DIR_APP_AUTHOR))
+                   .resolve(new BuildInfo().version.toString());
+    }
+
+    default Path getBackupDirectory() {
+        return Path.of(AppDirsFactory.getInstance()
+                                     .getUserDataDir(
+                                             OS.APP_DIR_APP_NAME,
+                                             "backups",
+                                             OS.APP_DIR_APP_AUTHOR));
+    }
+
+    default Path getFulltextIndexBaseDirectory() {
+        return Path.of(AppDirsFactory.getInstance()
+                                     .getUserDataDir(OS.APP_DIR_APP_NAME,
+                                             "lucene" + File.separator + SearchFieldConstants.VERSION,
+                                             OS.APP_DIR_APP_AUTHOR));
+    }
+
+    default Path getSslDirectory() {
+        return Path.of(AppDirsFactory.getInstance()
+                                     .getUserDataDir(OS.APP_DIR_APP_NAME,
+                                             "ssl",
+                                             OS.APP_DIR_APP_AUTHOR));
+    }
 }

src/main/java/org/jabref/gui/desktop/os/Windows.java

@@ -15,11 +15,9 @@
 import com.sun.jna.platform.win32.Shell32Util;
 import com.sun.jna.platform.win32.ShlObj;
 import com.sun.jna.platform.win32.Win32Exception;
-import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 public class Windows implements NativeDesktop {
-    private static final Logger LOGGER = LoggerFactory.getLogger(Windows.class);
 
     private static final String DEFAULT_EXECUTABLE_EXTENSION = ".exe";
 
@@ -89,7 +87,8 @@ public Path getDefaultFileChooserDirectory() {
                 return Path.of(Shell32Util.getFolderPath(ShlObj.CSIDL_MYDOCUMENTS));
             }
         } catch (Win32Exception e) {
-            LOGGER.error("Error accessing folder", e);
+            // needs to be non-static because of org.jabref.cli.Launcher.addLogToDisk
+            LoggerFactory.getLogger(Windows.class).error("Error accessing folder", e);
             return Path.of(System.getProperty("user.home"));
         }
     }