Remove apache commons logging in favor of slf4j + log4j for JAVA 9

build.gradle

@@ -138,7 +138,9 @@ dependencies {
     compile 'org.jsoup:jsoup:1.11.2'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
-    compile 'commons-logging:commons-logging:1.2'
+	// >1.8.0-beta is required for java 9 compatibility
+    compile 'org.slf4j:slf4j-api:1.8.0-beta0'
+    compile 'org.apache.logging.log4j:log4j-slf4j-impl:2.10.0'
     compile 'org.apache.logging.log4j:log4j-jcl:2.10.0'
     compile 'org.apache.logging.log4j:log4j-api:2.10.0'
     compile 'org.apache.logging.log4j:log4j-core:2.10.0'
@@ -167,7 +169,6 @@ dependencies {
     testCompile 'org.xmlunit:xmlunit-core:2.5.1'
     testCompile 'org.xmlunit:xmlunit-matchers:2.5.1'
     testCompile 'com.tngtech.archunit:archunit-junit:0.5.0'
-    testCompile 'org.slf4j:slf4j-jcl:1.7.25' // required by ArchUnit to enable logging over jcl
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit:4.0.+"
 

docs/adr/0002-use-slf4j-for-logging.md

@@ -0,0 +1,43 @@
+# Use slf4j together with log4j2 for logging
+
+* Up to version 4.1 JabRef uses apache-ommons-logging 1.2 for logging errors and messages. However, this is not compatible with java 9 and is superseded by log4j.
+* SLF4J provides a facade for several logging frameworks, including log4j and supports already java 9
+* Log4j is already defined as dependency and slf4j has already been required by a third party dependency
+
+## Considered Alternatives
+
+* [Log4j2](https://logging.apache.org/log4j/2.x/)
+* [SLF4J with Log4j2 binding](https://logging.apache.org/log4j/2.x/maven-artifacts.html)
+* [SLF4J with Logback binding](https://logback.qos.ch/)
+
+## Decision Outcome
+* We chose slf4j with log4j2 binding, because it only requires minimal changes to our logging infrastructure and it is claimed that  
+> Apache Log4j 2 is an upgrade to Log4j that provides significant improvements over its predecessor, Log4j 1.x, and      provides many of the improvements available in Logback while fixing some inherent problems in Logback’s architecture.
+* Furthermore, as slf4j is a facade for several loggers, the underlying implementation can easily be changed in the future
+
+
+## Pros and Cons of the Alternatives 
+
+### Log4j2
+
+* `+` Dependency already exists
+* `+` Java 9 support since version 2.10
+* `-` Direct dependency
+
+### SLF4J with log4j2 binding
+
+* `+` Supports other loggers as well
+* `+` Java 9 support
+* `+` Already defined
+* `+` Migration tool available
+* `-` Logger statements require a slight different syntax
+
+### SLF4J with Logback binding
+
+* `+` Migration tool available
+* `+` Native implementation of slf4j
+* `-` Java 9 support only available in alpha
+* `-` Different syntax than log4j/commons logging
+
+
+

src/main/java/org/jabref/FallbackExceptionHandler.java

@@ -1,14 +1,14 @@
 package org.jabref;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Catch and log any unhandled exceptions.
  */
 public class FallbackExceptionHandler implements Thread.UncaughtExceptionHandler {
 
-    private static final Log LOGGER = LogFactory.getLog(FallbackExceptionHandler.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(FallbackExceptionHandler.class);
 
     public static void installExceptionHandler() {
         Thread.setDefaultUncaughtExceptionHandler(new FallbackExceptionHandler());

src/main/java/org/jabref/JabRefException.java

@@ -1,11 +1,11 @@
 package org.jabref;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class JabRefException extends Exception {
 
-    private static final Log LOGGER = LogFactory.getLog(JabRefException.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(JabRefException.class);
     private String localizedMessage;
 
     public JabRefException(String message) {

src/main/java/org/jabref/JabRefExecutorService.java

@@ -9,8 +9,8 @@
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 
 /**
@@ -19,7 +19,7 @@
 public class JabRefExecutorService implements Executor {
 
     public static final JabRefExecutorService INSTANCE = new JabRefExecutorService();
-    private static final Log LOGGER = LogFactory.getLog(JabRefExecutorService.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(JabRefExecutorService.class);
     private final ExecutorService executorService = Executors.newCachedThreadPool(r -> {
         Thread thread = new Thread(r);
         thread.setName("JabRef CachedThreadPool");

src/main/java/org/jabref/JabRefGUI.java

@@ -34,20 +34,20 @@
 import org.jabref.model.database.shared.DatabaseNotSupportedException;
 import org.jabref.preferences.JabRefPreferences;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class JabRefGUI {
-    private static final Log LOGGER = LogFactory.getLog(JabRefGUI.class);
 
+    private static final Logger LOGGER = LoggerFactory.getLogger(JabRefGUI.class);
     private static JabRefFrame mainFrame;
 
     private final List<ParserResult> bibDatabases;
     private final boolean isBlank;
     private final List<ParserResult> failed = new ArrayList<>();
     private final List<ParserResult> toOpenTab = new ArrayList<>();
 
-    private String focusedFile;
+    private final String focusedFile;
 
     public JabRefGUI(List<ParserResult> argsDatabases, boolean isBlank) {
         this.bibDatabases = argsDatabases;

src/main/java/org/jabref/JabRefMain.java

@@ -31,15 +31,15 @@
 import org.jabref.model.entry.InternalBibtexFields;
 import org.jabref.preferences.JabRefPreferences;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * JabRef MainClass
  */
 public class JabRefMain extends Application {
 
-    private static final Log LOGGER = LogFactory.getLog(JabRefMain.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(JabRefMain.class);
     private static String[] arguments;
 
     public static void main(String[] args) {

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

@@ -51,12 +51,12 @@
 import org.jabref.preferences.SearchPreferences;
 
 import com.google.common.base.Throwables;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class ArgumentProcessor {
 
-    private static final Log LOGGER = LogFactory.getLog(ArgumentProcessor.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(ArgumentProcessor.class);
     private final JabRefCLI cli;
     private final List<ParserResult> parserResults;
     private final Mode startupMode;

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

@@ -12,12 +12,12 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class JabRefCLI {
 
-    private static final Log LOGGER = LogFactory.getLog(JabRefCLI.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(JabRefCLI.class);
     private final CommandLine cl;
     private List<String> leftOver;
 

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

@@ -146,12 +146,12 @@
 import com.google.common.eventbus.Subscribe;
 import com.jgoodies.forms.builder.FormBuilder;
 import com.jgoodies.forms.layout.FormLayout;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class BasePanel extends JPanel implements ClipboardOwner {
 
-    private static final Log LOGGER = LogFactory.getLog(BasePanel.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(BasePanel.class);
 
     // Divider size for BaseFrame split pane. 0 means non-resizable.
     private static final int SPLIT_PANE_DIVIDER_SIZE = 4;

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

@@ -21,12 +21,12 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.identifier.DOI;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class ClipBoardManager implements ClipboardOwner {
 
-    private static final Log LOGGER = LogFactory.getLog(ClipBoardManager.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(ClipBoardManager.class);
 
     private final Clipboard clipboard;
 

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

@@ -11,12 +11,12 @@
 
 import com.airhacks.afterburner.injection.Injector;
 import com.airhacks.afterburner.injection.PresenterFactory;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class DefaultInjector implements PresenterFactory {
 
-    private static final Log LOGGER = LogFactory.getLog(DefaultInjector.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(DefaultInjector.class);
 
     /**
      * This method takes care of creating dependencies.

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

@@ -45,16 +45,16 @@
 import org.jabref.model.entry.IEEETranEntryTypes;
 
 import com.jgoodies.forms.builder.ButtonBarBuilder;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Dialog that prompts the user to choose a type for an entry.
  * Returns null if canceled.
  */
 public class EntryTypeDialog extends JabRefDialog implements ActionListener {
 
-    private static final Log LOGGER = LogFactory.getLog(EntryTypeDialog.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(EntryTypeDialog.class);
     private static final int COLUMN = 3;
     private final JabRefFrame frame;
     private final CancelAction cancelAction = new CancelAction();

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

@@ -82,8 +82,8 @@
 import org.jabref.preferences.JabRefPreferences;
 
 import com.jgoodies.forms.builder.ButtonBarBuilder;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * GUI Dialog for the feature "Find unlinked files".
@@ -99,7 +99,7 @@ public class FindUnlinkedFilesDialog extends JabRefDialog {
     public static final String ACTION_SHORT_DESCRIPTION = Localization
             .lang("Searches for unlinked PDF files on the file system");
 
-    private static final Log LOGGER = LogFactory.getLog(FindUnlinkedFilesDialog.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(FindUnlinkedFilesDialog.class);
     private static final String GLOBAL_PREFS_WORKING_DIRECTORY_KEY = "findUnlinkedFilesWD";
 
     private static final String GLOBAL_PREFS_DIALOG_SIZE_KEY = "findUnlinkedFilesDialogSize";

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

@@ -19,8 +19,8 @@
 import org.jabref.model.entry.specialfields.SpecialField;
 import org.jabref.preferences.JabRefPreferences;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Static variables for graphics files and keyboard shortcuts.
@@ -45,7 +45,7 @@ public class GUIGlobals {
     public static final Color ENTRY_EDITOR_LABEL_COLOR = new Color(100, 100, 150); // Empty field, blue.
 
     static final Color INACTIVE_TABBED_COLOR = Color.black; // inactive Database
-    private static final Log LOGGER = LogFactory.getLog(GUIGlobals.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(GUIGlobals.class);
     private static final Map<String, JLabel> TABLE_ICONS = new HashMap<>(); // Contains table icon mappings. Set up
     static final Color ACTIVE_TABBED_COLOR = ENTRY_EDITOR_LABEL_COLOR.darker(); // active Database (JTabbedPane)
 

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

@@ -33,8 +33,8 @@
 
 import de.jensd.fx.glyphs.materialdesignicons.MaterialDesignIcon;
 import de.jensd.fx.glyphs.materialdesignicons.MaterialDesignIconView;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class IconTheme {
 
@@ -45,7 +45,7 @@ public class IconTheme {
     public static final Color DEFAULT_DISABLED_COLOR = JabRefPreferences.getInstance().getColor(JabRefPreferences.ICON_DISABLED_COLOR);
     public static Font FONT;
     private static final String DEFAULT_ICON_PATH = "/images/external/red.png";
-    private static final Log LOGGER = LogFactory.getLog(IconTheme.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(IconTheme.class);
     private static final Map<String, String> KEY_TO_ICON = readIconThemeFile(
             IconTheme.class.getResource("/images/Icons.properties"), "/images/external/");
 

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

@@ -14,12 +14,12 @@
 import org.jabref.gui.fieldeditors.JTextAreaWithHighlighting;
 import org.jabref.logic.search.SearchQueryHighlightListener;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class JEditorPaneWithHighlighting extends JEditorPane implements SearchQueryHighlightListener {
 
-    private static final Log LOGGER = LogFactory.getLog(JTextAreaWithHighlighting.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(JTextAreaWithHighlighting.class);
 
     public void highlightPattern(Optional<Pattern> highlightPattern) {
         Highlighter highlighter = getHighlighter();

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

@@ -143,15 +143,15 @@
 import org.jabref.preferences.SearchPreferences;
 
 import com.google.common.eventbus.Subscribe;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import osx.macadapter.MacAdapter;
 
 /**
  * The main window of the application.
  */
 public class JabRefFrame extends JFrame implements OutputPrinter {
-    private static final Log LOGGER = LogFactory.getLog(JabRefFrame.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(JabRefFrame.class);
 
     // Frame titles.
     private static final String FRAME_TITLE = "JabRef";
@@ -653,7 +653,7 @@ public void windowClosing(WindowEvent e) {
             try {
                 new MacAdapter().registerMacEvents(this);
             } catch (Exception e) {
-                LOGGER.fatal("Could not interface with Mac OS X methods.", e);
+                LOGGER.error("Could not interface with Mac OS X methods.", e);
             }
         }
 

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

@@ -34,15 +34,15 @@
 import org.jabref.preferences.PreviewPreferences;
 
 import com.google.common.eventbus.Subscribe;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Displays an BibEntry using the given layout format.
  */
 public class PreviewPanel extends ScrollPane implements SearchQueryHighlightListener, EntryContainer {
 
-    private static final Log LOGGER = LogFactory.getLog(PreviewPanel.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(PreviewPanel.class);
 
     private final ClipBoardManager clipBoardManager;
     private final DialogService dialogService;