Add Debug to BackupManager

CHANGELOG.md

@@ -24,6 +24,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - 'Get full text' now also checks the file url. [#568](https://github.com/koppor/jabref/issues/568)
 - We refined the 'main directory not found' error message. [#9625](https://github.com/JabRef/jabref/pull/9625)
+- `log.txt` now contains debug messages. Debugging needs to be enabled explicitly. [#9678](https://github.com/JabRef/jabref/pull/9678)
+- `log.txt` does not contain entries for non-found files during PDF indexing. [#9678](https://github.com/JabRef/jabref/pull/9678)
 - We modified the `Add Group` dialog to use the most recently selected group hierarchical context [#9141](https://github.com/JabRef/jabref/issues/9141)
 
 

docs/code-howtos/logging.md

@@ -5,20 +5,44 @@ parent: Code Howtos
 
 JabRef uses the logging facade [SLF4j](https://www.slf4j.org). All log messages are passed internally to [tinylog](https://tinylog.org/v2/) which handles any filtering, formatting and writing of log messages.
 
-* Obtaining a logger for a class:
+Obtaining a logger for a class:
 
-    ```java
-    private static final Logger LOGGER = LoggerFactory.getLogger(<ClassName>.class);
-    ```
+```java
+private static final Logger LOGGER = LoggerFactory.getLogger(<ClassName>.class);
+```
 
-* If the logging event is caused by an exception, please add the exception to the log message as:
+Please always use `LOGGER.debug` for debugging.
 
-    ```java
-      catch (SomeException e) {
-         LOGGER.warn("Warning text.", e);
-         ...
-      }
-    ```
+Example:
+
+```java
+String example = "example";
+LOGGER.debug("Some state {}", example);
+```
+
+Enable logging in `tinylog.properties`:
+
+```properties
+[email protected] = debug
+```
+
+If the logging event is caused by an exception, please add the exception to the log message as:
+
+```java
+  catch (SomeException e) {
+     LOGGER.warn("Warning text.", e);
+     ...
+  }
+```
+
+When running tests, `tinylog-test.properties` is used.
+It is located under `src/test/resources`. As default, only `info` is logged.
+When developing, it makes sense to use `debug` as log level.
+One can change the log level per class using the pattern `level@class=debug` is set to `debug`.
+In the `.properties` file, this is done for `org.jabref.model.entry.BibEntry`.
+
+## Further reading
+
+SLF4J also support parameterized logging, e.g. if you want to print out multiple arguments in a log statement use a pair of curly braces (`{}`). 
+Head to <https://www.slf4j.org/faq.html#logging_performance> for examples.
 
-* SLF4J also support parameterized logging, e.g. if you want to print out multiple arguments in a log statement use a pair of curly braces. [Examples](https://www.slf4j.org/faq.html#logging\_performance)
-* When running tests, `tinylog-test.properties` is used. It is located under `src/test/resources`. As default, only `info` is logged. When developing, it makes sense to use `debug` as log level. One can change the log level per class using the pattern `level@class=debug` is set to `debug`. In the `.properties` file, this is done for `org.jabref.model.entry.BibEntry`.

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

@@ -105,7 +105,7 @@ private static void addLogToDisk() {
         // https://tinylog.org/v2/configuration/#shared-file-writer
         Map<String, String> configuration = Map.of(
                 "writerFile", "shared file",
-                "writerFile.level", "info",
+                "writerFile.level", "debug",
                 "writerFile.file", directory.resolve("log.txt").toString(),
                 "writerFile.charset", "UTF-8");
 

src/main/java/org/jabref/gui/collab/entryadd/EntryAdd.java

@@ -8,6 +8,8 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 
+import com.google.common.base.MoreObjects;
+
 public final class EntryAdd extends DatabaseChange {
     private final BibEntry addedEntry;
 
@@ -28,4 +30,11 @@ public void applyChange(NamedCompound undoEdit) {
     public BibEntry getAddedEntry() {
         return addedEntry;
     }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("addedEntry", addedEntry)
+                          .toString();
+    }
 }

src/main/java/org/jabref/gui/collab/entrychange/EntryChange.java

@@ -11,6 +11,8 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 
+import com.google.common.base.MoreObjects;
+
 public final class EntryChange extends DatabaseChange {
     private final BibEntry oldEntry;
     private final BibEntry newEntry;
@@ -46,4 +48,12 @@ public void applyChange(NamedCompound undoEdit) {
 
         undoEdit.addEdit(changeEntryEdit);
     }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("oldEntry", oldEntry)
+                          .add("newEntry", newEntry)
+                          .toString();
+    }
 }

src/main/java/org/jabref/gui/collab/entrydelete/EntryDelete.java

@@ -8,6 +8,8 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 
+import com.google.common.base.MoreObjects;
+
 public final class EntryDelete extends DatabaseChange {
     private final BibEntry deletedEntry;
 
@@ -28,4 +30,11 @@ public void applyChange(NamedCompound undoEdit) {
     public BibEntry getDeletedEntry() {
         return deletedEntry;
     }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("deletedEntry", deletedEntry)
+                          .toString();
+    }
 }

src/main/java/org/jabref/gui/collab/groupchange/GroupChange.java

@@ -11,6 +11,8 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.groups.GroupTreeNode;
 
+import com.google.common.base.MoreObjects;
+
 public final class GroupChange extends DatabaseChange {
     private final GroupDiff groupDiff;
 
@@ -53,4 +55,11 @@ public void applyChange(NamedCompound undoEdit) {
     public GroupDiff getGroupDiff() {
         return groupDiff;
     }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("groupDiff", groupDiff)
+                          .toString();
+    }
 }

src/main/java/org/jabref/gui/collab/metedatachange/MetadataChange.java

@@ -7,6 +7,8 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 
+import com.google.common.base.MoreObjects;
+
 public final class MetadataChange extends DatabaseChange {
     private final MetaDataDiff metaDataDiff;
 
@@ -29,4 +31,11 @@ public void applyChange(NamedCompound undoEdit) {
     public MetaDataDiff getMetaDataDiff() {
         return metaDataDiff;
     }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("metaDataDiff", metaDataDiff)
+                          .toString();
+    }
 }

src/main/java/org/jabref/gui/collab/preamblechange/PreambleChange.java

@@ -8,6 +8,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 
+import com.google.common.base.MoreObjects;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -32,4 +33,11 @@ public void applyChange(NamedCompound undoEdit) {
     public PreambleDiff getPreambleDiff() {
         return preambleDiff;
     }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("preambleDiff", preambleDiff)
+                          .toString();
+    }
 }

src/main/java/org/jabref/gui/collab/stringadd/BibTexStringAdd.java

@@ -9,6 +9,7 @@
 import org.jabref.model.database.KeyCollisionException;
 import org.jabref.model.entry.BibtexString;
 
+import com.google.common.base.MoreObjects;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -36,4 +37,11 @@ public void applyChange(NamedCompound undoEdit) {
     public BibtexString getAddedString() {
         return addedString;
     }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("addedString", addedString)
+                          .toString();
+    }
 }

src/main/java/org/jabref/gui/collab/stringchange/BibTexStringChange.java

@@ -8,6 +8,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibtexString;
 
+import com.google.common.base.MoreObjects;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -40,4 +41,12 @@ public BibtexString getOldString() {
     public BibtexString getNewString() {
         return newString;
     }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("oldString", oldString)
+                          .add("newString", newString)
+                          .toString();
+    }
 }

src/main/java/org/jabref/gui/collab/stringdelete/BibTexStringDelete.java

@@ -8,6 +8,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibtexString;
 
+import com.google.common.base.MoreObjects;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -35,4 +36,11 @@ public void applyChange(NamedCompound undoEdit) {
     public BibtexString getDeletedString() {
         return deletedString;
     }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("deletedString", deletedString)
+                          .toString();
+    }
 }

src/main/java/org/jabref/gui/collab/stringrename/BibTexStringRename.java

@@ -8,6 +8,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibtexString;
 
+import com.google.common.base.MoreObjects;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -45,4 +46,12 @@ public BibtexString getOldString() {
     public BibtexString getNewString() {
         return newString;
     }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("oldString", oldString)
+                          .add("newString", newString)
+                          .toString();
+    }
 }

src/main/java/org/jabref/gui/dialogs/BackupUIManager.java

@@ -70,6 +70,7 @@ private static Optional<ParserResult> showReviewBackupDialog(DialogService dialo
 
             return DefaultTaskExecutor.runInJavaFXThread(() -> {
                 List<DatabaseChange> changes = DatabaseChangeList.compareAndGetChanges(originalDatabase, backupDatabase, changeResolverFactory);
+                LOGGER.debug("changes: {}", changes);
                 DatabaseChangesResolverDialog reviewBackupDialog = new DatabaseChangesResolverDialog(
                         changes,
                         originalDatabase, "Review Backup"

src/main/java/org/jabref/logic/autosaveandbackup/BackupManager.java

@@ -139,20 +139,26 @@ public static void shutdown(BibDatabaseContext bibDatabaseContext) {
      * In the case of an exception <code>true</code> is returned to ensure that the user checks the output.
      */
     public static boolean backupFileDiffers(Path originalPath) {
+        LOGGER.debug("originalPath path: {}", originalPath);
         Path discardedFile = determineDiscardedFile(originalPath);
         if (Files.exists(discardedFile)) {
+            LOGGER.debug("discardedFile {} exists", discardedFile);
             try {
                 Files.delete(discardedFile);
             } catch (IOException e) {
                 LOGGER.error("Could not remove discarded file {}", discardedFile, e);
+                LOGGER.debug("backupFileDiffers for {}: true", originalPath);
                 return true;
             }
+            LOGGER.debug("backupFileDiffers for {}: false", originalPath);
             return false;
         }
-        return getLatestBackupPath(originalPath).map(latestBackupPath -> {
+        LOGGER.debug("discardedFile {} does not exist", discardedFile);
+        Boolean result = getLatestBackupPath(originalPath).map(latestBackupPath -> {
+            LOGGER.debug("Latest backup path: {}", latestBackupPath);
             FileTime latestBackupFileLastModifiedTime;
             try {
-                 latestBackupFileLastModifiedTime = Files.getLastModifiedTime(latestBackupPath);
+                latestBackupFileLastModifiedTime = Files.getLastModifiedTime(latestBackupPath);
             } catch (IOException e) {
                 LOGGER.debug("Could not get timestamp of backup file {}", latestBackupPath, e);
                 // If we cannot get the timestamp, we do show any warning
@@ -179,6 +185,8 @@ public static boolean backupFileDiffers(Path originalPath) {
                 return true;
             }
         }).orElse(false);
+        LOGGER.debug("backupFileDiffers for {}: {}", originalPath, result);
+        return result;
     }
 
     /**

src/main/java/org/jabref/logic/pdf/search/indexing/PdfIndexer.java

@@ -188,7 +188,7 @@ private void writeToIndex(BibEntry entry, LinkedFile linkedFile) {
         }
         Optional<Path> resolvedPath = linkedFile.findIn(databaseContext, filePreferences);
         if (resolvedPath.isEmpty()) {
-            LOGGER.warn("Could not find {}", linkedFile.getLink());
+            LOGGER.debug("Could not find {}", linkedFile.getLink());
             return;
         }
         try {

src/main/java/org/jabref/model/database/BibDatabaseContext.java

@@ -248,13 +248,17 @@ public static Path getFulltextIndexBasePath() {
 
     public Path getFulltextIndexPath() {
         Path appData = getFulltextIndexBasePath();
+        Path indexPath;
 
         if (getDatabasePath().isPresent()) {
-            LOGGER.info("Index path for {} is {}", getDatabasePath().get(), appData);
-            return appData.resolve(String.valueOf(this.getDatabasePath().get().hashCode()));
+            indexPath = appData.resolve(String.valueOf(this.getDatabasePath().get().hashCode()));
+            LOGGER.debug("Index path for {} is {}", getDatabasePath().get(), indexPath);
+            return indexPath;
         }
 
-        return appData.resolve("unsaved");
+        indexPath = appData.resolve("unsaved");
+        LOGGER.debug("Using index for unsaved database: {}", indexPath);
+        return indexPath;
     }
 
     @Override

src/main/resources/tinylog.properties

@@ -5,3 +5,7 @@ writerAzure = application insights
 
 # More shrunk exception logs. See https://tinylog.org/v2/configuration/#strip-stack-trace-elements for details
 exception = strip: jdk.internal
+
+#[email protected] = debug
+[email protected] = debug
+[email protected] = debug