More conservative write

CHANGELOG.md

@@ -13,6 +13,9 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Changed
 
+- We changed the writing method of a `.bib` file: Existing files should have been modified instead of being replaced.
+- When JabRef writes a `.bib` file, it makes first a backup (`.bak`) of the `.bib`.
+- When JabRef writes a `.bib` file, it first attempts to write into a separate local directory.
 - We improved the Citavi Importer to also import so called Knowledge-items into the field `comment` of the corresponding entry [#9025](https://github.com/JabRef/jabref/issues/9025)
 - We removed wrapping of string constants when writing to a `.bib` file.
 - We changed the button label from "Return to JabRef" to "Return to library" to better indicate the purpose of the action.

build.gradle

@@ -216,6 +216,12 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
+    testImplementation ('com.google.jimfs:jimfs:1.2') {
+        exclude group: "com.google.auto.service"
+        exclude group: "com.google.code.findbugs"
+        exclude group: "org.checkerframework"
+    }
+
     checkstyle 'com.puppycrawl.tools:checkstyle:10.3.2'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'

docs/decisions/0026-safe-file-writing-by-writing-to-a-temporary-file-in-another-filder.md

@@ -0,0 +1,34 @@
+---
+parent: Decision Records
+nav_order: 26
+---
+# Safe File Writing by Writing to a Temporary File in Another Folder
+
+## Context and Problem Statement
+
+JabRef needs to write to the .bib file. A .bib file of a user should never be damaged. JabRef needs to provide a way to do "safe" writing of a bib file.
+
+## Considered Options
+
+* Create a temporary file in a local folder and copy after successful write
+* Create temporary file next to bib file and atomically move it to the original file
+
+## Decision Outcome
+
+Chosen option: "Create a temporary file in a local folder and copy after successful write", because good usage of Dropbox outweighs potential recovery scenarios
+
+## Pros and Cons of the Options
+
+### Create a temporary file in a local folder and copy after successful write
+
+* Good, because Keeps directory of .bib file clean
+* Good, because Keeping file access rights is simple as the file content is replaced, not the file itself
+* Bad, because Error recovery is hard
+
+### Create temporary file next to bib file and atomically move it to the original file
+
+This implementation is available at [Marty Lamb's AtomicFileOutputStream](https://github.com/martylamb/atomicfileoutputstream/blob/master/src/main/java/com/martiansoftware/io/AtomicFileOutputStream.java)
+and [Apache Zookeepr's AtomicFileOutputStream](https://github.com/apache/zookeeper/blob/master/zookeeper-server/src/main/java/org/apache/zookeeper/common/AtomicFileOutputStream.java).
+
+* Good, because Atomic move is an all-or-nothing move
+* Bad, because Makes issues with Dropbox, OneDrive, ...

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

@@ -77,8 +77,8 @@ private void openWindow(Stage mainStage) {
         if (guiPreferences.isWindowMaximised()) {
             mainStage.setMaximized(true);
         } else if ((Screen.getScreens().size() == 1) && isWindowPositionOutOfBounds()) {
-            // corrects the Window, if its outside of the mainscreen
-            LOGGER.debug("The Jabref Window is outside the Main Monitor\n");
+            // corrects the Window, if it is outside the mainscreen
+            LOGGER.debug("The Jabref window is outside the main screen\n");
             mainStage.setX(0);
             mainStage.setY(0);
             mainStage.setWidth(1024);

src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java

@@ -231,7 +231,7 @@ private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding,
         GeneralPreferences generalPreferences = this.preferences.getGeneralPreferences();
         SavePreferences savePreferences = this.preferences.getSavePreferences()
                                                       .withSaveType(saveType);
-        try (AtomicFileWriter fileWriter = new AtomicFileWriter(file, encoding, savePreferences.shouldMakeBackup())) {
+        try (AtomicFileWriter fileWriter = new AtomicFileWriter(file, encoding)) {
             BibDatabaseContext bibDatabaseContext = libraryTab.getBibDatabaseContext();
             BibWriter bibWriter = new BibWriter(fileWriter, bibDatabaseContext.getDatabase().getNewLineSeparator());
             BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(bibWriter, generalPreferences, savePreferences, entryTypesManager);

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

@@ -107,7 +107,7 @@ public static boolean backupFileDiffers(Path originalPath) {
         }
 
         try {
-            return Files.mismatch(originalPath, backupPath) != -1L;
+            return !Files.isSameFile(originalPath, backupPath);
         } catch (IOException e) {
             LOGGER.debug("Could not compare original file and backup file.", e);
             // User has to investigate in this case