Merge remote-tracking branch 'upstream/master' into fileDescr

* upstream/master:
  Don't highlight odd rows in file list editor (#3223)
  Fix assertion by removing typo (#3220)
  Update assertion to change of online reference (#3221)
  Put in null return
  Reformatted code, renamed method, added try/catch
  Fix null return
  Changed from Path to Optional<Path>
  Added logic to check whether linked file already exists

CHANGELOG.md

@@ -39,6 +39,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the arrow keys in the search bar did not work as expected [#3081](https://github.com/JabRef/jabref/issues/3081)
 - We fixed wrong hotkey being displayed at "automatically file links" in the entry editor
 - We fixed an issue where metadata syncing with local and shared database were unstable. It will also fix syncing groups and sub-groups in database. [#2284](https://github.com/JabRef/jabref/issues/2284)
+- We fixed an issue where renaming a linked file would fail silently if a file with the same name existed.  Added support for overriding existing file at user discretion. [#3172] (https://github.com/JabRef/jabref/issues/3172)
 - We fixed an issue where the "Remove group and subgroups" operation did not remove group information from entries in the group [#3190](https://github.com/JabRef/jabref/issues/3190)
 - We fixed an issue where it was possible to leave the entry editor with an imbalance of braces. [#3167](https://github.com/JabRef/jabref/issues/3167)
 - Renaming files now truncates the filename to not exceed the limit of 255 chars [#2622](https://github.com/JabRef/jabref/issues/2622)

src/main/java/org/jabref/gui/entryeditor/EntryEditor.css

@@ -31,3 +31,7 @@
     -fx-text-fill: text-area-foreground;
     -fx-text-origin: baseline;
 }
+
+.list-cell:odd {
+    -fx-background-color: text-area-background;
+}

src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

@@ -30,6 +30,7 @@
 import org.jabref.logic.cleanup.MoveFilesCleanup;
 import org.jabref.logic.cleanup.RenamePdfCleanup;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
@@ -182,7 +183,8 @@ public void rename() {
                     Localization.lang("Cancel"));
 
             if (confirm) {
-                pdfCleanup.cleanup(entry);
+                Optional<Path> fileConflictCheck = pdfCleanup.findExistingFile(linkedFile, entry);
+                performRenameWithConflictCheck(file, pdfCleanup, targetFileName, fileConflictCheck);
             }
         } else {
             dialogService.showErrorDialogAndWait(
@@ -191,6 +193,23 @@ public void rename() {
         }
     }
 
+    private void performRenameWithConflictCheck(Optional<Path> file, RenamePdfCleanup pdfCleanup, String targetFileName, Optional<Path> fileConflictCheck) {
+        boolean confirm;
+        if (!fileConflictCheck.isPresent()) {
+            pdfCleanup.cleanup(entry);
+        } else {
+            confirm = dialogService.showConfirmationDialogAndWait(
+                    Localization.lang("File exists"),
+                    Localization.lang("'%0' exists. Overwrite file?", targetFileName),
+                    Localization.lang("Overwrite"),
+                    Localization.lang("Cancel"));
+            if (confirm) {
+                FileUtil.renameFile(fileConflictCheck.get(), file.get(), true);
+                pdfCleanup.cleanup(entry);
+            }
+        }
+    }
+
     public void moveToDefaultDirectory() {
         if (linkedFile.isOnlineLink()) {
             // Cannot move remote links

src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java

@@ -10,6 +10,7 @@
 import java.util.Objects;
 import java.util.Optional;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import org.jabref.logic.layout.LayoutFormatterPreferences;
 import org.jabref.logic.util.io.FileUtil;
@@ -158,4 +159,29 @@ public String getTargetFileName(LinkedFile flEntry, BibEntry entry) {
     public int getUnsuccessfulRenames() {
         return unsuccessfulRenames;
     }
+
+    /**
+    * Check to see if a file already exists in the target directory.  Search is not case sensitive.
+    * @param flEntry
+    * @param entry
+    * @return First identified path that matches an existing file.  This name can be used in subsequent calls to override the existing file.
+    */
+    public Optional<Path> findExistingFile(LinkedFile flEntry, BibEntry entry) {
+        String targetFileName = getTargetFileName(flEntry, entry);
+        // The .get() is legal without check because the method will always return a value.
+        Path targetFilePath = flEntry.findIn(databaseContext,
+                fileDirectoryPreferences).get().getParent().resolve(targetFileName);
+        Path oldFilePath = flEntry.findIn(databaseContext, fileDirectoryPreferences).get();
+        //Check if file already exists in directory with different case.
+        //This is necessary because other entries may have such a file.
+        Optional<Path> matchedByDiffCase = Optional.empty();
+        try (Stream<Path> stream = Files.list(oldFilePath.getParent())) {
+            matchedByDiffCase = stream
+                    .filter(name -> name.toString().equalsIgnoreCase(targetFilePath.toString()))
+                    .findFirst();
+        } catch (IOException e) {
+            LOGGER.error("Could not get the list of files in target directory", e);
+        }
+        return matchedByDiffCase;
+    }
 }

src/test/java/org/jabref/gui/importer/fetcher/OAI2HandlerFetcherTest.java

@@ -72,7 +72,7 @@ public void testParse() throws Throwable {
 
             Assert.assertEquals(Optional.of("Heavy Particles from Inflation"), be.getField("title"));
             Assert.assertTrue(be.getField("abstract").isPresent());
-            Assert.assertEquals(Optional.of("23 pages"), be.getField("comments"));
+            Assert.assertEquals(Optional.of("23 pages"), be.getField("comment"));
             Assert.assertEquals(Optional.of("CERN-PH-TH/2004-151"), be.getField("reportno"));
         } catch (SAXException e) {
             throw e.getException();

src/test/java/org/jabref/logic/importer/fetcher/IsbnViaEbookDeFetcherTest.java

@@ -65,12 +65,12 @@ public void authorsAreCorrectlyFormatted() throws Exception {
         bibEntry.setField("title", "Fundamentals of Business Process Management");
         bibEntry.setField("publisher", "Springer");
         bibEntry.setField("year", "2015");
-        bibEntry.setField("author", "Dumas, Marlon and Rosa, Marcello La and Mendling, Jan and Reijers, Hajo");
+        bibEntry.setField("author", "Dumas, Marlon and Rosa, Marcello La and Mendling, Jan and Reijers, Hajo A.");
         bibEntry.setField("date", "2015-04-12");
         bibEntry.setField("ean", "9783642434730");
         bibEntry.setField("isbn", "3642434738");
         bibEntry.setField("pagetotal", "428");
-        bibEntry.setField("url", "http://www.ebook.de/de/product/23955263/marlon_dumas_marcello_la_rosa_jan_mendling_hajo_reijers_fundamentals_of_business_process_management.html");
+        bibEntry.setField("url", "http://www.ebook.de/de/product/23955263/marlon_dumas_marcello_la_rosa_jan_mendling_hajo_a_reijers_fundamentals_of_business_process_management.html");
 
         Optional<BibEntry> fetchedEntry = fetcher.performSearchById("3642434738");
         assertEquals(Optional.of(bibEntry), fetchedEntry);