Add feature relinking moved file

CHANGELOG.md

@@ -21,6 +21,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - When pasting HTML into the abstract or a comment field, the hypertext is automatically converted to Markdown. [#10558](https://github.com/JabRef/jabref/issues/10558)
 - We added the possibility to redownload files that had been present but are no longer in the specified location. [#10848](https://github.com/JabRef/jabref/issues/10848)
 - We added the citation key pattern `[camelN]`. Equivalent to the first N words of the `[camel]` pattern.
+- We added file relinking functionality after a file is moved when clicking the "Automatically set file links" button. Implementation based and improved upon work done in closed issue [#10526]. [#9798]
 
 ### Changed
 

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

@@ -1,5 +1,6 @@
 package org.jabref.cli;
 
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
@@ -188,7 +189,7 @@ private Optional<ParserResult> importFile(Path file, String importFormat) {
         }
     }
 
-    public void processArguments() {
+    public void processArguments() throws FileNotFoundException {
         uiCommands.clear();
 
         if ((startupMode == Mode.INITIAL_START) && cli.isShowVersion()) {
@@ -711,7 +712,7 @@ private void resetPreferences(String value) {
         }
     }
 
-    private void automaticallySetFileLinks(List<ParserResult> loaded) {
+    private void automaticallySetFileLinks(List<ParserResult> loaded) throws FileNotFoundException {
         for (ParserResult parserResult : loaded) {
             BibDatabase database = parserResult.getDatabase();
             LOGGER.info(Localization.lang("Automatically setting file links"));

src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java

@@ -1,5 +1,6 @@
 package org.jabref.gui.externalfiles;
 
+import java.io.FileNotFoundException;
 import java.util.List;
 
 import javax.swing.undo.UndoManager;
@@ -55,7 +56,7 @@ public void execute() {
 
         Task<AutoSetFileLinksUtil.LinkFilesResult> linkFilesTask = new Task<>() {
             @Override
-            protected AutoSetFileLinksUtil.LinkFilesResult call() {
+            protected AutoSetFileLinksUtil.LinkFilesResult call() throws FileNotFoundException {
                 return util.linkAssociatedFiles(entries, nc);
             }
 

src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java

@@ -1,6 +1,8 @@
 package org.jabref.gui.externalfiles;
 
+import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.nio.file.FileVisitOption;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
@@ -30,23 +32,25 @@
 
 public class AutoSetFileLinksUtil {
 
+    record RelinkedResults(List<LinkedFile> relinkedFiles, List<String> exceptions) { }
+
     public static class LinkFilesResult {
         private final List<BibEntry> changedEntries = new ArrayList<>();
-        private final List<IOException> fileExceptions = new ArrayList<>();
+        private final List<String> fileExceptions = new ArrayList<String>();
 
         protected void addBibEntry(BibEntry bibEntry) {
             changedEntries.add(bibEntry);
         }
 
-        protected void addFileException(IOException exception) {
+        protected void addFileException(String exception) {
             fileExceptions.add(exception);
         }
 
         public List<BibEntry> getChangedEntries() {
             return changedEntries;
         }
 
-        public List<IOException> getFileExceptions() {
+        public List<String> getFileExceptions() {
             return fileExceptions;
         }
     }
@@ -66,7 +70,7 @@ private AutoSetFileLinksUtil(List<Path> directories, FilePreferences filePrefere
         this.filePreferences = filePreferences;
     }
 
-    public LinkFilesResult linkAssociatedFiles(List<BibEntry> entries, NamedCompound ce) {
+    public LinkFilesResult linkAssociatedFiles(List<BibEntry> entries, NamedCompound ce) throws FileNotFoundException {
         LinkFilesResult result = new LinkFilesResult();
 
         for (BibEntry entry : entries) {
@@ -75,7 +79,7 @@ public LinkFilesResult linkAssociatedFiles(List<BibEntry> entries, NamedCompound
             try {
                 linkedFiles = findAssociatedNotLinkedFiles(entry);
             } catch (IOException e) {
-                result.addFileException(e);
+                result.addFileException(String.valueOf(e));
                 LOGGER.error("Problem finding files", e);
             }
 
@@ -94,10 +98,18 @@ public LinkFilesResult linkAssociatedFiles(List<BibEntry> entries, NamedCompound
                         entry.addFile(linkedFile);
                     });
                 }
-
                 if (changed) {
                     result.addBibEntry(entry);
                 }
+                // Run Relinking Process
+                RelinkedResults relink = relinkingFiles(entry.getFiles());
+                entry.setFiles(relink.relinkedFiles);
+                if (!relink.relinkedFiles().isEmpty()) {
+                    result.addBibEntry(entry);
+                }
+                for (String e : (relink.exceptions)) {
+                    result.addFileException(e);
+                }
             }
         }
         return result;
@@ -127,16 +139,60 @@ public List<LinkedFile> findAssociatedNotLinkedFiles(BibEntry entry) throws IOEx
 
             if (!fileAlreadyLinked) {
                 Optional<ExternalFileType> type = FileUtil.getFileExtension(foundFile)
-                                                            .map(extension -> ExternalFileTypes.getExternalFileTypeByExt(extension, filePreferences))
-                                                            .orElse(Optional.of(new UnknownExternalFileType("")));
+                                                          .map(extension -> ExternalFileTypes.getExternalFileTypeByExt(extension, filePreferences))
+                                                          .orElse(Optional.of(new UnknownExternalFileType("")));
 
                 String strType = type.isPresent() ? type.get().getName() : "";
                 Path relativeFilePath = FileUtil.relativize(foundFile, directories);
                 LinkedFile linkedFile = new LinkedFile("", relativeFilePath, strType);
                 linkedFiles.add(linkedFile);
             }
         }
-
         return linkedFiles;
     }
+
+    public RelinkedResults relinkingFiles(List<LinkedFile> listlinked) throws FileNotFoundException {
+        List<LinkedFile> changedFiles = new ArrayList<>();
+        List<String> exceptions = new ArrayList<>();
+
+        for (LinkedFile file : listlinked) {
+            Path path = Path.of(file.getLink());
+            if (!Files.exists(path)) {
+                Path filePath = Path.of(file.getLink());
+                // May need to put some limit since it can cause considerable performance problems.
+                String directoryPath = filePath.getParent().getParent().toString();
+
+                String fileNameString = filePath.getFileName().toString();
+
+                List<Path> fileLocations = searchFileInDirectoryAndSubdirectories(Path.of(directoryPath), fileNameString);
+                if (!fileLocations.isEmpty()) {
+                    // File locations is a list but as stated in the link below, it is a rare case. But can be solved if time allows.
+                    // https://github.com/JabRef/jabref/issues/9798#issuecomment-1524155132
+                    file.setLink(fileLocations.get(0).toString());
+                    changedFiles.add(file);
+                } else {
+                    exceptions.add(fileNameString);
+                    throw new FileNotFoundException();
+                }
+            }
+        }
+        return new RelinkedResults(changedFiles, exceptions);
+    }
+
+    public List<Path> searchFileInDirectoryAndSubdirectories(Path directory, String targetFileName) {
+        List<Path> paths = new ArrayList<>();
+        try {
+            Files.walk(directory, Integer.MAX_VALUE, FileVisitOption.FOLLOW_LINKS)
+                 .filter(path -> Files.isRegularFile(path))
+                 .filter(path -> path.getFileName().toString().equals(targetFileName))
+                 .forEach(paths::add);
+        } catch (IOException e) {
+            // Handle any exceptions here
+        }
+        List<Path> output = new ArrayList<>();
+        for (Path p : paths) {
+            output.add(p);
+        }
+        return output;
+    }
 }

src/main/java/org/jabref/gui/remote/CLIMessageHandler.java

@@ -1,5 +1,6 @@
 package org.jabref.gui.remote;
 
+import java.io.FileNotFoundException;
 import java.util.Arrays;
 
 import javafx.application.Platform;
@@ -42,6 +43,9 @@ public void handleCommandLineArguments(String[] message) {
             Platform.runLater(() -> JabRefGUI.getMainFrame().handleUiCommands(argumentProcessor.getUiCommands()));
         } catch (ParseException e) {
             LOGGER.error("Error when parsing CLI args", e);
+        } catch (
+                FileNotFoundException e) {
+            throw new RuntimeException(e);
         }
     }
 }

src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java

@@ -2,6 +2,8 @@
 
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.TreeSet;
@@ -26,7 +28,6 @@
 import static org.mockito.Mockito.when;
 
 public class AutoSetFileLinksUtilTest {
-
     private final FilePreferences filePreferences = mock(FilePreferences.class);
     private final AutoLinkPreferences autoLinkPrefs = new AutoLinkPreferences(
             AutoLinkPreferences.CitationKeyDependency.START,
@@ -47,7 +48,7 @@ public void setUp(@TempDir Path folder) throws Exception {
     }
 
     @Test
-    public void findAssociatedNotLinkedFilesSuccess() throws Exception {
+    public void testFindAssociatedNotLinkedFilesSuccess() throws Exception {
         when(databaseContext.getFileDirectories(any())).thenReturn(Collections.singletonList(path.getParent()));
         List<LinkedFile> expected = Collections.singletonList(new LinkedFile("", Path.of("CiteKey.pdf"), "PDF"));
         AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, filePreferences, autoLinkPrefs);
@@ -56,10 +57,78 @@ public void findAssociatedNotLinkedFilesSuccess() throws Exception {
     }
 
     @Test
-    public void findAssociatedNotLinkedFilesForEmptySearchDir() throws Exception {
+    public void testFindAssociatedNotLinkedFilesForEmptySearchDir() throws Exception {
         when(filePreferences.shouldStoreFilesRelativeToBibFile()).thenReturn(false);
         AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, filePreferences, autoLinkPrefs);
         List<LinkedFile> actual = util.findAssociatedNotLinkedFiles(entry);
         assertEquals(Collections.emptyList(), actual);
     }
+
+        /* @BeforeEach
+    public void setUp(@TempDir Path folder) throws Exception {
+        A = folder.resolve("A");
+        Files.createDirectory(A);
+        B = folder.resolve("B");
+        Files.createDirectory(B);
+        path = A.resolve("CiteKey.pdf");
+        Files.createFile(path);
+        entry.setCitationKey("CiteKey");
+        when(filePreferences.getExternalFileTypes())
+                .thenReturn(FXCollections.observableSet(new TreeSet<>(ExternalFileTypes.getDefaultExternalFileTypes())));
+    } */
+
+    @Test
+    public void testFileLinksAfterMoving() throws Exception {
+        // Run "Automatically set file links" - check that the bib file was not modified
+        path = path.getParent();
+
+        Path A = path.resolve("A");
+        Files.createDirectory(A);
+        Path B = path.resolve("B");
+        Files.createDirectory(B);
+        Path filePath = A.resolve("Test.pdf");
+        Files.createFile(filePath);
+        entry.setCitationKey("Test");
+
+        LinkedFile linkedFile = new LinkedFile("desc", filePath, "PDF");
+        List<LinkedFile> listLinked = new ArrayList<>();
+        listLinked.add(linkedFile);
+        entry.setFiles(listLinked);
+
+        Path destination = B.resolve("Test.pdf");
+        Files.move(A.resolve("Test.pdf"), destination, StandardCopyOption.REPLACE_EXISTING);
+
+        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, filePreferences, autoLinkPrefs);
+        AutoSetFileLinksUtil.RelinkedResults results = util.relinkingFiles(entry.getFiles());
+        List<LinkedFile> list = results.relinkedFiles();
+        List<String> exceptions = results.exceptions();
+        assertEquals(Collections.emptyList(), exceptions);
+
+        // Change Entry to match required result and run method on bib
+        LinkedFile linkedDestFile = new LinkedFile("desc", B.resolve("Test.pdf"), "PDF");
+        List<LinkedFile> listLinked2 = new ArrayList<>();
+        listLinked2.add(linkedDestFile);
+        entry.setFiles(listLinked2);
+        assertEquals(entry.getFiles(), list);
+
+        // After this point, tested different extension along with the case where document has multiple file references
+        Path filePath2 = B.resolve("Test1.txt");
+        Files.createFile(filePath2);
+        linkedFile = new LinkedFile("desc", filePath2, "TXT");
+        listLinked.add(linkedFile);
+        entry.setFiles(listLinked);
+
+        destination = A.resolve("Test1.txt");
+        Files.move(B.resolve("Test1.txt"), destination, StandardCopyOption.REPLACE_EXISTING);
+        util = new AutoSetFileLinksUtil(databaseContext, filePreferences, autoLinkPrefs);
+        results = util.relinkingFiles(entry.getFiles());
+        list = results.relinkedFiles();
+        exceptions = results.exceptions();
+
+        listLinked2.clear();
+        listLinked2.add(new LinkedFile("desc", B.resolve("Test.pdf"), "PDF"));
+        listLinked2.add(new LinkedFile("desc", A.resolve("Test1.txt"), "TXT"));
+
+        assertEquals(listLinked2, list);
+    }
 }