Resolve requested "nitpicks" and warnings.

CHANGELOG.md

@@ -27,6 +27,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added ability to export in CFF (Citation File Format) [#10661](https://github.com/JabRef/jabref/issues/10661).
 - We added ability to push entries to TeXworks. [#3197](https://github.com/JabRef/jabref/issues/3197)
 - We added the ability to zoom in and out in the document viewer using <kbd>Ctrl</kbd> + <kbd>Scroll</kbd>. [#10964](https://github.com/JabRef/jabref/pull/10964)
+- We added a Cleanup for removing non-existent files and grouped the related options [#10929](https://github.com/JabRef/jabref/issues/10929)
 
 ### Changed
 

src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.fxml

@@ -14,26 +14,39 @@
         <ToggleGroup fx:id="timestampCleanup"/>
       </fx:define>
 
-
-      <CheckBox fx:id="cleanUpDOI" text="%Move DOIs from note and URL field to DOI field and remove http prefix" />
-      <CheckBox fx:id="cleanUpEprint" text="%Move preprint information from 'URL' and 'journal' field to the 'eprint' field" />
-      <CheckBox fx:id="cleanUpURL" text="%Move URL in note field to url field" />
-      <CheckBox fx:id="cleanUpISSN" text="%Reformat ISSN" />
-      <CheckBox fx:id="cleanUpUpgradeExternalLinks" />
-      <CheckBox fx:id="cleanUpMovePDF" />
-      <CheckBox fx:id="cleanUpMakePathsRelative" text="%Make paths of linked files relative (if possible)" />
-      <CheckBox fx:id="cleanUpRenamePDF" text="%Rename PDFs to given filename format pattern" />
-      <VBox prefHeight="40.0" prefWidth="451.0" spacing="10.0">
-          <Label fx:id="cleanupRenamePDFLabel" />
-          <CheckBox fx:id="cleanUpRenamePDFonlyRelativePaths" text="%Rename only PDFs having a relative path" />
-       <VBox.margin>
-          <Insets left="20.0" />
-       </VBox.margin>
+      <Label text="Miscellanous" />
+      <VBox>
+         <VBox.margin>
+            <Insets left="20.0" />
+         </VBox.margin>
+         <CheckBox fx:id="cleanUpDOI" text="%Move DOIs from note and URL field to DOI field and remove http prefix" />
+         <CheckBox fx:id="cleanUpEprint" text="%Move preprint information from 'URL' and 'journal' field to the 'eprint' field" />
+         <CheckBox fx:id="cleanUpURL" text="%Move URL in note field to url field" />
+         <CheckBox fx:id="cleanUpISSN" text="%Reformat ISSN" />
+         <CheckBox fx:id="cleanUpBiblatex" text="%Convert to biblatex format (e.g., store publication date in date field)" />
+         <CheckBox fx:id="cleanUpBibtex" text="%Convert to BibTeX format (e.g., store publication date in year and month fields)" />
+         <CheckBox fx:id="cleanUpTimestampToCreationDate" text="%Convert timestamp field to field 'creationdate'" />
+         <CheckBox fx:id="cleanUpTimestampToModificationDate" text="%Convert timestamp field to field 'modificationdate'" />
+      </VBox>
+
+      <Label text="File Related" />
+      <VBox>
+         <VBox.margin>
+            <Insets left="20.0" />
+         </VBox.margin>
+         <CheckBox fx:id="cleanUpUpgradeExternalLinks" />
+         <CheckBox fx:id="cleanUpMovePDF" />
+         <CheckBox fx:id="cleanUpMakePathsRelative" text="%Make paths of linked files relative (if possible)" />
+         <CheckBox fx:id="cleanUpRenamePDF" text="%Rename PDFs to given filename format pattern" />
+         <VBox prefHeight="40.0" prefWidth="451.0" spacing="10.0">
+            <Label fx:id="cleanupRenamePDFLabel" />
+            <CheckBox fx:id="cleanUpRenamePDFonlyRelativePaths" text="%Rename only PDFs having a relative path" />
+         <VBox.margin>
+            <Insets left="20.0" />
+         </VBox.margin>
+         </VBox>
+         <CheckBox fx:id="cleanUpDeletedFiles" text="Remove links to non existent files" />
       </VBox>
-      <CheckBox fx:id="cleanUpBiblatex" text="%Convert to biblatex format (e.g., store publication date in date field)" />
-      <CheckBox fx:id="cleanUpBibtex" text="%Convert to BibTeX format (e.g., store publication date in year and month fields)" />
-      <CheckBox fx:id="cleanUpTimestampToCreationDate" text="%Convert timestamp field to field 'creationdate'" />
-      <CheckBox fx:id="cleanUpTimestampToModificationDate" text="%Convert timestamp field to field 'modificationdate'" />
             <FieldFormatterCleanupsPanel fx:id="formatterCleanupsPanel" />
  <padding>
     <Insets bottom="10.0" left="15.0" right="10.0" top="10.0" />

src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.java

@@ -33,6 +33,7 @@ public class CleanupPresetPanel extends VBox {
     @FXML private CheckBox cleanUpMakePathsRelative;
     @FXML private CheckBox cleanUpRenamePDF;
     @FXML private CheckBox cleanUpRenamePDFonlyRelativePaths;
+    @FXML private CheckBox cleanUpDeletedFiles;
     @FXML private CheckBox cleanUpUpgradeExternalLinks;
     @FXML private CheckBox cleanUpBiblatex;
     @FXML private CheckBox cleanUpBibtex;
@@ -71,6 +72,7 @@ private void init(CleanupPreferences cleanupPreferences, FilePreferences filePre
                                             .concat(": ")
                                             .concat(filePreferences.getFileNamePattern());
         cleanupRenamePDFLabel.setText(currentPattern);
+
         cleanUpBibtex.selectedProperty().addListener(
                 (observable, oldValue, newValue) -> {
                     if (newValue) {
@@ -109,6 +111,7 @@ private void updateDisplay(CleanupPreferences preset) {
         cleanUpRenamePDF.setSelected(preset.isActive(CleanupPreferences.CleanupStep.RENAME_PDF));
         cleanUpRenamePDFonlyRelativePaths.setSelected(preset.isActive(CleanupPreferences.CleanupStep.RENAME_PDF_ONLY_RELATIVE_PATHS));
         cleanUpUpgradeExternalLinks.setSelected(preset.isActive(CleanupPreferences.CleanupStep.CLEAN_UP_UPGRADE_EXTERNAL_LINKS));
+        cleanUpDeletedFiles.setSelected(preset.isActive(CleanupPreferences.CleanupStep.CLEAN_UP_DELETED_LINKED_FILES));
         cleanUpBiblatex.setSelected(preset.isActive(CleanupPreferences.CleanupStep.CONVERT_TO_BIBLATEX));
         cleanUpBibtex.setSelected(preset.isActive(CleanupPreferences.CleanupStep.CONVERT_TO_BIBTEX));
         cleanUpTimestampToCreationDate.setSelected(preset.isActive(CleanupPreferences.CleanupStep.CONVERT_TIMESTAMP_TO_CREATIONDATE));
@@ -150,6 +153,9 @@ public CleanupPreferences getCleanupPreset() {
         if (cleanUpUpgradeExternalLinks.isSelected()) {
             activeJobs.add(CleanupPreferences.CleanupStep.CLEAN_UP_UPGRADE_EXTERNAL_LINKS);
         }
+        if (cleanUpDeletedFiles.isSelected()) {
+            activeJobs.add(CleanupPreferences.CleanupStep.CLEAN_UP_DELETED_LINKED_FILES);
+        }
         if (cleanUpBiblatex.isSelected()) {
             activeJobs.add(CleanupPreferences.CleanupStep.CONVERT_TO_BIBLATEX);
         }

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

@@ -67,6 +67,8 @@ private CleanupJob toJob(CleanupPreferences.CleanupStep action) {
                     new RenamePdfCleanup(true, databaseContext, filePreferences);
             case CLEAN_UP_UPGRADE_EXTERNAL_LINKS ->
                     new UpgradePdfPsToFileCleanup();
+            case CLEAN_UP_DELETED_LINKED_FILES ->
+                    new RemoveLinksToNotExistentFiles(databaseContext, filePreferences);
             case CONVERT_TO_BIBLATEX ->
                     new ConvertToBiblatexCleanup();
             case CONVERT_TO_BIBTEX ->

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

@@ -0,0 +1,52 @@
+package org.jabref.logic.cleanup;
+
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+
+import org.jabref.model.FieldChange;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.LinkedFile;
+import org.jabref.model.util.OptionalUtil;
+import org.jabref.preferences.FilePreferences;
+
+public class RemoveLinksToNotExistentFiles implements CleanupJob {
+    private final BibDatabaseContext databaseContext;
+    private final FilePreferences filePreferences;
+
+    public RemoveLinksToNotExistentFiles(BibDatabaseContext databaseContext, FilePreferences filePreferences) {
+        this.databaseContext = Objects.requireNonNull(databaseContext);
+        this.filePreferences = Objects.requireNonNull(filePreferences);
+    }
+
+    @Override
+    public List<FieldChange> cleanup(BibEntry entry) {
+        List<LinkedFile> files = entry.getFiles();
+        List<LinkedFile> cleanedUpFiles = new ArrayList<>();
+        boolean changed = false;
+        for (LinkedFile file : files) {
+            if (file.isOnlineLink()) {
+                cleanedUpFiles.add(file);
+            } else {
+                Optional<Path> oldFile = file.findIn(databaseContext, filePreferences);
+
+                if (oldFile.isEmpty()) {
+                    changed = true;
+                } else {
+                    cleanedUpFiles.add(file);
+                }
+            }
+        }
+
+        if (changed) {
+            Optional<FieldChange> changes = entry.setFiles(cleanedUpFiles);
+            return OptionalUtil.toList(changes);
+        }
+
+        return Collections.emptyList();
+    }
+}

src/main/java/org/jabref/preferences/CleanupPreferences.java

@@ -88,6 +88,7 @@ public enum CleanupStep {
          * Collects file links from the pdf or ps field, and adds them to the list contained in the file field.
          */
         CLEAN_UP_UPGRADE_EXTERNAL_LINKS,
+        CLEAN_UP_DELETED_LINKED_FILES,
         /**
          * Converts to biblatex format
          */

src/test/java/org/jabref/logic/cleanup/RemoveLinksToNotExistentFilesTest.java

@@ -0,0 +1,163 @@
+package org.jabref.logic.cleanup;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+
+import org.jabref.logic.bibtex.FileFieldWriter;
+import org.jabref.model.FieldChange;
+import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.LinkedFile;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.entry.types.StandardEntryType;
+import org.jabref.model.metadata.MetaData;
+import org.jabref.preferences.FilePreferences;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+public class RemoveLinksToNotExistentFilesTest {
+    private Path fileBefore;
+    private BibEntry entry;
+    private RemoveLinksToNotExistentFiles removeLinks;
+
+    @BeforeEach
+    void setUp(@TempDir Path bibFolder) throws IOException {
+        // The folder where the files should be moved to
+        Path newFileFolder = bibFolder.resolve("pdf");
+        Files.createDirectory(newFileFolder);
+
+        Path originalFileFolder = bibFolder.resolve("files");
+        Path testBibFolder = bibFolder.resolve("test.bib");
+        Files.createDirectory(originalFileFolder);
+        fileBefore = originalFileFolder.resolve("test.pdf");
+        Files.createFile(fileBefore);
+
+        MetaData metaData = new MetaData();
+        metaData.setDefaultFileDirectory(newFileFolder.toAbsolutePath().toString());
+
+        BibDatabaseContext databaseContext = new BibDatabaseContext(new BibDatabase(), metaData);
+        Files.createFile(testBibFolder);
+        databaseContext.setDatabasePath(testBibFolder);
+
+        LinkedFile fileField = new LinkedFile("", fileBefore.toAbsolutePath(), "");
+
+        // Entry with one online and one normal linked file
+        entry = new BibEntry(StandardEntryType.Article)
+                .withField(StandardField.AUTHOR, "Shatakshi Sharma and Bhim Singh and Sukumar Mishra")
+                .withField(StandardField.DATE, "April 2020")
+                .withField(StandardField.YEAR, "2020")
+                .withField(StandardField.DOI, "10.1109/TII.2019.2935531")
+                .withField(StandardField.FILE, FileFieldWriter.getStringRepresentation(List.of(
+                    new LinkedFile("", "https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8801912", "PDF"),
+                    fileField)))
+                .withField(StandardField.ISSUE, "4")
+                .withField(StandardField.ISSN, "1941-0050")
+                .withField(StandardField.JOURNALTITLE, "IEEE Transactions on Industrial Informatics")
+                .withField(StandardField.PAGES, "2346--2356")
+                .withField(StandardField.PUBLISHER, "IEEE")
+                .withField(StandardField.TITLE, "Economic Operation and Quality Control in PV-BES-DG-Based Autonomous System")
+                .withField(StandardField.VOLUME, "16")
+                .withField(StandardField.KEYWORDS, "Batteries, Generators, Economics, Power quality, State of charge, Harmonic analysis, Control systems, Battery, diesel generator (DG), distributed generation, power quality, photovoltaic (PV), voltage source converter (VSC)");
+
+        FilePreferences filePreferences = mock(FilePreferences.class);
+        when(filePreferences.shouldStoreFilesRelativeToBibFile()).thenReturn(false);
+        removeLinks = new RemoveLinksToNotExistentFiles(databaseContext, filePreferences);
+    }
+
+    @Test
+    void deleteFileInEntryWithMultipleFileLinks() throws IOException {
+        LinkedFile fileField = new LinkedFile("", fileBefore.toAbsolutePath(), "");
+        FieldChange expectedChange = new FieldChange(entry, StandardField.FILE,
+            FileFieldWriter.getStringRepresentation(List.of(
+            new LinkedFile("", "https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8801912", "PDF"),
+            fileField)),
+            FileFieldWriter.getStringRepresentation(new LinkedFile("", "https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8801912", "PDF"))
+        );
+        BibEntry expectedEntry = new BibEntry(StandardEntryType.Article)
+                .withField(StandardField.AUTHOR, "Shatakshi Sharma and Bhim Singh and Sukumar Mishra")
+                .withField(StandardField.DATE, "April 2020")
+                .withField(StandardField.YEAR, "2020")
+                .withField(StandardField.DOI, "10.1109/TII.2019.2935531")
+                .withField(StandardField.FILE, FileFieldWriter.getStringRepresentation(
+                    new LinkedFile("", "https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8801912", "PDF")))
+                .withField(StandardField.ISSUE, "4")
+                .withField(StandardField.ISSN, "1941-0050")
+                .withField(StandardField.JOURNALTITLE, "IEEE Transactions on Industrial Informatics")
+                .withField(StandardField.PAGES, "2346--2356")
+                .withField(StandardField.PUBLISHER, "IEEE")
+                .withField(StandardField.TITLE, "Economic Operation and Quality Control in PV-BES-DG-Based Autonomous System")
+                .withField(StandardField.VOLUME, "16")
+                .withField(StandardField.KEYWORDS, "Batteries, Generators, Economics, Power quality, State of charge, Harmonic analysis, Control systems, Battery, diesel generator (DG), distributed generation, power quality, photovoltaic (PV), voltage source converter (VSC)");
+
+        Files.delete(fileBefore);
+        List<FieldChange> changes = removeLinks.cleanup(entry);
+
+        assertEquals(List.of(expectedChange), changes);
+        assertEquals(expectedEntry, entry);
+    }
+
+    @Test
+    void keepLinksToExistingFiles() {
+        LinkedFile fileField = new LinkedFile("", fileBefore.toAbsolutePath(), "");
+        BibEntry expectedEntry = new BibEntry(StandardEntryType.Article)
+                .withField(StandardField.AUTHOR, "Shatakshi Sharma and Bhim Singh and Sukumar Mishra")
+                .withField(StandardField.DATE, "April 2020")
+                .withField(StandardField.YEAR, "2020")
+                .withField(StandardField.DOI, "10.1109/TII.2019.2935531")
+                .withField(StandardField.FILE, FileFieldWriter.getStringRepresentation(List.of(
+                    new LinkedFile("", "https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8801912", "PDF"),
+                    fileField)))
+                .withField(StandardField.ISSUE, "4")
+                .withField(StandardField.ISSN, "1941-0050")
+                .withField(StandardField.JOURNALTITLE, "IEEE Transactions on Industrial Informatics")
+                .withField(StandardField.PAGES, "2346--2356")
+                .withField(StandardField.PUBLISHER, "IEEE")
+                .withField(StandardField.TITLE, "Economic Operation and Quality Control in PV-BES-DG-Based Autonomous System")
+                .withField(StandardField.VOLUME, "16")
+                .withField(StandardField.KEYWORDS, "Batteries, Generators, Economics, Power quality, State of charge, Harmonic analysis, Control systems, Battery, diesel generator (DG), distributed generation, power quality, photovoltaic (PV), voltage source converter (VSC)");
+
+        List<FieldChange> changes = removeLinks.cleanup(entry);
+
+        assertEquals(List.of(), changes);
+        assertEquals(expectedEntry, entry);
+    }
+
+    @Test
+    void deleteLinkedFile() throws IOException {
+        LinkedFile fileField = new LinkedFile("", fileBefore.toAbsolutePath(), "");
+
+        // There is only one linked file in entry
+        entry.setField(StandardField.FILE, FileFieldWriter.getStringRepresentation(fileField));
+        FieldChange expectedChange = new FieldChange(entry, StandardField.FILE,
+            FileFieldWriter.getStringRepresentation(fileField),
+            null);
+        BibEntry expectedEntry = new BibEntry(StandardEntryType.Article)
+                .withField(StandardField.AUTHOR, "Shatakshi Sharma and Bhim Singh and Sukumar Mishra")
+                .withField(StandardField.DATE, "April 2020")
+                .withField(StandardField.YEAR, "2020")
+                .withField(StandardField.DOI, "10.1109/TII.2019.2935531")
+                .withField(StandardField.ISSUE, "4")
+                .withField(StandardField.ISSN, "1941-0050")
+                .withField(StandardField.JOURNALTITLE, "IEEE Transactions on Industrial Informatics")
+                .withField(StandardField.PAGES, "2346--2356")
+                .withField(StandardField.PUBLISHER, "IEEE")
+                .withField(StandardField.TITLE, "Economic Operation and Quality Control in PV-BES-DG-Based Autonomous System")
+                .withField(StandardField.VOLUME, "16")
+                .withField(StandardField.KEYWORDS, "Batteries, Generators, Economics, Power quality, State of charge, Harmonic analysis, Control systems, Battery, diesel generator (DG), distributed generation, power quality, photovoltaic (PV), voltage source converter (VSC)");
+
+        Files.delete(fileBefore);
+        List<FieldChange> changes = removeLinks.cleanup(entry);
+
+        assertEquals(List.of(expectedChange), changes);
+        assertEquals(expectedEntry, entry);
+    }
+}