Add eprint cleanup

CHANGELOG.md

@@ -16,6 +16,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the behavior of the field formatting dialog such that the `bibtexkey` is not changed when formatting all fields or all text fields.
 - We added a "Move file to file directory and rename file" option for simultaneously moving and renaming of document file. [#4166](https://github.com/JabRef/jabref/issues/4166)
 - Use integrated graphics card instead of discrete on macOS [#4070](https://github.com/JabRef/jabref/issues/4070)
+- We added a cleanup operation that detects an arXiv identifier in the note, journal or url field and moves it to the `eprint` field.
+ Because of this change, the last-used cleanup operations were reset.
 - We changed the minimum required version of Java to 1.8.0_171, as this is the latest release for which the automatic Java update works. [4093](https://github.com/JabRef/jabref/issues/4093)
 - The special fields like `Printed` and `Read status` now show gray icons when the row is hovered.
 - We added a button in the tab header which allows you to close the database with one click. https://github.com/JabRef/jabref/issues/494

src/main/java/org/jabref/gui/actions/CleanupAction.java

@@ -10,7 +10,6 @@
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.gui.util.BackgroundTask;
-import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.cleanup.CleanupWorker;
 import org.jabref.logic.l10n.Localization;
@@ -23,11 +22,6 @@ public class CleanupAction implements BaseAction {
  private final BasePanel panel;
  private final DialogService dialogService;
 
- /**
- * Global variable to count unsuccessful renames
- */
- private int unsuccessfulRenames;
-
  private boolean isCanceled;
  private int modifiedEntriesCount;
  private final JabRefPreferences preferences;
@@ -44,13 +38,31 @@ public void action() {
  if (isCanceled) {
  return;
  }
- CleanupDialog cleanupDialog = new CleanupDialog(panel.getBibDatabaseContext(), preferences.getCleanupPreset());
+ CleanupDialog cleanupDialog = new CleanupDialog(panel.getBibDatabaseContext(), preferences.getCleanupPreset(), preferences.getFilePreferences());
 
  Optional<CleanupPreset> chosenPreset = cleanupDialog.showAndWait();
- chosenPreset.ifPresent(cleanupPreset ->
- BackgroundTask.wrap(() -> cleanup(cleanupPreset))
- .onSuccess(x -> showResults())
- .executeWith(Globals.TASK_EXECUTOR));
+
+ if (chosenPreset.isPresent()) {
+ if (chosenPreset.get().isRenamePDFActive() && preferences.getBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN)) {
+ boolean confirmed = dialogService.showConfirmationDialogWithOptOutAndWait(Localization.lang("Autogenerate PDF Names"),
+ Localization.lang("Auto-generating PDF-Names does not support undo. Continue?"),
+ Localization.lang("Autogenerate PDF Names"),
+ Localization.lang("Cancel"),
+ Localization.lang("Disable this confirmation dialog"),
+ optOut -> Globals.prefs.putBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN, !optOut));
+
+ if (!confirmed) {
+ isCanceled = true;
+ return;
+ }
+ }
+
+ preferences.setCleanupPreset(chosenPreset.get());
+
+ BackgroundTask.wrap(() -> cleanup(chosenPreset.get()))
+ .onSuccess(result -> showResults())
+ .executeWith(Globals.TASK_EXECUTOR);
+ }
  }
 
  public void init() {
@@ -111,21 +123,6 @@ private void showResults() {
  private void cleanup(CleanupPreset cleanupPreset) {
  preferences.setCleanupPreset(cleanupPreset);
 
- if (cleanupPreset.isRenamePDF() && preferences.getBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN)) {
-
- boolean confirmed = DefaultTaskExecutor.runInJavaFXThread(() -> dialogService.showConfirmationDialogWithOptOutAndWait(Localization.lang("Autogenerate PDF Names"),
- Localization.lang("Auto-generating PDF-Names does not support undo. Continue?"),
- Localization.lang("Autogenerate PDF Names"),
- Localization.lang("Cancel"),
- Localization.lang("Disable this confirmation dialog"),
- optOut -> Globals.prefs.putBoolean(JabRefPreferences.ASK_AUTO_NAMING_PDFS_AGAIN, !optOut)));
-
- if (!confirmed) {
- isCanceled = true;
- return;
- }
- }
-
  for (BibEntry entry : panel.getSelectedEntries()) {
  // undo granularity is on entry level
  NamedCompound ce = new NamedCompound(Localization.lang("Cleanup entry"));

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

@@ -6,15 +6,16 @@
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.metadata.FilePreferences;
 
 public class CleanupDialog extends BaseDialog<CleanupPreset> {
 
- public CleanupDialog(BibDatabaseContext databaseContext, CleanupPreset initialPreset) {
+ public CleanupDialog(BibDatabaseContext databaseContext, CleanupPreset initialPreset, FilePreferences filePreferences) {
  setTitle(Localization.lang("Cleanup entries"));
  getDialogPane().setPrefSize(600, 600);
  getDialogPane().getButtonTypes().setAll(ButtonType.OK, ButtonType.CANCEL);
 
- CleanupPresetPanel presetPanel = new CleanupPresetPanel(databaseContext, initialPreset);
+ CleanupPresetPanel presetPanel = new CleanupPresetPanel(databaseContext, initialPreset, filePreferences);
  getDialogPane().setContent(presetPanel);
  setResultConverter(button -> {
  if (button == ButtonType.OK) {

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

@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.geometry.Insets?>
+<?import javafx.scene.control.CheckBox?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.layout.VBox?>
+<fx:root xmlns:fx="http://javafx.com/fxml/1" spacing="10.0" type="VBox" xmlns="http://javafx.com/javafx/8.0.121"
+ fx:controller="org.jabref.gui.cleanup.CleanupPresetPanel">
+
+ <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="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 spacing="5.0">
+ <Label fx:id="cleanupRenamePDFLabel"/>
+ <CheckBox fx:id="cleanUpRenamePDFonlyRelativePaths" text="%Rename only PDFs having a relative path"/>
+ <VBox.margin>
+ <Insets left="40.0"/>
+ </VBox.margin>
+ </VBox>
+
+ <CheckBox fx:id="cleanUpBiblatex"
+ text="%Convert to biblatex format (for example, move the value of the 'journal' field to 'journaltitle')"/>
+ <CheckBox fx:id="cleanUpBibtex"
+ text="%Convert to BibTeX format (for example, move the value of the 'journaltitle' field to 'journal')"/>
+
+ <VBox fx:id="formatterContainer"/>
+
+</fx:root>

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

@@ -6,124 +6,103 @@
 import java.util.Optional;
 import java.util.Set;
 
-import javafx.scene.Group;
+import javafx.fxml.FXML;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.Label;
-import javafx.scene.control.ScrollPane;
-import javafx.scene.layout.GridPane;
+import javafx.scene.layout.VBox;
 
-import org.jabref.Globals;
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.cleanup.Cleanups;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.FieldName;
-import org.jabref.preferences.JabRefPreferences;
+import org.jabref.model.metadata.FilePreferences;
 
-public class CleanupPresetPanel extends ScrollPane {
+import com.airhacks.afterburner.views.ViewLoader;
+
+public class CleanupPresetPanel extends VBox {
 
  private final BibDatabaseContext databaseContext;
- private CheckBox cleanUpDOI;
- private CheckBox cleanUpISSN;
- private CheckBox cleanUpMovePDF;
- private CheckBox cleanUpMakePathsRelative;
- private CheckBox cleanUpRenamePDF;
- private CheckBox cleanUpRenamePDFonlyRelativePaths;
- private CheckBox cleanUpUpgradeExternalLinks;
- private CheckBox cleanUpBiblatex;
- private CheckBox cleanUpBibtex;
+ @FXML private Label cleanupRenamePDFLabel;
+ @FXML private CheckBox cleanUpDOI;
+ @FXML private CheckBox cleanUpEprint;
+ @FXML private CheckBox cleanUpISSN;
+ @FXML private CheckBox cleanUpMovePDF;
+ @FXML private CheckBox cleanUpMakePathsRelative;
+ @FXML private CheckBox cleanUpRenamePDF;
+ @FXML private CheckBox cleanUpRenamePDFonlyRelativePaths;
+ @FXML private CheckBox cleanUpUpgradeExternalLinks;
+ @FXML private CheckBox cleanUpBiblatex;
+ @FXML private CheckBox cleanUpBibtex;
+ @FXML private VBox formatterContainer;
  private FieldFormatterCleanupsPanel cleanUpFormatters;
 
- private CleanupPreset cleanupPreset;
-
- public CleanupPresetPanel(BibDatabaseContext databaseContext, CleanupPreset cleanupPreset) {
- this.cleanupPreset = Objects.requireNonNull(cleanupPreset);
+ public CleanupPresetPanel(BibDatabaseContext databaseContext, CleanupPreset cleanupPreset, FilePreferences filePreferences) {
  this.databaseContext = Objects.requireNonNull(databaseContext);
- init();
+
+ // Load FXML
+ ViewLoader.view(this)
+ .root(this)
+ .load();
+
+ init(cleanupPreset, filePreferences);
  }
 
- private void init() {
- cleanUpDOI = new CheckBox(
- Localization.lang("Move DOIs from note and URL field to DOI field and remove http prefix"));
- cleanUpISSN = new CheckBox(Localization.lang("Reformat ISSN"));
- Optional<Path> firstExistingDir = databaseContext
- .getFirstExistingFileDir(JabRefPreferences.getInstance().getFilePreferences());
+ private void init(CleanupPreset cleanupPreset, FilePreferences filePreferences) {
+ Optional<Path> firstExistingDir = databaseContext.getFirstExistingFileDir(filePreferences);
  if (firstExistingDir.isPresent()) {
- cleanUpMovePDF = new CheckBox(Localization.lang("Move linked files to default file directory %0",
- firstExistingDir.get().toString()));
+ cleanUpMovePDF.setText(Localization.lang("Move linked files to default file directory %0", firstExistingDir.get().toString()));
  } else {
- cleanUpMovePDF = new CheckBox(Localization.lang("Move linked files to default file directory %0", "..."));
- cleanUpMovePDF.setDisable(true);
+ cleanUpMovePDF.setText(Localization.lang("Move linked files to default file directory %0", "..."));
+
  // Since the directory does not exist, we cannot move it to there. So, this option is not checked - regardless of the presets stored in the preferences.
+ cleanUpMovePDF.setDisable(true);
  cleanUpMovePDF.setSelected(false);
  }
- cleanUpMakePathsRelative = new CheckBox(
- Localization.lang("Make paths of linked files relative (if possible)"));
- cleanUpRenamePDF = new CheckBox(Localization.lang("Rename PDFs to given filename format pattern"));
- cleanUpRenamePDF.selectedProperty().addListener(
- event -> cleanUpRenamePDFonlyRelativePaths.setDisable(!cleanUpRenamePDF.isSelected()));
- cleanUpRenamePDFonlyRelativePaths = new CheckBox(Localization.lang("Rename only PDFs having a relative path"));
- cleanUpUpgradeExternalLinks = new CheckBox(
- Localization.lang("Upgrade external PDF/PS links to use the '%0' field.", FieldName.FILE));
- cleanUpBiblatex = new CheckBox(Localization.lang(
- "Convert to biblatex format (for example, move the value of the 'journal' field to 'journaltitle')"));
- cleanUpBibtex = new CheckBox(Localization.lang(
- "Convert to BibTeX format (for example, move the value of the 'journaltitle' field to 'journal')"));
- Group biblatexConversion = new Group(); // Only make "to Biblatex" or "to BibTeX" selectable
- biblatexConversion.getChildren().add(cleanUpBiblatex);
- biblatexConversion.getChildren().add(cleanUpBibtex);
-
- cleanUpFormatters = new FieldFormatterCleanupsPanel(Localization.lang("Run field formatter:"),
- Cleanups.DEFAULT_SAVE_ACTIONS);
 
- updateDisplay(cleanupPreset);
+ cleanUpRenamePDFonlyRelativePaths.disableProperty().bind(cleanUpRenamePDF.selectedProperty().not());
 
- GridPane container = new GridPane();
- container.add(cleanUpDOI, 0, 0);
- container.add(cleanUpUpgradeExternalLinks, 0, 1);
- container.add(cleanUpMovePDF, 0, 2);
- container.add(cleanUpMakePathsRelative, 0, 3);
- container.add(cleanUpRenamePDF, 0, 4);
- String currentPattern = Localization.lang("Filename format pattern").concat(": ");
- currentPattern = currentPattern.concat(Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN));
- container.add(new Label(currentPattern), 0, 5);
- container.add(cleanUpRenamePDFonlyRelativePaths, 0, 6);
- container.add(cleanUpBibtex, 0, 7);
- container.add(cleanUpBiblatex, 0, 8);
- container.add(cleanUpISSN, 0, 9);
- container.add(cleanUpFormatters, 0, 10);
-
- setContent(container);
- setVbarPolicy(ScrollBarPolicy.AS_NEEDED);
+ cleanUpUpgradeExternalLinks.setText(Localization.lang("Upgrade external PDF/PS links to use the '%0' field.", FieldName.FILE));
+
+ cleanUpFormatters = new FieldFormatterCleanupsPanel(Localization.lang("Run field formatter:"), Cleanups.DEFAULT_SAVE_ACTIONS);
+ formatterContainer.getChildren().setAll(cleanUpFormatters);
+
+ String currentPattern = Localization.lang("Filename format pattern")
+ .concat(": ")
+ .concat(filePreferences.getFileNamePattern());
+ cleanupRenamePDFLabel.setText(currentPattern);
+
+ updateDisplay(cleanupPreset);
  }
 
  private void updateDisplay(CleanupPreset preset) {
- cleanUpDOI.setSelected(preset.isCleanUpDOI());
+ cleanUpDOI.setSelected(preset.isActive(CleanupPreset.CleanupStep.CLEAN_UP_DOI));
+ cleanUpEprint.setSelected(preset.isActive(CleanupPreset.CleanupStep.CLEANUP_EPRINT));
  if (!cleanUpMovePDF.isDisabled()) {
- cleanUpMovePDF.setSelected(preset.isMovePDF());
+ cleanUpMovePDF.setSelected(preset.isActive(CleanupPreset.CleanupStep.MOVE_PDF));
  }
- cleanUpMakePathsRelative.setSelected(preset.isMakePathsRelative());
- cleanUpRenamePDF.setSelected(preset.isRenamePDF());
- cleanUpRenamePDFonlyRelativePaths.setSelected(preset.isRenamePdfOnlyRelativePaths());
- cleanUpRenamePDFonlyRelativePaths.setDisable(!cleanUpRenamePDF.isSelected());
- cleanUpUpgradeExternalLinks.setSelected(preset.isCleanUpUpgradeExternalLinks());
- cleanUpBiblatex.setSelected(preset.isConvertToBiblatex());
- cleanUpBibtex.setSelected(preset.isConvertToBibtex());
- cleanUpISSN.setSelected(preset.isCleanUpISSN());
+ cleanUpMakePathsRelative.setSelected(preset.isActive(CleanupPreset.CleanupStep.MAKE_PATHS_RELATIVE));
+ cleanUpRenamePDF.setSelected(preset.isRenamePDFActive());
+ cleanUpRenamePDFonlyRelativePaths.setSelected(preset.isActive(CleanupPreset.CleanupStep.RENAME_PDF_ONLY_RELATIVE_PATHS));
+ cleanUpUpgradeExternalLinks.setSelected(preset.isActive(CleanupPreset.CleanupStep.CLEAN_UP_UPGRADE_EXTERNAL_LINKS));
+ cleanUpBiblatex.setSelected(preset.isActive(CleanupPreset.CleanupStep.CONVERT_TO_BIBLATEX));
+ cleanUpBibtex.setSelected(preset.isActive(CleanupPreset.CleanupStep.CONVERT_TO_BIBTEX));
+ cleanUpISSN.setSelected(preset.isActive(CleanupPreset.CleanupStep.CLEAN_UP_ISSN));
  cleanUpFormatters.setValues(preset.getFormatterCleanups());
  }
 
  public CleanupPreset getCleanupPreset() {
-
  Set<CleanupPreset.CleanupStep> activeJobs = EnumSet.noneOf(CleanupPreset.CleanupStep.class);
 
  if (cleanUpMovePDF.isSelected()) {
  activeJobs.add(CleanupPreset.CleanupStep.MOVE_PDF);
  }
-
  if (cleanUpDOI.isSelected()) {
  activeJobs.add(CleanupPreset.CleanupStep.CLEAN_UP_DOI);
  }
+ if (cleanUpEprint.isSelected()) {
+ activeJobs.add(CleanupPreset.CleanupStep.CLEANUP_EPRINT);
+ }
  if (cleanUpISSN.isSelected()) {
  activeJobs.add(CleanupPreset.CleanupStep.CLEAN_UP_ISSN);
  }
@@ -149,7 +128,6 @@ public CleanupPreset getCleanupPreset() {
 
  activeJobs.add(CleanupPreset.CleanupStep.FIX_FILE_LINKS);
 
- cleanupPreset = new CleanupPreset(activeJobs, cleanUpFormatters.getFormatterCleanups());
- return cleanupPreset;
+ return new CleanupPreset(activeJobs, cleanUpFormatters.getFormatterCleanups());
  }
 }

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

@@ -103,7 +103,7 @@ private void buildLayout() {
  actionsList = new ListView<>(actions);
  actionsList.getSelectionModel().setSelectionMode(SelectionMode.SINGLE);
  new ViewModelListCellFactory<FieldFormatterCleanup>()
- .withText(action -> action.getFormatter().getName())
+ .withText(action -> action.getField() + ": " + action.getFormatter().getName())
  .withTooltip(action -> action.getFormatter().getDescription())
  .install(actionsList);
  add(actionsList, 1, 1, 3, 1);