Add eprint cleanup (#4445)

* Adds a cleanup operation that detects an arXiv identifier in the note, journal or url field and moves it to the `eprint` field. I also took the opportunity to convert the cleanup panel to FXML and somewhat simplified/refactored the code around the cleanup. * Implement feedback * Fix cleanup
JabRef · Nov 7, 2018 · 144522d · 144522d
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diff --git a/CHANGELOG.md b/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

diff --git a/src/main/java/org/jabref/gui/actions/CleanupAction.java b/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"));

diff --git a/src/main/java/org/jabref/gui/cleanup/CleanupDialog.java b/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) {

diff --git a/src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.fxml b/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>
diff --git a/src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.java b/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());
     }
 }
diff --git a/src/main/java/org/jabref/gui/cleanup/FieldFormatterCleanupsPanel.java b/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);