Merge remote-tracking branch 'upstream/main' into jabrefonline

* upstream/main: Added auto-key-generation task to task-progress (JabRef#7797) cleanup temporary files, use prefix "jabref-" (JabRef#7811) Add easier how-to for checklist (JabRef#7813) Fix annotation + package of ACMPortalParserTest (JabRef#7812) Implemented a select all button for the library import function (issue JabRef#7786) (JabRef#7808) Fix for issue 4682 : Restructuring the side pane structure having additional functionality and merging the remove group menus (JabRef#7714)
JabRef · Jun 11, 2021 · d5d4ed6 · d5d4ed6
2 parents 6388a41 + 475b298
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -7,12 +7,12 @@ The title of the PR must not reference an issue, because GitHub does not support
 
 
 <!-- 
-- Go through the list below. If a task has been completed, mark it done by using `[x]`.
-- Please don't remove any items, just leave them unchecked if they are not applicable.
+- Go through the list below. Please don't remove any items.
+- [x] done; [ ] not done / not applicable
 -->
 
-- [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
-- [ ] Tests created for changes (if applicable)
-- [ ] Manually tested changed features in running JabRef (always required)
-- [ ] Screenshots added in PR description (for UI changes)
-- [ ] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not created an issue at <https://github.com/JabRef/user-documentation/issues> or, even better, submitted a pull request to the documentation repository.
+- [] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
+- [] Tests created for changes (if applicable)
+- [] Manually tested changed features in running JabRef (always required)
+- [] Screenshots added in PR description (for UI changes)
+- [] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not created an issue at <https://github.com/JabRef/user-documentation/issues> or, even better, submitted a pull request to the documentation repository.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,9 +21,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added two new fields to track the creation and most recent modification date and time for each entry. [koppor#130](https://github.com/koppor/jabref/issues/130)
 - We added a feature that allows the user to copy highlighted text in the preview window. [#6962](https://github.com/JabRef/jabref/issues/6962)
 - We added a feature that allows you to create new BibEntry via paste arxivId [#2292](https://github.com/JabRef/jabref/issues/2292)
+- We added a add group functionality at the bottom of the side pane. [#4682](https://github.com/JabRef/jabref/issues/4682)
 - We added a feature that allows the user to choose whether to trust the target site when unable to find a valid certification path from the file download site. [#7616](https://github.com/JabRef/jabref/issues/7616)
 - We added a feature that allows the user to open all linked files of multiple selected entries by "Open file" option. [#6966](https://github.com/JabRef/jabref/issues/6966)
 - We added a keybinding preset for new entries. [#7705](https://github.com/JabRef/jabref/issues/7705)
+- We added a select all button for the library import function. [#7786](https://github.com/JabRef/jabref/issues/7786)
+- We added auto-key-generation progress to the background task list. [#7267](https://github.com/JabRef/jabref/issues/7267)
 
 ### Changed
 
@@ -38,6 +41,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We improved the linking of the `python3` interpreter via the shebang to dynamically use the systems default Python. Related to [JabRef-Browser-Extension #177](https://github.com/JabRef/JabRef-Browser-Extension/issues/177)
 - Automatically found pdf files now have the linking button to the far left and uses a link icon with a plus instead of a briefcase. The file name also has lowered opacity(70%) until added. [#3607](https://github.com/JabRef/jabref/issues/3607)
 - We simplified the select entry type form by splitting it into two parts ("Recommended" and "Others") based on internal usage data. [#6730](https://github.com/JabRef/jabref/issues/6730)
+- We improved the submenu list by merging the'Remove group' having two options, with or without subgroups. [#4682](https://github.com/JabRef/jabref/issues/4682)
 - The export to MS Office XML now uses the month name for the field `Month` instead of the two digit number [forum#2685](https://discourse.jabref.org/t/export-month-as-text-not-number/2685)
 - We reintroduced missing default keybindings for new entries. [#7346](https://github.com/JabRef/jabref/issues/7346) [#7439](https://github.com/JabRef/jabref/issues/7439)
 - Lists of available fields are now sorted alphabetically. [#7716](https://github.com/JabRef/jabref/issues/7716)
@@ -88,6 +92,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where font size of the preferences dialog does not update with the rest of the GUI. [#7416](https://github.com/JabRef/jabref/issues/7416)
 - We fixed an issue in which a linked online file consisting of a web page was saved as an invalid pdf file upon being downloaded. The user is now notified when downloading a linked file results in an HTML file. [#7452](https://github.com/JabRef/jabref/issues/7452)
 - We fixed an issue where opening BibTex file (doubleclick) from Folder with spaces not working. [#6487](https://github.com/JabRef/jabref/issues/6487)
+- We fixed the header title in the Add Group/Subgroup Dialog box. [#4682](https://github.com/JabRef/jabref/issues/4682)
 - We fixed an issue with saving large `.bib` files [#7265](https://github.com/JabRef/jabref/issues/7265)
 - We fixed an issue with very large page numbers [#7590](https://github.com/JabRef/jabref/issues/7590)
 - We fixed an issue where the file extension is missing on saving the library file on linux [#7451](https://github.com/JabRef/jabref/issues/7451)
@@ -108,6 +113,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Removed
 
+- We removed add group button beside the filter group tab. [#4682](https://github.com/JabRef/jabref/issues/4682)
+
 ## [5.2] – 2020-12-24
 
 ### Added

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -506,7 +506,7 @@ private Node createToolbar() {
 
                 new HBox(
                         pushToApplicationButton,
-                        factory.createIconButton(StandardActions.GENERATE_CITE_KEYS, new GenerateCitationKeyAction(this, dialogService, stateManager)),
+                        factory.createIconButton(StandardActions.GENERATE_CITE_KEYS, new GenerateCitationKeyAction(this, dialogService, stateManager, taskExecutor, prefs)),
                         factory.createIconButton(StandardActions.CLEANUP_ENTRIES, new CleanupAction(this, prefs, dialogService, stateManager))
                 ),
 
@@ -727,7 +727,7 @@ private MenuBar createMenu() {
                 new SeparatorMenuItem(),
 
                 factory.createMenuItem(StandardActions.REPLACE_ALL, new ReplaceStringAction(this, stateManager)),
-                factory.createMenuItem(StandardActions.GENERATE_CITE_KEYS, new GenerateCitationKeyAction(this, dialogService, stateManager)),
+                factory.createMenuItem(StandardActions.GENERATE_CITE_KEYS, new GenerateCitationKeyAction(this, dialogService, stateManager, taskExecutor, prefs)),
 
                 new SeparatorMenuItem(),
 

diff --git a/src/main/java/org/jabref/gui/citationkeypattern/GenerateCitationKeyAction.java b/src/main/java/org/jabref/gui/citationkeypattern/GenerateCitationKeyAction.java
@@ -1,19 +1,22 @@
 package org.jabref.gui.citationkeypattern;
 
 import java.util.List;
+import java.util.function.Consumer;
 
 import org.jabref.gui.DialogService;
-import org.jabref.gui.Globals;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.actions.ActionHelper;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableKeyChange;
 import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.DefaultTaskExecutor;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.preferences.PreferencesService;
 
 public class GenerateCitationKeyAction extends SimpleCommand {
 
@@ -24,10 +27,15 @@ public class GenerateCitationKeyAction extends SimpleCommand {
     private List<BibEntry> entries;
     private boolean isCanceled;
 
-    public GenerateCitationKeyAction(JabRefFrame frame, DialogService dialogService, StateManager stateManager) {
+    private final TaskExecutor taskExecutor;
+    private final PreferencesService preferencesService;
+
+    public GenerateCitationKeyAction(JabRefFrame frame, DialogService dialogService, StateManager stateManager, TaskExecutor taskExecutor, PreferencesService preferencesService) {
         this.frame = frame;
         this.dialogService = dialogService;
         this.stateManager = stateManager;
+        this.taskExecutor = taskExecutor;
+        this.preferencesService = preferencesService;
 
         this.executable.bind(ActionHelper.needsEntriesSelected(stateManager));
     }
@@ -45,20 +53,26 @@ public void execute() {
 
         checkOverwriteKeysChosen();
 
-        BackgroundTask.wrap(this::generateKeys)
-                      .executeWith(Globals.TASK_EXECUTOR);
+        if (!this.isCanceled) {
+            BackgroundTask backgroundTask = this.generateKeysInBackground();
+            backgroundTask.showToUser(true);
+            backgroundTask.titleProperty().set(Localization.lang("Autogenerate citation keys"));
+            backgroundTask.messageProperty().set(Localization.lang("%0/%1 entries", 0, entries.size()));
+
+            backgroundTask.executeWith(this.taskExecutor);
+        }
     }
 
-    public static boolean confirmOverwriteKeys(DialogService dialogService) {
-        if (Globals.prefs.getCitationKeyPatternPreferences().shouldWarnBeforeOverwriteCiteKey()) {
+    public static boolean confirmOverwriteKeys(DialogService dialogService, PreferencesService preferencesService) {
+        if (preferencesService.getCitationKeyPatternPreferences().shouldWarnBeforeOverwriteCiteKey()) {
             return dialogService.showConfirmationDialogWithOptOutAndWait(
                     Localization.lang("Overwrite keys"),
                     Localization.lang("One or more keys will be overwritten. Continue?"),
                     Localization.lang("Overwrite keys"),
                     Localization.lang("Cancel"),
                     Localization.lang("Do not ask again"),
-                    optOut -> Globals.prefs.storeCitationKeyPatternPreferences(
-                            Globals.prefs.getCitationKeyPatternPreferences().withWarnBeforeOverwriteCiteKey(!optOut)));
+                    optOut -> preferencesService.storeCitationKeyPatternPreferences(
+                            preferencesService.getCitationKeyPatternPreferences().withWarnBeforeOverwriteCiteKey(!optOut)));
         } else {
             // Always overwrite keys by default
             return true;
@@ -67,11 +81,11 @@ public static boolean confirmOverwriteKeys(DialogService dialogService) {
 
     private void checkOverwriteKeysChosen() {
         // We don't want to generate keys for entries which already have one thus remove the entries
-        if (Globals.prefs.getCitationKeyPatternPreferences().shouldAvoidOverwriteCiteKey()) {
+        if (this.preferencesService.getCitationKeyPatternPreferences().shouldAvoidOverwriteCiteKey()) {
             entries.removeIf(BibEntry::hasCitationKey);
             // if we're going to override some citation keys warn the user about it
         } else if (entries.parallelStream().anyMatch(BibEntry::hasCitationKey)) {
-            boolean overwriteKeys = confirmOverwriteKeys(dialogService);
+            boolean overwriteKeys = confirmOverwriteKeys(dialogService, this.preferencesService);
 
             // The user doesn't want to override citation keys
             if (!overwriteKeys) {
@@ -80,30 +94,54 @@ private void checkOverwriteKeysChosen() {
         }
     }
 
-    private void generateKeys() {
-        if (isCanceled) {
-            return;
-        }
-
-        stateManager.getActiveDatabase().ifPresent(databaseContext -> {
-            // generate the new citation keys for each entry
-            final NamedCompound compound = new NamedCompound(Localization.lang("Autogenerate citation keys"));
-            CitationKeyGenerator keyGenerator =
-                    new CitationKeyGenerator(databaseContext, Globals.prefs.getCitationKeyPatternPreferences());
-            for (BibEntry entry : entries) {
-                keyGenerator.generateAndSetKey(entry)
-                            .ifPresent(fieldChange -> compound.addEdit(new UndoableKeyChange(fieldChange)));
+    private BackgroundTask generateKeysInBackground() {
+        return new BackgroundTask<Void>() {
+
+            private NamedCompound compound;
+
+            @Override
+            protected Void call() {
+                    if (isCanceled) {
+                        return null;
+                    }
+                    DefaultTaskExecutor.runInJavaFXThread(() -> {
+                        updateProgress(0, entries.size());
+                        messageProperty().set(Localization.lang("%0/%1 entries", 0, entries.size()));
+                    });
+                    stateManager.getActiveDatabase().ifPresent(databaseContext -> {
+                        // generate the new citation keys for each entry
+                        compound = new NamedCompound(Localization.lang("Autogenerate citation keys"));
+                        CitationKeyGenerator keyGenerator =
+                                new CitationKeyGenerator(databaseContext, preferencesService.getCitationKeyPatternPreferences());
+                        int entriesDone = 0;
+                        for (BibEntry entry : entries) {
+                            keyGenerator.generateAndSetKey(entry)
+                                        .ifPresent(fieldChange -> compound.addEdit(new UndoableKeyChange(fieldChange)));
+                            entriesDone++;
+                            int finalEntriesDone = entriesDone;
+                            DefaultTaskExecutor.runInJavaFXThread(() -> {
+                                updateProgress(finalEntriesDone, entries.size());
+                                messageProperty().set(Localization.lang("%0/%1 entries", finalEntriesDone, entries.size()));
+                            });
+                        }
+                        compound.end();
+                    });
+                    return null;
             }
-            compound.end();
 
-            // register the undo event only if new citation keys were generated
-            if (compound.hasEdits()) {
-                frame.getUndoManager().addEdit(compound);
+            @Override
+            public BackgroundTask<Void> onSuccess(Consumer<Void> onSuccess) {
+                // register the undo event only if new citation keys were generated
+                if (compound.hasEdits()) {
+                    frame.getUndoManager().addEdit(compound);
+                }
+
+                frame.getCurrentLibraryTab().markBaseChanged();
+                dialogService.notify(formatOutputMessage(Localization.lang("Generated citation key for"), entries.size()));
+                return super.onSuccess(onSuccess);
             }
+        };
 
-            frame.getCurrentLibraryTab().markBaseChanged();
-            dialogService.notify(formatOutputMessage(Localization.lang("Generated citation key for"), entries.size()));
-        });
     }
 
     private String formatOutputMessage(String start, int count) {

diff --git a/src/main/java/org/jabref/gui/citationkeypattern/GenerateCitationKeySingleAction.java b/src/main/java/org/jabref/gui/citationkeypattern/GenerateCitationKeySingleAction.java
@@ -32,7 +32,7 @@ public GenerateCitationKeySingleAction(BibEntry entry, BibDatabaseContext databa
 
     @Override
     public void execute() {
-        if (!entry.hasCitationKey() || GenerateCitationKeyAction.confirmOverwriteKeys(dialogService)) {
+        if (!entry.hasCitationKey() || GenerateCitationKeyAction.confirmOverwriteKeys(dialogService, preferencesService)) {
             new CitationKeyGenerator(databaseContext, preferencesService.getCitationKeyPatternPreferences())
                     .generateAndSetKey(entry)
                     .ifPresent(change -> undoManager.addEdit(new UndoableKeyChange(change)));

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialogHeader.java b/src/main/java/org/jabref/gui/groups/GroupDialogHeader.java
@@ -0,0 +1,5 @@
+package org.jabref.gui.groups;
+
+public enum GroupDialogHeader {
+    GROUP, SUBGROUP
+}
diff --git a/src/main/java/org/jabref/gui/groups/GroupDialogView.java b/src/main/java/org/jabref/gui/groups/GroupDialogView.java
@@ -67,15 +67,19 @@ public class GroupDialogView extends BaseDialog<AbstractGroup> {
     private final ControlsFxVisualizer validationVisualizer = new ControlsFxVisualizer();
     private final GroupDialogViewModel viewModel;
 
-    public GroupDialogView(DialogService dialogService, BibDatabaseContext currentDatabase, PreferencesService preferencesService, AbstractGroup editedGroup) {
-        viewModel = new GroupDialogViewModel(dialogService, currentDatabase, preferencesService, editedGroup);
+    public GroupDialogView(DialogService dialogService, BibDatabaseContext currentDatabase, PreferencesService preferencesService, AbstractGroup editedGroup, GroupDialogHeader groupDialogHeader) {
+        viewModel = new GroupDialogViewModel(dialogService, currentDatabase, preferencesService, editedGroup, groupDialogHeader);
 
         ViewLoader.view(this)
                   .load()
                   .setAsDialogPane(this);
 
         if (editedGroup == null) {
-            this.setTitle(Localization.lang("Add subgroup"));
+            if (groupDialogHeader == GroupDialogHeader.GROUP) {
+                this.setTitle(Localization.lang("Add group"));
+            } else if (groupDialogHeader == GroupDialogHeader.SUBGROUP) {
+                this.setTitle(Localization.lang("Add subgroup"));
+            }
         } else {
             this.setTitle(Localization.lang("Edit group") + " " + editedGroup.getName());
         }

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java b/src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java
@@ -107,12 +107,14 @@ public class GroupDialogViewModel {
     private final PreferencesService preferencesService;
     private final BibDatabaseContext currentDatabase;
     private final AbstractGroup editedGroup;
+    private final GroupDialogHeader groupDialogHeader;
 
-    public GroupDialogViewModel(DialogService dialogService, BibDatabaseContext currentDatabase, PreferencesService preferencesService, AbstractGroup editedGroup) {
+    public GroupDialogViewModel(DialogService dialogService, BibDatabaseContext currentDatabase, PreferencesService preferencesService, AbstractGroup editedGroup, GroupDialogHeader groupDialogHeader) {
         this.dialogService = dialogService;
         this.preferencesService = preferencesService;
         this.currentDatabase = currentDatabase;
         this.editedGroup = editedGroup;
+        this.groupDialogHeader = groupDialogHeader;
 
         setupValidation();
         setValues();

diff --git a/src/main/java/org/jabref/gui/groups/GroupTree.css b/src/main/java/org/jabref/gui/groups/GroupTree.css
@@ -102,8 +102,18 @@
     -fx-translate-x: -0.4em;
 }
 
-#newGroupButton {
-    -fx-padding: 0.1em 1.5em 0.1em 1.5em;
+#addNewGroup:active {
+    -fx-border-width: 0px;
+    -fx-background-color: -jr-theme;
+    -fx-padding: 0.5em;
+    -fx-text-fill: -jr-white;
+}
+
+#addNewGroup:inactive {
+    -fx-border-width: 0px;
+    -fx-background-color: -jr-icon-background-active;
+    -fx-padding: 0.5em;
+    -fx-text-fill:-jr-black;
 }
 
 #groupFilterBar {
@@ -116,3 +126,7 @@
 #groupFilterBar .glyph-icon {
     -fx-font-size: 2em;
 }
+
+#groupBar .glyph-icon {
+    -fx-font-size: 2em;
+}