From 65245999ba988d81e1c1e39e738445f2dbcf4eaf Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 08:32:21 +0100
Subject: [PATCH 01/61] Bump mockito-core from 2.25.0 to 2.25.1 (#4771)

Bumps [mockito-core](https://github.com/mockito/mockito) from 2.25.0 to 2.25.1.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v2.25.0...v2.25.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 0a45aab3885..599dd191bfe 100644
--- a/build.gradle
+++ b/build.gradle
@@ -167,7 +167,7 @@ dependencies {
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
-    testCompile 'org.mockito:mockito-core:2.25.0'
+    testCompile 'org.mockito:mockito-core:2.25.1'
     testCompile 'com.github.tomakehurst:wiremock:2.21.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'

From d64494e517893e71e2f1cdafa9ed826c0c1935b9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 08:32:44 +0100
Subject: [PATCH 02/61] Bump junit-vintage-engine from 5.4.0 to 5.4.1 (#4772)

Bumps [junit-vintage-engine](https://github.com/junit-team/junit5) from 5.4.0 to 5.4.1.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/compare/r5.4.0...r5.4.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 599dd191bfe..c329ea2d3c5 100644
--- a/build.gradle
+++ b/build.gradle
@@ -162,7 +162,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.4.0'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.0'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'

From 8a1fbe1ee6f1ed6aa47ebe989081fd7e3825ecb8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 08:34:05 +0100
Subject: [PATCH 03/61] Bump archunit-junit5-api from 0.9.3 to 0.10.1 (#4773)

Bumps [archunit-junit5-api](https://github.com/TNG/ArchUnit) from 0.9.3 to 0.10.1.
- [Release notes](https://github.com/TNG/ArchUnit/releases)
- [Commits](https://github.com/TNG/ArchUnit/compare/v0.9.3...v0.10.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index c329ea2d3c5..9b75a95267f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -173,7 +173,7 @@ dependencies {
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
     testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.3'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.3'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.1'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 

From 52696f04b518f4093fea32aff0c2f80b540dab67 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 10:50:00 +0100
Subject: [PATCH 04/61] Bump wiremock from 2.21.0 to 2.22.0 (#4776)

Bumps [wiremock](https://github.com/tomakehurst/wiremock) from 2.21.0 to 2.22.0.
- [Release notes](https://github.com/tomakehurst/wiremock/releases)
- [Changelog](https://github.com/tomakehurst/wiremock/blob/master/release-settings.gradle)
- [Commits](https://github.com/tomakehurst/wiremock/compare/2.21.0...2.22.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9b75a95267f..0b8f14c6198 100644
--- a/build.gradle
+++ b/build.gradle
@@ -168,7 +168,7 @@ dependencies {
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
     testCompile 'org.mockito:mockito-core:2.25.1'
-    testCompile 'com.github.tomakehurst:wiremock:2.21.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.22.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'

From 39f7690c2c3ec76a9747b2e65e77d31d1c741dba Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 10:50:18 +0100
Subject: [PATCH 05/61] Bump junit-jupiter from 5.4.0 to 5.4.1 (#4775)

Bumps [junit-jupiter](https://github.com/junit-team/junit5) from 5.4.0 to 5.4.1.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/compare/r5.4.0...r5.4.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 0b8f14c6198..1bee7bc1732 100644
--- a/build.gradle
+++ b/build.gradle
@@ -161,7 +161,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.1'
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.0'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.1'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
 

From 2512657ea02908057787dfb124ed0bcb84df07e9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 10:50:38 +0100
Subject: [PATCH 06/61] Bump junit-platform-launcher from 1.4.0 to 1.4.1
 (#4774)

Bumps [junit-platform-launcher](https://github.com/junit-team/junit5) from 1.4.0 to 1.4.1.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/commits)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 1bee7bc1732..70d2bc30c2b 100644
--- a/build.gradle
+++ b/build.gradle
@@ -163,7 +163,7 @@ dependencies {
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.4.1'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.4.1'
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'

From 2b791c306070f08e31b5218b4de1f818fb25a49e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2019 10:51:02 +0100
Subject: [PATCH 07/61] Bump archunit-junit5-engine from 0.9.3 to 0.10.1
 (#4777)

Bumps [archunit-junit5-engine](https://github.com/TNG/ArchUnit) from 0.9.3 to 0.10.1.
- [Release notes](https://github.com/TNG/ArchUnit/releases)
- [Commits](https://github.com/TNG/ArchUnit/compare/v0.9.3...v0.10.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 70d2bc30c2b..9673626d496 100644
--- a/build.gradle
+++ b/build.gradle
@@ -172,7 +172,7 @@ dependencies {
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.3'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.1'
     testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.1'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"

From 90376f40fe0acc9b4b85c5574292e3997d3975f5 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 19 Mar 2019 23:29:48 +0100
Subject: [PATCH 08/61] Fix opening of entry editor (#4784)

Fixes #4762. The problem was that the NotificationPane was hiding the entry editor/preview.
---
 src/main/java/org/jabref/gui/BasePanel.java | 40 ++++++---------------
 1 file changed, 11 insertions(+), 29 deletions(-)

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index ea88315f304..96d68e870dd 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -25,7 +25,6 @@
 import javafx.scene.Node;
 import javafx.scene.control.ScrollPane;
 import javafx.scene.control.SplitPane;
-import javafx.scene.layout.AnchorPane;
 import javafx.scene.layout.StackPane;
 
 import org.jabref.Globals;
@@ -191,7 +190,7 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         if (file.isPresent()) {
             // Register so we get notifications about outside changes to the file.
             changeMonitor = Optional.of(new DatabaseChangeMonitor(bibDatabaseContext, Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR));
-            changePane = new DatabaseChangePane(mainTable.getPane(), bibDatabaseContext, changeMonitor.get());
+            changePane = new DatabaseChangePane(splitPane, bibDatabaseContext, changeMonitor.get());
             getChildren().add(changePane);
         } else {
             if (bibDatabaseContext.getDatabase().hasEntries()) {
@@ -394,7 +393,7 @@ private void setupActions() {
                                                                          .withPreviewPanelEnabled(enabled)
                                                                          .build();
             Globals.prefs.storePreviewPreferences(newPreviewPreferences);
-            DefaultTaskExecutor.runInJavaFXThread(() -> setPreviewActiveBasePanels(enabled));
+            setPreviewActive(enabled);
         });
 
         actions.put(Actions.NEXT_PREVIEW_STYLE, this::nextPreviewStyle);
@@ -776,13 +775,9 @@ public void setupMainPanel() {
         createMainTable();
 
         ScrollPane pane = mainTable.getPane();
-        AnchorPane anchorPane = new AnchorPane(pane);
-        AnchorPane.setBottomAnchor(pane, 0.0);
-        AnchorPane.setTopAnchor(pane, 0.0);
-        AnchorPane.setLeftAnchor(pane, 0.0);
-        AnchorPane.setRightAnchor(pane, 0.0);
-        splitPane.getItems().add(anchorPane);
-        this.getChildren().setAll(splitPane);
+        pane.setFitToHeight(true);
+        pane.setFitToWidth(true);
+        splitPane.getItems().add(pane);
 
         // Set up name autocompleter for search:
         instantiateSearchAutoCompleter();
@@ -845,17 +840,13 @@ public EntryEditor getEntryEditor() {
      * @param entry The entry to edit.
      */
     public void showAndEdit(BibEntry entry) {
-        DefaultTaskExecutor.runInJavaFXThread(() -> {
+        showBottomPane(BasePanelMode.SHOWING_EDITOR);
 
-            showBottomPane(BasePanelMode.SHOWING_EDITOR);
-
-            if (entry != getShowing()) {
-                entryEditor.setEntry(entry);
-                showing = entry;
-            }
-            entryEditor.requestFocus();
-
-        });
+        if (entry != getShowing()) {
+            entryEditor.setEntry(entry);
+            showing = entry;
+        }
+        entryEditor.requestFocus();
     }
 
     private void showBottomPane(BasePanelMode newMode) {
@@ -1150,15 +1141,6 @@ public String formatOutputMessage(String start, int count) {
         return String.format("%s %d %s.", start, count, (count > 1 ? Localization.lang("entries") : Localization.lang("entry")));
     }
 
-    /**
-     * Set the preview active state for all BasePanel instances.
-     */
-    private void setPreviewActiveBasePanels(boolean enabled) {
-        for (int i = 0; i < frame.getTabbedPane().getTabs().size(); i++) {
-            frame.getBasePanelAt(i).setPreviewActive(enabled);
-        }
-    }
-
     private void setPreviewActive(boolean enabled) {
         if (enabled) {
             showPreview();

From 6c61664a8f715e4011064ddca5cb0ace0b803131 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Wed, 20 Mar 2019 20:48:13 +0100
Subject: [PATCH 09/61] Fix NPE in Duplicate Resolver Dialog (#4791)

* Fix NPE in Duplicate Resolver Dialog


Fixes #4785

* Fix NPE in review dialog

Fixes #4786
---
 src/main/java/org/jabref/gui/DuplicateResolverDialog.java      | 2 +-
 src/main/java/org/jabref/gui/PreviewPanel.java                 | 2 +-
 .../java/org/jabref/gui/collab/EntryAddChangeViewModel.java    | 2 +-
 src/main/java/org/jabref/gui/search/SearchResultFrame.java     | 3 ++-
 4 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
index 858a7c7e7f2..fa1b2b92b96 100644
--- a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
+++ b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
@@ -39,8 +39,8 @@ public enum DuplicateResolverResult {
 
     public DuplicateResolverDialog(BibEntry one, BibEntry two, DuplicateResolverType type, BibDatabaseContext database) {
         this.setTitle(Localization.lang("Possible duplicate entries"));
-        init(one, two, type);
         this.database = database;
+        init(one, two, type);
     }
 
     private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
diff --git a/src/main/java/org/jabref/gui/PreviewPanel.java b/src/main/java/org/jabref/gui/PreviewPanel.java
index 796fafdd016..ff26ee6765b 100644
--- a/src/main/java/org/jabref/gui/PreviewPanel.java
+++ b/src/main/java/org/jabref/gui/PreviewPanel.java
@@ -84,7 +84,7 @@ public class PreviewPanel extends ScrollPane implements SearchQueryHighlightList
 
     /**
      * @param panel           (may be null) Only set this if the preview is associated to the main window.
-     * @param databaseContext Used for resolving pdf directories for links. Must not be null.
+     * @param databaseContext Used for resolving pdf directories for links. Must not be null, just pass a new empty BibDatabaseContext()
      */
     public PreviewPanel(BasePanel panel, BibDatabaseContext databaseContext, KeyBindingRepository keyBindingRepository, PreviewPreferences preferences, DialogService dialogService, ExternalFileTypes externalFileTypes) {
         this.databaseContext = Objects.requireNonNull(databaseContext);
diff --git a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
index 8284f544cab..c5849decfef 100644
--- a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
@@ -29,7 +29,7 @@ public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
 
     @Override
     public Node description() {
-        PreviewPanel previewPanel = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
         previewPanel.setEntry(diskEntry);
         return previewPanel;
     }
diff --git a/src/main/java/org/jabref/gui/search/SearchResultFrame.java b/src/main/java/org/jabref/gui/search/SearchResultFrame.java
index 9977866efad..376de69855e 100644
--- a/src/main/java/org/jabref/gui/search/SearchResultFrame.java
+++ b/src/main/java/org/jabref/gui/search/SearchResultFrame.java
@@ -55,6 +55,7 @@
 import org.jabref.logic.bibtex.comparator.FieldComparator;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.search.SearchQuery;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.FieldProperty;
@@ -122,7 +123,7 @@ private void init(String title) {
         searchResultFrame.setTitle(title);
         searchResultFrame.setIconImages(IconTheme.getLogoSet());
 
-        preview = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), frame.getDialogService(), ExternalFileTypes.getInstance());
+        preview = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), frame.getDialogService(), ExternalFileTypes.getInstance());
 
         sortedEntries = new SortedList<>(entries, new EntryComparator(false, true, FieldName.AUTHOR));
         model = (DefaultEventTableModel<BibEntry>) GlazedListsSwing.eventTableModelWithThreadProxyList(sortedEntries,

From 29e9d4971954a80510134800499fd65563e3b280 Mon Sep 17 00:00:00 2001
From: samiyac <samiya17094@iiitd.ac.in>
Date: Fri, 22 Mar 2019 01:57:11 +0530
Subject: [PATCH 10/61] Shortens text fields in Required Fields Tab

---
 src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java  | 2 +-
 src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java b/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
index bbd23b29d97..26f22eb2b6f 100644
--- a/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
@@ -103,7 +103,7 @@ private void setupPanel(BibEntry entry, boolean compressed, SuggestionProviders
         }
 
         ColumnConstraints columnExpand = new ColumnConstraints();
-        columnExpand.setHgrow(Priority.ALWAYS);
+        columnExpand.setPercentWidth(60);
 
         ColumnConstraints columnDoNotContract = new ColumnConstraints();
         columnDoNotContract.setMinWidth(Region.USE_PREF_SIZE);
diff --git a/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml b/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
index 99d6d3f7601..32160f0c544 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
+++ b/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
@@ -6,5 +6,5 @@
 <fx:root xmlns:fx="http://javafx.com/fxml/1" type="HBox" xmlns="http://javafx.com/javafx/8.0.112"
          fx:controller="org.jabref.gui.fieldeditors.BibtexKeyEditor">
     <EditorTextField fx:id="textField"/>
-    <Button fx:id="generateCiteKeyButton" styleClass="icon-button"/>
+    <Button fx:id="generateCiteKeyButton" text="Generate" styleClass="icon-button"/>
 </fx:root>

From 48ed0bae4c59b370bfb1be01328f99c06c141f5b Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 25 Mar 2019 17:36:02 +0100
Subject: [PATCH 11/61] fix npe

---
 .../java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
index 22f4c9a80b9..e4b658036a0 100644
--- a/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
@@ -46,7 +46,7 @@ public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
 
     @Override
     public Node description() {
-        PreviewPanel previewPanel = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
         previewPanel.setEntry(memEntry);
         return previewPanel;
     }

From e14b567425cdd2a49efcf56b0e4eafd0b96f1c1a Mon Sep 17 00:00:00 2001
From: Matthias Geiger <matthias.geiger@uni-bamberg.de>
Date: Mon, 25 Mar 2019 17:54:03 +0100
Subject: [PATCH 12/61] Followup of #4784 - fixes remaining issues of #4762
 (#4806)

* followup of #4784 - fixes remaining issues of #4762

* use Path instead of File

Co-authored-by: matthiasgeiger <matthias.geiger@uni-bamberg.de>
---
 src/main/java/org/jabref/gui/BasePanel.java   | 41 ++++++++++---------
 .../gui/exporter/SaveDatabaseAction.java      |  2 +-
 2 files changed, 23 insertions(+), 20 deletions(-)

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index 96d68e870dd..b64b181f60a 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -1,6 +1,5 @@
 package org.jabref.gui;
 
-import java.io.File;
 import java.io.IOException;
 import java.io.StringReader;
 import java.lang.reflect.InvocationTargetException;
@@ -115,7 +114,6 @@ public class BasePanel extends StackPane {
 
     private final BibDatabaseContext bibDatabaseContext;
     private final MainTableDataModel tableModel;
-    private final DatabaseChangePane changePane;
 
     private final CitationStyleCache citationStyleCache;
     private final FileAnnotationCache annotationCache;
@@ -138,6 +136,7 @@ public class BasePanel extends StackPane {
     // As most enums, this must not be null
     private BasePanelMode mode = BasePanelMode.SHOWING_NOTHING;
     private SplitPane splitPane;
+    private DatabaseChangePane changePane;
     private boolean saving;
 
     // AutoCompleter used in the search bar
@@ -186,22 +185,6 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         // ensure that all entry changes mark the panel as changed
         this.bibDatabaseContext.getDatabase().registerListener(this);
 
-        Optional<File> file = bibDatabaseContext.getDatabaseFile();
-        if (file.isPresent()) {
-            // Register so we get notifications about outside changes to the file.
-            changeMonitor = Optional.of(new DatabaseChangeMonitor(bibDatabaseContext, Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR));
-            changePane = new DatabaseChangePane(splitPane, bibDatabaseContext, changeMonitor.get());
-            getChildren().add(changePane);
-        } else {
-            if (bibDatabaseContext.getDatabase().hasEntries()) {
-                // if the database is not empty and no file is assigned,
-                // the database came from an import and has to be treated somehow
-                // -> mark as changed
-                this.baseChanged = true;
-            }
-            changePane = null;
-        }
-
         this.getDatabase().registerListener(new UpdateTimestampListener(Globals.prefs));
 
         this.entryEditor = new EntryEditor(this, preferences.getEntryEditorPreferences(), Globals.getFileUpdateMonitor(), dialogService, externalFileTypes, Globals.TASK_EXECUTOR);
@@ -790,6 +773,22 @@ public void setupMainPanel() {
         dividerPositionSubscription = EasyBind.monadic(Bindings.valueAt(splitPane.getDividers(), 0))
                                               .flatMap(SplitPane.Divider::positionProperty)
                                               .subscribe((observable, oldValue, newValue) -> saveDividerLocation(newValue));
+
+        // Add changePane in case a file is present - otherwise just add the splitPane to the panel
+        Optional<Path> file = bibDatabaseContext.getDatabasePath();
+        if (file.isPresent()) {
+            // create changeMonitor and changePane so we get notifications about outside changes to the file.
+            resetChangeMonitorAndChangePane();
+        } else {
+            if (bibDatabaseContext.getDatabase().hasEntries()) {
+                // if the database is not empty and no file is assigned,
+                // the database came from an import and has to be treated somehow
+                // -> mark as changed
+                this.baseChanged = true;
+            }
+            changePane = null;
+            getChildren().add(splitPane);
+        }
     }
 
     /**
@@ -1182,9 +1181,13 @@ public FileAnnotationCache getAnnotationCache() {
         return annotationCache;
     }
 
-    public void resetChangeMonitor() {
+    public void resetChangeMonitorAndChangePane() {
         changeMonitor.ifPresent(DatabaseChangeMonitor::unregister);
         changeMonitor = Optional.of(new DatabaseChangeMonitor(bibDatabaseContext, Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR));
+
+        changePane = new DatabaseChangePane(splitPane, bibDatabaseContext, changeMonitor.get());
+
+        this.getChildren().setAll(changePane);
     }
 
     public void updateTimeStamp() {
diff --git a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
index f1bfe5c0739..b743b7fa199 100644
--- a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
@@ -211,7 +211,7 @@ public void saveAs(Path file) {
         save();
 
         // Reinstall AutosaveManager and BackupManager
-        panel.resetChangeMonitor();
+        panel.resetChangeMonitorAndChangePane();
         if (readyForAutosave(context)) {
             AutosaveManager autosaver = AutosaveManager.start(context);
             autosaver.registerListener(new AutosaveUIManager(panel));

From 8e6b1772ef9f3486e6fe1d459d1b77f78018f335 Mon Sep 17 00:00:00 2001
From: Tim Kilian <mail@timkilian.pl>
Date: Tue, 26 Mar 2019 16:14:40 +0100
Subject: [PATCH 13/61] Fix do not clear wanted special characters (#4770)

---
 CHANGELOG.md                                              | 2 +-
 .../jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java | 6 ++++--
 .../logic/bibtexkeypattern/BibtexKeyGeneratorTest.java    | 8 ++++++++
 3 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9e14888432a..1450b5b5201 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -99,7 +99,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
-
+- We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
 
 
 
diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
index 6e10ac5ff8f..6309b297168 100644
--- a/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
+++ b/src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java
@@ -133,6 +133,9 @@ public String generateKey(BibEntry entry) {
                         label = applyModifiers(label, parts, 1);
                     }
 
+                    // Remove all illegal characters from the label.
+                    label = cleanKey(label, bibtexKeyPatternPreferences.isEnforceLegalKey());
+
                     stringBuilder.append(label);
 
                 } else {
@@ -143,8 +146,7 @@ public String generateKey(BibEntry entry) {
             LOGGER.warn("Cannot make label", e);
         }
 
-        // Remove all illegal characters from the key.
-        key = cleanKey(stringBuilder.toString(), bibtexKeyPatternPreferences.isEnforceLegalKey());
+        key = stringBuilder.toString();
 
         // Remove Regular Expressions while generating Keys
         String regex = bibtexKeyPatternPreferences.getKeyPatternRegex();
diff --git a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
index 3857cfb6c8b..ad6e2d86e1c 100644
--- a/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
+++ b/src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java
@@ -1073,4 +1073,12 @@ public void generateKeyWithYearAuthUpperTitleSentenceCaseModifier() throws Excep
         assertEquals("NewtonMaxwellEtAl_2019_TheInterestingTitleLongerThanThreeWords", BibtexKeyGenerator.generateKey(entry, "[authors2]_[year]_[title:capitalize]"));
     }
 
+    @Test
+    public void generateKeyWithMinusInCitationStyleOutsideAField() throws Exception {
+        BibEntry entry = new BibEntry();
+        entry.setField("author", AUTHOR_STRING_FIRSTNAME_FULL_LASTNAME_FULL_COUNT_1);
+        entry.setField("year", "2019");
+
+        assertEquals("Newton-2019", BibtexKeyGenerator.generateKey(entry, "[auth]-[year]"));
+    }
 }

From 83c8022697bef2756d238ad401adc6697ada467f Mon Sep 17 00:00:00 2001
From: Yash  Kothari <yashkothari199767@gmail.com>
Date: Tue, 26 Mar 2019 21:16:14 +0530
Subject: [PATCH 14/61] Fix closing of library not handling backup and autosave
 manager shutdown (#4794)

---
 src/main/java/org/jabref/gui/JabRefFrame.java | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index ff496a25e09..1cf05c35116 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -1154,6 +1154,10 @@ public void addTab(BasePanel basePanel, boolean raisePanel) {
             // add tab
             Tab newTab = new Tab(basePanel.getTabTitle(), basePanel);
             tabbedPane.getTabs().add(newTab);
+            newTab.setOnCloseRequest(event -> {
+                closeTab((BasePanel) newTab.getContent());
+                event.consume();
+            });
 
             // update all tab titles
             updateAllTabTitles();
@@ -1340,6 +1344,8 @@ private void closeTab(BasePanel panel) {
         if (panel.isModified() && (context.getLocation() == DatabaseLocation.LOCAL)) {
             if (confirmClose(panel)) {
                 removeTab(panel);
+            } else {
+                return;
             }
         } else if (context.getLocation() == DatabaseLocation.SHARED) {
             context.convertToLocalDatabase();

From 44163bfe151a6a09b8f1b355698a1c550a41ec16 Mon Sep 17 00:00:00 2001
From: Johannes Manner <johannes.manner@web.de>
Date: Wed, 27 Mar 2019 15:37:11 +0100
Subject: [PATCH 15/61] Change latex command handling only for XML Chars
 (#4379)

* Change latex command handling only for XML Chars

* Added Test for DocbookExporter

* Hopefully fixed travis error and added changelog entry

* Update DocbookExporterTest.java

* Resolve jupiter problem

* Update DocbookExporterTest.java
---
 CHANGELOG.md                                  |  1 +
 .../jabref/logic/layout/format/XMLChars.java  |  8 +-
 .../logic/exporter/DocbookExporterTest.java   | 74 +++++++++++++++++++
 3 files changed, 82 insertions(+), 1 deletion(-)
 create mode 100644 src/test/java/org/jabref/logic/exporter/DocbookExporterTest.java

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1450b5b5201..d5983623107 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We changed the latex command removal for docbook exporter. [#3838](https://github.com/JabRef/jabref/issues/3838)
 - We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
   - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
   - DOI/URL: General -> Optional
diff --git a/src/main/java/org/jabref/logic/layout/format/XMLChars.java b/src/main/java/org/jabref/logic/layout/format/XMLChars.java
index 59c98142969..4a3ada367a7 100644
--- a/src/main/java/org/jabref/logic/layout/format/XMLChars.java
+++ b/src/main/java/org/jabref/logic/layout/format/XMLChars.java
@@ -30,7 +30,8 @@ public String format(String fieldText) {
             return fieldText;
         }
 
-        String formattedFieldText = firstFormat(fieldText);
+        String latexCommandFree = removeLatexCommands(fieldText);
+        String formattedFieldText = firstFormat(latexCommandFree);
 
         for (Map.Entry<String, String> entry : XML_CHARS.entrySet()) {
             String s = entry.getKey();
@@ -42,6 +43,11 @@ public String format(String fieldText) {
         return restFormat(formattedFieldText);
     }
 
+    private String removeLatexCommands(String fieldText) {
+        LatexToUnicodeFormatter latexToUnicode = new LatexToUnicodeFormatter();
+        return latexToUnicode.format(fieldText);
+    }
+
     private static String firstFormat(String s) {
         return s.replaceAll("&|\\\\&", "&#x0026;").replace("--", "&#x2013;");
     }
diff --git a/src/test/java/org/jabref/logic/exporter/DocbookExporterTest.java b/src/test/java/org/jabref/logic/exporter/DocbookExporterTest.java
new file mode 100644
index 00000000000..a10a91ec6ff
--- /dev/null
+++ b/src/test/java/org/jabref/logic/exporter/DocbookExporterTest.java
@@ -0,0 +1,74 @@
+package org.jabref.logic.exporter;
+
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.jabref.logic.layout.LayoutFormatterPreferences;
+import org.jabref.logic.xmp.XmpPreferences;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import org.mockito.Answers;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.Mockito.mock;
+
+public class DocbookExporterTest {
+
+    public BibDatabaseContext databaseContext = new BibDatabaseContext();;
+    public Charset charset = StandardCharsets.UTF_8;
+
+    private Exporter exportFormat;
+
+    @BeforeEach
+    public void setUp() {
+        List<TemplateExporter> customFormats = new ArrayList<>();
+        LayoutFormatterPreferences layoutPreferences = mock(LayoutFormatterPreferences.class, Answers.RETURNS_DEEP_STUBS);
+        SavePreferences savePreferences = mock(SavePreferences.class);
+        XmpPreferences xmpPreferences = mock(XmpPreferences.class);
+        ExporterFactory exporterFactory = ExporterFactory.create(customFormats, layoutPreferences, savePreferences, xmpPreferences);
+
+        exportFormat = exporterFactory.getExporterByName("docbook4").get();
+    }
+
+    @Test
+    public void testCorruptedTitleBraces(@TempDir Path testFolder) throws Exception {
+        Path tmpFile = testFolder.resolve("testBraces");
+
+        BibEntry entry = new BibEntry();
+        entry.setField("title", "Peptidomics of the larval {\\protect{{D}rosophila melanogaster}} central nervous system.");
+
+        List<BibEntry> entries = Arrays.asList(entry);
+
+        exportFormat.export(databaseContext, tmpFile, charset, entries);
+
+        List<String> lines = Files.readAllLines(tmpFile);
+        assertEquals(20, lines.size());
+        assertEquals("   <citetitle pubwork=\"article\">Peptidomics of the larval Drosophila melanogaster central nervous system.</citetitle>", lines.get(9));
+    }
+
+    @Test
+    public void testCorruptedTitleUnicode(@TempDir Path testFolder) throws Exception {
+        Path tmpFile = testFolder.resolve("testBraces");
+
+        BibEntry entry = new BibEntry();
+        entry.setField("title", "Insect neuropeptide bursicon homodimers induce innate immune and stress genes during molting by activating the {NF}-$\\kappa$B transcription factor Relish.");
+
+        List<BibEntry> entries = Arrays.asList(entry);
+
+        exportFormat.export(databaseContext, tmpFile, charset, entries);
+
+        List<String> lines = Files.readAllLines(tmpFile);
+        assertEquals(20, lines.size());
+        assertEquals("   <citetitle pubwork=\"article\">Insect neuropeptide bursicon homodimers induce innate immune and stress genes during molting by activating the NF&#45;&#954;B transcription factor Relish.</citetitle>", lines.get(9));
+    }
+
+}

From ef5710c464612fc363f5e2f20b96b21463473236 Mon Sep 17 00:00:00 2001
From: Manuel <WtfJoke@users.noreply.github.com>
Date: Wed, 27 Mar 2019 18:58:45 +0100
Subject: [PATCH 16/61] Searchable/Filterable preferences (#4415)

* add search box to preferences

* replace deprecated method call

* Fix codestyle/checkstyle

* Add Preferences Search Handler

still work in progress
mapping search to preference and start searching it
still needs a way to filter the found items

* Remove unused variable

* Add a list of filtered preftabs instead of filtered preftabnames

* :tada: Add the actual filtering of the elements

* Favor SimpleListProperty over SimpleObjectProperty

* Fix Imports

also be explicit about method visibility

* Add filtering of labels

* Remove some unneeded member variables

* extract filterBy methods

* Fix Type of ListProperty

* Remove todo

Verified this is not the case: label names dont contain tab names

* Reformat code

* Favor regular List over ObservableList

* Use existing translated text for prompt

* Revert: Favor regular List over ObservableList

because build (guiTest) fails

* Favor regular List over ObservableList

is not the cause of the build failure

* Adding search highlight while filtering

* Replacing map by multimaps and changing the mapping relation

* Fixing checkstyle error

* Added Locale.ROOT when converting to lower case

* Removed redundant comments

* Removed LabeledWrapper inner class and refactored PreferencesSearchHandler

* Fixed checkstyle error

* add bidiretional binding to searchProperty

* Added change listener on searchBox and removed search text property

Co-authored-by: Yash Kothari <yashkothari199767@gmail.com>
---
 .../gui/preferences/PreferencesDialog.css     |  4 +
 .../gui/preferences/PreferencesDialog.java    | 21 +++-
 .../preferences/PreferencesSearchHandler.java | 98 +++++++++++++++++++
 3 files changed, 119 insertions(+), 4 deletions(-)
 create mode 100644 src/main/java/org/jabref/gui/preferences/PreferencesSearchHandler.java

diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css
index f79bfba706e..8407e1276de 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.css
@@ -12,3 +12,7 @@
 .preferencePaneContainer {
     -fx-padding: 0em 1em 0em 3em;
 }
+
+*:search-highlight {
+	-fx-background-color: -jr-light-red;
+}
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
index e966cd2eb66..a64fa630780 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
@@ -1,6 +1,7 @@
 package org.jabref.gui.preferences;
 
 import java.util.List;
+import java.util.Locale;
 import java.util.prefs.BackingStoreException;
 
 import javafx.collections.FXCollections;
@@ -12,6 +13,7 @@
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.ListView;
 import javafx.scene.control.ScrollPane;
+import javafx.scene.control.TextField;
 import javafx.scene.control.Tooltip;
 import javafx.scene.layout.BorderPane;
 import javafx.scene.layout.Priority;
@@ -127,6 +129,15 @@ private void construct() {
                                                 .withText(PrefsTab::getTabName)
                                                 .install(tabsList);
 
+        TextField searchBox = new TextField();
+        searchBox.setPromptText(Localization.lang("Search"));
+
+        PreferencesSearchHandler searchHandler = new PreferencesSearchHandler(preferenceTabs);
+        tabsList.itemsProperty().bindBidirectional(searchHandler.filteredPreferenceTabsProperty());
+        searchBox.textProperty().addListener((observable, previousText, newText) -> {
+            searchHandler.filterTabs(newText.toLowerCase(Locale.ROOT));
+        });
+
         VBox buttonContainer = new VBox();
         buttonContainer.setAlignment(Pos.BOTTOM_LEFT);
         buttonContainer.setSpacing(3.0);
@@ -155,9 +166,11 @@ private void construct() {
         VBox.setVgrow(tabsList, Priority.ALWAYS);
         VBox.setVgrow(spacer, Priority.SOMETIMES);
         vBox.getChildren().addAll(
-                                  tabsList,
-                                  spacer,
-                                  buttonContainer);
+                searchBox,
+                tabsList,
+                spacer,
+                buttonContainer
+        );
 
         container.setLeft(vBox);
 
@@ -230,7 +243,7 @@ private void storeAllSettings() {
 
         GUIGlobals.updateEntryEditorColors();
         frame.setupAllTables();
-        frame.output(Localization.lang("Preferences recorded."));
+        dialogService.notify(Localization.lang("Preferences recorded."));
     }
 
     public void setValues() {
diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesSearchHandler.java b/src/main/java/org/jabref/gui/preferences/PreferencesSearchHandler.java
new file mode 100644
index 00000000000..4478d88f75e
--- /dev/null
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesSearchHandler.java
@@ -0,0 +1,98 @@
+package org.jabref.gui.preferences;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Locale;
+
+import javafx.beans.property.ListProperty;
+import javafx.beans.property.SimpleListProperty;
+import javafx.collections.FXCollections;
+import javafx.css.PseudoClass;
+import javafx.scene.Node;
+import javafx.scene.Parent;
+import javafx.scene.control.Labeled;
+
+import com.google.common.collect.ArrayListMultimap;
+
+class PreferencesSearchHandler {
+
+    private static PseudoClass labelHighlight = PseudoClass.getPseudoClass("search-highlight");
+    private final List<PrefsTab> preferenceTabs;
+    private final ListProperty<PrefsTab> filteredPreferenceTabs;
+    private final ArrayListMultimap<PrefsTab, Labeled> preferenceTabsLabelNames;
+    private final ArrayList<Labeled> highlightedLabels = new ArrayList<>();
+
+    PreferencesSearchHandler(List<PrefsTab> preferenceTabs) {
+        this.preferenceTabs = preferenceTabs;
+        this.preferenceTabsLabelNames = getPrefsTabLabelMap();
+        this.filteredPreferenceTabs = new SimpleListProperty<>(FXCollections.observableArrayList(preferenceTabs));
+    }
+
+    public void filterTabs(String text) {
+        clearHighlights();
+        if (text.isEmpty()) {
+            clearSearch();
+            return;
+        }
+
+        filteredPreferenceTabs.clear();
+        for (PrefsTab tab : preferenceTabsLabelNames.keySet()) {
+            boolean tabContainsLabel = false;
+            for (Labeled labeled : preferenceTabsLabelNames.get(tab)) {
+                if (labelContainsText(labeled, text)) {
+                    tabContainsLabel = true;
+                    highlightLabel(labeled);
+                }
+            }
+            boolean tabNameIsMatchedByQuery = tab.getTabName().toLowerCase(Locale.ROOT).contains(text);
+            if (tabContainsLabel || tabNameIsMatchedByQuery) {
+                filteredPreferenceTabs.add(tab);
+            }
+        }
+    }
+
+    private boolean labelContainsText(Labeled labeled, String text) {
+        return labeled.getText().toLowerCase(Locale.ROOT).contains(text);
+    }
+
+    private void highlightLabel(Labeled labeled) {
+        labeled.pseudoClassStateChanged(labelHighlight, true);
+        highlightedLabels.add(labeled);
+    }
+
+    private void clearHighlights() {
+        highlightedLabels.forEach(labeled -> labeled.pseudoClassStateChanged(labelHighlight, false));
+    }
+
+    private void clearSearch() {
+        filteredPreferenceTabs.setAll(preferenceTabs);
+    }
+
+    /*
+     * Traverse all nodes of a PrefsTab and return a
+     * mapping from PrefsTab to all its Labeled type nodes.
+     */
+    private ArrayListMultimap<PrefsTab, Labeled> getPrefsTabLabelMap() {
+        ArrayListMultimap<PrefsTab, Labeled> prefsTabLabelMap = ArrayListMultimap.create();
+        for (PrefsTab prefsTab : preferenceTabs) {
+            Node builder = prefsTab.getBuilder();
+            if (builder instanceof Parent) {
+                Parent parentBuilder = (Parent) builder;
+                for (Node child : parentBuilder.getChildrenUnmodifiable()) {
+                    if (child instanceof Labeled) {
+                        Labeled labeled = (Labeled) child;
+                        if (!labeled.getText().isEmpty()) {
+                            prefsTabLabelMap.put(prefsTab, labeled);
+                        }
+                    }
+                }
+            }
+        }
+        return prefsTabLabelMap;
+    }
+
+    protected ListProperty<PrefsTab> filteredPreferenceTabsProperty() {
+        return filteredPreferenceTabs;
+    }
+
+}

From ce7293dc4ea0ba8cb56deff62419ac6fe0ea11fe Mon Sep 17 00:00:00 2001
From: Samiya Caur <36728314+samiyac@users.noreply.github.com>
Date: Wed, 27 Mar 2019 23:40:39 +0530
Subject: [PATCH 17/61] Item Count in a group updated correctly (#4807)

* Item Count in a group updated correctly

* Added comments

* changes
---
 src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java b/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java
index c31c9ce6dd9..cb17247dd0c 100644
--- a/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java
+++ b/src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java
@@ -55,6 +55,7 @@ public class GroupNodeViewModel {
     private final BooleanBinding allSelectedEntriesMatched;
     private final TaskExecutor taskExecutor;
     private final CustomLocalDragboard localDragBoard;
+    private final ObservableList<BibEntry> entriesList;
 
     public GroupNodeViewModel(BibDatabaseContext databaseContext, StateManager stateManager, TaskExecutor taskExecutor, GroupTreeNode groupNode, CustomLocalDragboard localDragBoard) {
         this.databaseContext = Objects.requireNonNull(databaseContext);
@@ -84,7 +85,9 @@ public GroupNodeViewModel(BibDatabaseContext databaseContext, StateManager state
         expandedProperty.addListener((observable, oldValue, newValue) -> groupNode.getGroup().setExpanded(newValue));
 
         // Register listener
-        databaseContext.getDatabase().getEntries().addListener(this::onDatabaseChanged);
+        // The wrapper created by the FXCollections will set a weak listener on the wrapped list. This weak listener gets garbage collected. Hence, we need to maintain a reference to this list.
+        entriesList = databaseContext.getDatabase().getEntries();
+        entriesList.addListener(this::onDatabaseChanged);
 
         ObservableList<Boolean> selectedEntriesMatchStatus = EasyBind.map(stateManager.getSelectedEntries(), groupNode::matches);
         anySelectedEntriesMatched = BindingsHelper.any(selectedEntriesMatchStatus, matched -> matched);

From 133fbaa376e779ab515f763f7a6986a0ba4f37ce Mon Sep 17 00:00:00 2001
From: Yash  Kothari <yashkothari199767@gmail.com>
Date: Thu, 28 Mar 2019 13:34:47 +0530
Subject: [PATCH 18/61] Fix removing entries when source-code-field is out of
 focus (#4769)

Fixes #4764
---
 .../org/jabref/gui/entryeditor/SourceTab.java | 28 +++++++++----------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
index 89f97ffbf2e..2752103316d 100644
--- a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
@@ -145,7 +145,7 @@ protected void bindToEntry(BibEntry entry) {
         // and update source code for every change of entry field values
         BindingsHelper.bindContentBidirectional(entry.getFieldsObservable(), codeArea.focusedProperty(), onFocus -> {
             if (!onFocus) {
-                storeSource(codeArea.textProperty().getValue());
+                storeSource(entry, codeArea.textProperty().getValue());
             }
         }, fields -> {
             DefaultTaskExecutor.runAndWaitInJavaFXThread(() -> {
@@ -163,8 +163,8 @@ protected void bindToEntry(BibEntry entry) {
 
     }
 
-    private void storeSource(String text) {
-        if ((currentEntry == null) || text.isEmpty()) {
+    private void storeSource(BibEntry outOfFocusEntry, String text) {
+        if ((outOfFocusEntry == null) || text.isEmpty()) {
             return;
         }
 
@@ -197,42 +197,42 @@ private void storeSource(String text) {
             String newKey = newEntry.getCiteKeyOptional().orElse(null);
 
             if (newKey != null) {
-                currentEntry.setCiteKey(newKey);
+                outOfFocusEntry.setCiteKey(newKey);
             } else {
-                currentEntry.clearCiteKey();
+                outOfFocusEntry.clearCiteKey();
             }
 
             // First, remove fields that the user has removed.
-            for (Map.Entry<String, String> field : currentEntry.getFieldMap().entrySet()) {
+            for (Map.Entry<String, String> field : outOfFocusEntry.getFieldMap().entrySet()) {
                 String fieldName = field.getKey();
                 String fieldValue = field.getValue();
 
                 if (InternalBibtexFields.isDisplayableField(fieldName) && !newEntry.hasField(fieldName)) {
                     compound.addEdit(
-                            new UndoableFieldChange(currentEntry, fieldName, fieldValue, null));
-                    currentEntry.clearField(fieldName);
+                                     new UndoableFieldChange(outOfFocusEntry, fieldName, fieldValue, null));
+                    outOfFocusEntry.clearField(fieldName);
                 }
             }
 
             // Then set all fields that have been set by the user.
             for (Map.Entry<String, String> field : newEntry.getFieldMap().entrySet()) {
                 String fieldName = field.getKey();
-                String oldValue = currentEntry.getField(fieldName).orElse(null);
+                String oldValue = outOfFocusEntry.getField(fieldName).orElse(null);
                 String newValue = field.getValue();
                 if (!Objects.equals(oldValue, newValue)) {
                     // Test if the field is legally set.
                     new LatexFieldFormatter(fieldFormatterPreferences)
                             .format(newValue, fieldName);
 
-                    compound.addEdit(new UndoableFieldChange(currentEntry, fieldName, oldValue, newValue));
-                    currentEntry.setField(fieldName, newValue);
+                    compound.addEdit(new UndoableFieldChange(outOfFocusEntry, fieldName, oldValue, newValue));
+                    outOfFocusEntry.setField(fieldName, newValue);
                 }
             }
 
             // See if the user has changed the entry type:
-            if (!Objects.equals(newEntry.getType(), currentEntry.getType())) {
-                compound.addEdit(new UndoableChangeType(currentEntry, currentEntry.getType(), newEntry.getType()));
-                currentEntry.setType(newEntry.getType());
+            if (!Objects.equals(newEntry.getType(), outOfFocusEntry.getType())) {
+                compound.addEdit(new UndoableChangeType(outOfFocusEntry, outOfFocusEntry.getType(), newEntry.getType()));
+                outOfFocusEntry.setType(newEntry.getType());
             }
             compound.end();
             undoManager.addEdit(compound);

From a9115a256107620fcfbb7c087f1e89e14a632b0d Mon Sep 17 00:00:00 2001
From: Robin <robin.lichtenthaeler@web.de>
Date: Thu, 28 Mar 2019 12:07:14 +0100
Subject: [PATCH 19/61] put renaming of file entries in JavaFX thread for
 cleanup (#4818)

---
 src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java b/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
index 4016081e60b..72912ed73de 100644
--- a/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
+++ b/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
@@ -7,6 +7,7 @@
 import java.util.Objects;
 import java.util.Optional;
 
+import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.externalfiles.LinkedFileHandler;
 import org.jabref.model.FieldChange;
 import org.jabref.model.cleanup.CleanupJob;
@@ -54,8 +55,8 @@ public List<FieldChange> cleanup(BibEntry entry) {
         }
 
         if (changed) {
-            Optional<FieldChange> changes = entry.setFiles(files);
-            return OptionalUtil.toList(changes);
+            Optional<FieldChange> fileFieldChanged = DefaultTaskExecutor.runInJavaFXThread(() -> entry.setFiles(files));
+            return OptionalUtil.toList(fileFieldChanged);
         }
 
         return Collections.emptyList();

From a731679333d3c8b91a3a24c69b6a7bd9151639e2 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Thu, 28 Mar 2019 18:48:08 +0100
Subject: [PATCH 20/61] Remove unused swing code (#4787)

* Remove unused swing code

* Implement feedback and fix tests
---
 src/main/java/org/jabref/JabRefGUI.java       |  23 +-
 src/main/java/org/jabref/gui/BasePanel.java   |  34 --
 .../jabref/gui/DuplicateResolverDialog.java   |   2 +-
 src/main/java/org/jabref/gui/GUIGlobals.java  |   8 -
 .../gui/JEditorPaneWithHighlighting.java      |  57 ---
 src/main/java/org/jabref/gui/JabRefFrame.java |  26 --
 .../jabref/gui/actions/ChangeTypeAction.java  |  52 ---
 .../jabref/gui/actions/CopyDoiUrlAction.java  |  18 +-
 .../gui/actions/MnemonicAwareAction.java      |  44 --
 .../jabref/gui/actions/StandardActions.java   |   5 +
 .../BibtexKeyPatternPanel.java                |  18 +-
 .../gui/cleanup/CleanupActionsListModel.java  |  81 ----
 .../CustomizeGeneralFieldsDialogView.java     |   6 +-
 .../jabref/gui/entryeditor/EntryEditor.java   |   2 +-
 .../externalfiles/DownloadExternalFile.java   | 345 ----------------
 .../JTextAreaWithHighlighting.java            | 173 --------
 .../gui/fieldeditors/LinkedFileViewModel.java |  10 +-
 .../fieldeditors/contextmenu/EditorMenus.java |  11 +-
 .../ConfirmCloseFileListEntryEditor.java      |  14 -
 .../gui/filelist/FileListEntryEditor.java     | 386 ------------------
 .../gui/groups/GroupTreeCellRenderer.java     | 114 ------
 .../java/org/jabref/gui/help/HelpAction.java  |  58 +--
 .../gui/importer/fetcher/WebSearchPane.java   |   3 +-
 .../org/jabref/gui/keyboard/KeyBinder.java    |  29 --
 .../org/jabref/gui/maintable/MainTable.java   |  14 +-
 .../jabref/gui/maintable/RightClickMenu.java  |   4 +-
 .../jabref/gui/menus/ChangeEntryTypeMenu.java |  91 +----
 .../gui/openoffice/OpenOfficePanel.java       |   4 +-
 .../jabref/gui/preferences/AdvancedTab.java   |   2 +-
 .../org/jabref/gui/preferences/FileTab.java   |   5 +-
 .../jabref/gui/preferences/GeneralTab.java    |   4 +-
 .../gui/preferences/NameFormatterTab.java     |   3 +-
 .../gui/preferences/TableColumnsTab.java      |  57 +--
 .../org/jabref/gui/util/ControlHelper.java    |  10 -
 .../gui/util/component/CheckBoxMessage.java   |  37 --
 .../component/JTextAreaWithPlaceholder.java   |  90 ----
 .../component/JTextFieldWithPlaceholder.java  |  91 -----
 .../java/org/jabref/gui/worker/CallBack.java  |  11 -
 .../java/org/jabref/logic/net/URLUtil.java    |  57 ++-
 src/main/resources/l10n/JabRef_en.properties  |  10 -
 .../cleanup/CleanupActionsListModelTest.java  |  94 -----
 41 files changed, 147 insertions(+), 1956 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/JEditorPaneWithHighlighting.java
 delete mode 100644 src/main/java/org/jabref/gui/actions/ChangeTypeAction.java
 delete mode 100644 src/main/java/org/jabref/gui/actions/MnemonicAwareAction.java
 delete mode 100644 src/main/java/org/jabref/gui/cleanup/CleanupActionsListModel.java
 delete mode 100644 src/main/java/org/jabref/gui/externalfiles/DownloadExternalFile.java
 delete mode 100644 src/main/java/org/jabref/gui/fieldeditors/JTextAreaWithHighlighting.java
 delete mode 100644 src/main/java/org/jabref/gui/filelist/ConfirmCloseFileListEntryEditor.java
 delete mode 100644 src/main/java/org/jabref/gui/filelist/FileListEntryEditor.java
 delete mode 100644 src/main/java/org/jabref/gui/groups/GroupTreeCellRenderer.java
 delete mode 100644 src/main/java/org/jabref/gui/keyboard/KeyBinder.java
 delete mode 100644 src/main/java/org/jabref/gui/util/component/CheckBoxMessage.java
 delete mode 100644 src/main/java/org/jabref/gui/util/component/JTextAreaWithPlaceholder.java
 delete mode 100644 src/main/java/org/jabref/gui/util/component/JTextFieldWithPlaceholder.java
 delete mode 100644 src/main/java/org/jabref/gui/worker/CallBack.java
 delete mode 100644 src/test/java/org/jabref/cleanup/CleanupActionsListModelTest.java

diff --git a/src/main/java/org/jabref/JabRefGUI.java b/src/main/java/org/jabref/JabRefGUI.java
index 57214d9ef9f..203dcf03386 100644
--- a/src/main/java/org/jabref/JabRefGUI.java
+++ b/src/main/java/org/jabref/JabRefGUI.java
@@ -65,17 +65,7 @@ public JabRefGUI(Stage mainStage, List<ParserResult> argsDatabases, boolean isBl
     }
 
     private void openWindow(Stage mainStage) {
-        // Set antialiasing on everywhere. This only works in JRE >= 1.5.
-        // Or... it doesn't work, period.
-        // TODO test and maybe remove this! I found this commented out with no additional info ( payload@lavabit.com )
-        // Enabled since JabRef 2.11 beta 4
-        System.setProperty("swing.aatext", "true");
-        // Default is "on".
-        // "lcd" instead of "on" because of http://wiki.netbeans.org/FaqFontRendering and http://docs.oracle.com/javase/6/docs/technotes/guides/2d/flags.html#aaFonts
-        System.setProperty("awt.useSystemAAFontSettings", "lcd");
-
-        // look and feel. This MUST be the first thing to do before loading any Swing-specific code!
-        setLookAndFeel();
+        applyFontRenderingTweak();
 
         // If the option is enabled, open the last edited libraries, if any.
         if (!isBlank && Globals.prefs.getBoolean(JabRefPreferences.OPEN_LAST_EDITED)) {
@@ -242,9 +232,9 @@ private boolean isLoaded(File fileToOpen) {
         return false;
     }
 
-    private void setLookAndFeel() {
-        // On Linux, Java FX fonts look blurry per default. This can be improved by using a non-default rendering
-        // setting. See https://github.com/woky/javafx-hates-linux
+    private void applyFontRenderingTweak() {
+        // On Linux, Java FX fonts look blurry per default. This can be improved by using a non-default rendering setting.
+        // See https://github.com/woky/javafx-hates-linux
         if (Globals.prefs.getBoolean(JabRefPreferences.FX_FONT_RENDERING_TWEAK)) {
             System.setProperty("prism.text", "t2k");
             System.setProperty("prism.lcdtext", "true");
@@ -254,9 +244,4 @@ private void setLookAndFeel() {
     public static JabRefFrame getMainFrame() {
         return mainFrame;
     }
-
-    // Only used for testing, other than that do NOT set the mainFrame...
-    public static void setMainFrame(JabRefFrame mainFrame) {
-        JabRefGUI.mainFrame = mainFrame;
-    }
 }
diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index b64b181f60a..2ccfcdcc927 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -63,7 +63,6 @@
 import org.jabref.gui.specialfields.SpecialFieldViewModel;
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableChangeType;
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.gui.undo.UndoableInsertEntry;
 import org.jabref.gui.undo.UndoableRemoveEntry;
@@ -1011,39 +1010,6 @@ public BibDatabase getDatabase() {
         return bibDatabaseContext.getDatabase();
     }
 
-    public void changeTypeOfSelectedEntries(String newType) {
-        List<BibEntry> bes = mainTable.getSelectedEntries();
-        changeType(bes, newType);
-    }
-
-    private void changeType(List<BibEntry> entries, String newType) {
-        if ((entries == null) || (entries.isEmpty())) {
-            LOGGER.error("At least one entry must be selected to be able to change the type.");
-            return;
-        }
-
-        if (entries.size() > 1) {
-            boolean proceed = dialogService.showConfirmationDialogAndWait(Localization.lang("Change entry type"), Localization.lang("Multiple entries selected. Do you want to change the type of all these to '%0'?"));
-            if (!proceed) {
-                return;
-            }
-        }
-
-        NamedCompound compound = new NamedCompound(Localization.lang("Change entry type"));
-        for (BibEntry entry : entries) {
-            compound.addEdit(new UndoableChangeType(entry, entry.getType(), newType));
-            DefaultTaskExecutor.runInJavaFXThread(() -> {
-                entry.setType(newType);
-            });
-        }
-
-        output(formatOutputMessage(Localization.lang("Changed type to '%0' for", newType), entries.size()));
-        compound.end();
-        getUndoManager().addEdit(compound);
-        markBaseChanged();
-        updateEntryEditorIfShowing();
-    }
-
     public boolean showDeleteConfirmationDialog(int numberOfEntries) {
         if (Globals.prefs.getBoolean(JabRefPreferences.CONFIRM_DELETE)) {
             String title = Localization.lang("Delete entry");
diff --git a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
index fa1b2b92b96..a56da356f6f 100644
--- a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
+++ b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
@@ -116,7 +116,7 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
 
         getDialogPane().setContent(borderPane);
         Button helpButton = (Button) this.getDialogPane().lookupButton(help);
-        helpButton.setOnAction(evt -> helpCommand.getCommand().execute());
+        helpButton.setOnAction(evt -> helpCommand.execute());
     }
 
     public BibEntry getMergedEntry() {
diff --git a/src/main/java/org/jabref/gui/GUIGlobals.java b/src/main/java/org/jabref/gui/GUIGlobals.java
index e1f145054ff..12d55f69bbe 100644
--- a/src/main/java/org/jabref/gui/GUIGlobals.java
+++ b/src/main/java/org/jabref/gui/GUIGlobals.java
@@ -10,9 +10,6 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.preferences.JabRefPreferences;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 /**
  * Static variables for graphics files and keyboard shortcuts.
  */
@@ -32,11 +29,6 @@ public class GUIGlobals {
 
     public static final String UNTITLED_TITLE = Localization.lang("untitled");
 
-    //	Colors.
-    public static final Color ENTRY_EDITOR_LABEL_COLOR = new Color(100, 100, 150); // Empty field, blue.
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(GUIGlobals.class);
-
     private GUIGlobals() {
     }
 
diff --git a/src/main/java/org/jabref/gui/JEditorPaneWithHighlighting.java b/src/main/java/org/jabref/gui/JEditorPaneWithHighlighting.java
deleted file mode 100644
index 71235c5d08e..00000000000
--- a/src/main/java/org/jabref/gui/JEditorPaneWithHighlighting.java
+++ /dev/null
@@ -1,57 +0,0 @@
-package org.jabref.gui;
-
-import java.util.Optional;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.swing.JEditorPane;
-import javax.swing.text.BadLocationException;
-import javax.swing.text.DefaultHighlighter;
-import javax.swing.text.Document;
-import javax.swing.text.Highlighter;
-import javax.swing.text.LayeredHighlighter.LayerPainter;
-
-import org.jabref.gui.fieldeditors.JTextAreaWithHighlighting;
-import org.jabref.logic.search.SearchQueryHighlightListener;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class JEditorPaneWithHighlighting extends JEditorPane implements SearchQueryHighlightListener {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(JTextAreaWithHighlighting.class);
-
-    public void highlightPattern(Optional<Pattern> highlightPattern) {
-        Highlighter highlighter = getHighlighter();
-        highlighter.removeAllHighlights();
-
-        if ((highlightPattern == null) || !highlightPattern.isPresent()) {
-            return;
-        }
-
-        String text = getDocumentText();
-
-        Matcher matcher = highlightPattern.get().matcher(text);
-        LayerPainter painter = DefaultHighlighter.DefaultPainter;
-        while (matcher.find()) {
-            try {
-                highlighter.addHighlight(matcher.start(), matcher.end(), painter);
-            } catch (BadLocationException ble) {
-                // should not occur if matcher works right
-                LOGGER.warn("Highlighting not possible, bad location", ble);
-            }
-        }
-    }
-
-    private String getDocumentText() {
-        Document doc = getDocument();
-        String text;
-        try {
-            text = doc.getText(0, doc.getLength());
-        } catch (Exception e) {
-            LOGGER.error("Error while getting document text");
-            text = "";
-        }
-        return text;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 1cf05c35116..838f5d459f0 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -550,32 +550,6 @@ public void changed(ObservableValue<? extends Boolean> observable, Boolean oldVa
         });
 
         setCenter(splitPane);
-
-        /*
-        GridBagLayout gbl = new GridBagLayout();
-        GridBagConstraints con = new GridBagConstraints();
-        con.fill = GridBagConstraints.BOTH;
-        con.anchor = GridBagConstraints.WEST;
-        JPanel status = new JPanel();
-        status.setLayout(gbl);
-        con.weighty = 0;
-        con.weightx = 0;
-        con.gridwidth = 1;
-        con.insets = new Insets(0, 2, 0, 0);
-        gbl.setConstraints(statusLabel, con);
-        status.add(statusLabel);
-        con.weightx = 1;
-        con.insets = new Insets(0, 4, 0, 0);
-        con.gridwidth = 1;
-        gbl.setConstraints(statusLine, con);
-        status.add(statusLine);
-        con.weightx = 0;
-        con.gridwidth = GridBagConstraints.REMAINDER;
-        con.insets = new Insets(2, 4, 2, 2);
-        gbl.setConstraints(progressBar, con);
-        status.add(progressBar);
-        statusLabel.setForeground(GUIGlobals.ENTRY_EDITOR_LABEL_COLOR.darker());
-        */
     }
 
     private void setDividerPosition() {
diff --git a/src/main/java/org/jabref/gui/actions/ChangeTypeAction.java b/src/main/java/org/jabref/gui/actions/ChangeTypeAction.java
deleted file mode 100644
index b7b907a662c..00000000000
--- a/src/main/java/org/jabref/gui/actions/ChangeTypeAction.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package org.jabref.gui.actions;
-
-import java.awt.event.ActionEvent;
-import java.util.Collections;
-import java.util.List;
-
-import javax.swing.AbstractAction;
-import javax.swing.undo.UndoManager;
-
-import javafx.scene.control.MenuItem;
-
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableChangeType;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.EntryType;
-
-public class ChangeTypeAction extends AbstractAction {
-
-    private final String type;
-    private final BasePanel panel;
-
-    public ChangeTypeAction(EntryType type, BasePanel bp) {
-        super(type.getName());
-        this.type = type.getName();
-        panel = bp;
-    }
-
-    @Override
-    public void actionPerformed(ActionEvent evt) {
-        panel.changeTypeOfSelectedEntries(type);
-    }
-
-    public static MenuItem as(EntryType type, BibEntry entry, UndoManager undoManager) {
-        return as(type, Collections.singletonList(entry), undoManager);
-    }
-
-    public static MenuItem as(EntryType type, List<BibEntry> entries, UndoManager undoManager) {
-        MenuItem menuItem = new MenuItem(type.getName());
-        menuItem.setOnAction(event -> {
-            NamedCompound compound = new NamedCompound(Localization.lang("Change entry type"));
-            for (BibEntry entry : entries) {
-                entry.setType(type)
-                        .ifPresent(change -> compound.addEdit(new UndoableChangeType(change)));
-            }
-
-            undoManager.addEdit(compound);
-        });
-        return menuItem;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java b/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
index aa8ee344abe..51adf9ba8b3 100644
--- a/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
+++ b/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
@@ -1,10 +1,7 @@
 package org.jabref.gui.actions;
 
-import java.awt.event.ActionEvent;
 import java.util.Optional;
 
-import javax.swing.AbstractAction;
-
 import javafx.scene.control.TextArea;
 
 import org.jabref.Globals;
@@ -15,24 +12,17 @@
 /**
  * Copies the doi url to the clipboard
  */
-public class CopyDoiUrlAction extends AbstractAction {
-
-    private TextArea component = null;
-    private String identifier;
+public class CopyDoiUrlAction extends SimpleCommand {
 
-    public CopyDoiUrlAction(String identifier) {
-        super(Localization.lang("Copy DOI url"));
-        this.identifier = identifier;
-    }
+    private TextArea component;
 
     public CopyDoiUrlAction(TextArea component) {
-        this(component.getText());
         this.component = component;
     }
 
     @Override
-    public void actionPerformed(ActionEvent e) {
-        identifier = component == null ? identifier : component.getText();
+    public void execute() {
+        String identifier = component.getText();
 
         Optional<String> urlOptional = DOI.parse(identifier).map(DOI::getURIAsASCIIString);
         if (urlOptional.isPresent()) {
diff --git a/src/main/java/org/jabref/gui/actions/MnemonicAwareAction.java b/src/main/java/org/jabref/gui/actions/MnemonicAwareAction.java
deleted file mode 100644
index b1bfa9f87d5..00000000000
--- a/src/main/java/org/jabref/gui/actions/MnemonicAwareAction.java
+++ /dev/null
@@ -1,44 +0,0 @@
-package org.jabref.gui.actions;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.Icon;
-
-import org.jabref.gui.icon.IconTheme;
-
-/**
- * This class extends {@link AbstractAction} with the ability to set
- * the mnemonic key based on a '&' character inserted in front of
- * the desired mnemonic letter. This is done by setting the action's
- * name using putValue(NAME, actionname).
- * This facilitates localized mnemonics.
- */
-public abstract class MnemonicAwareAction extends AbstractAction {
-
-    public MnemonicAwareAction() { }
-
-    public MnemonicAwareAction(Icon icon) {
-        if (icon instanceof IconTheme.FontBasedIcon) {
-            putValue(Action.SMALL_ICON, ((IconTheme.FontBasedIcon) icon).createSmallIcon());
-            putValue(Action.LARGE_ICON_KEY, icon);
-        } else {
-            putValue(Action.SMALL_ICON, icon);
-        }
-    }
-
-    @Override
-    public void putValue(String key, Object value) {
-        if (key.equals(Action.NAME)) {
-            String name = value.toString();
-            int i = name.indexOf('&');
-            if (i >= 0) {
-                char mnemonic = Character.toUpperCase(name.charAt(i + 1));
-                putValue(Action.MNEMONIC_KEY, (int) mnemonic);
-                value = name.substring(0, i) + name.substring(i + 1);
-            } else {
-                value = name;
-            }
-        }
-        super.putValue(key, value);
-    }
-}
diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
index 6e7493f32d7..2c91ff5c4b5 100644
--- a/src/main/java/org/jabref/gui/actions/StandardActions.java
+++ b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -91,6 +91,7 @@ public enum StandardActions implements Action {
     OPEN_FILE(Localization.lang("Open file"), Localization.lang("Open file"), IconTheme.JabRefIcons.FILE, KeyBinding.OPEN_FILE),
     OPEN_CONSOLE(Localization.lang("Open terminal here"), Localization.lang("Open terminal here"), IconTheme.JabRefIcons.CONSOLE, KeyBinding.OPEN_CONSOLE),
     COPY_LINKED_FILES(Localization.lang("Copy linked files to folder...")),
+    COPY_DOI(Localization.lang("Copy DOI url")),
     ABBREVIATE(Localization.lang("Abbreviate journal names")),
     ABBREVIATE_ISO("ISO", Localization.lang("Abbreviate journal names of the selected entries (ISO abbreviation)"), KeyBinding.ABBREVIATE),
     ABBREVIATE_MEDLINE("MEDLINE", Localization.lang("Abbreviate journal names of the selected entries (MEDLINE abbreviation)")),
@@ -138,6 +139,10 @@ public enum StandardActions implements Action {
     SET_FILE_LINKS(Localization.lang("Automatically set file links"), KeyBinding.AUTOMATICALLY_LINK_FILES),
 
     HELP(Localization.lang("Online help"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
+    HELP_KEY_PATTERNS(Localization.lang("Help on key patterns"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
+    HELP_REGEX_SEARCH(Localization.lang("Help on regular expression search"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
+    HELP_NAME_FORMATTER(Localization.lang("Help on Name Formatting"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
+    HELP_SPECIAL_FIELDS(Localization.lang("Help on special fields"), IconTheme.JabRefIcons.HELP, KeyBinding.HELP),
     WEB_MENU(Localization.lang("JabRef resources")),
     OPEN_WEBPAGE(Localization.lang("Website"), Localization.lang("Opens JabRef's website")),
     OPEN_FACEBOOK("Facebook", Localization.lang("Opens JabRef's Facebook page"), IconTheme.JabRefIcons.FACEBOOK),
diff --git a/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java b/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
index e3796c623ee..e1e81d2bc03 100644
--- a/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
+++ b/src/main/java/org/jabref/gui/bibtexkeypattern/BibtexKeyPatternPanel.java
@@ -1,7 +1,5 @@
 package org.jabref.gui.bibtexkeypattern;
 
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
 import java.util.HashMap;
 import java.util.Locale;
 import java.util.Map;
@@ -30,15 +28,9 @@
 
 public class BibtexKeyPatternPanel extends Pane {
 
-    // used by both BibtexKeyPatternPanel and TabLabelPAttern
-    protected final GridBagLayout gbl = new GridBagLayout();
-    protected final GridBagConstraints con = new GridBagConstraints();
-
     // default pattern
     protected final TextField defaultPat = new TextField();
 
-    private final int COLUMNS = 2;
-
     // one field for each type
     private final Map<String, TextField> textFields = new HashMap<>();
     private final BasePanel panel;
@@ -64,7 +56,8 @@ private void buildGUI() {
         int rowIndex = 1;
         int columnIndex = 0;
         // The header - can be removed
-        for (int i = 0; i < COLUMNS; i++) {
+        int columnsNumber = 2;
+        for (int i = 0; i < columnsNumber; i++) {
             Label label = new Label(Localization.lang("Entry type"));
             Label keyPattern = new Label(Localization.lang("Key pattern"));
             gridPane.add(label, ++columnIndex, rowIndex);
@@ -93,7 +86,7 @@ private void buildGUI() {
 
             textFields.put(type.getName().toLowerCase(Locale.ROOT), textField);
 
-            if (columnIndex == (COLUMNS - 1)) {
+            if (columnIndex == (columnsNumber - 1)) {
                 columnIndex = 0;
                 rowIndex++;
             } else {
@@ -104,7 +97,7 @@ private void buildGUI() {
         rowIndex++;
 
         ActionFactory factory = new ActionFactory(Globals.prefs.getKeyBindingRepository());
-        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on key patterns"), HelpFile.BIBTEX_KEY_PATTERN).getCommand());
+        Button help = factory.createIconButton(StandardActions.HELP_KEY_PATTERNS, new HelpAction(HelpFile.BIBTEX_KEY_PATTERN));
         gridPane.add(help, 1, rowIndex);
 
         Button btnDefaultAll1 = new Button(Localization.lang("Reset all"));
@@ -138,8 +131,7 @@ private void fillPatternUsingPanelData(AbstractBibtexKeyPattern keypatterns) {
     }
 
     protected GlobalBibtexKeyPattern getKeyPatternAsGlobalBibtexKeyPattern() {
-        GlobalBibtexKeyPattern res = GlobalBibtexKeyPattern.fromPattern(
-                                                                        JabRefPreferences.getInstance().get(JabRefPreferences.DEFAULT_BIBTEX_KEY_PATTERN));
+        GlobalBibtexKeyPattern res = GlobalBibtexKeyPattern.fromPattern(Globals.prefs.get(JabRefPreferences.DEFAULT_BIBTEX_KEY_PATTERN));
         fillPatternUsingPanelData(res);
         return res;
     }
diff --git a/src/main/java/org/jabref/gui/cleanup/CleanupActionsListModel.java b/src/main/java/org/jabref/gui/cleanup/CleanupActionsListModel.java
deleted file mode 100644
index f7bf8a5e463..00000000000
--- a/src/main/java/org/jabref/gui/cleanup/CleanupActionsListModel.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package org.jabref.gui.cleanup;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-
-import javax.swing.ListModel;
-import javax.swing.event.ListDataEvent;
-import javax.swing.event.ListDataListener;
-
-import org.jabref.model.cleanup.FieldFormatterCleanup;
-import org.jabref.model.cleanup.FieldFormatterCleanups;
-
-public class CleanupActionsListModel implements ListModel<FieldFormatterCleanup> {
-
-    private List<FieldFormatterCleanup> cleanupActions;
-    private final List<ListDataListener> listeners = new ArrayList<>();
-
-
-    public CleanupActionsListModel(List<FieldFormatterCleanup> cleanupAction) {
-        Objects.requireNonNull(cleanupAction);
-        this.cleanupActions = cleanupAction;
-
-    }
-
-    public void addCleanupAction(FieldFormatterCleanup action) {
-        if (!cleanupActions.contains(action)) {
-            cleanupActions.add(action);
-            for (ListDataListener listener : listeners) {
-                listener.intervalAdded(new ListDataEvent(action, ListDataEvent.INTERVAL_ADDED, cleanupActions.size(),
-                        cleanupActions.size()));
-            }
-        }
-    }
-
-    /**
-     * Removes the action at the specified index from the list.
-     * Removal is only done when index {@code >=0} and index {@code<=} list size
-     * @param index The index to remove
-     */
-    public void removeAtIndex(int index) {
-
-        if ((index >= 0) && (index < cleanupActions.size())) {
-            FieldFormatterCleanup action = cleanupActions.remove(index);
-            for (ListDataListener listener : listeners) {
-                listener.intervalRemoved(new ListDataEvent(action, ListDataEvent.INTERVAL_REMOVED, index, index));
-            }
-        }
-    }
-
-    public List<FieldFormatterCleanup> getAllActions() {
-        return cleanupActions;
-    }
-
-    @Override
-    public int getSize() {
-        return cleanupActions.size();
-    }
-
-    @Override
-    public FieldFormatterCleanup getElementAt(int index) {
-        return cleanupActions.get(index);
-    }
-
-    @Override
-    public void addListDataListener(ListDataListener l) {
-        listeners.add(l);
-    }
-
-    @Override
-    public void removeListDataListener(ListDataListener l) {
-        listeners.remove(l);
-    }
-
-    public void reset(FieldFormatterCleanups defaultFormatters) {
-        cleanupActions = new ArrayList<>(defaultFormatters.getConfiguredActions());
-        for (ListDataListener listener : listeners) {
-            listener.contentsChanged(new ListDataEvent(this, ListDataEvent.CONTENTS_CHANGED, 0, cleanupActions.size()));
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/gui/customizefields/CustomizeGeneralFieldsDialogView.java b/src/main/java/org/jabref/gui/customizefields/CustomizeGeneralFieldsDialogView.java
index a36f44bb86d..e2e6fe781fb 100644
--- a/src/main/java/org/jabref/gui/customizefields/CustomizeGeneralFieldsDialogView.java
+++ b/src/main/java/org/jabref/gui/customizefields/CustomizeGeneralFieldsDialogView.java
@@ -36,11 +36,7 @@ public CustomizeGeneralFieldsDialogView() {
                   .load()
                   .setAsDialogPane(this);
 
-        HelpAction helpCommand = new HelpAction(HelpFile.GENERAL_FIELDS);
-        //HelpAction is written with Swing, not JavaFX, so runCommand() cannot be used normally.  Here I am reaching into
-        //the command and running execute.  When HelpAction is converted to JavaFX,
-        //the following will need to be changed.
-        ControlHelper.setAction(helpButton, getDialogPane(), event -> helpCommand.getCommand().execute());
+        ControlHelper.setAction(helpButton, getDialogPane(), event -> new HelpAction(HelpFile.GENERAL_FIELDS).execute());
         ControlHelper.setAction(resetButton, getDialogPane(), event -> resetFields());
         ControlHelper.setAction(okButton, getDialogPane(), event -> saveFieldsAndCloseDialog());
 
diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
index 450da9e98d9..4ebdb2b1b72 100644
--- a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
+++ b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -376,7 +376,7 @@ private void setupToolBar() {
         typeLabel.setText(typedEntry.getTypeForDisplay());
 
         // Add type change menu
-        ContextMenu typeMenu = new ChangeEntryTypeMenu(preferences.getKeyBindings()).getChangeEntryTypePopupMenu(entry, databaseContext, undoManager);
+        ContextMenu typeMenu = new ChangeEntryTypeMenu().getChangeEntryTypePopupMenu(entry, databaseContext, undoManager);
         typeLabel.setOnMouseClicked(event -> typeMenu.show(typeLabel, Side.RIGHT, 0, 0));
         typeChangeButton.setOnMouseClicked(event -> typeMenu.show(typeChangeButton, Side.RIGHT, 0, 0));
         // Add menu for fetching bibliographic information
diff --git a/src/main/java/org/jabref/gui/externalfiles/DownloadExternalFile.java b/src/main/java/org/jabref/gui/externalfiles/DownloadExternalFile.java
deleted file mode 100644
index b4e1ad794db..00000000000
--- a/src/main/java/org/jabref/gui/externalfiles/DownloadExternalFile.java
+++ /dev/null
@@ -1,345 +0,0 @@
-package org.jabref.gui.externalfiles;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.List;
-import java.util.Optional;
-
-import javax.swing.SwingUtilities;
-
-import org.jabref.Globals;
-import org.jabref.JabRefExecutorService;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.filelist.FileListEntryEditor;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.net.URLDownload;
-import org.jabref.logic.util.OS;
-import org.jabref.logic.util.io.FileUtil;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.LinkedFile;
-import org.jabref.preferences.JabRefPreferences;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * This class handles the download of an external file. Typically called when the user clicks
- * the "Download" button in a FileListEditor shown in an EntryEditor.
- * <p/>
- * The FileListEditor constructs the DownloadExternalFile instance, then calls the download()
- * method passing a reference to itself as a callback. The download() method asks for the URL,
- * then starts the download. When the download is completed, it calls the downloadCompleted()
- * method on the callback FileListEditor, which then needs to take care of linking to the file.
- * The local filename is passed as an argument to the downloadCompleted() method.
- * <p/>
- * If the download is canceled, or failed, the user is informed. The callback is never called.
- */
-public class DownloadExternalFile {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(DownloadExternalFile.class);
-
-    private final BibDatabaseContext databaseContext;
-    private final BibEntry entry;
-    private final DialogService dialogService;
-
-    private FileListEntryEditor editor;
-    private boolean downloadFinished;
-    private boolean dontShowDialog;
-
-    public DownloadExternalFile(DialogService dialogService, BibDatabaseContext databaseContext, BibEntry entry) {
-        this.dialogService = dialogService;
-        this.databaseContext = databaseContext;
-        this.entry = entry;
-    }
-
-    /**
-     * Look for the last '.' in the link, and return the following characters.
-     * This gives the extension for most reasonably named links.
-     *
-     * @param link The link
-     * @return The suffix, excluding the dot (e.g. "pdf")
-     */
-    public static String getSuffix(final String link) {
-        String strippedLink = link;
-        try {
-            // Try to strip the query string, if any, to get the correct suffix:
-            URL url = new URL(link);
-            if ((url.getQuery() != null) && (url.getQuery().length() < (link.length() - 1))) {
-                strippedLink = link.substring(0, link.length() - url.getQuery().length() - 1);
-            }
-        } catch (MalformedURLException e) {
-            // Don't report this error, since this getting the suffix is a non-critical
-            // operation, and this error will be triggered and reported elsewhere.
-        }
-        // First see if the stripped link gives a reasonable suffix:
-        String suffix;
-        int strippedLinkIndex = strippedLink.lastIndexOf('.');
-        if ((strippedLinkIndex <= 0) || (strippedLinkIndex == (strippedLink.length() - 1))) {
-            suffix = null;
-        } else {
-            suffix = strippedLink.substring(strippedLinkIndex + 1);
-        }
-        if (!ExternalFileTypes.getInstance().isExternalFileTypeByExt(suffix)) {
-            // If the suffix doesn't seem to give any reasonable file type, try
-            // with the non-stripped link:
-            int index = link.lastIndexOf('.');
-            if ((index <= 0) || (index == (link.length() - 1))) {
-                // No occurrence, or at the end
-                // Check if there are path separators in the suffix - if so, it is definitely
-                // not a proper suffix, so we should give up:
-                if (strippedLink.substring(strippedLinkIndex + 1).indexOf('/') >= 1) {
-                    return "";
-                } else {
-                    return suffix; // return the first one we found, anyway.
-                }
-            } else {
-                // Check if there are path separators in the suffix - if so, it is definitely
-                // not a proper suffix, so we should give up:
-                if (link.substring(index + 1).indexOf('/') >= 1) {
-                    return "";
-                } else {
-                    return link.substring(index + 1);
-                }
-            }
-        } else {
-            return suffix;
-        }
-    }
-
-    /**
-     * Start a download.
-     *
-     * @param callback The object to which the filename should be reported when download
-     *                 is complete.
-     */
-    public void download(final DownloadCallback callback) throws IOException {
-        dontShowDialog = false;
-
-        Optional<String> res = dialogService.showInputDialogAndWait(Localization.lang("Download file"), Localization.lang("Enter URL to download"));
-
-        if (res.isPresent()) {
-            URL url;
-            try {
-                url = new URL(res.get());
-            } catch (MalformedURLException ex1) {
-                dialogService.showErrorDialogAndWait(Localization.lang("Download file"),
-                        Localization.lang("Invalid URL"));
-
-                return;
-            }
-            download(url, callback);
-        }
-    }
-
-    public void download(URL url, final DownloadCallback callback) throws IOException {
-        // TODO: what if this takes long time?
-        // TODO: stop editor dialog if this results in an error?
-        String mimeType = new URLDownload(url).getMimeType();
-        download(url, mimeType, callback);
-    }
-
-    private Optional<ExternalFileType> getExternalFileType(String mimeType) {
-        Optional<ExternalFileType> suggestedType = Optional.empty();
-        if (mimeType != null) {
-            LOGGER.debug("MIME Type suggested: " + mimeType);
-            suggestedType = ExternalFileTypes.getInstance().getExternalFileTypeByMimeType(mimeType);
-        }
-        return suggestedType;
-    }
-
-    /**
-     * Start a download.
-     *
-     * @param callback The object to which the filename should be reported when download
-     *                 is complete.
-     */
-    public void download(URL url, String mimeType, final DownloadCallback callback) throws IOException {
-        Optional<ExternalFileType> fileType = getExternalFileType(mimeType);
-
-        // First of all, start the download itself in the background to a temporary file:
-        final Path tempFile = Files.createTempFile("jabref_download", "tmp");
-        tempFile.toFile().deleteOnExit();
-
-        final URLDownload fileDownload = new URLDownload(url);
-
-        JabRefExecutorService.INSTANCE.execute(() -> {
-            try {
-                fileDownload.toFile(tempFile);
-            } catch (IOException e) {
-                dontShowDialog = true;
-                if ((editor != null) && editor.isVisible()) {
-                    editor.setVisible(false, false);
-                }
-
-                LOGGER.info("Error while downloading " + "'" + url + "'", e);
-
-                dialogService.showErrorDialogAndWait(Localization.lang("Download file"), Localization.lang("Invalid URL") + ": " + e.getMessage());
-
-                return;
-            }
-            // Download finished: call the method that stops the progress bar etc.:
-            SwingUtilities.invokeLater(DownloadExternalFile.this::downloadFinished);
-        });
-
-        // Then, while the download is proceeding, let the user choose the details of the file:
-        String suffix;
-        if (fileType.isPresent()) {
-            suffix = fileType.get().getExtension();
-        } else {
-            // If we did not find a file type from the MIME type, try based on extension:
-            suffix = getSuffix(url.toString());
-            if (suffix == null) {
-                suffix = "";
-            }
-            fileType = ExternalFileTypes.getInstance().getExternalFileTypeByExt(suffix);
-        }
-        String suggestedName = getSuggestedFileName(suffix);
-        List<String> fDirectory = databaseContext.getFileDirectories(Globals.prefs.getFilePreferences());
-        String directory;
-        if (fDirectory.isEmpty()) {
-            directory = null;
-        } else {
-            directory = fDirectory.get(0);
-        }
-        final String suggestDir = directory == null ? System.getProperty("user.home") : directory;
-        File file = new File(new File(suggestDir), suggestedName);
-        LinkedFile fileListEntry = new LinkedFile("", file.getCanonicalPath(), fileType.map(ExternalFileType::getName).orElse(""));
-        editor = new FileListEntryEditor(fileListEntry, true, false, databaseContext, true);
-        editor.getProgressBar().setIndeterminate(true);
-        editor.setOkEnabled(false);
-        editor.setExternalConfirm(closeEntry -> {
-            File f = directory == null ? new File(closeEntry.getLink()) : expandFilename(directory, closeEntry.getLink());
-            if (f.isDirectory()) {
-                dialogService.showErrorDialogAndWait(Localization.lang("Download file"),
-                        Localization.lang("Target file cannot be a directory."));
-
-                return false;
-            }
-            if (f.exists()) {
-                return dialogService.showConfirmationDialogAndWait(Localization.lang("Download file"),
-                        Localization.lang("'%0' exists. Overwrite file?", f.getName()), Localization.lang("Overwrite file"),
-                        Localization.lang("Cancel"));
-
-            } else {
-                return true;
-            }
-        });
-        if (dontShowDialog) {
-            return;
-        } else {
-            editor.setVisible(true, false);
-        }
-        // Editor closed. Go on:
-        if (editor.okPressed()) {
-            File toFile = directory == null ? new File(fileListEntry.getLink()) : expandFilename(directory,
-                    fileListEntry.getLink());
-            String dirPrefix;
-            if (directory == null) {
-                dirPrefix = null;
-            } else {
-                if (directory.endsWith(OS.FILE_SEPARATOR)) {
-                    dirPrefix = directory;
-                } else {
-                    dirPrefix = directory + OS.FILE_SEPARATOR;
-                }
-            }
-
-            boolean success = FileUtil.copyFile(tempFile, Paths.get(toFile.toURI()), true);
-            if (!success) {
-                // OOps, the file exists!
-                LOGGER.error("File already exists! DownloadExternalFile.download()");
-            }
-
-            // If the local file is in or below the main file directory, change the
-            // path to relative:
-            if ((dirPrefix != null) && fileListEntry.getLink().startsWith(directory)
-                    && (fileListEntry.getLink().length() > dirPrefix.length())) {
-                fileListEntry = new LinkedFile(fileListEntry.getDescription(),
-                        fileListEntry.getLink().substring(dirPrefix.length()), fileListEntry.getFileType());
-            }
-            callback.downloadComplete(fileListEntry);
-
-            if (!Files.deleteIfExists(tempFile)) {
-                LOGGER.info("Cannot delete temporary file");
-            }
-        } else {
-            // Canceled. Just delete the temp file:
-            if (downloadFinished && !Files.deleteIfExists(tempFile)) {
-                LOGGER.info("Cannot delete temporary file");
-            }
-        }
-    }
-
-    /**
-     * Construct a File object pointing to the file linked, whether the link is
-     * absolute or relative to the main directory.
-     *
-     * @param directory The main directory.
-     * @param link      The absolute or relative link.
-     * @return The expanded File.
-     */
-    private File expandFilename(String directory, String link) {
-        File toFile = new File(link);
-        // If this is a relative link, we should perhaps append the directory:
-        String dirPrefix = directory + OS.FILE_SEPARATOR;
-        if (!toFile.isAbsolute()) {
-            toFile = new File(dirPrefix + link);
-        }
-        return toFile;
-    }
-
-    /**
-     * This is called by the download thread when download is completed.
-     */
-    private void downloadFinished() {
-        downloadFinished = true;
-        editor.getProgressBar().setVisible(false);
-        editor.getProgressBarLabel().setVisible(false);
-        editor.setOkEnabled(true);
-        editor.getProgressBar().setValue(editor.getProgressBar().getMaximum());
-    }
-
-    private String getSuggestedFileName(String suffix) {
-        String plannedName = FileUtil.createFileNameFromPattern(databaseContext.getDatabase(), entry,
-                Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN));
-
-        if (!suffix.isEmpty()) {
-            plannedName += "." + suffix;
-        }
-
-        /*
-        * [ 1548875 ] download pdf produces unsupported filename
-        *
-        * http://sourceforge.net/tracker/index.php?func=detail&aid=1548875&group_id=92314&atid=600306
-        * FIXME: rework this! just allow alphanumeric stuff or so?
-        * https://msdn.microsoft.com/en-us/library/windows/desktop/aa365247(v=vs.85).aspx#naming_conventions
-        * http://superuser.com/questions/358855/what-characters-are-safe-in-cross-platform-file-names-for-linux-windows-and-os
-        * https://support.apple.com/en-us/HT202808
-        */
-        if (OS.WINDOWS) {
-            plannedName = plannedName.replaceAll("\\?|\\*|\\<|\\>|\\||\\\"|\\:|\\.$|\\[|\\]", "");
-        } else if (OS.OS_X) {
-            plannedName = plannedName.replace(":", "");
-        }
-
-        return plannedName;
-    }
-
-    /**
-     * Callback interface that users of this class must implement in order to receive
-     * notification when download is complete.
-     */
-    @FunctionalInterface
-    public interface DownloadCallback {
-
-        void downloadComplete(LinkedFile file);
-    }
-}
diff --git a/src/main/java/org/jabref/gui/fieldeditors/JTextAreaWithHighlighting.java b/src/main/java/org/jabref/gui/fieldeditors/JTextAreaWithHighlighting.java
deleted file mode 100644
index 05bb4c791b4..00000000000
--- a/src/main/java/org/jabref/gui/fieldeditors/JTextAreaWithHighlighting.java
+++ /dev/null
@@ -1,173 +0,0 @@
-package org.jabref.gui.fieldeditors;
-
-import java.awt.event.ActionEvent;
-import java.util.Optional;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.swing.AbstractAction;
-import javax.swing.KeyStroke;
-import javax.swing.text.BadLocationException;
-import javax.swing.text.DefaultHighlighter;
-import javax.swing.text.Document;
-import javax.swing.text.Highlighter;
-import javax.swing.text.Keymap;
-import javax.swing.undo.CannotRedoException;
-import javax.swing.undo.CannotUndoException;
-import javax.swing.undo.UndoManager;
-
-import org.jabref.Globals;
-import org.jabref.gui.actions.Actions;
-import org.jabref.gui.util.component.JTextAreaWithPlaceholder;
-import org.jabref.logic.search.SearchQueryHighlightListener;
-import org.jabref.preferences.JabRefPreferences;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class JTextAreaWithHighlighting extends JTextAreaWithPlaceholder implements SearchQueryHighlightListener {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(JTextAreaWithHighlighting.class);
-
-    private Optional<Pattern> highlightPattern = Optional.empty();
-
-    private UndoManager undo;
-
-    public JTextAreaWithHighlighting() {
-        this("");
-    }
-
-    public JTextAreaWithHighlighting(String text) {
-        this(text, "");
-    }
-
-    /**
-     * Creates a text area with the ability to highlight parts of the content.
-     * It also defines a placeholder which will be displayed the content is empty.
-     *
-     * @param text
-     * @param placeholder
-     */
-    public JTextAreaWithHighlighting(String text, String placeholder) {
-        super(text, placeholder);
-        setupUndoRedo();
-        setupPasteListener();
-    }
-
-    private void setupPasteListener() {
-        // Bind paste command to KeyBinds.PASTE
-        getInputMap().put(Globals.getKeyPrefs().getKey(org.jabref.gui.keyboard.KeyBinding.PASTE), Actions.PASTE);
-    }
-
-    private void setupUndoRedo() {
-        undo = new UndoManager();
-        Document doc = getDocument();
-
-        // Listen for undo and redo events
-        doc.addUndoableEditListener(evt -> undo.addEdit(evt.getEdit()));
-
-        // Create an undo action and add it to the text component
-        getActionMap().put("Undo", new AbstractAction("Undo") {
-
-            @Override
-            public void actionPerformed(ActionEvent evt) {
-                try {
-                    if (undo.canUndo()) {
-                        undo.undo();
-                    }
-                } catch (CannotUndoException ignored) {
-                    // Ignored
-                }
-            }
-        });
-
-        // Bind the undo action to ctl-Z
-        getInputMap().put(Globals.getKeyPrefs().getKey(org.jabref.gui.keyboard.KeyBinding.UNDO), "Undo");
-
-        // Create a redo action and add it to the text component
-        getActionMap().put("Redo", new AbstractAction(Actions.REDO.name()) {
-
-            @Override
-            public void actionPerformed(ActionEvent evt) {
-                try {
-                    if (undo.canRedo()) {
-                        undo.redo();
-                    }
-                } catch (CannotRedoException ignored) {
-                    // Ignored
-                }
-            }
-        });
-
-        // Bind the redo action to ctrl-Y
-        boolean bind = true;
-        KeyStroke redoKey = Globals.getKeyPrefs().getKey(org.jabref.gui.keyboard.KeyBinding.REDO);
-        if (Globals.prefs.getBoolean(JabRefPreferences.EDITOR_EMACS_KEYBINDINGS)) {
-            // If emacs is enabled, check if we have a conflict at keys
-            // If yes, do not bind
-            // Typically, we have: CTRL+y is "yank" in emacs and REDO in 'normal' settings
-            // The Emacs key bindings are stored in the keymap, not in the input map.
-            Keymap keymap = getKeymap();
-            KeyStroke[] keys = keymap.getBoundKeyStrokes();
-            int i = 0;
-            while ((i < keys.length) && !keys[i].equals(redoKey)) {
-                i++;
-            }
-            if (i < keys.length) {
-                // conflict found -> do not bind
-                bind = false;
-            }
-        }
-        if (bind) {
-            getInputMap().put(redoKey, "Redo");
-        }
-    }
-
-    /**
-     * Highlight words in the Textarea
-     *
-     * @param words to highlight
-     */
-    private void highLight() {
-        // highlight all characters that appear in charsToHighlight
-        Highlighter highlighter = getHighlighter();
-        highlighter.removeAllHighlights();
-
-        if ((highlightPattern == null) || !highlightPattern.isPresent()) {
-            return;
-        }
-        String content = getText();
-        if (content.isEmpty()) {
-            return;
-        }
-
-        highlightPattern.ifPresent(pattern -> {
-            Matcher matcher = pattern.matcher(content);
-            while (matcher.find()) {
-                try {
-                    highlighter.addHighlight(matcher.start(), matcher.end(), DefaultHighlighter.DefaultPainter);
-                } catch (BadLocationException ble) {
-                    // should not occur if matcher works right
-                    LOGGER.warn("Highlighting not possible, bad location", ble);
-                }
-            }
-        });
-
-    }
-
-    @Override
-    public void setText(String text) {
-        super.setText(text);
-        highLight();
-        if (undo != null) {
-            undo.discardAllEdits();
-        }
-    }
-
-    @Override
-    public void highlightPattern(Optional<Pattern> highlightPattern) {
-        this.highlightPattern = highlightPattern;
-        highLight();
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
index 68da8aec6f5..c4f11bb73b3 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
@@ -26,7 +26,6 @@
 import org.jabref.gui.AbstractViewModel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.desktop.JabRefDesktop;
-import org.jabref.gui.externalfiles.DownloadExternalFile;
 import org.jabref.gui.externalfiles.FileDownloadTask;
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
@@ -38,6 +37,7 @@
 import org.jabref.logic.externalfiles.LinkedFileHandler;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.URLDownload;
+import org.jabref.logic.net.URLUtil;
 import org.jabref.logic.xmp.XmpPreferences;
 import org.jabref.logic.xmp.XmpUtilWriter;
 import org.jabref.model.database.BibDatabaseContext;
@@ -439,12 +439,8 @@ private Optional<ExternalFileType> inferFileTypeFromMimeType(URLDownload urlDown
     }
 
     private Optional<ExternalFileType> inferFileTypeFromURL(String url) {
-        String extension = DownloadExternalFile.getSuffix(url);
-        if (extension != null) {
-            return ExternalFileTypes.getInstance().getExternalFileTypeByExt(extension);
-        } else {
-            return Optional.empty();
-        }
+        return URLUtil.getSuffix(url)
+                      .flatMap(extension -> ExternalFileTypes.getInstance().getExternalFileTypeByExt(extension));
     }
 
     public LinkedFile getFile() {
diff --git a/src/main/java/org/jabref/gui/fieldeditors/contextmenu/EditorMenus.java b/src/main/java/org/jabref/gui/fieldeditors/contextmenu/EditorMenus.java
index 575403025f0..baaabbe8f93 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/contextmenu/EditorMenus.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/contextmenu/EditorMenus.java
@@ -4,9 +4,6 @@
 import java.util.List;
 import java.util.function.Supplier;
 
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-
 import javafx.scene.control.CustomMenuItem;
 import javafx.scene.control.Label;
 import javafx.scene.control.MenuItem;
@@ -15,7 +12,10 @@
 import javafx.scene.control.TextInputControl;
 import javafx.scene.control.Tooltip;
 
+import org.jabref.Globals;
+import org.jabref.gui.actions.ActionFactory;
 import org.jabref.gui.actions.CopyDoiUrlAction;
+import org.jabref.gui.actions.StandardActions;
 import org.jabref.logic.formatter.bibtexfields.CleanupURLFormatter;
 import org.jabref.logic.formatter.bibtexfields.NormalizeNamesFormatter;
 import org.jabref.logic.l10n.Localization;
@@ -74,9 +74,8 @@ public static Supplier<List<MenuItem>> getNameMenu(final TextInputControl textIn
      */
     public static Supplier<List<MenuItem>> getDOIMenu(TextArea textArea) {
         return () -> {
-            AbstractAction copyDoiUrlAction = new CopyDoiUrlAction(textArea);
-            MenuItem copyDoiUrlMenuItem = new MenuItem((String) copyDoiUrlAction.getValue(Action.NAME));
-            copyDoiUrlMenuItem.setOnAction(event -> copyDoiUrlAction.actionPerformed(null));
+            ActionFactory factory = new ActionFactory(Globals.getKeyPrefs());
+            MenuItem copyDoiUrlMenuItem = factory.createMenuItem(StandardActions.COPY_DOI, new CopyDoiUrlAction(textArea));
 
             List<MenuItem> menuItems = new ArrayList<>();
             menuItems.add(copyDoiUrlMenuItem);
diff --git a/src/main/java/org/jabref/gui/filelist/ConfirmCloseFileListEntryEditor.java b/src/main/java/org/jabref/gui/filelist/ConfirmCloseFileListEntryEditor.java
deleted file mode 100644
index 92e92a8eaa9..00000000000
--- a/src/main/java/org/jabref/gui/filelist/ConfirmCloseFileListEntryEditor.java
+++ /dev/null
@@ -1,14 +0,0 @@
-package org.jabref.gui.filelist;
-
-import org.jabref.model.entry.LinkedFile;
-
-/**
- * An implementation of this interface is called to confirm whether a FileListEntryEditor
- * is ready to close when Ok is pressed, or whether there is a problem that needs to be
- * resolved first.
- */
-@FunctionalInterface
-public interface ConfirmCloseFileListEntryEditor {
-
-    boolean confirmClose(LinkedFile entry);
-}
diff --git a/src/main/java/org/jabref/gui/filelist/FileListEntryEditor.java b/src/main/java/org/jabref/gui/filelist/FileListEntryEditor.java
deleted file mode 100644
index fc590f146e2..00000000000
--- a/src/main/java/org/jabref/gui/filelist/FileListEntryEditor.java
+++ /dev/null
@@ -1,386 +0,0 @@
-package org.jabref.gui.filelist;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.Collection;
-import java.util.List;
-import java.util.Optional;
-import java.util.regex.Pattern;
-
-import javax.swing.AbstractAction;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.DefaultComboBoxModel;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JProgressBar;
-import javax.swing.JTextField;
-import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
-import javax.swing.event.DocumentEvent;
-import javax.swing.event.DocumentListener;
-
-import org.jabref.Globals;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.desktop.JabRefDesktop;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.externalfiletype.UnknownExternalFileType;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.gui.util.FileDialogConfiguration;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.io.FileUtil;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.LinkedFile;
-import org.jabref.model.util.FileHelper;
-import org.jabref.preferences.JabRefPreferences;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import com.jgoodies.forms.builder.FormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * This class produces a dialog box for editing a single file link from a Bibtex entry.
- *
- * The information to be edited includes the file description, the link itself and the
- * file type. The dialog also includes convenience buttons for quick linking.
- *
- * For use when downloading files, this class also offers a progress bar and a "Downloading..."
- * label that can be hidden when the download is complete.
- * @deprecated Use {@link LinkedFileEditDialogView}
- */
-@Deprecated
-public class FileListEntryEditor {
-
-    private static final Pattern REMOTE_LINK_PATTERN = Pattern.compile("[a-z]+://.*");
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(FileListEntryEditor.class);
-    private final JTextField link = new JTextField();
-    private final JTextField description = new JTextField();
-    private final JButton ok = new JButton(Localization.lang("OK"));
-    private final JComboBox<ExternalFileType> types;
-    private final JProgressBar prog = new JProgressBar(SwingConstants.HORIZONTAL);
-    private final JLabel downloadLabel = new JLabel(Localization.lang("Downloading..."));
-    private JDialog dialog;
-    //Do not make this variable final, as then the lambda action listener will fail on compile
-    private JabRefFrame frame;
-    private boolean showSaveDialog;
-    private ConfirmCloseFileListEntryEditor externalConfirm;
-    private LinkedFile entry;
-    //Do not make this variable final, as then the lambda action listener will fail on compiöe
-    private BibDatabaseContext databaseContext;
-    private final ActionListener browsePressed = e -> {
-        String fileText = link.getText().trim();
-        Optional<Path> file = FileHelper.expandFilename(this.databaseContext, fileText,
-                Globals.prefs.getFilePreferences());
-
-        Path workingDir = file.orElse(Paths.get(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)));
-        String fileName = Paths.get(fileText).getFileName().toString();
-
-        FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                .withInitialDirectory(workingDir)
-                .withInitialFileName(fileName).build();
-
-        Optional<Path> path;
-        if (showSaveDialog) {
-            path = DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().showFileSaveDialog(fileDialogConfiguration));
-        } else {
-            path = DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().showFileOpenDialog(fileDialogConfiguration));
-        }
-
-        path.ifPresent(newFile -> {
-            // Store the directory for next time:
-            Globals.prefs.put(JabRefPreferences.WORKING_DIRECTORY, newFile.toString());
-
-            // If the file is below the file directory, make the path relative:
-            List<Path> fileDirectories = this.databaseContext
-                    .getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
-            newFile = FileUtil.relativize(newFile, fileDirectories);
-
-            link.setText(newFile.toString());
-            link.requestFocus();
-        });
-    };
-    private boolean okPressed;
-
-    private boolean okDisabledExternally;
-    private boolean openBrowseWhenShown;
-
-    private boolean dontOpenBrowseUntilDisposed;
-
-    public FileListEntryEditor(LinkedFile entry, boolean showProgressBar, boolean showOpenButton, BibDatabaseContext databaseContext, boolean showSaveDialog) {
-        this(entry, showProgressBar, showOpenButton, databaseContext);
-        this.showSaveDialog = showSaveDialog;
-    }
-
-    public FileListEntryEditor(LinkedFile entry, boolean showProgressBar, boolean showOpenButton, BibDatabaseContext databaseContext) {
-        this.entry = entry;
-        this.databaseContext = databaseContext;
-
-        ActionListener okAction = e -> {
-            // If OK button is disabled, ignore this event:
-            if (!ok.isEnabled()) {
-                return;
-            }
-            // If necessary, ask the external confirm object whether we are ready to close.
-            if (externalConfirm != null) {
-                // Construct an updated FileListEntry:
-                storeSettings(entry);
-                if (!externalConfirm.confirmClose(entry)) {
-                    return;
-                }
-            }
-            dialog.dispose();
-            storeSettings(FileListEntryEditor.this.entry);
-            okPressed = true;
-        };
-        types = new JComboBox<>();
-        types.addItemListener(itemEvent -> {
-            if (!okDisabledExternally) {
-                ok.setEnabled(types.getSelectedItem() != null);
-            }
-        });
-
-        FormLayout fileDialog = new FormLayout(
-                "left:pref, 4dlu, fill:400dlu, 4dlu, fill:pref, 4dlu, fill:pref",
-                "p, 8dlu, p, 8dlu, p");
-        FormBuilder builder = FormBuilder.create().layout(fileDialog);
-        builder.add(Localization.lang("Link")).xy(1, 1);
-        builder.add(link).xy(3, 1);
-
-        final JButton browseBut = new JButton(Localization.lang("Browse"));
-        browseBut.addActionListener(browsePressed);
-        builder.add(browseBut).xy(5, 1);
-        JButton open = new JButton(Localization.lang("Open"));
-        if (showOpenButton) {
-            builder.add(open).xy(7, 1);
-        }
-        builder.add(Localization.lang("Description")).xy(1, 3);
-        builder.add(description).xyw(3, 3, 5);
-        builder.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-        builder.add(Localization.lang("File type")).xy(1, 5);
-        builder.add(types).xyw(3, 5, 5);
-        if (showProgressBar) {
-            builder.appendRows("2dlu, p");
-            builder.add(downloadLabel).xy(1, 7);
-            builder.add(prog).xyw(3, 7, 3);
-        }
-
-        ButtonBarBuilder bb = new ButtonBarBuilder();
-        bb.addGlue();
-        bb.addRelatedGap();
-        bb.addButton(ok);
-        JButton cancel = new JButton(Localization.lang("Cancel"));
-        bb.addButton(cancel);
-        bb.addGlue();
-        bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        ok.addActionListener(okAction);
-        // Add OK action to the two text fields to simplify entering:
-        link.addActionListener(okAction);
-        description.addActionListener(okAction);
-
-        open.addActionListener(e -> openFile());
-
-        AbstractAction cancelAction = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                dialog.dispose();
-            }
-        };
-        cancel.addActionListener(cancelAction);
-
-        // Key bindings:
-        ActionMap am = builder.getPanel().getActionMap();
-        InputMap im = builder.getPanel().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", cancelAction);
-
-        link.getDocument().addDocumentListener(new DocumentListener() {
-
-            @Override
-            public void insertUpdate(DocumentEvent documentEvent) {
-                checkExtension();
-            }
-
-            @Override
-            public void removeUpdate(DocumentEvent documentEvent) {
-                // Do nothing
-            }
-
-            @Override
-            public void changedUpdate(DocumentEvent documentEvent) {
-                checkExtension();
-            }
-
-        });
-
-        dialog = new JDialog();
-        dialog.setTitle(Localization.lang("Select files"));
-        dialog.setModal(true);
-        dialog.getContentPane().add(builder.getPanel(), BorderLayout.CENTER);
-        dialog.getContentPane().add(bb.getPanel(), BorderLayout.SOUTH);
-        dialog.pack();
-        dialog.addWindowListener(new WindowAdapter() {
-
-            @Override
-            public void windowActivated(WindowEvent event) {
-                if (openBrowseWhenShown && !dontOpenBrowseUntilDisposed) {
-                    dontOpenBrowseUntilDisposed = true;
-                    SwingUtilities.invokeLater(() -> browsePressed.actionPerformed(new ActionEvent(browseBut, 0, "")));
-                }
-            }
-
-            @Override
-            public void windowClosed(WindowEvent event) {
-                dontOpenBrowseUntilDisposed = false;
-            }
-        });
-        setValues(entry);
-    }
-
-    private void checkExtension() {
-        if ((types.getSelectedIndex() == -1) && (!link.getText().trim().isEmpty())) {
-
-            // Check if this looks like a remote link:
-            if (FileListEntryEditor.REMOTE_LINK_PATTERN.matcher(link.getText()).matches()) {
-                Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByExt("html");
-                if (type.isPresent()) {
-                    types.setSelectedItem(type.get());
-                    return;
-                }
-            }
-
-            // Try to guess the file type:
-            String theLink = link.getText().trim();
-            ExternalFileTypes.getInstance().getExternalFileTypeForName(theLink).ifPresent(types::setSelectedItem);
-        }
-    }
-
-    private void openFile() {
-        ExternalFileType type = (ExternalFileType) types.getSelectedItem();
-        if (type != null) {
-            try {
-                JabRefDesktop.openExternalFileAnyFormat(databaseContext, link.getText(), Optional.of(type));
-            } catch (IOException e) {
-                LOGGER.error("File could not be opened", e);
-            }
-        }
-    }
-
-    public void setExternalConfirm(ConfirmCloseFileListEntryEditor eC) {
-        this.externalConfirm = eC;
-    }
-
-    public void setOkEnabled(boolean enabled) {
-        okDisabledExternally = !enabled;
-        ok.setEnabled(enabled);
-    }
-
-    public JProgressBar getProgressBar() {
-        return prog;
-    }
-
-    public JLabel getProgressBarLabel() {
-        return downloadLabel;
-    }
-
-    public void setEntry(LinkedFile entry) {
-        this.entry = entry;
-        setValues(entry);
-    }
-
-    public void setVisible(boolean visible, boolean openBrowse) {
-        openBrowseWhenShown = openBrowse && Globals.prefs.getBoolean(JabRefPreferences.ALLOW_FILE_AUTO_OPEN_BROWSE);
-        if (visible) {
-            okPressed = false;
-        }
-        String title;
-        if (showSaveDialog) {
-            title = Localization.lang("Save file");
-        } else {
-            title = Localization.lang("Select files");
-        }
-        dialog.setTitle(title);
-        dialog.setVisible(visible);
-    }
-
-    public boolean isVisible() {
-        return (dialog != null) && dialog.isVisible();
-    }
-
-    private void setValues(LinkedFile entry) {
-        description.setText(entry.getDescription());
-        link.setText(entry.getLink());
-
-        Collection<ExternalFileType> list = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
-
-        types.setModel(new DefaultComboBoxModel<>(list.toArray(new ExternalFileType[list.size()])));
-        types.setSelectedIndex(-1);
-        // See what is a reasonable selection for the type combobox:
-        Optional<ExternalFileType> fileType = ExternalFileTypes.getInstance().fromLinkedFile(entry, false);
-        if (fileType.isPresent() && !(fileType.get() instanceof UnknownExternalFileType)) {
-            types.setSelectedItem(fileType.get());
-        } else if ((entry.getLink() != null) && (!entry.getLink().isEmpty())) {
-            checkExtension();
-        }
-    }
-
-    private void storeSettings(LinkedFile listEntry) {
-        String descriptionText = this.description.getText().trim();
-        String fileLink = "";
-        // See if we should trim the file link to be relative to the file directory:
-        try {
-            List<String> dirs = databaseContext.getFileDirectories(Globals.prefs.getFilePreferences());
-            if (dirs.isEmpty()) {
-                fileLink = this.link.getText().trim();
-            } else {
-                boolean found = false;
-                for (String dir : dirs) {
-                    String canPath = (new File(dir)).getCanonicalPath();
-                    File fl = new File(this.link.getText().trim());
-                    if (fl.isAbsolute()) {
-                        String flPath = fl.getCanonicalPath();
-                        if ((flPath.length() > canPath.length()) && (flPath.startsWith(canPath))) {
-                            fileLink = fl.getCanonicalPath().substring(canPath.length() + 1);
-                            found = true;
-                            break;
-                        }
-                    }
-                }
-                if (!found) {
-                    fileLink = this.link.getText().trim();
-                }
-            }
-        } catch (IOException ex) {
-            // Don't think this should happen, but set the file link directly as a fallback:
-            fileLink = this.link.getText().trim();
-        }
-
-        ExternalFileType type = (ExternalFileType) types.getSelectedItem();
-
-        listEntry.setDescription(descriptionText);
-        listEntry.setFileType(type.getName());
-        listEntry.setLink(fileLink);
-    }
-
-    public boolean okPressed() {
-        return okPressed;
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/groups/GroupTreeCellRenderer.java b/src/main/java/org/jabref/gui/groups/GroupTreeCellRenderer.java
deleted file mode 100644
index 4b128b2593d..00000000000
--- a/src/main/java/org/jabref/gui/groups/GroupTreeCellRenderer.java
+++ /dev/null
@@ -1,114 +0,0 @@
-package org.jabref.gui.groups;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-
-import javax.swing.BorderFactory;
-import javax.swing.JLabel;
-import javax.swing.JTree;
-import javax.swing.border.Border;
-import javax.swing.tree.DefaultTreeCellRenderer;
-
-import org.jabref.model.groups.GroupTreeNode;
-
-/**
- * Renders a GroupTreeNode using its group's getName() method, rather that its toString() method.
- */
-public class GroupTreeCellRenderer extends DefaultTreeCellRenderer {
-
-    /** The cell over which the user is currently dragging */
-    private Object highlight1Cell;
-    private List<GroupTreeNode> overlappingGroups = new ArrayList<>();
-    private List<GroupTreeNode> matchingGroups = new ArrayList<>();
-    private Object highlightBorderCell;
-
-    @Override
-    public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf,
-            int row, boolean tmpHasFocus) {
-        // show as selected
-        selected = (Objects.equals(highlight1Cell, value)) || sel;
-        Component c = super.getTreeCellRendererComponent(tree, value, selected, expanded, leaf, row, tmpHasFocus);
-        // this is sometimes called from deep within somewhere, with a dummy
-        // value (probably for layout etc.), so we've got to check here!
-        if (!(value instanceof GroupTreeNodeViewModel)) {
-            return c;
-        }
-        if (!(c instanceof JLabel)) {
-            return c; // sanity check
-        }
-
-        GroupTreeNodeViewModel viewModel = (GroupTreeNodeViewModel) value;
-        JLabel label = (JLabel) c;
-
-        Border border;
-        if (Objects.equals(highlightBorderCell, value)) {
-            border = BorderFactory.createLineBorder(Color.BLACK);
-        } else {
-            border = BorderFactory.createEmptyBorder();
-        }
-        if (label.getBorder() != border) {
-            label.setBorder(border);
-        }
-
-        Boolean red = printInRed(viewModel) && !selected; // do not print currently selected node in red
-        Boolean underlined = printUnderlined(viewModel);
-        StringBuilder sb = new StringBuilder(60);
-        sb.append("<html>");
-        if (red) {
-            sb.append("<font color=\"#FF0000\">");
-        }
-        if (underlined) {
-            sb.append("<u>");
-        }
-        if (viewModel.printInItalics()) {
-            sb.append("<i>");
-        }
-        sb.append(viewModel.getName());
-        if (viewModel.printInItalics()) {
-            sb.append("</i>");
-        }
-        if (underlined) {
-            sb.append("</u>");
-        }
-        if (red) {
-            sb.append("</font>");
-        }
-        sb.append("</html>");
-
-        String text = sb.toString();
-        if (!label.getText().equals(text)) {
-            label.setText(text);
-        }
-        label.setToolTipText(viewModel.getDescription());
-
-        return c;
-    }
-
-    private boolean printInRed(GroupTreeNodeViewModel viewModel) {
-        if (viewModel.isAllEntriesGroup()) {
-            // Do not print all entries group in red
-            return false;
-        }
-
-        return overlappingGroups.contains(viewModel.getNode());
-    }
-
-    private boolean printUnderlined(GroupTreeNodeViewModel viewModel) {
-        if (viewModel.isAllEntriesGroup()) {
-            // Do not underline all entries group
-            return false;
-        }
-        return matchingGroups.contains(viewModel.getNode());
-    }
-
-    /**
-     * Highlights the specified cells (by drawing a border around it), or disables highlight if highlightBorderCell ==
-     * null.
-     */
-    public void setHighlightBorderCell(Object highlightBorderCell) {
-        this.highlightBorderCell = highlightBorderCell;
-    }
-}
diff --git a/src/main/java/org/jabref/gui/help/HelpAction.java b/src/main/java/org/jabref/gui/help/HelpAction.java
index d18d3f0b34b..603e055abaf 100644
--- a/src/main/java/org/jabref/gui/help/HelpAction.java
+++ b/src/main/java/org/jabref/gui/help/HelpAction.java
@@ -1,68 +1,39 @@
 package org.jabref.gui.help;
 
-import java.awt.event.ActionEvent;
 import java.util.HashSet;
 import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import javax.swing.Action;
-import javax.swing.Icon;
-import javax.swing.KeyStroke;
-
 import org.jabref.Globals;
-import org.jabref.gui.actions.MnemonicAwareAction;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.desktop.JabRefDesktop;
-import org.jabref.gui.icon.IconTheme;
 import org.jabref.logic.help.HelpFile;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.preferences.JabRefPreferences;
 
 /**
  * This Action keeps a reference to a URL. When activated, it shows the help
  * Dialog unless it is already visible, and shows the URL in it.
  */
-public class HelpAction extends MnemonicAwareAction {
+public class HelpAction extends SimpleCommand {
 
     /**
      * New languages of the help have to be added here
      */
-    private static final Set<String> AVAIABLE_LANG_FILES = Stream.of("en", "de", "fr", "in", "ja")
-            .collect(Collectors.toCollection(HashSet::new));
+    private static final Set<String> AVAILABLE_LANG_FILES = Stream.of("en", "de", "fr", "in", "ja")
+                                                                  .collect(Collectors.toCollection(HashSet::new));
 
     private HelpFile helpPage;
 
-
-    public HelpAction(String title, String tooltip, HelpFile helpPage, KeyStroke key) {
-        this(title, tooltip, helpPage, IconTheme.JabRefIcons.HELP.getSmallIcon());
-        putValue(Action.ACCELERATOR_KEY, key);
-    }
-
-    private HelpAction(String title, String tooltip, HelpFile helpPage, Icon icon) {
-        super(icon);
-        this.helpPage = helpPage;
-        putValue(Action.NAME, title);
-        putValue(Action.SHORT_DESCRIPTION, tooltip);
-    }
-
-    public HelpAction(String tooltip, HelpFile helpPage) {
-        this(Localization.lang("Help"), tooltip, helpPage, IconTheme.JabRefIcons.HELP.getSmallIcon());
-    }
-
-    public HelpAction(HelpFile helpPage, Icon icon) {
-        this(Localization.lang("Help"), Localization.lang("Help"), helpPage, icon);
-    }
-
     public HelpAction(HelpFile helpPage) {
-        this(Localization.lang("Help"), Localization.lang("Help"), helpPage, IconTheme.JabRefIcons.HELP.getSmallIcon());
+        this.helpPage = helpPage;
     }
 
     public static void openHelpPage(HelpFile helpPage) {
         String lang = Globals.prefs.get(JabRefPreferences.LANGUAGE);
         StringBuilder sb = new StringBuilder("https://help.jabref.org/");
 
-        if (AVAIABLE_LANG_FILES.contains(lang)) {
+        if (AVAILABLE_LANG_FILES.contains(lang)) {
             sb.append(lang);
             sb.append("/");
         } else {
@@ -72,15 +43,6 @@ public static void openHelpPage(HelpFile helpPage) {
         JabRefDesktop.openBrowserShowPopup(sb.toString());
     }
 
-    public void setHelpFile(HelpFile urlPart) {
-        this.helpPage = urlPart;
-    }
-
-    @Override
-    public void actionPerformed(ActionEvent e) {
-        openHelpPage(helpPage);
-    }
-
     public static SimpleCommand getMainHelpPageCommand() {
         return new SimpleCommand() {
             @Override
@@ -90,12 +52,8 @@ public void execute() {
         };
     }
 
-    public SimpleCommand getCommand() {
-        return new SimpleCommand() {
-            @Override
-            public void execute() {
-                openHelpPage(helpPage);
-            }
-        };
+    @Override
+    public void execute() {
+        openHelpPage(helpPage);
     }
 }
diff --git a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java
index 30ee0635043..b3851939465 100644
--- a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java
+++ b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java
@@ -59,8 +59,7 @@ protected Node createContentPane() {
         ActionFactory factory = new ActionFactory(preferences.getKeyBindingRepository());
         EasyBind.subscribe(viewModel.selectedFetcherProperty(), fetcher -> {
             if ((fetcher != null) && fetcher.getHelpPage().isPresent()) {
-                HelpAction helpCommand = new HelpAction(fetcher.getHelpPage().get());
-                Button helpButton = factory.createIconButton(StandardActions.HELP, helpCommand.getCommand());
+                Button helpButton = factory.createIconButton(StandardActions.HELP, new HelpAction(fetcher.getHelpPage().get()));
                 helpButtonContainer.getChildren().setAll(helpButton);
             } else {
                 helpButtonContainer.getChildren().clear();
diff --git a/src/main/java/org/jabref/gui/keyboard/KeyBinder.java b/src/main/java/org/jabref/gui/keyboard/KeyBinder.java
deleted file mode 100644
index 1944bd038cd..00000000000
--- a/src/main/java/org/jabref/gui/keyboard/KeyBinder.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package org.jabref.gui.keyboard;
-
-import javax.swing.Action;
-import javax.swing.ActionMap;
-import javax.swing.InputMap;
-import javax.swing.JComponent;
-import javax.swing.JRootPane;
-
-import org.jabref.Globals;
-
-public class KeyBinder {
-
-    private KeyBinder() {
-    }
-
-    /**
-     * Binds ESC-Key to cancel button
-     *
-     * @param rootPane     the pane to bind the action to. Typically, this variable is retrieved by this.getRootPane();
-     * @param cancelAction the action to bind
-     */
-    public static void bindCloseDialogKeyToCancelAction(JRootPane rootPane, Action cancelAction) {
-        InputMap im = rootPane.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        ActionMap am = rootPane.getActionMap();
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", cancelAction);
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/maintable/MainTable.java b/src/main/java/org/jabref/gui/maintable/MainTable.java
index d852104c1fd..892116fb337 100644
--- a/src/main/java/org/jabref/gui/maintable/MainTable.java
+++ b/src/main/java/org/jabref/gui/maintable/MainTable.java
@@ -83,17 +83,17 @@ public MainTable(MainTableDataModel model, JabRefFrame frame,
         this.getColumns().addAll(new MainTableColumnFactory(database, preferences.getColumnPreferences(), externalFileTypes, panel.getUndoManager(), frame.getDialogService()).createColumns());
 
         new ViewModelTableRowFactory<BibEntryTableViewModel>()
-                                                              .withOnMouseClickedEvent((entry, event) -> {
+                .withOnMouseClickedEvent((entry, event) -> {
                                                                   if (event.getClickCount() == 2) {
                                                                       panel.showAndEdit(entry.getEntry());
                                                                   }
                                                               })
-                                                              .withContextMenu(entry -> RightClickMenu.create(entry, keyBindingRepository, panel, Globals.getKeyPrefs(), frame.getDialogService()))
-                                                              .setOnDragDetected(this::handleOnDragDetected)
-                                                              .setOnDragDropped(this::handleOnDragDropped)
-                                                              .setOnDragOver(this::handleOnDragOver)
-                                                              .setOnMouseDragEntered(this::handleOnDragEntered)
-                                                              .install(this);
+                .withContextMenu(entry -> RightClickMenu.create(entry, keyBindingRepository, panel, frame.getDialogService()))
+                .setOnDragDetected(this::handleOnDragDetected)
+                .setOnDragDropped(this::handleOnDragDropped)
+                .setOnDragOver(this::handleOnDragOver)
+                .setOnMouseDragEntered(this::handleOnDragEntered)
+                .install(this);
 
         /*for (Entry<String, SortType> entries : preferences.getColumnPreferences().getSortTypesForColumns().entrySet()) {
             Optional<TableColumn<BibEntryTableViewModel, ?>> column = this.getColumns().stream().filter(col -> entries.getKey().equals(col.getText())).findFirst();
diff --git a/src/main/java/org/jabref/gui/maintable/RightClickMenu.java b/src/main/java/org/jabref/gui/maintable/RightClickMenu.java
index 3070a50a2b7..66b1c5c3765 100644
--- a/src/main/java/org/jabref/gui/maintable/RightClickMenu.java
+++ b/src/main/java/org/jabref/gui/maintable/RightClickMenu.java
@@ -29,7 +29,7 @@
 
 public class RightClickMenu {
 
-    public static ContextMenu create(BibEntryTableViewModel entry, KeyBindingRepository keyBindingRepository, BasePanel panel, KeyBindingRepository keyBindings, DialogService dialogService) {
+    public static ContextMenu create(BibEntryTableViewModel entry, KeyBindingRepository keyBindingRepository, BasePanel panel, DialogService dialogService) {
         ContextMenu contextMenu = new ContextMenu();
         ActionFactory factory = new ActionFactory(keyBindingRepository);
 
@@ -79,7 +79,7 @@ public static ContextMenu create(BibEntryTableViewModel entry, KeyBindingReposit
 
         contextMenu.getItems().add(new SeparatorMenuItem());
 
-        contextMenu.getItems().add(new ChangeEntryTypeMenu(keyBindings).getChangeEntryTypeMenu(entry.getEntry(), panel.getBibDatabaseContext(), panel.getUndoManager()));
+        contextMenu.getItems().add(new ChangeEntryTypeMenu().getChangeEntryTypeMenu(entry.getEntry(), panel.getBibDatabaseContext(), panel.getUndoManager()));
         contextMenu.getItems().add(factory.createMenuItem(StandardActions.MERGE_WITH_FETCHED_ENTRY, getFetchEntryData(panel)));
         contextMenu.getItems().add(factory.createMenuItem(StandardActions.ATTACH_FILE, new AttachFileAction(panel, dialogService)));
         contextMenu.getItems().add(factory.createMenuItem(StandardActions.MERGE_ENTRIES, mergeEntries(panel)));
diff --git a/src/main/java/org/jabref/gui/menus/ChangeEntryTypeMenu.java b/src/main/java/org/jabref/gui/menus/ChangeEntryTypeMenu.java
index f65f4517030..eb7ca539262 100644
--- a/src/main/java/org/jabref/gui/menus/ChangeEntryTypeMenu.java
+++ b/src/main/java/org/jabref/gui/menus/ChangeEntryTypeMenu.java
@@ -1,14 +1,8 @@
 package org.jabref.gui.menus;
 
-import java.awt.Font;
 import java.util.Collection;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.KeyStroke;
 import javax.swing.undo.UndoManager;
 
 import javafx.collections.ObservableList;
@@ -17,11 +11,9 @@
 import javafx.scene.control.MenuItem;
 import javafx.scene.control.SeparatorMenuItem;
 
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.actions.ChangeTypeAction;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.undo.CountingUndoManager;
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.gui.undo.UndoableChangeType;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.EntryTypes;
 import org.jabref.model.database.BibDatabaseContext;
@@ -32,23 +24,20 @@
 import org.jabref.model.entry.IEEETranEntryTypes;
 
 public class ChangeEntryTypeMenu {
-    public final Map<String, KeyStroke> entryShortCuts = new HashMap<>();
-
-    public ChangeEntryTypeMenu(KeyBindingRepository keyBindings) {
-        entryShortCuts.put(BibtexEntryTypes.ARTICLE.getName(), keyBindings.getKey(KeyBinding.NEW_ARTICLE));
-        entryShortCuts.put(BibtexEntryTypes.BOOK.getName(), keyBindings.getKey(KeyBinding.NEW_BOOK));
-        entryShortCuts.put(BibtexEntryTypes.PHDTHESIS.getName(), keyBindings.getKey(KeyBinding.NEW_PHDTHESIS));
-        entryShortCuts.put(BibtexEntryTypes.INBOOK.getName(), keyBindings.getKey(KeyBinding.NEW_MASTERSTHESIS));
-        entryShortCuts.put(BibtexEntryTypes.INBOOK.getName(), keyBindings.getKey(KeyBinding.NEW_INBOOK));
-        entryShortCuts.put(BibtexEntryTypes.PROCEEDINGS.getName(), keyBindings.getKey(KeyBinding.NEW_PROCEEDINGS));
-        entryShortCuts.put(BibtexEntryTypes.UNPUBLISHED.getName(), keyBindings.getKey(KeyBinding.NEW_UNPUBLISHED));
-        entryShortCuts.put(BibtexEntryTypes.TECHREPORT.getName(), keyBindings.getKey(KeyBinding.NEW_TECHREPORT));
+
+    public ChangeEntryTypeMenu() {
+
     }
 
-    public JMenu getChangeEntryTypeMenu(BasePanel panel) {
-        JMenu menu = new JMenu(Localization.lang("Change entry type"));
-        populateChangeEntryTypeMenu(menu, panel);
-        return menu;
+    public static MenuItem createMenuItem(EntryType type, BibEntry entry, UndoManager undoManager) {
+        MenuItem menuItem = new MenuItem(type.getName());
+        menuItem.setOnAction(event -> {
+            NamedCompound compound = new NamedCompound(Localization.lang("Change entry type"));
+            entry.setType(type)
+                 .ifPresent(change -> compound.addEdit(new UndoableChangeType(change)));
+            undoManager.addEdit(compound);
+        });
+        return menuItem;
     }
 
     public ContextMenu getChangeEntryTypePopupMenu(BibEntry entry, BibDatabaseContext bibDatabaseContext, CountingUndoManager undoManager) {
@@ -95,61 +84,11 @@ private void populateSubMenu(ObservableList<MenuItem> items, String text, List<E
 
     private void populate(ObservableList<MenuItem> items, Collection<EntryType> types, BibEntry entry, UndoManager undoManager) {
         for (EntryType type : types) {
-            items.add(ChangeTypeAction.as(type, entry, undoManager));
+            items.add(createMenuItem(type, entry, undoManager));
         }
     }
 
     private void populate(Menu menu, Collection<EntryType> types, BibEntry entry, UndoManager undoManager) {
         populate(menu.getItems(), types, entry, undoManager);
     }
-
-    /**
-     * Remove all types from the menu. Then cycle through all available
-     * types, and add them.
-     */
-    private void populateChangeEntryTypeMenu(JMenu menu, BasePanel panel) {
-        menu.removeAll();
-
-        // biblatex?
-        if (panel.getBibDatabaseContext().isBiblatexMode()) {
-            for (EntryType type : EntryTypes.getAllValues(BibDatabaseMode.BIBLATEX)) {
-                menu.add(new ChangeTypeAction(type, panel));
-            }
-
-            List<EntryType> customTypes = EntryTypes.getAllCustomTypes(BibDatabaseMode.BIBLATEX);
-            if (!customTypes.isEmpty()) {
-                menu.addSeparator();
-                // custom types
-                createEntryTypeSection(panel, menu, "Custom Entries", customTypes);
-            }
-        } else {
-            // Bibtex
-            createEntryTypeSection(panel, menu, "BibTeX Entries", BibtexEntryTypes.ALL);
-            menu.addSeparator();
-            // ieeetran
-            createEntryTypeSection(panel, menu, "IEEETran Entries", IEEETranEntryTypes.ALL);
-
-            List<EntryType> customTypes = EntryTypes.getAllCustomTypes(BibDatabaseMode.BIBTEX);
-            if (!customTypes.isEmpty()) {
-                menu.addSeparator();
-                // custom types
-                createEntryTypeSection(panel, menu, "Custom Entries", customTypes);
-            }
-        }
-    }
-
-    private void createEntryTypeSection(BasePanel panel, JMenu menu, String title, List<? extends EntryType> types) {
-        // bibtex
-        JMenuItem header = new JMenuItem(title);
-        Font font = new Font(menu.getFont().getName(), Font.ITALIC, menu.getFont().getSize());
-        header.setFont(font);
-        header.setEnabled(false);
-        if (!types.isEmpty()) {
-            menu.add(header);
-        }
-
-        for (EntryType type : types) {
-            menu.add(new ChangeTypeAction(type, panel));
-        }
-    }
 }
diff --git a/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java b/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
index 7d2c1c20e70..c56e7606c29 100644
--- a/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
+++ b/src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
@@ -117,9 +117,7 @@ public OpenOfficePanel(JabRefFrame frame, JabRefPreferences jabRefPreferences, O
         manualConnect.setTooltip(new Tooltip(Localization.lang("Manual connect")));
         manualConnect.setMaxWidth(Double.MAX_VALUE);
 
-        HelpAction helpCommand = new HelpAction(HelpFile.OPENOFFICE_LIBREOFFICE);
-
-        help = factory.createIconButton(StandardActions.HELP, helpCommand.getCommand());
+        help = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.OPENOFFICE_LIBREOFFICE));
         help.setMaxWidth(Double.MAX_VALUE);
 
         selectDocument = new Button();
diff --git a/src/main/java/org/jabref/gui/preferences/AdvancedTab.java b/src/main/java/org/jabref/gui/preferences/AdvancedTab.java
index 4a8dbf0a075..03f67d319cb 100644
--- a/src/main/java/org/jabref/gui/preferences/AdvancedTab.java
+++ b/src/main/java/org/jabref/gui/preferences/AdvancedTab.java
@@ -80,7 +80,7 @@ public AdvancedTab(DialogService dialogService, JabRefPreferences prefs) {
         p.getChildren().add(remoteServerPort);
 
         ActionFactory factory = new ActionFactory(preferences.getKeyBindingRepository());
-        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.REMOTE).getCommand());
+        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.REMOTE));
         help.setMaxWidth(Double.MAX_VALUE);
         p.getChildren().add(help);
 
diff --git a/src/main/java/org/jabref/gui/preferences/FileTab.java b/src/main/java/org/jabref/gui/preferences/FileTab.java
index 4067cf08751..060afb272cd 100644
--- a/src/main/java/org/jabref/gui/preferences/FileTab.java
+++ b/src/main/java/org/jabref/gui/preferences/FileTab.java
@@ -143,8 +143,7 @@ public FileTab(DialogService dialogService, JabRefPreferences prefs) {
         matchExactKeyOnly.setToggleGroup(autolinkGroup);
         useRegExpComboBox.setToggleGroup(autolinkGroup);
 
-        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on regular expression search"),
-                                                                                    HelpFile.REGEX_SEARCH).getCommand());
+        Button help = factory.createIconButton(StandardActions.HELP_REGEX_SEARCH, new HelpAction(HelpFile.REGEX_SEARCH));
         builder.add(help, 3, 16);
         builder.add(runAutoFileSearch, 1, 17);
         builder.add(allowFileAutoOpenBrowse, 1, 18);
@@ -157,7 +156,7 @@ public FileTab(DialogService dialogService, JabRefPreferences prefs) {
         builder.add(autosave, 1, 20);
         builder.add(localAutoSave, 1, 21);
 
-        Button helpAutosave = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.AUTOSAVE).getCommand());
+        Button helpAutosave = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.AUTOSAVE));
         builder.add(helpAutosave, 2, 21);
     }
 
diff --git a/src/main/java/org/jabref/gui/preferences/GeneralTab.java b/src/main/java/org/jabref/gui/preferences/GeneralTab.java
index c7f3759755d..4dacdd38e8a 100644
--- a/src/main/java/org/jabref/gui/preferences/GeneralTab.java
+++ b/src/main/java/org/jabref/gui/preferences/GeneralTab.java
@@ -95,7 +95,7 @@ public GeneralTab(DialogService dialogService, JabRefPreferences prefs) {
         builder.add(defOwnerField, 2, 10);
         builder.add(overwriteOwner, 3, 10);
 
-        Button helpOwner = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.OWNER).getCommand());
+        Button helpOwner = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.OWNER));
         builder.add(helpOwner, 4, 10);
 
         builder.add(useTimeStamp, 1, 13);
@@ -105,7 +105,7 @@ public GeneralTab(DialogService dialogService, JabRefPreferences prefs) {
         builder.add(fieldName, 3, 13);
         builder.add(timeStampField, 4, 13);
 
-        Button helpTimestamp = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.TIMESTAMP).getCommand());
+        Button helpTimestamp = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.TIMESTAMP));
         builder.add(helpTimestamp, 6, 13);
 
         builder.add(updateTimeStamp, 1, 14);
diff --git a/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java b/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java
index da1f649fb2c..bfc0de4fbfd 100644
--- a/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java
+++ b/src/main/java/org/jabref/gui/preferences/NameFormatterTab.java
@@ -151,8 +151,7 @@ public NameFormatterTab(JabRefPreferences prefs) {
             }
         });
 
-        Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on Name Formatting"),
-                                                                                    HelpFile.CUSTOM_EXPORTS_NAME_FORMATTER).getCommand());
+        Button help = factory.createIconButton(StandardActions.HELP_NAME_FORMATTER, new HelpAction(HelpFile.CUSTOM_EXPORTS_NAME_FORMATTER));
         HBox toolbar = new HBox();
         toolbar.getChildren().addAll(addName, addLast, add, delete, help);
         tabPanel.setBottom(toolbar);
diff --git a/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java b/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
index fe9dd582df7..38c252b642c 100644
--- a/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
+++ b/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
@@ -1,15 +1,11 @@
 package org.jabref.gui.preferences;
 
-import java.awt.event.ActionEvent;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Locale;
 
-import javax.swing.AbstractAction;
-
 import javafx.beans.property.SimpleDoubleProperty;
 import javafx.beans.property.SimpleStringProperty;
 import javafx.collections.FXCollections;
@@ -50,7 +46,7 @@ class TableColumnsTab extends Pane implements PrefsTab {
 
     private final JabRefPreferences prefs;
     private boolean tableChanged;
-    private final TableView colSetup;
+    private final TableView<TableRow> colSetup;
     private final JabRefFrame frame;
 
     private final CheckBox urlColumn;
@@ -229,8 +225,7 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
 
         ActionFactory factory = new ActionFactory(prefs.getKeyBindingRepository());
 
-        Button helpButton = factory.createIconButton(StandardActions.HELP, new HelpAction(Localization.lang("Help on special fields"),
-                                                                                          HelpFile.SPECIAL_FIELDS).getCommand());
+        Button helpButton = factory.createIconButton(StandardActions.HELP_SPECIAL_FIELDS, new HelpAction(HelpFile.SPECIAL_FIELDS));
 
         rankingColumn = new CheckBox(Localization.lang("Show rank"));
         qualityColumn = new CheckBox(Localization.lang("Show quality"));
@@ -299,7 +294,7 @@ public TableColumnsTab(JabRefPreferences prefs, JabRefFrame frame) {
         builder.add(tabPanel, 1, 5);
         Button buttonOrder = new Button("Update to current column order");
         buttonOrder.setPrefSize(300, 30);
-        buttonOrder.setOnAction(e -> new UpdateOrderAction());
+        buttonOrder.setOnAction(e -> updateOrderAction());
         builder.add(buttonOrder, 1, 7);
     }
 
@@ -517,23 +512,16 @@ public void storeSettings() {
 
     }
 
-    class UpdateOrderAction extends AbstractAction {
-
-        public UpdateOrderAction() {
-            super(Localization.lang("Update to current column order"));
+    private void updateOrderAction() {
+        BasePanel panel = frame.getCurrentBasePanel();
+        if (panel == null) {
+            return;
         }
+        // idea: sort elements according to value stored in hash, keep
+        // everything not inside hash/mainTable as it was
+        final HashMap<String, Integer> map = new HashMap<>();
 
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            BasePanel panel = frame.getCurrentBasePanel();
-            if (panel == null) {
-                return;
-            }
-            // idea: sort elements according to value stored in hash, keep
-            // everything not inside hash/mainTable as it was
-            final HashMap<String, Integer> map = new HashMap<>();
-
-            // first element (#) not inside data
+        // first element (#) not inside data
             /*
             for (TableColumn<BibEntry, ?> column : panel.getMainTable().getColumns()) {
                 String name = column.getText();
@@ -542,19 +530,18 @@ public void actionPerformed(ActionEvent e) {
                 }
             }
             */
-            Collections.sort(data, (o1, o2) -> {
-                Integer n1 = map.get(o1.getName());
-                Integer n2 = map.get(o2.getName());
-                if ((n1 == null) || (n2 == null)) {
-                    return 0;
-                }
-                return n1.compareTo(n2);
-            });
+        data.sort((o1, o2) -> {
+            Integer n1 = map.get(o1.getName());
+            Integer n2 = map.get(o2.getName());
+            if ((n1 == null) || (n2 == null)) {
+                return 0;
+            }
+            return n1.compareTo(n2);
+        });
 
-            colSetup.setItems(data);
-            colSetup.refresh();
-            tableChanged = true;
-        }
+        colSetup.setItems(data);
+        colSetup.refresh();
+        tableChanged = true;
     }
 
     @Override
diff --git a/src/main/java/org/jabref/gui/util/ControlHelper.java b/src/main/java/org/jabref/gui/util/ControlHelper.java
index b5d139b338a..ca9b703880a 100644
--- a/src/main/java/org/jabref/gui/util/ControlHelper.java
+++ b/src/main/java/org/jabref/gui/util/ControlHelper.java
@@ -3,9 +3,6 @@
 import java.util.function.Consumer;
 import java.util.function.UnaryOperator;
 
-import javax.swing.JComponent;
-
-import javafx.embed.swing.SwingNode;
 import javafx.event.ActionEvent;
 import javafx.event.Event;
 import javafx.scene.Parent;
@@ -24,13 +21,6 @@ public static void setAction(ButtonType buttonType, DialogPane dialogPane, Consu
         }));
     }
 
-    public static void setSwingContent(DialogPane dialogPane, JComponent content) {
-        SwingNode node = new SwingNode();
-        node.setContent(content);
-        node.setVisible(true);
-        dialogPane.setContent(node);
-    }
-
     public static boolean childIsFocused(Parent node) {
         return node.isFocused() || node.getChildrenUnmodifiable().stream().anyMatch(child -> {
             if (child instanceof Parent) {
diff --git a/src/main/java/org/jabref/gui/util/component/CheckBoxMessage.java b/src/main/java/org/jabref/gui/util/component/CheckBoxMessage.java
deleted file mode 100644
index 99aa890ca7d..00000000000
--- a/src/main/java/org/jabref/gui/util/component/CheckBoxMessage.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package org.jabref.gui.util.component;
-
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-
-import javax.swing.JCheckBox;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.SwingConstants;
-
-public class CheckBoxMessage extends JPanel {
-
-    private final JCheckBox cb;
-
-
-    public CheckBoxMessage(String message, String cbText, boolean defaultValue) {
-        cb = new JCheckBox(cbText, defaultValue);
-        GridBagLayout gbl = new GridBagLayout();
-        setLayout(gbl);
-        GridBagConstraints con = new GridBagConstraints();
-        con.gridwidth = GridBagConstraints.REMAINDER;
-
-        JLabel lab = new JLabel(message + '\n');
-        cb.setHorizontalAlignment(SwingConstants.LEFT);
-        gbl.setConstraints(lab, con);
-        add(lab);
-        con.anchor = GridBagConstraints.WEST;
-        con.insets = new Insets(10, 0, 0, 0);
-        gbl.setConstraints(cb, con);
-        add(cb);
-    }
-
-    public boolean isSelected() {
-        return cb.isSelected();
-    }
-}
diff --git a/src/main/java/org/jabref/gui/util/component/JTextAreaWithPlaceholder.java b/src/main/java/org/jabref/gui/util/component/JTextAreaWithPlaceholder.java
deleted file mode 100644
index 0c0c0b06acb..00000000000
--- a/src/main/java/org/jabref/gui/util/component/JTextAreaWithPlaceholder.java
+++ /dev/null
@@ -1,90 +0,0 @@
-package org.jabref.gui.util.component;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-
-import javax.swing.JTextArea;
-import javax.swing.UIManager;
-
-/**
- * A text area which displays a predefined text the same way as {@link JTextFieldWithPlaceholder} does.
- */
-public class JTextAreaWithPlaceholder extends JTextArea implements KeyListener {
-
-    private final String textWhenNotFocused;
-
-    public JTextAreaWithPlaceholder() {
-        this("");
-    }
-
-    /**
-     * Additionally to {@link JTextAreaWithPlaceholder#JTextAreaWithPlaceholder(String)}
-     * this also sets the initial text of the text field component.
-     *
-     * @param content as the text of the textfield
-     * @param placeholder as the placeholder of the textfield
-     */
-    public JTextAreaWithPlaceholder(String content, String placeholder) {
-        this(placeholder);
-        setText(content);
-    }
-
-    /**
-     * This will create a {@link JTextArea} with a placeholder text. The placeholder
-     * will always be displayed if the text of the {@link JTextArea} is empty.
-     *
-     * @param placeholder as the placeholder of the textarea
-     */
-    public JTextAreaWithPlaceholder(String placeholder) {
-        super();
-        this.setEditable(true);
-        this.setText("");
-        this.textWhenNotFocused = placeholder;
-    }
-
-    @Override
-    protected void paintComponent(Graphics graphics) {
-        super.paintComponent(graphics);
-
-        if (this.getText().isEmpty()) {
-            Font prev = graphics.getFont();
-            Color prevColor = graphics.getColor();
-            graphics.setColor(UIManager.getColor("textInactiveText"));
-            int textHeight = graphics.getFontMetrics().getHeight();
-            int x = this.getInsets().left;
-            Graphics2D g2d = (Graphics2D) graphics;
-            RenderingHints hints = g2d.getRenderingHints();
-            g2d.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
-            g2d.drawString(textWhenNotFocused, x, textHeight + this.getInsets().top);
-            g2d.setRenderingHints(hints);
-            graphics.setFont(prev);
-            graphics.setColor(prevColor);
-        }
-    }
-
-    @Override
-    public void keyTyped(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-
-    @Override
-    public void keyPressed(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-
-    @Override
-    public void keyReleased(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/gui/util/component/JTextFieldWithPlaceholder.java b/src/main/java/org/jabref/gui/util/component/JTextFieldWithPlaceholder.java
deleted file mode 100644
index b676b20adb4..00000000000
--- a/src/main/java/org/jabref/gui/util/component/JTextFieldWithPlaceholder.java
+++ /dev/null
@@ -1,91 +0,0 @@
-package org.jabref.gui.util.component;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-
-import javax.swing.JTextField;
-import javax.swing.UIManager;
-
-/**
- * A text field which displays a predefined text (e.g. "Search") if the text field is empty.
- * This is similar to a html5 input element with a defined placeholder attribute.
- * Implementation based on https://gmigdos.wordpress.com/2010/03/30/java-a-custom-jtextfield-for-searching/
- */
-public class JTextFieldWithPlaceholder extends JTextField implements KeyListener {
-
-    private final String textWhenNotFocused;
-
-    /**
-     * Additionally to {@link JTextFieldWithPlaceholder#JTextFieldWithPlaceholder(String)}
-     * this also sets the initial text of the text field component.
-     *
-     * @param content as the text of the textfield
-     * @param placeholder as the placeholder of the textfield
-     */
-    public JTextFieldWithPlaceholder(String content, String placeholder) {
-        this(placeholder);
-        setText(content);
-    }
-
-    /**
-     * This will create a {@link JTextField} with a placeholder text. The placeholder
-     * will always be displayed if the text of the {@link JTextField} is empty.
-     *
-     * @param placeholder as the placeholder of the textfield
-     */
-    public JTextFieldWithPlaceholder(String placeholder) {
-        super();
-        this.setEditable(true);
-        this.setText("");
-        this.textWhenNotFocused = placeholder;
-    }
-
-    @Override
-    protected void paintComponent(Graphics graphics) {
-        super.paintComponent(graphics);
-
-        if (this.getText().isEmpty()) {
-            int height = this.getHeight();
-            Font prev = graphics.getFont();
-            Color prevColor = graphics.getColor();
-            graphics.setColor(UIManager.getColor("textInactiveText"));
-            int textHeight = graphics.getFontMetrics().getHeight();
-            int textBottom = (((height - textHeight) / 2) + textHeight) - 4;
-            int x = this.getInsets().left;
-            Graphics2D g2d = (Graphics2D) graphics;
-            RenderingHints hints = g2d.getRenderingHints();
-            g2d.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
-            g2d.drawString(textWhenNotFocused, x, textBottom);
-            g2d.setRenderingHints(hints);
-            graphics.setFont(prev);
-            graphics.setColor(prevColor);
-        }
-    }
-
-    @Override
-    public void keyTyped(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-
-    @Override
-    public void keyPressed(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-
-    @Override
-    public void keyReleased(KeyEvent e) {
-        if (this.getText().isEmpty()) {
-            this.repaint();
-        }
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/worker/CallBack.java b/src/main/java/org/jabref/gui/worker/CallBack.java
deleted file mode 100644
index 4fa4c6eb60e..00000000000
--- a/src/main/java/org/jabref/gui/worker/CallBack.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package org.jabref.gui.worker;
-
-/**
- * Represents a task that is to be executed on the GUI thread
- */
-@FunctionalInterface
-public interface CallBack {
-
-    void update();
-
-}
diff --git a/src/main/java/org/jabref/logic/net/URLUtil.java b/src/main/java/org/jabref/logic/net/URLUtil.java
index 05644fd4a18..e927d6933ff 100644
--- a/src/main/java/org/jabref/logic/net/URLUtil.java
+++ b/src/main/java/org/jabref/logic/net/URLUtil.java
@@ -6,7 +6,9 @@
 import java.net.URLDecoder;
 import java.nio.charset.StandardCharsets;
 import java.util.Objects;
+import java.util.Optional;
 
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.model.strings.StringUtil;
 
 import org.apache.http.client.utils.URIBuilder;
@@ -52,7 +54,7 @@ public static String cleanGoogleSearchURL(String url) {
             for (String pair: pairs) {
                 // "clean" url is decoded value of "url" parameter
                 if (pair.startsWith("url=")) {
-                    String value = pair.substring(pair.indexOf('=') + 1, pair.length());
+                    String value = pair.substring(pair.indexOf('=') + 1);
 
                     String decode = URLDecoder.decode(value, StandardCharsets.UTF_8.name());
                     // url?
@@ -102,4 +104,57 @@ private static String appendSegmentToPath(String path, String segment) {
         return path + "/" + segment;
     }
 
+    /**
+     * Look for the last '.' in the link, and return the following characters.
+     * This gives the extension for most reasonably named links.
+     *
+     * @param link The link
+     * @return The suffix, excluding the dot (e.g. "pdf")
+     */
+    public static Optional<String> getSuffix(final String link) {
+        String strippedLink = link;
+        try {
+            // Try to strip the query string, if any, to get the correct suffix:
+            URL url = new URL(link);
+            if ((url.getQuery() != null) && (url.getQuery().length() < (link.length() - 1))) {
+                strippedLink = link.substring(0, link.length() - url.getQuery().length() - 1);
+            }
+        } catch (MalformedURLException e) {
+            // Don't report this error, since this getting the suffix is a non-critical
+            // operation, and this error will be triggered and reported elsewhere.
+        }
+        // First see if the stripped link gives a reasonable suffix:
+        String suffix;
+        int strippedLinkIndex = strippedLink.lastIndexOf('.');
+        if ((strippedLinkIndex <= 0) || (strippedLinkIndex == (strippedLink.length() - 1))) {
+            suffix = null;
+        } else {
+            suffix = strippedLink.substring(strippedLinkIndex + 1);
+        }
+        if (!ExternalFileTypes.getInstance().isExternalFileTypeByExt(suffix)) {
+            // If the suffix doesn't seem to give any reasonable file type, try
+            // with the non-stripped link:
+            int index = link.lastIndexOf('.');
+            if ((index <= 0) || (index == (link.length() - 1))) {
+                // No occurrence, or at the end
+                // Check if there are path separators in the suffix - if so, it is definitely
+                // not a proper suffix, so we should give up:
+                if (strippedLink.substring(strippedLinkIndex + 1).indexOf('/') >= 1) {
+                    return Optional.empty();
+                } else {
+                    return Optional.of(suffix); // return the first one we found, anyway.
+                }
+            } else {
+                // Check if there are path separators in the suffix - if so, it is definitely
+                // not a proper suffix, so we should give up:
+                if (link.substring(index + 1).indexOf('/') >= 1) {
+                    return Optional.empty();
+                } else {
+                    return Optional.of(link.substring(index + 1));
+                }
+            }
+        } else {
+            return Optional.ofNullable(suffix);
+        }
+    }
 }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 6f889dd0133..c553d2896fa 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -280,9 +280,6 @@ Donate\ to\ JabRef=Donate to JabRef
 Down=Down
 
 Download\ file=Download file
-
-Downloading...=Downloading...
-
 duplicate\ removal=duplicate removal
 
 Duplicate\ string\ name=Duplicate string name
@@ -300,7 +297,6 @@ Each\ line\ must\ be\ of\ the\ following\ form=Each line must be of the followin
 Edit=Edit
 
 Edit\ entry=Edit entry
-Save\ file=Save file
 Edit\ file\ type=Edit file type
 
 Edit\ group=Edit group
@@ -390,7 +386,6 @@ File\ directory\ is\ not\ set\ or\ does\ not\ exist\!=File directory is not set
 File\ exists=File exists
 
 File\ not\ found=File not found
-File\ type=File type
 filename=filename
 
 Files\ opened=Files opened
@@ -927,8 +922,6 @@ Sublibrary\ from\ AUX=Sublibrary from AUX
 Switches\ between\ full\ and\ abbreviated\ journal\ name\ if\ the\ journal\ name\ is\ known.=Switches between full and abbreviated journal name if the journal name is known.
 
 Tabname=Tabname
-Target\ file\ cannot\ be\ a\ directory.=Target file cannot be a directory.
-
 Tertiary\ sort\ criterion=Tertiary sort criterion
 
 Test=Test
@@ -1097,7 +1090,6 @@ Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ %1.=Line %0: Found corrupted BibTeX k
 Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ %1\ (contains\ whitespaces).=Line %0: Found corrupted BibTeX key %1 (contains whitespaces).
 Line\ %0\:\ Found\ corrupted\ BibTeX\ key\ %1\ (comma\ missing).=Line %0: Found corrupted BibTeX key %1 (comma missing).
 No\ full\ text\ document\ found=No full text document found
-Update\ to\ current\ column\ order=Update to current column order
 Download\ from\ URL=Download from URL
 Rename\ field=Rename field
 Append\ field=Append field
@@ -1451,8 +1443,6 @@ Could\ not\ connect\ to\ %0=Could not connect to %0
 Warning\:\ %0\ out\ of\ %1\ entries\ have\ undefined\ title.=Warning: %0 out of %1 entries have undefined title.
 Warning\:\ %0\ out\ of\ %1\ entries\ have\ undefined\ BibTeX\ key.=Warning: %0 out of %1 entries have undefined BibTeX key.
 Added\ new\ '%0'\ entry.=Added new '%0' entry.
-Multiple\ entries\ selected.\ Do\ you\ want\ to\ change\ the\ type\ of\ all\ these\ to\ '%0'?=Multiple entries selected. Do you want to change the type of all these to '%0'?
-Changed\ type\ to\ '%0'\ for=Changed type to '%0' for
 Really\ delete\ the\ selected\ entry?=Really delete the selected entry?
 Really\ delete\ the\ %0\ selected\ entries?=Really delete the %0 selected entries?
 Keep\ merged\ entry\ only=Keep merged entry only
diff --git a/src/test/java/org/jabref/cleanup/CleanupActionsListModelTest.java b/src/test/java/org/jabref/cleanup/CleanupActionsListModelTest.java
deleted file mode 100644
index b44b0c572aa..00000000000
--- a/src/test/java/org/jabref/cleanup/CleanupActionsListModelTest.java
+++ /dev/null
@@ -1,94 +0,0 @@
-package org.jabref.cleanup;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-
-import javax.swing.event.ListDataEvent;
-import javax.swing.event.ListDataListener;
-
-import org.jabref.gui.cleanup.CleanupActionsListModel;
-import org.jabref.logic.cleanup.Cleanups;
-import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
-import org.jabref.model.cleanup.FieldFormatterCleanup;
-import org.jabref.model.cleanup.FieldFormatterCleanups;
-
-import org.junit.jupiter.api.Test;
-import org.mockito.ArgumentCaptor;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.verify;
-import static org.mockito.Mockito.verifyZeroInteractions;
-import static org.mockito.Mockito.when;
-
-public class CleanupActionsListModelTest {
-
-    @Test
-    public void resetFiresItemsChanged() throws Exception {
-        CleanupActionsListModel model = new CleanupActionsListModel(Collections.emptyList());
-        ListDataListener listener = mock(ListDataListener.class);
-        model.addListDataListener(listener);
-        FieldFormatterCleanups defaultFormatters = mock(FieldFormatterCleanups.class);
-
-        model.reset(defaultFormatters);
-
-        ArgumentCaptor<ListDataEvent> argument = ArgumentCaptor.forClass(ListDataEvent.class);
-        verify(listener).contentsChanged(argument.capture());
-        assertEquals(ListDataEvent.CONTENTS_CHANGED, argument.getValue().getType());
-    }
-
-    @Test
-    public void resetSetsFormattersToPassedList() throws Exception {
-        CleanupActionsListModel model = new CleanupActionsListModel(Collections.emptyList());
-        FieldFormatterCleanups defaultFormatters = mock(FieldFormatterCleanups.class);
-        List<FieldFormatterCleanup> formatters = Arrays.asList(new FieldFormatterCleanup("test", new ClearFormatter()));
-        when(defaultFormatters.getConfiguredActions()).thenReturn(formatters);
-
-        model.reset(defaultFormatters);
-
-        assertEquals(formatters, model.getAllActions());
-    }
-
-    public List<FieldFormatterCleanup> getDefaultFieldFormatterCleanups() {
-        FieldFormatterCleanups formatters = Cleanups.DEFAULT_SAVE_ACTIONS;
-        //new ArrayList because configured actions is an unmodifiable collection
-        return new ArrayList<>(formatters.getConfiguredActions());
-    }
-
-    @Test
-    public void removedAtIndexOkay() {
-
-        CleanupActionsListModel model = new CleanupActionsListModel(getDefaultFieldFormatterCleanups());
-        ListDataListener listener = mock(ListDataListener.class);
-        model.addListDataListener(listener);
-        model.removeAtIndex(0);
-
-        ArgumentCaptor<ListDataEvent> argument = ArgumentCaptor.forClass(ListDataEvent.class);
-        verify(listener).intervalRemoved(argument.capture());
-        assertEquals(ListDataEvent.INTERVAL_REMOVED, argument.getValue().getType());
-    }
-
-    @Test
-    public void removedAtIndexMinus1DoesNothing() {
-
-        CleanupActionsListModel model = new CleanupActionsListModel(getDefaultFieldFormatterCleanups());
-        ListDataListener listener = mock(ListDataListener.class);
-        model.addListDataListener(listener);
-        model.removeAtIndex(-1);
-
-        verifyZeroInteractions(listener);
-    }
-
-    @Test
-    public void removedAtIndexgreaterListSizeDoesNothing() {
-
-        CleanupActionsListModel model = new CleanupActionsListModel(getDefaultFieldFormatterCleanups());
-        ListDataListener listener = mock(ListDataListener.class);
-        model.addListDataListener(listener);
-        model.removeAtIndex((getDefaultFieldFormatterCleanups().size() + 1));
-
-        verifyZeroInteractions(listener);
-    }
-}

From 2c327259a45e744c7ad9a46ae35af3145940a830 Mon Sep 17 00:00:00 2001
From: Johannes Manner <johannes.manner@web.de>
Date: Fri, 29 Mar 2019 13:21:28 +0100
Subject: [PATCH 21/61] =?UTF-8?q?Moved=20cleanup=20out=20of=20background?=
 =?UTF-8?q?=20thread=20to=20stick=20with=20the=20architecture=E2=80=A6=20(?=
 =?UTF-8?q?#4823)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Moved cleanup out of background thread to stick with the architecture tests

* remove unused imports

* Had to split the URLUtil since another logic class used URLUtil functionality

* fixed checkstyle

* Update DOAJFetcher.java

* checkstyle III
---
 .../org/jabref/gui/actions/CleanupAction.java |  6 ++--
 .../gui/fieldeditors/LinkedFileViewModel.java |  1 -
 .../net => gui/fieldeditors}/URLUtil.java     | 29 +-----------------
 .../gui/fieldeditors/UrlEditorViewModel.java  |  1 -
 .../logic/cleanup/RenamePdfCleanup.java       |  5 ++--
 .../logic/importer/fetcher/DOAJFetcher.java   | 28 +++++++++++++++--
 .../importer/fetcher/DOAJFetcherTest.java     | 29 ++++++++++++++++++
 .../org/jabref/logic/net/URLUtilTest.java     | 30 ++-----------------
 8 files changed, 62 insertions(+), 67 deletions(-)
 rename src/main/java/org/jabref/{logic/net => gui/fieldeditors}/URLUtil.java (85%)

diff --git a/src/main/java/org/jabref/gui/actions/CleanupAction.java b/src/main/java/org/jabref/gui/actions/CleanupAction.java
index 648af8313b7..f2251d45616 100644
--- a/src/main/java/org/jabref/gui/actions/CleanupAction.java
+++ b/src/main/java/org/jabref/gui/actions/CleanupAction.java
@@ -9,7 +9,6 @@
 import org.jabref.gui.cleanup.CleanupDialog;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.gui.util.BackgroundTask;
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.cleanup.CleanupWorker;
 import org.jabref.logic.l10n.Localization;
@@ -59,9 +58,8 @@ public void action() {
 
             preferences.setCleanupPreset(chosenPreset.get());
 
-            BackgroundTask.wrap(() -> cleanup(chosenPreset.get()))
-                          .onSuccess(result -> showResults())
-                          .executeWith(Globals.TASK_EXECUTOR);
+            this.cleanup(chosenPreset.get());
+            this.showResults();
         }
     }
 
diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
index c4f11bb73b3..d902b93a233 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
@@ -37,7 +37,6 @@
 import org.jabref.logic.externalfiles.LinkedFileHandler;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.URLDownload;
-import org.jabref.logic.net.URLUtil;
 import org.jabref.logic.xmp.XmpPreferences;
 import org.jabref.logic.xmp.XmpUtilWriter;
 import org.jabref.model.database.BibDatabaseContext;
diff --git a/src/main/java/org/jabref/logic/net/URLUtil.java b/src/main/java/org/jabref/gui/fieldeditors/URLUtil.java
similarity index 85%
rename from src/main/java/org/jabref/logic/net/URLUtil.java
rename to src/main/java/org/jabref/gui/fieldeditors/URLUtil.java
index e927d6933ff..5ab4a3b8e87 100644
--- a/src/main/java/org/jabref/logic/net/URLUtil.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/URLUtil.java
@@ -1,4 +1,4 @@
-package org.jabref.logic.net;
+package org.jabref.gui.fieldeditors;
 
 import java.io.UnsupportedEncodingException;
 import java.net.MalformedURLException;
@@ -9,9 +9,6 @@
 import java.util.Optional;
 
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.model.strings.StringUtil;
-
-import org.apache.http.client.utils.URIBuilder;
 
 public class URLUtil {
     private static final String URL_EXP = "^(https?|ftp)://.+";
@@ -80,30 +77,6 @@ public static boolean isURL(String url) {
         return url.contains("://");
     }
 
-    /**
-     * @implNote slightly altered version based on https://gist.github.com/enginer/230e2dc2f1d213a825d5
-     */
-    public static URIBuilder addPath(URIBuilder base, String subPath) {
-        if (StringUtil.isBlank(subPath) || "/".equals(subPath)) {
-            return base;
-        } else {
-            base.setPath(appendSegmentToPath(base.getPath(), subPath));
-            return base;
-        }
-    }
-
-    private static String appendSegmentToPath(String path, String segment) {
-        if (StringUtil.isBlank(path)) {
-            path = "/";
-        }
-
-        if (path.charAt(path.length() - 1) == '/' || segment.startsWith("/")) {
-            return path + segment;
-        }
-
-        return path + "/" + segment;
-    }
-
     /**
      * Look for the last '.' in the link, and return the following characters.
      * This gives the extension for most reasonably named links.
diff --git a/src/main/java/org/jabref/gui/fieldeditors/UrlEditorViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/UrlEditorViewModel.java
index f370a1a89ad..e6b785b488a 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/UrlEditorViewModel.java
+++ b/src/main/java/org/jabref/gui/fieldeditors/UrlEditorViewModel.java
@@ -10,7 +10,6 @@
 import org.jabref.gui.desktop.JabRefDesktop;
 import org.jabref.logic.integrity.FieldCheckers;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.net.URLUtil;
 import org.jabref.model.strings.StringUtil;
 
 import org.fxmisc.easybind.EasyBind;
diff --git a/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java b/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
index 72912ed73de..4016081e60b 100644
--- a/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
+++ b/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java
@@ -7,7 +7,6 @@
 import java.util.Objects;
 import java.util.Optional;
 
-import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.externalfiles.LinkedFileHandler;
 import org.jabref.model.FieldChange;
 import org.jabref.model.cleanup.CleanupJob;
@@ -55,8 +54,8 @@ public List<FieldChange> cleanup(BibEntry entry) {
         }
 
         if (changed) {
-            Optional<FieldChange> fileFieldChanged = DefaultTaskExecutor.runInJavaFXThread(() -> entry.setFiles(files));
-            return OptionalUtil.toList(fileFieldChanged);
+            Optional<FieldChange> changes = entry.setFiles(files);
+            return OptionalUtil.toList(changes);
         }
 
         return Collections.emptyList();
diff --git a/src/main/java/org/jabref/logic/importer/fetcher/DOAJFetcher.java b/src/main/java/org/jabref/logic/importer/fetcher/DOAJFetcher.java
index 67bc0dc97ac..40b617a2301 100644
--- a/src/main/java/org/jabref/logic/importer/fetcher/DOAJFetcher.java
+++ b/src/main/java/org/jabref/logic/importer/fetcher/DOAJFetcher.java
@@ -16,10 +16,10 @@
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.Parser;
 import org.jabref.logic.importer.SearchBasedParserFetcher;
-import org.jabref.logic.net.URLUtil;
 import org.jabref.logic.util.OS;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
+import org.jabref.model.strings.StringUtil;
 
 import org.apache.http.client.utils.URIBuilder;
 import org.json.JSONArray;
@@ -165,12 +165,36 @@ public Optional<HelpFile> getHelpPage() {
     @Override
     public URL getURLForQuery(String query) throws URISyntaxException, MalformedURLException, FetcherException {
         URIBuilder uriBuilder = new URIBuilder(SEARCH_URL);
-        URLUtil.addPath(uriBuilder, query);
+        DOAJFetcher.addPath(uriBuilder, query);
         uriBuilder.addParameter("pageSize", "30"); // Number of results
         //uriBuilder.addParameter("page", "1"); // Page (not needed so far)
         return uriBuilder.build().toURL();
     }
 
+    /**
+     * @implNote slightly altered version based on https://gist.github.com/enginer/230e2dc2f1d213a825d5
+     */
+    public static URIBuilder addPath(URIBuilder base, String subPath) {
+        if (StringUtil.isBlank(subPath) || "/".equals(subPath)) {
+            return base;
+        } else {
+            base.setPath(appendSegmentToPath(base.getPath(), subPath));
+            return base;
+        }
+    }
+
+    private static String appendSegmentToPath(String path, String segment) {
+        if (StringUtil.isBlank(path)) {
+            path = "/";
+        }
+
+        if (path.charAt(path.length() - 1) == '/' || segment.startsWith("/")) {
+            return path + segment;
+        }
+
+        return path + "/" + segment;
+    }
+
     @Override
     public Parser getParser() {
         return inputStream -> {
diff --git a/src/test/java/org/jabref/logic/importer/fetcher/DOAJFetcherTest.java b/src/test/java/org/jabref/logic/importer/fetcher/DOAJFetcherTest.java
index 77a0a20b925..f49b0e21d17 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/DOAJFetcherTest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/DOAJFetcherTest.java
@@ -9,6 +9,7 @@
 import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.testutils.category.FetcherTest;
 
+import org.apache.http.client.utils.URIBuilder;
 import org.json.JSONObject;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -73,4 +74,32 @@ void testBibJSONConverter() {
     public void searchByEmptyQuery() throws Exception {
         assertEquals(Collections.emptyList(), fetcher.performSearch(""));
     }
+
+    @Test
+    void appendSingleWord() throws Exception {
+        URIBuilder builder = new URIBuilder("http://example.com/test");
+        DOAJFetcher.addPath(builder, "/example");
+        assertEquals("http://example.com/test/example", builder.build().toASCIIString());
+    }
+
+    @Test
+    void appendSingleWordWithSlash() throws Exception {
+        URIBuilder builder = new URIBuilder("http://example.com/test");
+        DOAJFetcher.addPath(builder, "/example");
+        assertEquals("http://example.com/test/example", builder.build().toASCIIString());
+    }
+
+    @Test
+    void appendSlash() throws Exception {
+        URIBuilder builder = new URIBuilder("http://example.com/test");
+        DOAJFetcher.addPath(builder, "/");
+        assertEquals("http://example.com/test", builder.build().toASCIIString());
+    }
+
+    @Test
+    void appendTwoWords() throws Exception {
+        URIBuilder builder = new URIBuilder("http://example.com/test");
+        DOAJFetcher.addPath(builder, "example two");
+        assertEquals("http://example.com/test/example%20two", builder.build().toASCIIString());
+    }
 }
diff --git a/src/test/java/org/jabref/logic/net/URLUtilTest.java b/src/test/java/org/jabref/logic/net/URLUtilTest.java
index 01f181eb465..6a6cfc12972 100644
--- a/src/test/java/org/jabref/logic/net/URLUtilTest.java
+++ b/src/test/java/org/jabref/logic/net/URLUtilTest.java
@@ -1,6 +1,7 @@
 package org.jabref.logic.net;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.jabref.gui.fieldeditors.URLUtil;
+
 import org.junit.jupiter.api.Test;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -73,31 +74,4 @@ void isURLshouldRejectInvalidURL() {
         assertFalse(URLUtil.isURL("google.com"));
     }
 
-    @Test
-    void appendSingleWord() throws Exception {
-        URIBuilder builder = new URIBuilder("http://example.com/test");
-        URLUtil.addPath(builder, "/example");
-        assertEquals("http://example.com/test/example", builder.build().toASCIIString());
-    }
-
-    @Test
-    void appendSingleWordWithSlash() throws Exception {
-        URIBuilder builder = new URIBuilder("http://example.com/test");
-        URLUtil.addPath(builder, "/example");
-        assertEquals("http://example.com/test/example", builder.build().toASCIIString());
-    }
-
-    @Test
-    void appendSlash() throws Exception {
-        URIBuilder builder = new URIBuilder("http://example.com/test");
-        URLUtil.addPath(builder, "/");
-        assertEquals("http://example.com/test", builder.build().toASCIIString());
-    }
-
-    @Test
-    void appendTwoWords() throws Exception {
-        URIBuilder builder = new URIBuilder("http://example.com/test");
-        URLUtil.addPath(builder, "example two");
-        assertEquals("http://example.com/test/example%20two", builder.build().toASCIIString());
-    }
 }

From ee0f42c02bf69f03015d654c7f3cb5f1cc976a83 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Fri, 29 Mar 2019 15:04:38 +0100
Subject: [PATCH 22/61] Fix overwriting of date in RIS import (#4821)

* Fix overwriting of date in RIS import

Now the first valid year is taken into account
Adjusted the tests to reflect the new behvaiour

* add changelog
---
 CHANGELOG.md                                  |  1 +
 .../importer/fileformat/RisImporter.java      | 28 +++++++++++++----
 .../importer/fileformat/RisImporterTest3.bib  |  1 -
 .../importer/fileformat/RisImporterTest6.bib  |  1 -
 .../fileformat/RisImporterTest8_date.bib      | 15 ++++++++++
 .../fileformat/RisImporterTest8_date.ris      | 30 +++++++++++++++++++
 6 files changed, 68 insertions(+), 8 deletions(-)
 create mode 100644 src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.bib
 create mode 100644 src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.ris

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d5983623107..a64512c0723 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -101,6 +101,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
 - We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
+- We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 
 
 
diff --git a/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java
index d778dd3d357..3adfa827d19 100644
--- a/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java
+++ b/src/main/java/org/jabref/logic/importer/fileformat/RisImporter.java
@@ -2,6 +2,9 @@
 
 import java.io.BufferedReader;
 import java.io.IOException;
+import java.time.Year;
+import java.time.format.DateTimeFormatter;
+import java.time.format.DateTimeParseException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -23,6 +26,7 @@
 public class RisImporter extends Importer {
 
     private static final Pattern RECOGNIZED_FORMAT_PATTERN = Pattern.compile("TY  - .*");
+    private static DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy");
 
     @Override
     public String getName() {
@@ -53,10 +57,12 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
         String linesAsString = reader.lines().reduce((line, nextline) -> line + "\n" + nextline).orElse("");
 
         String[] entries = linesAsString.replace("\u2013", "-").replace("\u2014", "--").replace("\u2015", "--")
-                .split("ER  -.*\\n");
+                                        .split("ER  -.*\\n");
 
         for (String entry1 : entries) {
 
+            boolean foundDate = false;
+
             String type = "";
             String author = "";
             String editor = "";
@@ -74,7 +80,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                 while (!done && (j < (lines.length - 1))) {
                     if ((lines[j + 1].length() >= 6) && !"  - ".equals(lines[j + 1].substring(2, 6))) {
                         if ((current.length() > 0) && !Character.isWhitespace(current.charAt(current.length() - 1))
-                                && !Character.isWhitespace(lines[j + 1].charAt(0))) {
+                            && !Character.isWhitespace(lines[j + 1].charAt(0))) {
                             current.append(' ');
                         }
                         current.append(lines[j + 1]);
@@ -123,7 +129,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                         fields.put(FieldName.TITLE, fields.get(FieldName.TITLE).replaceAll("\\s+", " ")); // Normalize whitespaces
                     } else if ("BT".equals(tag)) {
                         fields.put(FieldName.BOOKTITLE, value);
-                    } else if (("T2".equals(tag) || "J2".equals(tag) || "JA".equals(tag)) && (fields.get(FieldName.JOURNAL) == null || "".equals(fields.get(FieldName.JOURNAL)))) {
+                    } else if (("T2".equals(tag) || "J2".equals(tag) || "JA".equals(tag)) && ((fields.get(FieldName.JOURNAL) == null) || "".equals(fields.get(FieldName.JOURNAL)))) {
                         //if there is no journal title, then put second title as journal title
                         fields.put(FieldName.JOURNAL, value);
                     } else if ("JO".equals(tag) || "J1".equals(tag) || "JF".equals(tag)) {
@@ -187,8 +193,18 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                         }
                     } else if ("UR".equals(tag) || "L2".equals(tag) || "LK".equals(tag)) {
                         fields.put(FieldName.URL, value);
-                    } else if (("Y1".equals(tag) || "Y2".equals(tag) || "PY".equals(tag) || "DA".equals(tag)) && (value.length() >= 4)) {
-                        fields.put(FieldName.YEAR, value.substring(0, 4));
+                    } else if (!foundDate && (("Y1".equals(tag) || "Y2".equals(tag) || "PY".equals(tag) || "DA".equals(tag)) && (value.length() >= 4))) {
+                        String year = value.substring(0, 4);
+
+                        try {
+                            Year.parse(year, formatter);
+                            //if the year is parsebale we have found our date
+                            fields.put(FieldName.YEAR, value.substring(0, 4));
+                            foundDate = true;
+                        } catch (DateTimeParseException ex) {
+                            //We can't parse the year, we ignore it
+                        }
+
                         String[] parts = value.split("/");
                         if ((parts.length > 1) && !parts[1].isEmpty()) {
                             try {
@@ -210,7 +226,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                             comment = comment + OS.NEWLINE;
                         }
                         comment = comment + value;
-                    }  else if ("M3".equals(tag) || "DO".equals(tag)) {
+                    } else if ("M3".equals(tag) || "DO".equals(tag)) {
                         addDoi(fields, value);
                     } else if ("C3".equals(tag)) {
                         fields.put(FieldName.EVENTTITLE, value);
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest3.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest3.bib
index 13eb9b9a606..9bd2b47b290 100644
--- a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest3.bib
+++ b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest3.bib
@@ -4,7 +4,6 @@ @incollection{
   doi = {10.1201/b19107-2},
   issn = {978-1-4822-5326-9},
   journal = {Dermoscopy Image Analysis},
-  month = {#nov#},
   number = {0},
   pages = {1-22},
   publisher = {CRC Press},
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib
index e94772ff175..12a03af5704 100644
--- a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib
+++ b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest6.bib
@@ -4,7 +4,6 @@ @article{
   database = {PMC},
   issn = {1537-744X},
   journal = {The Scientific World Journal},
-  month = {#mar#},
   number = {PMC3654245},
   pages = {219840},
   publisher = {Hindawi Publishing Corporation},
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.bib b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.bib
new file mode 100644
index 00000000000..8c200fa3c7a
--- /dev/null
+++ b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.bib
@@ -0,0 +1,15 @@
+@article{,
+  author = {Valle-Delgado, J. J. and Molina-Bolívar, J. A. and Galisteo-González, F. and Gálvez-Ruiz, M. J. and Feiler, A. and Rutland, M. W.},
+  comment = {doi: 10.1063/1.1954747},
+  doi = {10.1063/1.1954747},
+  issn = {0021-9606},
+  journal = {J. Chem. Phys.},
+  month = {#jul#},
+  number = {3},
+  pages = {034708},
+  publisher = {American Institute of Physics},
+  title = {Hydration forces between silica surfaces: Experimental data and predictions from different theories},
+  url = {https://doi.org/10.1063/1.1954747},
+  volume = {123},
+  year = {2005}
+}
\ No newline at end of file
diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.ris b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.ris
new file mode 100644
index 00000000000..2ba45d82897
--- /dev/null
+++ b/src/test/resources/org/jabref/logic/importer/fileformat/RisImporterTest8_date.ris
@@ -0,0 +1,30 @@
+
+
+
+
+
+TY  - JOUR
+T1  - Hydration forces between silica surfaces: Experimental data and predictions from different theories
+AU  - Valle-Delgado,J. J. 
+AU  - Molina-Bolívar,J. A. 
+AU  - Galisteo-González,F. 
+AU  - Gálvez-Ruiz,M. J. 
+AU  - Feiler,A. 
+AU  - Rutland,M. W. 
+Y1  - 2005/07/15
+PY  - 2005
+DA  - 2005/07/15
+N1  - doi: 10.1063/1.1954747
+DO  - 10.1063/1.1954747
+T2  - The Journal of Chemical Physics
+JF  - The Journal of Chemical Physics
+JO  - J. Chem. Phys.
+SP  - 034708
+VL  - 123
+IS  - 3
+PB  - American Institute of Physics
+SN  - 0021-9606
+M3  - doi: 10.1063/1.1954747
+UR  - https://doi.org/10.1063/1.1954747
+Y2  - 2019/03/28
+ER  - 

From 3f48bf094ae29e46a58d62608fd8ecb2cdf7a11f Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 29 Mar 2019 15:45:03 +0100
Subject: [PATCH 23/61] Update BibtexKeyEditor.fxml

---
 src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml b/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
index 32160f0c544..7feb0fe3335 100644
--- a/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
+++ b/src/main/java/org/jabref/gui/fieldeditors/BibtexKeyEditor.fxml
@@ -6,5 +6,5 @@
 <fx:root xmlns:fx="http://javafx.com/fxml/1" type="HBox" xmlns="http://javafx.com/javafx/8.0.112"
          fx:controller="org.jabref.gui.fieldeditors.BibtexKeyEditor">
     <EditorTextField fx:id="textField"/>
-    <Button fx:id="generateCiteKeyButton" text="Generate" styleClass="icon-button"/>
+    <Button fx:id="generateCiteKeyButton" text="%Generate" styleClass="icon-button"/>
 </fx:root>

From 60148642e4c727198414e12d9a2f4d1a57c753af Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 29 Mar 2019 22:00:26 +0100
Subject: [PATCH 24/61] Remove "plain text import" feature (#4717)

---
 src/main/java/org/jabref/gui/JabRefFrame.java |   2 -
 .../actions/NewEntryFromPlainTextAction.java  |  54 --
 .../plaintextimport/TagToMarkedTextStore.java |  81 --
 .../gui/plaintextimport/TextInputDialog.java  | 735 ------------------
 src/main/resources/l10n/JabRef_en.properties  |  32 -
 5 files changed, 904 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/actions/NewEntryFromPlainTextAction.java
 delete mode 100644 src/main/java/org/jabref/gui/plaintextimport/TagToMarkedTextStore.java
 delete mode 100644 src/main/java/org/jabref/gui/plaintextimport/TextInputDialog.java

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 838f5d459f0..06ab62cb461 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -71,7 +71,6 @@
 import org.jabref.gui.actions.ManageJournalsAction;
 import org.jabref.gui.actions.NewDatabaseAction;
 import org.jabref.gui.actions.NewEntryAction;
-import org.jabref.gui.actions.NewEntryFromPlainTextAction;
 import org.jabref.gui.actions.NewSubLibraryAction;
 import org.jabref.gui.actions.OldDatabaseCommandWrapper;
 import org.jabref.gui.actions.OpenBrowserAction;
@@ -795,7 +794,6 @@ private MenuBar createMenu() {
         //@formatter:off
         library.getItems().addAll(
                 factory.createMenuItem(StandardActions.NEW_ENTRY, new NewEntryAction(this, dialogService, Globals.prefs)),
-                factory.createMenuItem(StandardActions.NEW_ENTRY_FROM_PLAINTEX, new NewEntryFromPlainTextAction(this, Globals.prefs.getUpdateFieldPreferences(), dialogService, Globals.prefs)),
                 factory.createMenuItem(StandardActions.DELETE_ENTRY, new OldDatabaseCommandWrapper(Actions.DELETE, this, Globals.stateManager)),
 
                 new SeparatorMenuItem(),
diff --git a/src/main/java/org/jabref/gui/actions/NewEntryFromPlainTextAction.java b/src/main/java/org/jabref/gui/actions/NewEntryFromPlainTextAction.java
deleted file mode 100644
index b4c3faa9a2b..00000000000
--- a/src/main/java/org/jabref/gui/actions/NewEntryFromPlainTextAction.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package org.jabref.gui.actions;
-
-import org.jabref.gui.DialogService;
-import org.jabref.gui.EntryTypeView;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.plaintextimport.TextInputDialog;
-import org.jabref.logic.util.UpdateField;
-import org.jabref.logic.util.UpdateFieldPreferences;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.EntryType;
-import org.jabref.preferences.JabRefPreferences;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class NewEntryFromPlainTextAction extends SimpleCommand {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(NewEntryFromPlainTextAction.class);
-
-    private final UpdateFieldPreferences prefs;
-    private final JabRefFrame jabRefFrame;
-    private final DialogService dialogService;
-    private final JabRefPreferences preferences;
-
-    public NewEntryFromPlainTextAction(JabRefFrame jabRefFrame, UpdateFieldPreferences prefs, DialogService dialogService, JabRefPreferences preferences) {
-        this.jabRefFrame = jabRefFrame;
-        this.prefs = prefs;
-        this.dialogService = dialogService;
-        this.preferences = preferences;
-
-    }
-
-    @Override
-    public void execute() {
-        if (jabRefFrame.getBasePanelCount() <= 0) {
-            LOGGER.error("Action 'New entry' must be disabled when no database is open.");
-            return;
-        }
-
-        EntryTypeView typeChoiceDialog = new EntryTypeView(jabRefFrame.getCurrentBasePanel(), dialogService, preferences);
-        EntryType selectedType = typeChoiceDialog.showAndWait().orElse(null);
-        if (selectedType == null) {
-            return;
-        }
-        BibEntry bibEntry = new BibEntry(selectedType);
-
-        TextInputDialog tidialog = new TextInputDialog(jabRefFrame, bibEntry);
-        tidialog.setVisible(true);
-        if (tidialog.okPressed()) {
-            UpdateField.setAutomaticFields(bibEntry, false, false, prefs);
-            jabRefFrame.getCurrentBasePanel().insertEntry(bibEntry);
-        }
-    }
-}
diff --git a/src/main/java/org/jabref/gui/plaintextimport/TagToMarkedTextStore.java b/src/main/java/org/jabref/gui/plaintextimport/TagToMarkedTextStore.java
deleted file mode 100644
index 9b191abdd1e..00000000000
--- a/src/main/java/org/jabref/gui/plaintextimport/TagToMarkedTextStore.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package org.jabref.gui.plaintextimport;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.swing.text.StyledDocument;
-
-/**
- * Save the textposition for tags in a recent TextInputDialog context
- */
-public class TagToMarkedTextStore {
-
-    private final Map<String, List<TMarkedStoreItem>> tagMap;
-
-    public TagToMarkedTextStore() {
-        tagMap = new HashMap<>();
-    }
-
-    /** appends a selection property for tag */
-    public void appendPosition(String tag, int start, int end) {
-        List<TMarkedStoreItem> ll = tagMap.get(tag);
-        if (ll == null) {
-            ll = new ArrayList<>();
-            tagMap.put(tag, ll);
-        }
-
-        ll.add(new TMarkedStoreItem(start, end));
-    }
-
-    /** insert selection properties for tag, old entries were deleted */
-    public void insertPosition(String tag, int start, int end) {
-        List<TMarkedStoreItem> ll = tagMap.get(tag);
-
-        if (ll == null) {
-            ll = new ArrayList<>();
-            tagMap.put(tag, ll);
-        } else {
-            ll.clear();
-        }
-
-        ll.add(new TMarkedStoreItem(start, end));
-    }
-
-    /** set the Style for the tag if an entry is available */
-    public void setStyleForTag(String tag, String style, StyledDocument doc) {
-        List<TMarkedStoreItem> ll = tagMap.get(tag);
-
-        if (ll != null) {
-            // iterate over all saved selections
-            for (TMarkedStoreItem item : ll) {
-                if (item != null) {
-                    doc.setCharacterAttributes(item.getStart(), item.getLength(), doc.getStyle(style), true);
-                }
-            }
-        }
-    }
-
-    private static class TMarkedStoreItem {
-
-        private final int start;
-        private final int end;
-
-
-        public TMarkedStoreItem(int start, int end) {
-            this.start = start;
-            this.end = end;
-        }
-
-        public int getStart() {
-            return start;
-        }
-
-        public int getLength() {
-            return end - start;
-        }
-
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/plaintextimport/TextInputDialog.java b/src/main/java/org/jabref/gui/plaintextimport/TextInputDialog.java
deleted file mode 100644
index f2aee0e94fa..00000000000
--- a/src/main/java/org/jabref/gui/plaintextimport/TextInputDialog.java
+++ /dev/null
@@ -1,735 +0,0 @@
-package org.jabref.gui.plaintextimport;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.GridLayout;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringWriter;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-import java.util.Optional;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.ActionMap;
-import javax.swing.BorderFactory;
-import javax.swing.ButtonGroup;
-import javax.swing.DefaultListCellRenderer;
-import javax.swing.Icon;
-import javax.swing.InputMap;
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JLabel;
-import javax.swing.JList;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButton;
-import javax.swing.JScrollPane;
-import javax.swing.JTabbedPane;
-import javax.swing.JTextArea;
-import javax.swing.JTextPane;
-import javax.swing.JToolBar;
-import javax.swing.ListSelectionModel;
-import javax.swing.ScrollPaneConstants;
-import javax.swing.border.TitledBorder;
-import javax.swing.event.ListSelectionEvent;
-import javax.swing.event.ListSelectionListener;
-import javax.swing.text.BadLocationException;
-import javax.swing.text.EditorKit;
-import javax.swing.text.Style;
-import javax.swing.text.StyleConstants;
-import javax.swing.text.StyleContext;
-import javax.swing.text.StyledDocument;
-
-import org.jabref.Globals;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.JabRefDialog;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.OSXCompatibleToolbar;
-import org.jabref.gui.icon.IconTheme;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.gui.util.FileDialogConfiguration;
-import org.jabref.gui.util.component.OverlayPanel;
-import org.jabref.logic.bibtex.BibEntryWriter;
-import org.jabref.logic.bibtex.LatexFieldFormatter;
-import org.jabref.logic.importer.ParserResult;
-import org.jabref.logic.importer.fileformat.FreeCiteImporter;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.OS;
-import org.jabref.logic.util.StandardFileType;
-import org.jabref.logic.util.UpdateField;
-import org.jabref.model.EntryTypes;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.EntryType;
-import org.jabref.model.entry.FieldName;
-import org.jabref.model.entry.FieldProperty;
-import org.jabref.model.entry.InternalBibtexFields;
-import org.jabref.preferences.JabRefPreferences;
-
-import com.jgoodies.forms.builder.ButtonBarBuilder;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * import from plain text => simple mark/copy/paste into bibtex entry
- * <p>
- * TODO
- * - change colors and fonts
- * - delete selected text
- * - make textarea editable
- * - create several bibtex entries in dialog
- * - if the dialog works with an existing entry (right click menu item), the cancel option doesn't work well
- */
-public class TextInputDialog extends JabRefDialog {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(TextInputDialog.class);
-
-    private final JButton okButton = new JButton(Localization.lang("Accept"));
-    private final JButton cancelButton = new JButton(Localization.lang("Cancel"));
-    private final JButton insertButton = new JButton(Localization.lang("Insert"));
-    private final JButton parseWithFreeCiteButton = new JButton(Localization.lang("Parse with FreeCite"));
-    private final JPanel panel1 = new JPanel();
-    private final JPanel buttons = new JPanel();
-    private final JPanel rawPanel = new JPanel();
-    private final JPanel sourcePanel = new JPanel();
-    private JList<String> fieldList;
-    private final JRadioButton override = new JRadioButton(Localization.lang("Override"));
-    private final JRadioButton append = new JRadioButton(Localization.lang("Append"));
-    private final JToolBar toolBar = new OSXCompatibleToolbar();
-
-    private final List<String> allFields = new ArrayList<>();
-    private final List<String> requiredFields = new ArrayList<>();
-    private final List<String> optionalFields = new ArrayList<>();
-
-    private final BibEntry entry;
-
-    private final JPopupMenu inputMenu = new JPopupMenu();
-    private StyledDocument document; // content from inputPane
-    private final JTextPane textPane = new JTextPane();
-    private final JTextArea sourcePreview = new JTextArea();
-
-    private final TagToMarkedTextStore markedTextStore;
-
-    private final JabRefFrame frame;
-
-    private boolean okPressed;
-
-
-    public TextInputDialog(JabRefFrame frame, BibEntry bibEntry) {
-        super(true, TextInputDialog.class);
-
-        this.frame = Objects.requireNonNull(frame);
-
-        entry = Objects.requireNonNull(bibEntry);
-        markedTextStore = new TagToMarkedTextStore();
-
-        jbInit();
-        pack();
-        updateSourceView();
-    }
-
-    private void jbInit() {
-        getContentPane().setLayout(new BorderLayout());
-        StringBuilder typeStr = new StringBuilder("Plain text import");
-        if (entry.getType() != null) {
-            typeStr.append(' ').append(Localization.lang("for")).append(' ').append(entry.getType());
-        }
-
-        this.setTitle(typeStr.toString());
-        getContentPane().add(panel1, BorderLayout.CENTER);
-
-        initRawPanel();
-        initButtonPanel();
-        initSourcePanel();
-
-        JTabbedPane tabbed = new JTabbedPane();
-
-        tabbed.add(rawPanel, Localization.lang("Raw source"));
-        tabbed.add(sourcePanel, Localization.lang("%0 source", frame.getCurrentBasePanel().getBibDatabaseContext().getMode().getFormattedName()));
-
-        // Panel Layout
-        panel1.setLayout(new BorderLayout());
-        panel1.add(tabbed, BorderLayout.CENTER);
-        panel1.add(buttons, BorderLayout.SOUTH);
-
-        // Key bindings:
-        ActionMap am = buttons.getActionMap();
-        InputMap im = buttons.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        im.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        am.put("close", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                dispose();
-            }
-        });
-    }
-
-    // Panel with text import functionality
-    private void initRawPanel() {
-        rawPanel.setLayout(new BorderLayout());
-
-        // Textarea
-        textPane.setEditable(false);
-
-        document = textPane.getStyledDocument();
-        addStylesToDocument();
-
-        try {
-            document.insertString(0, "", document.getStyle("regular"));
-        } catch (BadLocationException ex) {
-            LOGGER.warn("Problem setting style", ex);
-
-        }
-
-        OverlayPanel testPanel = new OverlayPanel(textPane, Localization.lang("paste text here"));
-
-        testPanel.setPreferredSize(new Dimension(450, 255));
-        testPanel.setMaximumSize(new Dimension(450, Integer.MAX_VALUE));
-
-        // Setup fields (required to be done before setting up popup menu)
-        fieldList = new JList<>(getAllFields());
-        fieldList.setCellRenderer(new SimpleCellRenderer(fieldList.getFont()));
-        ListSelectionModel listSelectionModel = fieldList.getSelectionModel();
-        listSelectionModel.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-        listSelectionModel.addListSelectionListener(new FieldListSelectionHandler());
-        fieldList.addMouseListener(new FieldListMouseListener());
-
-        // After the call to getAllFields
-        initPopupMenuAndToolbar();
-
-        //Add listener to components that can bring up popup menus.
-        MouseListener popupListener = new PopupListener(inputMenu);
-        textPane.addMouseListener(popupListener);
-        testPanel.addMouseListener(popupListener);
-
-        JPanel leftPanel = new JPanel(new BorderLayout());
-
-        leftPanel.add(toolBar, BorderLayout.NORTH);
-        leftPanel.add(testPanel, BorderLayout.CENTER);
-
-        JPanel inputPanel = setUpFieldListPanel();
-
-        // parse with FreeCite button
-        parseWithFreeCiteButton.addActionListener(event -> {
-            if (parseWithFreeCiteAndAddEntries()) {
-                okPressed = false; // we do not want to have the super method to handle our entries, we do it on our own
-                dispose();
-            }
-        });
-
-        rawPanel.add(leftPanel, BorderLayout.CENTER);
-        rawPanel.add(inputPanel, BorderLayout.EAST);
-
-        JLabel desc = new JLabel("<html><h3>" + Localization.lang("Plain text import") + "</h3><p>"
-                + Localization.lang("This is a simple copy and paste dialog. First load or paste some text into "
-                + "the text input area.<br>After that, you can mark text and assign it to a BibTeX field.")
-                + "</p></html>");
-        desc.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-
-        rawPanel.add(desc, BorderLayout.SOUTH);
-    }
-
-    private JPanel setUpFieldListPanel() {
-        JPanel inputPanel = new JPanel();
-
-        // Panel Layout
-        GridBagLayout gbl = new GridBagLayout();
-        GridBagConstraints con = new GridBagConstraints();
-        con.weightx = 0;
-        con.insets = new Insets(5, 5, 0, 5);
-        con.fill = GridBagConstraints.HORIZONTAL;
-
-        inputPanel.setLayout(gbl);
-
-        // Border
-        TitledBorder titledBorder1 = new TitledBorder(BorderFactory.createLineBorder(new Color(153, 153, 153), 2),
-                Localization.lang("Work options"));
-        inputPanel.setBorder(titledBorder1);
-        inputPanel.setMinimumSize(new Dimension(10, 10));
-
-        JScrollPane fieldScroller = new JScrollPane(fieldList);
-        fieldScroller.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED);
-
-        // insert buttons
-        insertButton.addActionListener(event -> insertTextForTag(override.isSelected()));
-
-        // Radio buttons
-        append.setToolTipText(Localization.lang("Append the selected text to BibTeX field"));
-        append.setMnemonic(KeyEvent.VK_A);
-        append.setSelected(true);
-
-        override.setToolTipText(Localization.lang("Override the BibTeX field by the selected text"));
-        override.setMnemonic(KeyEvent.VK_O);
-        override.setSelected(false);
-
-        //Group the radio buttons.
-        ButtonGroup group = new ButtonGroup();
-        group.add(append);
-        group.add(override);
-
-        JPanel radioPanel = new JPanel(new GridLayout(0, 1));
-        radioPanel.add(append);
-        radioPanel.add(override);
-
-        // insert sub components
-        JLabel label1 = new JLabel(Localization.lang("Available BibTeX fields"));
-        con.gridwidth = GridBagConstraints.REMAINDER;
-        gbl.setConstraints(label1, con);
-        inputPanel.add(label1);
-
-        con.gridwidth = GridBagConstraints.REMAINDER;
-        con.gridheight = 8;
-        con.weighty = 1;
-        con.fill = GridBagConstraints.BOTH;
-        gbl.setConstraints(fieldScroller, con);
-        inputPanel.add(fieldScroller);
-
-        con.fill = GridBagConstraints.HORIZONTAL;
-        con.weighty = 0;
-        con.gridwidth = 2;
-        gbl.setConstraints(radioPanel, con);
-        inputPanel.add(radioPanel);
-
-        con.gridwidth = GridBagConstraints.REMAINDER;
-        gbl.setConstraints(insertButton, con);
-        inputPanel.add(insertButton);
-        return inputPanel;
-    }
-
-    private void initPopupMenuAndToolbar() {
-        // copy/paste Menu
-        PasteAction pasteAction = new PasteAction();
-        ClearAction clearAction = new ClearAction();
-        JMenuItem pasteMI = new JMenuItem(pasteAction);
-
-        inputMenu.add(clearAction);
-        inputMenu.addSeparator();
-        inputMenu.add(pasteMI);
-        inputMenu.addSeparator();
-
-        // Right-click append/override
-        JMenu appendMenu = new JMenu(Localization.lang("Append"));
-        appendMenu.setToolTipText(Localization.lang("Append the selected text to BibTeX field"));
-        JMenu overrideMenu = new JMenu(Localization.lang("Override"));
-        overrideMenu.setToolTipText(Localization.lang("Override the BibTeX field by the selected text"));
-        for (String field : allFields) {
-            appendMenu.add(new JMenuItem(new MenuTextForTagAction(field, false)));
-            overrideMenu.add(new JMenuItem(new MenuTextForTagAction(field, true)));
-        }
-
-        inputMenu.add(appendMenu);
-        inputMenu.add(overrideMenu);
-
-        // Toolbar
-
-        toolBar.add(clearAction);
-        toolBar.setBorderPainted(false);
-        toolBar.addSeparator();
-        toolBar.add(pasteAction);
-        toolBar.add(new LoadAction());
-    }
-
-    private void initButtonPanel() {
-        okButton.addActionListener(event -> {
-            okPressed = true;
-            dispose();
-        });
-        cancelButton.addActionListener(event -> dispose());
-
-        ButtonBarBuilder bb = new ButtonBarBuilder(buttons);
-        buttons.setBorder(BorderFactory.createEmptyBorder(2, 2, 2, 2));
-        bb.addGlue();
-        bb.addButton(okButton);
-        bb.addButton(parseWithFreeCiteButton);
-        bb.addButton(cancelButton);
-        bb.addGlue();
-    }
-
-    // Panel with BibTeX source code
-    private void initSourcePanel() {
-        sourcePreview.setEditable(false);
-        sourcePreview.setFont(new Font("Monospaced", Font.PLAIN, Globals.prefs.getInt(JabRefPreferences.FONT_SIZE)));
-        JScrollPane paneScrollPane = new JScrollPane(sourcePreview);
-        paneScrollPane.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
-        paneScrollPane.setPreferredSize(new Dimension(500, 255));
-        paneScrollPane.setMinimumSize(new Dimension(10, 10));
-
-        sourcePanel.setLayout(new BorderLayout());
-        sourcePanel.add(paneScrollPane, BorderLayout.CENTER);
-    }
-
-    private void addStylesToDocument() {
-        //Initialize some styles.
-        Style defaultStyle = StyleContext.getDefaultStyleContext().getStyle(StyleContext.DEFAULT_STYLE);
-
-        Style regularStyle = document.addStyle("regular", defaultStyle);
-        StyleConstants.setFontFamily(defaultStyle, "SansSerif");
-        StyleConstants.setFontSize(defaultStyle, Globals.prefs.getInt(JabRefPreferences.FONT_SIZE));
-
-        Style s = document.addStyle("used", regularStyle);
-        StyleConstants.setBold(s, true);
-        StyleConstants.setForeground(s, Color.blue);
-
-        s = document.addStyle("marked", regularStyle);
-        StyleConstants.setBold(s, true);
-        StyleConstants.setForeground(s, Color.red);
-    }
-
-    private void insertTextForTag(boolean overrideField) {
-        String fieldName = fieldList.getSelectedValue();
-        if (fieldName != null) {
-            String txt = textPane.getSelectedText();
-
-            if (txt != null) {
-                int selectionStart = textPane.getSelectionStart();
-                int selectionEnd = textPane.getSelectionEnd();
-
-                // unselect text
-                textPane.setSelectionEnd(selectionStart);
-
-                // mark the selected text as "used"
-                document.setCharacterAttributes(selectionStart, selectionEnd - selectionStart,
-                        document.getStyle("marked"), true);
-
-                // override an existing entry
-                if (overrideField) {
-                    entry.setField(fieldName, txt);
-                    // erase old text selection
-                    markedTextStore.setStyleForTag(fieldName, "regular", document); // delete all previous styles
-                    markedTextStore.insertPosition(fieldName, selectionStart, selectionEnd); // insert new selection style
-                } else {
-                    // memorize the selection for text highlighting
-                    markedTextStore.appendPosition(fieldName, selectionStart, selectionEnd);
-
-                    // get old text from BibTeX tag
-                    Optional<String> old = entry.getField(fieldName);
-
-                    // merge old and selected text
-                    if (old.isPresent()) {
-                        // insert a new name with an additional "and"
-                        if (InternalBibtexFields.getFieldProperties(fieldName).contains(FieldProperty.PERSON_NAMES)) {
-                            entry.setField(fieldName, old.get() + " and " + txt);
-                        } else if (FieldName.KEYWORDS.equals(fieldName)) {
-                            // Add keyword
-                            entry.addKeyword(txt, Globals.prefs.getKeywordDelimiter());
-                        } else {
-                            entry.setField(fieldName, old.get() + txt);
-                        }
-                    } else {
-                        // "null"+"txt" Strings forbidden
-                        entry.setField(fieldName, txt);
-                    }
-                }
-                // make the new data in BibTeX source code visible
-                updateSourceView();
-            }
-        }
-    }
-
-    public boolean okPressed() {
-        return okPressed;
-    }
-
-    /**
-     * tries to parse the pasted reference with freecite
-     *
-     * @return true if successful, false otherwise
-     */
-    private boolean parseWithFreeCiteAndAddEntries() {
-        FreeCiteImporter fimp = new FreeCiteImporter(Globals.prefs.getImportFormatPreferences());
-        String text = textPane.getText();
-
-        // we have to remove line breaks (but keep empty lines)
-        // otherwise, the result is broken
-        text = text.replace(OS.NEWLINE.concat(OS.NEWLINE), "##NEWLINE##");
-        // possible URL line breaks are removed completely.
-        text = text.replace("/".concat(OS.NEWLINE), "/");
-        text = text.replace(OS.NEWLINE, " ");
-        text = text.replace("##NEWLINE##", OS.NEWLINE);
-
-        ParserResult importerResult = fimp.importEntries(text);
-        if (importerResult.hasWarnings()) {
-            frame.showMessage(importerResult.getErrorMessage());
-        }
-        List<BibEntry> importedEntries = importerResult.getDatabase().getEntries();
-        if (importedEntries.isEmpty()) {
-            return false;
-        } else {
-            UpdateField.setAutomaticFields(importedEntries, false, false, Globals.prefs.getUpdateFieldPreferences());
-
-            importedEntries.forEach(entry -> frame.getCurrentBasePanel().insertEntry(entry));
-            return true;
-        }
-    }
-
-    // update the bibtex source view and available List
-    private void updateSourceView() {
-        StringWriter sw = new StringWriter(200);
-        try {
-            new BibEntryWriter(new LatexFieldFormatter(Globals.prefs.getLatexFieldFormatterPreferences()),
-                    false).write(entry, sw, frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
-            sourcePreview.setText(sw.getBuffer().toString());
-        } catch (IOException ex) {
-            LOGGER.error("Error in entry" + ": " + ex.getMessage(), ex);
-        }
-
-        fieldList.clearSelection();
-    }
-
-    private String[] getAllFields() {
-        Optional<EntryType> type = EntryTypes.getType(entry.getType(),
-                frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
-        if (type.isPresent()) {
-            allFields.addAll(type.get().getAllFields());
-            requiredFields.addAll(type.get().getRequiredFieldsFlat());
-            optionalFields.addAll(type.get().getPrimaryOptionalFields());
-        }
-        for (String field : InternalBibtexFields.getAllPublicFieldNames()) {
-            if (!allFields.contains(field)) {
-                allFields.add(field);
-            }
-        }
-        return allFields.toArray(new String[allFields.size()]);
-    }
-
-    private class PasteAction extends BasicAction {
-
-        public PasteAction() {
-            super(Localization.lang("Paste"), Localization.lang("Paste from clipboard"),
-                    IconTheme.JabRefIcons.PASTE.getIcon());
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            String data = Globals.clipboardManager.getContents();
-            int selStart = textPane.getSelectionStart();
-            int selEnd = textPane.getSelectionEnd();
-            if ((selEnd - selStart) > 0) {
-                textPane.replaceSelection("");
-            }
-            int cPos = textPane.getCaretPosition();
-            try {
-                document.insertString(cPos, data, document.getStyle("regular"));
-            } catch (BadLocationException ex) {
-                LOGGER.warn("Could not paste text", ex);
-            }
-        }
-    }
-
-    private class LoadAction extends BasicAction {
-
-        public LoadAction() {
-            super(Localization.lang("Open"), Localization.lang("Open file"), IconTheme.JabRefIcons.OPEN.getIcon());
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            try {
-                FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                        .addExtensionFilter(Localization.lang("Plain text"), StandardFileType.TXT)
-                        .withDefaultExtension(Localization.lang("Plain text"), StandardFileType.TXT)
-                        .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)).build();
-                DialogService ds = frame.getDialogService();
-
-                Optional<Path> path = DefaultTaskExecutor
-                        .runInJavaFXThread(() -> ds.showFileOpenDialog(fileDialogConfiguration));
-
-                if (path.isPresent()) {
-                    Path file = path.get();
-                    document.remove(0, document.getLength());
-                    EditorKit eKit = textPane.getEditorKit();
-                    if (eKit != null) {
-                        try (InputStream fis = Files.newInputStream(file)) {
-                            eKit.read(fis, document, 0);
-                            document.setLogicalStyle(0, document.getStyle("regular"));
-                        }
-                    }
-                }
-            } catch (BadLocationException | IOException ex) {
-                LOGGER.warn("Problem reading or inserting file", ex);
-            }
-        }
-    }
-
-    private class ClearAction extends BasicAction {
-
-        public ClearAction() {
-            super(Localization.lang("Clear"), Localization.lang("Clear inputarea"), IconTheme.JabRefIcons.NEW.getIcon());
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            textPane.setText("");
-        }
-    }
-
-    class FieldListSelectionHandler implements ListSelectionListener {
-
-        private int lastIndex = -1;
-
-        @Override
-        public void valueChanged(ListSelectionEvent e) {
-            ListSelectionModel lsm = (ListSelectionModel) e.getSource();
-
-            int index = lsm.getAnchorSelectionIndex();
-            if (index != lastIndex) {
-                boolean isAdjusting = e.getValueIsAdjusting();
-
-                if (!isAdjusting) {
-                    if (lastIndex > -1) {
-                        String tag1 = fieldList.getModel().getElementAt(lastIndex);
-                        markedTextStore.setStyleForTag(tag1, "used", document);
-                    }
-
-                    String tag2 = fieldList.getModel().getElementAt(index);
-                    markedTextStore.setStyleForTag(tag2, "marked", document);
-
-                    lastIndex = index;
-                }
-            }
-        }
-    }
-
-    // simple JList Renderer
-    // based on : Advanced JList Programming at developers.sun.com
-    private class SimpleCellRenderer extends DefaultListCellRenderer {
-
-        private final Font baseFont;
-        private final Font usedFont;
-        private final Icon okIcon = IconTheme.JabRefIcons.PLAIN_TEXT_IMPORT_DONE.getSmallIcon();
-        private final Icon needIcon = IconTheme.JabRefIcons.PLAIN_TEXT_IMPORT_TODO.getSmallIcon();
-        private final Color requiredColor = new Color(230, 235, 255);
-        private final Color optionalColor = new Color(230, 255, 230);
-
-
-        public SimpleCellRenderer(Font normFont) {
-            baseFont = normFont;
-            usedFont = baseFont.deriveFont(Font.ITALIC);
-        }
-
-        /* This is the only method defined by ListCellRenderer.  We just
-         * reconfigure the Jlabel each time we're called.
-         */
-        @Override
-        public Component getListCellRendererComponent(JList<?> list, Object value, // value to display
-                                                      int index, // cell index
-                                                      boolean iss, // is the cell selected
-                                                      boolean chf) // the list and the cell have the focus
-        {
-            /* The DefaultListCellRenderer class will take care of
-             * the JLabels text property, it's foreground and background
-             * colors, and so on.
-             */
-            super.getListCellRendererComponent(list, value, index, iss, chf);
-
-            /* We additionally set the JLabels icon property here.
-             */
-            String s = value.toString();
-            if (entry.hasField(s)) {
-                this.setForeground(Color.gray);
-                this.setFont(usedFont);
-                this.setIcon(okIcon);
-                this.setToolTipText(Localization.lang("Filled"));
-            } else {
-                this.setIcon(needIcon);
-                this.setToolTipText(Localization.lang("Field is missing"));
-            }
-            if (requiredFields.contains(s)) {
-                this.setBackground(requiredColor);
-            } else if (optionalFields.contains(s)) {
-                this.setBackground(optionalColor);
-            }
-            return this;
-        }
-    }
-
-    private class FieldListMouseListener extends MouseAdapter {
-
-        @Override
-        public void mouseClicked(MouseEvent e) {
-            if (e.getClickCount() == 2) {
-                insertTextForTag(override.isSelected());
-            }
-        }
-    }
-
-    private class MenuTextForTagAction extends AbstractAction {
-
-        private final String field;
-        private final Boolean overrideField;
-
-
-        public MenuTextForTagAction(String field, Boolean overrideField) {
-            super(field);
-            this.field = field;
-            this.overrideField = overrideField;
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            // To enable correct marking of used values
-            fieldList.setSelectedValue(field, false);
-            insertTextForTag(overrideField);
-        }
-    }
-}
-
-class PopupListener extends MouseAdapter {
-
-    private final JPopupMenu popMenu;
-
-
-    public PopupListener(JPopupMenu menu) {
-        popMenu = menu;
-    }
-
-    @Override
-    public void mousePressed(MouseEvent e) {
-        maybeShowPopup(e);
-    }
-
-    @Override
-    public void mouseReleased(MouseEvent e) {
-        maybeShowPopup(e);
-    }
-
-    private void maybeShowPopup(MouseEvent e) {
-        if (e.isPopupTrigger()) {
-            popMenu.show(e.getComponent(), e.getX(), e.getY());
-        }
-    }
-}
-
-abstract class BasicAction extends AbstractAction {
-
-    public BasicAction(String text, String description, Icon icon) {
-        super(text, icon);
-        putValue(Action.SHORT_DESCRIPTION, description);
-    }
-
-    public BasicAction(String text) {
-        super(text);
-    }
-
-    @Override
-    public abstract void actionPerformed(ActionEvent e);
-}
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index c553d2896fa..3a6655432a7 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -61,12 +61,10 @@ any\ field\ that\ matches\ the\ regular\ expression\ <b>%0</b>=any field that ma
 
 Appearance=Appearance
 
-Append=Append
 Append\ contents\ from\ a\ BibTeX\ library\ into\ the\ currently\ viewed\ library=Append contents from a BibTeX library into the currently viewed library
 
 Append\ library=Append library
 
-Append\ the\ selected\ text\ to\ BibTeX\ field=Append the selected text to BibTeX field
 Application=Application
 
 Apply=Apply
@@ -93,8 +91,6 @@ AUX\ file\ import=AUX file import
 
 Available\ export\ formats=Available export formats
 
-Available\ BibTeX\ fields=Available BibTeX fields
-
 Available\ import\ formats=Available import formats
 
 Backup\ old\ file\ when\ saving=Backup old file when saving
@@ -401,9 +397,6 @@ First\ select\ the\ entries\ you\ want\ keys\ to\ be\ generated\ for.=First sele
 Fit\ table\ horizontally\ on\ screen=Fit table horizontally on screen
 
 Float=Float
-
-for=for
-
 Format\:\ Tab\:field;field;...\ (e.g.\ General\:url;pdf;note...)=Format\: Tab\:field;field;... (e.g. General\:url;pdf;note...)
 
 Format\ of\ author\ and\ editor\ names=Format of author and editor names
@@ -501,13 +494,7 @@ Importing\ in\ unknown\ format=Importing in unknown format
 Include\ subgroups\:\ When\ selected,\ view\ entries\ contained\ in\ this\ group\ or\ its\ subgroups=Include subgroups: When selected, view entries contained in this group or its subgroups
 
 Independent\ group\:\ When\ selected,\ view\ only\ this\ group's\ entries=Independent group: When selected, view only this group's entries
-
-Work\ options=Work options
-
 I\ Agree=I Agree
-
-Insert=Insert
-
 Insert\ rows=Insert rows
 
 Intersection=Intersection
@@ -663,13 +650,7 @@ or=or
 
 Output\ or\ export\ file=Output or export file
 
-Override=Override
-
 Override\ default\ file\ directories=Override default file directories
-
-Override\ the\ BibTeX\ field\ by\ the\ selected\ text=Override the BibTeX field by the selected text
-
-
 Overwrite=Overwrite
 
 Overwrite\ keys=Overwrite keys
@@ -682,7 +663,6 @@ Paste=Paste
 paste\ entries=paste entries
 
 paste\ entry=paste entry
-Paste\ from\ clipboard=Paste from clipboard
 
 Pasted=Pasted
 
@@ -694,8 +674,6 @@ PDF\ does\ not\ exist=PDF does not exist
 
 File\ has\ no\ attached\ annotations=File has no attached annotations
 
-Plain\ text\ import=Plain text import
-
 Please\ enter\ a\ name\ for\ the\ group.=Please enter a name for the group.
 
 Please\ enter\ a\ search\ term.\ For\ example,\ to\ search\ all\ fields\ for\ <b>Smith</b>,\ enter\:<p><tt>smith</tt><p>To\ search\ the\ field\ <b>Author</b>\ for\ <b>Smith</b>\ and\ the\ field\ <b>Title</b>\ for\ <b>electrical</b>,\ enter\:<p><tt>author\=smith\ and\ title\=electrical</tt>=Please enter a search term. For example, to search all fields for <b>Smith</b>, enter:<p><tt>smith</tt><p>To search the field <b>Author</b> for <b>Smith</b> and the field <b>Title</b> for <b>electrical</b>, enter:<p><tt>author=smith and title=electrical</tt>
@@ -735,8 +713,6 @@ Pushed\ citations\ to\ %0=Pushed citations to %0
 
 Quit\ JabRef=Quit JabRef
 
-Raw\ source=Raw source
-
 Redo=Redo
 
 Refine\ supergroup\:\ When\ selected,\ view\ entries\ contained\ in\ both\ this\ group\ and\ its\ supergroup=Refine supergroup: When selected, view entries contained in both this group and its supergroup
@@ -925,9 +901,6 @@ Tabname=Tabname
 Tertiary\ sort\ criterion=Tertiary sort criterion
 
 Test=Test
-
-paste\ text\ here=paste text here
-
 The\ chosen\ date\ format\ for\ new\ entries\ is\ not\ valid=The chosen date format for new entries is not valid
 
 The\ chosen\ encoding\ '%0'\ could\ not\ encode\ the\ following\ characters\:=The chosen encoding '%0' could not encode the following characters:
@@ -1112,7 +1085,6 @@ Export\ entries\ in\ their\ original\ order=Export entries in their original ord
 Error\ opening\ file\ '%0'.=Error opening file '%0'.
 
 Formatter\ not\ found\:\ %0=Formatter not found: %0
-Clear\ inputarea=Clear inputarea
 
 Could\ not\ save,\ file\ locked\ by\ another\ JabRef\ instance.=Could not save, file locked by another JabRef instance.
 Current\ tmp\ value=Current tmp value
@@ -1226,7 +1198,6 @@ Use\ the\ BIB\ file\ location\ as\ primary\ file\ directory=Use the BIB file loc
 Could\ not\ run\ the\ gnuclient/emacsclient\ program.\ Make\ sure\ you\ have\ the\ emacsclient/gnuclient\ program\ installed\ and\ available\ in\ the\ PATH.=Could not run the gnuclient/emacsclient program. Make sure you have the emacsclient/gnuclient program installed and available in the PATH.
 You\ must\ select\ either\ a\ valid\ style\ file,\ or\ use\ one\ of\ the\ default\ styles.=You must select either a valid style file, or use one of the default styles.
 
-This\ is\ a\ simple\ copy\ and\ paste\ dialog.\ First\ load\ or\ paste\ some\ text\ into\ the\ text\ input\ area.<br>After\ that,\ you\ can\ mark\ text\ and\ assign\ it\ to\ a\ BibTeX\ field.=This is a simple copy and paste dialog. First load or paste some text into the text input area.<br>After that, you can mark text and assign it to a BibTeX field.
 This\ feature\ generates\ a\ new\ library\ based\ on\ which\ entries\ are\ needed\ in\ an\ existing\ LaTeX\ document.=This feature generates a new library based on which entries are needed in an existing LaTeX document.
 
 First\ select\ entries\ to\ clean\ up.=First select entries to clean up.
@@ -1278,7 +1249,6 @@ Select\ directory=Select directory
 Select\ files=Select files
 BibTeX\ entry\ creation=BibTeX entry creation
 Unable\ to\ connect\ to\ FreeCite\ online\ service.=Unable to connect to FreeCite online service.
-Parse\ with\ FreeCite=Parse with FreeCite
 BibTeX\ key\ patterns=BibTeX key patterns
 Changed\ special\ field\ settings=Changed special field settings
 Clear\ priority=Clear priority
@@ -1466,8 +1436,6 @@ unexpected\ opening\ curly\ bracket=unexpected opening curly bracket
 capital\ letters\ are\ not\ masked\ using\ curly\ brackets\ {}=capital letters are not masked using curly brackets {}
 should\ contain\ a\ four\ digit\ number=should contain a four digit number
 should\ contain\ a\ valid\ page\ number\ range=should contain a valid page number range
-Filled=Filled
-Field\ is\ missing=Field is missing
 Search\ %0=Search %0
 
 Search\ results\ in\ all\ libraries\ for\ %0=Search results in all libraries for %0

From 91d779ad9385f1132a929c9bab6ce73b49ea4f98 Mon Sep 17 00:00:00 2001
From: Samiya Caur <36728314+samiyac@users.noreply.github.com>
Date: Sat, 30 Mar 2019 02:43:04 +0530
Subject: [PATCH 25/61] Relativizes paths to aux files (#4792)

* Relativizes paths to aux files

* relativize code shifted to FileHelper

* changes

* Shortens text fields in Required Fields Tab

* Removing irrelevant changes

* Implemented requested changes

* Implemented changes

* Delete irrelevant code
---
 .../org/jabref/gui/groups/GroupDialog.java    | 24 +++++++++-
 .../LibraryPropertiesDialog.fxml              | 10 ++--
 .../LibraryPropertiesDialogView.java          | 17 ++++++-
 .../LibraryPropertiesDialogViewModel.java     | 19 ++++++++
 .../logic/exporter/MetaDataSerializer.java    |  2 +
 .../logic/importer/util/GroupsParser.java     | 13 +++---
 .../logic/importer/util/MetaDataParser.java   | 10 +++-
 .../model/database/BibDatabaseContext.java    |  2 +-
 .../org/jabref/model/groups/TexGroup.java     | 46 ++++++++++++++++---
 .../org/jabref/model/metadata/MetaData.java   | 25 +++++++++-
 .../org/jabref/model/util/FileHelper.java     | 13 ++++++
 src/main/resources/l10n/JabRef_en.properties  |  1 +
 .../exporter/BibtexDatabaseWriterTest.java    |  3 +-
 .../logic/exporter/GroupSerializerTest.java   |  3 +-
 .../importer/fileformat/BibtexParserTest.java |  4 +-
 .../logic/importer/util/GroupsParserTest.java | 25 +++++-----
 .../org/jabref/model/groups/TexGroupTest.java | 24 +++++++++-
 17 files changed, 202 insertions(+), 39 deletions(-)

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
index 94c9f519fa7..2285db635ac 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDialog.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -1,8 +1,10 @@
 package org.jabref.gui.groups;
 
 import java.io.IOException;
+import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Optional;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
@@ -45,6 +47,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.search.SearchQuery;
 import org.jabref.logic.util.StandardFileType;
+import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.Keyword;
@@ -58,6 +61,7 @@
 import org.jabref.model.groups.SearchGroup;
 import org.jabref.model.groups.TexGroup;
 import org.jabref.model.groups.WordKeywordGroup;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.preferences.JabRefPreferences;
 
@@ -90,6 +94,7 @@ class GroupDialog extends BaseDialog<AbstractGroup> {
     private final RadioButton unionButton = new RadioButton(Localization.lang("Include subgroups: When selected, view entries contained in this group or its subgroups"));
     private final DialogService dialogService;
     private final JabRefPreferences prefs;
+    private final BasePanel basePanel;
 
     // for KeywordGroup
     private final TextField keywordGroupSearchTerm = new TextField();
@@ -144,6 +149,7 @@ public GroupDialog(DialogService dialogService, BasePanel basePanel, JabRefPrefe
 
         this.dialogService = dialogService;
         this.prefs = prefs;
+        this.basePanel = basePanel;
 
         // set default values (overwritten if editedGroup != null)
         keywordGroupSearchField.setText(prefs.get(JabRefPreferences.GROUPS_DEFAULT_FIELD));
@@ -330,7 +336,7 @@ groupName, getContext(),
                         }
                     } else if (texRadioButton.isSelected()) {
                         resultingGroup = new TexGroup(groupName, getContext(),
-                                Paths.get(texGroupFilePath.getText().trim()), new DefaultAuxParser(new BibDatabase()), Globals.getFileUpdateMonitor());
+                                                      Paths.get(texGroupFilePath.getText().trim()), new DefaultAuxParser(new BibDatabase()), Globals.getFileUpdateMonitor(), basePanel.getBibDatabaseContext().getMetaData());
                     }
 
                     resultingGroup.setColor(colorField.getValue());
@@ -610,7 +616,21 @@ private void openBrowseDialog() {
             .addExtensionFilter(StandardFileType.AUX)
             .withDefaultExtension(StandardFileType.AUX)
             .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)).build();
-        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> texGroupFilePath.setText(file.toAbsolutePath().toString()));
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> texGroupFilePath.setText(relativize(file.toAbsolutePath()).toString()));
+    }
+
+    private Path relativize(Path path) {
+        List<Path> fileDirectories = getFileDirectoriesAsPaths();
+        return FileUtil.relativize(path, fileDirectories);
+    }
+
+    private List<Path> getFileDirectoriesAsPaths() {
+        List<Path> fileDirs = new ArrayList<>();
+        MetaData metaData = basePanel.getBibDatabaseContext().getMetaData();
+        metaData.getLaTexFileDirectory(prefs.getFilePreferences().getUser())
+                .ifPresent(laTexFileDirectory -> fileDirs.add(laTexFileDirectory));
+
+        return fileDirs;
     }
 
     private String fromTextFlowToHTMLString(TextFlow textFlow) {
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
index 126d9e959b6..2cb00861431 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml
@@ -26,6 +26,7 @@
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
                         <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="SOMETIMES" />
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="ALWAYS" />
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="ALWAYS" />
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
                         <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="ALWAYS" />
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
@@ -40,10 +41,13 @@
                         <Label text="%User-specific file directory" GridPane.rowIndex="3" />
                         <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
                         <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
+                        <Label text="%LaTex file directory" GridPane.rowIndex="4" />
+                        <TextField fx:id="laTexFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="4" />
+                        <Button fx:id="browseLatexFileDir" mnemonicParsing="false" onAction="#browseLaTexFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="4" />
                         <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Override default file directories" GridPane.columnSpan="3" GridPane.rowIndex="1" />
-                        <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Library protection" GridPane.columnSpan="3" GridPane.rowIndex="4" />
-                        <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." GridPane.columnSpan="3" GridPane.rowIndex="5" />
-                        <Label styleClass="sectionHeader" text="%Export sort order" GridPane.rowIndex="6" />
+                        <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Library protection" GridPane.columnSpan="3" GridPane.rowIndex="5" />
+                        <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." GridPane.columnSpan="3" GridPane.rowIndex="6" />
+                        <Label styleClass="sectionHeader" text="%Export sort order" GridPane.rowIndex="7" />
                     </children>
                 </GridPane>
             </children>
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
index 8ed238faf8a..58002962d84 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
@@ -1,6 +1,7 @@
 package org.jabref.gui.libraryproperties;
 
 import java.nio.charset.Charset;
+import java.nio.file.Paths;
 import java.util.Optional;
 
 import javax.inject.Inject;
@@ -36,6 +37,7 @@ public class LibraryPropertiesDialogView extends BaseDialog<Void> {
     @FXML private Button browseGeneralFileDir;
     @FXML private TextField userSpecificFileDirectory;
     @FXML private Button browseUserSpefiicFileDir;
+    @FXML private TextField laTexFileDirectory;
     @FXML private CheckBox protect;
     @Inject private PreferencesService preferencesService;
 
@@ -70,6 +72,7 @@ private void initialize() {
 
         generalFileDirectory.textProperty().bindBidirectional(viewModel.generalFileDirectoryPropertyProperty());
         userSpecificFileDirectory.textProperty().bindBidirectional(viewModel.userSpecificFileDirectoryProperty());
+        laTexFileDirectory.textProperty().bindBidirectional(viewModel.LaTexFileDirectoryProperty());
 
         encoding.itemsProperty().bind(viewModel.encodingsProperty());
         encoding.valueProperty().bindBidirectional(viewModel.selectedEncodingProperty());
@@ -112,6 +115,11 @@ public void browseUserSpecificFileDirectory(ActionEvent event) {
         viewModel.browseUserDir();
     }
 
+    @FXML
+    void browseLaTexFileDirectory(ActionEvent event) {
+        viewModel.browseLaTexDir();
+    }
+
     private void storeSettings() {
         //FIXME: Move to viewModel until fieldFormatterCleanupsPanel is property implemented
         MetaData metaData = panel.getBibDatabaseContext().getMetaData();
@@ -134,6 +142,13 @@ private void storeSettings() {
             metaData.setUserFileDirectory(preferencesService.getUser(), text);
         }
 
+        text = viewModel.LaTexFileDirectoryProperty().getValue();
+        if (text.isEmpty()) {
+            metaData.clearLaTexFileDirectory(preferencesService.getUser());
+        } else {
+            metaData.setLaTexFileDirectory(preferencesService.getUser(), Paths.get(text));
+        }
+
         if (viewModel.libraryProtectedProperty().getValue()) {
             metaData.markAsProtected();
         } else {
@@ -165,7 +180,7 @@ private void storeSettings() {
 
         boolean changed = saveOrderConfigChanged || encodingChanged
                           || viewModel.generalFileDirChanged() || viewModel.userFileDirChanged()
-                          || viewModel.protectedValueChanged() || saveActionsChanged;
+                          || viewModel.protectedValueChanged() || saveActionsChanged || viewModel.LaTexFileDirChanged();
         // ... if so, mark base changed. Prevent the Undo button from removing
         // change marking:
         if (changed) {
diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
index 05f3982d7e0..e7791d7a534 100644
--- a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
+++ b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
@@ -1,6 +1,7 @@
 package org.jabref.gui.libraryproperties;
 
 import java.nio.charset.Charset;
+import java.nio.file.Path;
 import java.util.Optional;
 
 import javafx.beans.property.BooleanProperty;
@@ -25,6 +26,7 @@ public class LibraryPropertiesDialogViewModel {
 
     private final StringProperty generalFileDirectoryProperty = new SimpleStringProperty("");
     private final StringProperty userSpecificFileDirectoryProperty = new SimpleStringProperty("");
+    private final StringProperty laTexFileDirectoryProperty = new SimpleStringProperty("");
     private final ListProperty<Charset> encodingsProperty = new SimpleListProperty<>(FXCollections.observableArrayList(Encodings.getCharsets()));
     private final ObjectProperty<Charset> selectedEncodingPropety = new SimpleObjectProperty<>(Encodings.getCharsets().get(0));
     private final BooleanProperty libraryProtectedProperty = new SimpleBooleanProperty();
@@ -36,6 +38,7 @@ public class LibraryPropertiesDialogViewModel {
 
     private final String oldUserSpecificFileDir;
     private final String oldGeneralFileDir;
+    private final String oldLaTexFileDir;
     private final boolean oldLibraryProtected;
 
     public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogService, PreferencesService preferencesService) {
@@ -59,8 +62,11 @@ public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogSer
         Optional<String> fileDI = metaData.getUserFileDirectory(preferencesService.getUser());
         fileDI.ifPresent(userSpecificFileDirectoryProperty::setValue);
 
+        metaData.getLaTexFileDirectory(preferencesService.getUser()).map(Path::toString).ifPresent(laTexFileDirectoryProperty::setValue);
+
         oldUserSpecificFileDir = generalFileDirectoryProperty.getValue();
         oldGeneralFileDir = userSpecificFileDirectoryProperty.getValue();
+        oldLaTexFileDir = laTexFileDirectoryProperty.getValue();
 
         libraryProtectedProperty.setValue(metaData.isProtected());
         oldLibraryProtected = libraryProtectedProperty.getValue();
@@ -74,6 +80,10 @@ public StringProperty userSpecificFileDirectoryProperty() {
         return this.userSpecificFileDirectoryProperty;
     }
 
+    public StringProperty LaTexFileDirectoryProperty() {
+        return this.laTexFileDirectoryProperty;
+    }
+
     public ListProperty<Charset> encodingsProperty() {
         return this.encodingsProperty;
     }
@@ -90,6 +100,10 @@ public void browseUserDir() {
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> userSpecificFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
     }
 
+    public void browseLaTexDir() {
+        dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> laTexFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
+    }
+
     public BooleanProperty libraryProtectedProperty() {
         return this.libraryProtectedProperty;
     }
@@ -102,6 +116,10 @@ public boolean userFileDirChanged() {
         return !oldUserSpecificFileDir.equals(userSpecificFileDirectoryProperty.getValue());
     }
 
+    public boolean LaTexFileDirChanged() {
+        return !oldLaTexFileDir.equals(laTexFileDirectoryProperty.getValue());
+    }
+
     public boolean protectedValueChanged() {
         return !oldLibraryProtected == libraryProtectedProperty.getValue();
     }
@@ -113,4 +131,5 @@ public BooleanProperty encodingDisableProperty() {
     public BooleanProperty protectDisableProperty() {
         return protectDisableProperty;
     }
+
 }
diff --git a/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java b/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
index 92944665575..b75253685d4 100644
--- a/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
+++ b/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
@@ -43,6 +43,8 @@ public static Map<String, String> getSerializedStringMap(MetaData metaData,
                 path -> stringyMetaData.put(MetaData.FILE_DIRECTORY, Collections.singletonList(path.trim())));
         metaData.getUserFileDirectories().forEach((user, path) -> stringyMetaData
                 .put(MetaData.FILE_DIRECTORY + '-' + user, Collections.singletonList(path.trim())));
+        metaData.getLaTexFileDirectories().forEach((user, path) -> stringyMetaData
+                .put(MetaData.FILE_DIRECTORY + "Latex-" + user, Collections.singletonList(path.toString().trim())));
 
         for (ContentSelector selector: metaData.getContentSelectorList()) {
                 stringyMetaData.put(MetaData.SELECTOR_META_PREFIX + selector.getFieldName(), selector.getValues());
diff --git a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
index ca04fafd0ca..4c9365b0dd8 100644
--- a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
+++ b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
@@ -24,6 +24,7 @@
 import org.jabref.model.groups.SearchGroup;
 import org.jabref.model.groups.TexGroup;
 import org.jabref.model.groups.WordKeywordGroup;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -35,7 +36,7 @@ public class GroupsParser {
     private GroupsParser() {
     }
 
-    public static GroupTreeNode importGroups(List<String> orderedData, Character keywordSeparator, FileUpdateMonitor fileMonitor)
+    public static GroupTreeNode importGroups(List<String> orderedData, Character keywordSeparator, FileUpdateMonitor fileMonitor, MetaData metaData)
             throws ParseException {
         try {
             GroupTreeNode cursor = null;
@@ -52,7 +53,7 @@ public static GroupTreeNode importGroups(List<String> orderedData, Character key
                     throw new ParseException("Expected \"" + string + "\" to contain whitespace");
                 }
                 int level = Integer.parseInt(string.substring(0, spaceIndex));
-                AbstractGroup group = GroupsParser.fromString(string.substring(spaceIndex + 1), keywordSeparator, fileMonitor);
+                AbstractGroup group = GroupsParser.fromString(string.substring(spaceIndex + 1), keywordSeparator, fileMonitor, metaData);
                 GroupTreeNode newNode = GroupTreeNode.fromGroup(group);
                 if (cursor == null) {
                     // create new root
@@ -84,7 +85,7 @@ public static GroupTreeNode importGroups(List<String> orderedData, Character key
      * @throws ParseException If an error occurred and a group could not be created,
      *                        e.g. due to a malformed regular expression.
      */
-    public static AbstractGroup fromString(String s, Character keywordSeparator, FileUpdateMonitor fileMonitor)
+    public static AbstractGroup fromString(String s, Character keywordSeparator, FileUpdateMonitor fileMonitor, MetaData metaData)
             throws ParseException {
         if (s.startsWith(MetadataSerializationConfiguration.KEYWORD_GROUP_ID)) {
             return keywordGroupFromString(s, keywordSeparator);
@@ -108,13 +109,13 @@ public static AbstractGroup fromString(String s, Character keywordSeparator, Fil
             return automaticKeywordGroupFromString(s);
         }
         if (s.startsWith(MetadataSerializationConfiguration.TEX_GROUP_ID)) {
-            return texGroupFromString(s, fileMonitor);
+            return texGroupFromString(s, fileMonitor, metaData);
         }
 
         throw new ParseException("Unknown group: " + s);
     }
 
-    private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor fileMonitor) throws ParseException {
+    private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor fileMonitor, MetaData metaData) throws ParseException {
         QuotedStringTokenizer tok = new QuotedStringTokenizer(string.substring(MetadataSerializationConfiguration.TEX_GROUP_ID
                 .length()), MetadataSerializationConfiguration.GROUP_UNIT_SEPARATOR, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
 
@@ -122,7 +123,7 @@ private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor
         GroupHierarchyType context = GroupHierarchyType.getByNumberOrDefault(Integer.parseInt(tok.nextToken()));
         try {
             Path path = Paths.get(tok.nextToken());
-            TexGroup newGroup = new TexGroup(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor);
+            TexGroup newGroup = new TexGroup(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
             addGroupDetails(tok, newGroup);
             return newGroup;
         } catch (InvalidPathException | IOException ex) {
diff --git a/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java b/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
index ecd8e4ba4cf..1c3a9b211c5 100644
--- a/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
+++ b/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
@@ -3,6 +3,8 @@
 import java.io.IOException;
 import java.io.Reader;
 import java.io.StringReader;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -60,12 +62,18 @@ public MetaData parse(MetaData metaData, Map<String, String> data, Character key
             } else if (entry.getKey().startsWith(MetaData.SELECTOR_META_PREFIX)) {
                 metaData.addContentSelector(ContentSelectors.parse(entry.getKey().substring(MetaData.SELECTOR_META_PREFIX.length()), StringUtil.unquote(entry.getValue(), MetaData.ESCAPE_CHARACTER)));
                 continue;
+            } else if (entry.getKey().startsWith(MetaData.FILE_DIRECTORY + "Latex-")) {
+                // The user name comes directly after "FILE_DIRECTORYLatex-"
+                String user = entry.getKey().substring(MetaData.FILE_DIRECTORY.length() + 6);
+                Path path = Paths.get(getSingleItem(value)).normalize();
+                metaData.setLaTexFileDirectory(user, path);
+                continue;
             }
 
             switch (entry.getKey()) {
                 case MetaData.GROUPSTREE:
                 case MetaData.GROUPSTREE_LEGACY:
-                    metaData.setGroups(GroupsParser.importGroups(value, keywordSeparator, fileMonitor));
+                    metaData.setGroups(GroupsParser.importGroups(value, keywordSeparator, fileMonitor, metaData));
                     break;
                 case MetaData.SAVE_ACTIONS:
                     metaData.setSaveActions(Cleanups.parse(value));
diff --git a/src/main/java/org/jabref/model/database/BibDatabaseContext.java b/src/main/java/org/jabref/model/database/BibDatabaseContext.java
index adabb5805ed..3acdf7b484e 100644
--- a/src/main/java/org/jabref/model/database/BibDatabaseContext.java
+++ b/src/main/java/org/jabref/model/database/BibDatabaseContext.java
@@ -185,7 +185,7 @@ public Optional<Path> getFirstExistingFileDir(FilePreferences preferences) {
      * metadata can specify a general directory and/or a user-specific directory or the preferences can specify one. <p>
      * The settings are prioritized in the following order and the first defined setting is used:
      * <ol>
-     *     <li>metdata</li>
+     *     <li>metadata</li>
      *     <li>user-specific directory</li>
      *     <li>preferences directory</li>
      *     <li>BIB file directory</li>
diff --git a/src/main/java/org/jabref/model/groups/TexGroup.java b/src/main/java/org/jabref/model/groups/TexGroup.java
index 92a47028eae..ab350c486d5 100644
--- a/src/main/java/org/jabref/model/groups/TexGroup.java
+++ b/src/main/java/org/jabref/model/groups/TexGroup.java
@@ -1,13 +1,18 @@
 package org.jabref.model.groups;
 
 import java.io.IOException;
+import java.net.InetAddress;
 import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Objects;
 import java.util.Set;
 
 import org.jabref.model.auxparser.AuxParser;
 import org.jabref.model.auxparser.AuxParserResult;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.metadata.MetaData;
+import org.jabref.model.util.FileHelper;
 import org.jabref.model.util.FileUpdateListener;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -22,13 +27,21 @@ public class TexGroup extends AbstractGroup implements FileUpdateListener {
     private Set<String> keysUsedInAux = null;
     private final FileUpdateMonitor fileMonitor;
     private AuxParser auxParser;
+    private final MetaData metaData;
+    private String user;
 
-    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor) throws IOException {
+    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData, String user) throws IOException {
         super(name, context);
-        this.filePath = Objects.requireNonNull(filePath);
+        this.metaData = metaData;
+        this.user = user;
+        this.filePath = expandPath(Objects.requireNonNull(filePath));
         this.auxParser = auxParser;
         this.fileMonitor = fileMonitor;
-        fileMonitor.addListenerForFile(filePath, this);
+        fileMonitor.addListenerForFile(this.filePath, this);
+    }
+
+    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+        this(name, context, filePath, auxParser, fileMonitor, metaData, System.getProperty("user.name") + '-' + InetAddress.getLocalHost().getHostName());
     }
 
     @Override
@@ -49,7 +62,7 @@ public boolean isDynamic() {
     @Override
     public AbstractGroup deepCopy() {
         try {
-            return new TexGroup(name.getValue(), context, filePath, auxParser, fileMonitor);
+            return new TexGroup(name.getValue(), context, filePath, auxParser, fileMonitor, metaData);
         } catch (IOException ex) {
             // This should never happen because we were able to monitor the file just fine until now
             LOGGER.error("Problem creating copy of group", ex);
@@ -62,7 +75,7 @@ public boolean equals(Object o) {
         if (this == o) {
             return true;
         }
-        if (o == null || getClass() != o.getClass()) {
+        if ((o == null) || (getClass() != o.getClass())) {
             return false;
         }
         if (!super.equals(o)) {
@@ -75,7 +88,7 @@ public boolean equals(Object o) {
     @Override
     public String toString() {
         return "TexGroup{" +
-                "filePath=" + filePath +
+               "filePath=" + filePath +
                 ", keysUsedInAux=" + keysUsedInAux +
                 ", auxParser=" + auxParser +
                 ", fileMonitor=" + fileMonitor +
@@ -88,7 +101,7 @@ public int hashCode() {
     }
 
     public Path getFilePath() {
-        return filePath;
+        return relativize(filePath);
     }
 
     @Override
@@ -96,4 +109,23 @@ public void fileUpdated() {
         // Reset previous parse result
         keysUsedInAux = null;
     }
+
+    private Path relativize(Path path) {
+        List<Path> fileDirectories = getFileDirectoriesAsPaths();
+        return FileHelper.relativize(path, fileDirectories);
+    }
+
+    private Path expandPath(Path path) {
+        List<Path> fileDirectories = getFileDirectoriesAsPaths();
+        return FileHelper.expandFilenameAsPath(path.toString(), fileDirectories).orElse(path);
+    }
+
+    private List<Path> getFileDirectoriesAsPaths() {
+        List<Path> fileDirs = new ArrayList<>();
+
+        metaData.getLaTexFileDirectory(user)
+                .ifPresent(laTexFileDirectory -> fileDirs.add(laTexFileDirectory));
+
+        return fileDirs;
+    }
 }
diff --git a/src/main/java/org/jabref/model/metadata/MetaData.java b/src/main/java/org/jabref/model/metadata/MetaData.java
index 94b105eadac..7fc52e99842 100644
--- a/src/main/java/org/jabref/model/metadata/MetaData.java
+++ b/src/main/java/org/jabref/model/metadata/MetaData.java
@@ -1,6 +1,7 @@
 package org.jabref.model.metadata;
 
 import java.nio.charset.Charset;
+import java.nio.file.Path;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -42,6 +43,7 @@ public class MetaData {
     private final EventBus eventBus = new EventBus();
     private final Map<String, String> citeKeyPatterns = new HashMap<>(); // <BibType, Pattern>
     private final Map<String, String> userFileDirectory = new HashMap<>(); // <User, FilePath>
+    private final Map<String, Path> laTexFileDirectory = new HashMap<>(); // <User, FilePath>
     private GroupTreeNode groupsRoot;
     private Charset encoding;
     private SaveOrderConfig saveOrderConfig;
@@ -50,8 +52,8 @@ public class MetaData {
     private BibDatabaseMode mode;
     private boolean isProtected;
     private String defaultFileDirectory;
-    private ContentSelectors contentSelectors = new ContentSelectors();
-    private Map<String, List<String>> unkownMetaData = new HashMap<>();
+    private final ContentSelectors contentSelectors = new ContentSelectors();
+    private final Map<String, List<String>> unkownMetaData = new HashMap<>();
     private boolean isEventPropagationEnabled = true;
 
     /**
@@ -209,6 +211,20 @@ public void clearUserFileDirectory(String user) {
         postChange();
     }
 
+    public Optional<Path> getLaTexFileDirectory(String user) {
+        return Optional.ofNullable(laTexFileDirectory.get(user));
+    }
+
+    public void setLaTexFileDirectory(String user, Path path) {
+        laTexFileDirectory.put(Objects.requireNonNull(user), Objects.requireNonNull(path));
+        postChange();
+    }
+
+    public void clearLaTexFileDirectory(String user) {
+        laTexFileDirectory.remove(user);
+        postChange();
+    }
+
     public void markAsNotProtected() {
         isProtected = false;
         postChange();
@@ -285,6 +301,10 @@ public Map<String, String> getUserFileDirectories() {
         return Collections.unmodifiableMap(userFileDirectory);
     }
 
+    public Map<String, Path> getLaTexFileDirectories() {
+        return Collections.unmodifiableMap(laTexFileDirectory);
+    }
+
     public Map<String, List<String>> getUnknownMetaData() {
         return Collections.unmodifiableMap(unkownMetaData);
     }
@@ -310,6 +330,7 @@ public boolean equals(Object o) {
                 && Objects.equals(saveOrderConfig, metaData.saveOrderConfig)
                 && Objects.equals(citeKeyPatterns, metaData.citeKeyPatterns)
                 && Objects.equals(userFileDirectory, metaData.userFileDirectory)
+               && Objects.equals(laTexFileDirectory, metaData.laTexFileDirectory)
                 && Objects.equals(defaultCiteKeyPattern, metaData.defaultCiteKeyPattern)
                 && Objects.equals(saveActions, metaData.saveActions) && (mode == metaData.mode)
                 && Objects.equals(defaultFileDirectory, metaData.defaultFileDirectory)
diff --git a/src/main/java/org/jabref/model/util/FileHelper.java b/src/main/java/org/jabref/model/util/FileHelper.java
index e86e4686429..b2864ff5811 100644
--- a/src/main/java/org/jabref/model/util/FileHelper.java
+++ b/src/main/java/org/jabref/model/util/FileHelper.java
@@ -175,4 +175,17 @@ private static boolean isUrl(String url) {
             return false;
         }
     }
+
+    public static Path relativize(Path path, List<Path> fileDirectories) {
+        if (!path.isAbsolute()) {
+            return path;
+        }
+
+        for (Path directory : fileDirectories) {
+            if (path.startsWith(directory)) {
+                return directory.relativize(path);
+            }
+        }
+        return path;
+    }
 }
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 3a6655432a7..0258d204ee7 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1118,6 +1118,7 @@ Ensure\ unique\ keys\ using\ letters\ (b,\ c,\ ...)=Ensure unique keys using let
 
 General\ file\ directory=General file directory
 User-specific\ file\ directory=User-specific file directory
+LaTex\ file\ directory=LaTex file directory
 Search\ failed\:\ illegal\ search\ expression=Search failed: illegal search expression
 Show\ ArXiv\ column=Show ArXiv column
 
diff --git a/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java b/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java
index a7f2ef36a4c..c0d3994dbfc 100644
--- a/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java
+++ b/src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java
@@ -485,12 +485,13 @@ void writeProtectedFlag() throws Exception {
     void writeFileDirectories() throws Exception {
         metaData.setDefaultFileDirectory("\\Literature\\");
         metaData.setUserFileDirectory("defaultOwner-user", "D:\\Documents");
+        metaData.setLaTexFileDirectory("defaultOwner-user", Paths.get("D:\\Latex"));
 
         databaseWriter.savePartOfDatabase(bibtexContext, Collections.emptyList());
 
         assertEquals(OS.NEWLINE + "@Comment{jabref-meta: fileDirectory:\\\\Literature\\\\;}" + OS.NEWLINE +
                 OS.NEWLINE + "@Comment{jabref-meta: fileDirectory-defaultOwner-user:D:\\\\Documents;}"
-                + OS.NEWLINE, stringWriter.toString());
+                     + OS.NEWLINE + OS.NEWLINE + "@Comment{jabref-meta: fileDirectoryLatex-defaultOwner-user:D:\\\\Latex;}" + OS.NEWLINE, stringWriter.toString());
     }
 
     @Test
diff --git a/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java b/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
index b1560a3aa65..b8625babeb4 100644
--- a/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
+++ b/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
@@ -22,6 +22,7 @@
 import org.jabref.model.groups.SearchGroup;
 import org.jabref.model.groups.TexGroup;
 import org.jabref.model.groups.WordKeywordGroup;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
 import org.junit.jupiter.api.BeforeEach;
@@ -115,7 +116,7 @@ public void serializeSingleAutomaticPersonGroup() {
 
     @Test
     public void serializeSingleTexGroup() throws Exception {
-        TexGroup group = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor());
+        TexGroup group = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), new MetaData());
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 TexGroup:myTexGroup;0;path/To/File;1;;;;"), serialization);
     }
diff --git a/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java b/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
index 116cfd198aa..04fca15aff8 100644
--- a/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
+++ b/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
@@ -1474,10 +1474,12 @@ void parseDoesNotRecognizeDatabaseIDasUserComment() throws Exception {
     void integrationTestFileDirectories() throws IOException {
         ParserResult result = parser.parse(
                 new StringReader("@comment{jabref-meta: fileDirectory:\\\\Literature\\\\;}"
-                        + "@comment{jabref-meta: fileDirectory-defaultOwner-user:D:\\\\Documents;}"));
+                        + "@comment{jabref-meta: fileDirectory-defaultOwner-user:D:\\\\Documents;}"
+                         + "@comment{jabref-meta: fileDirectoryLatex-defaultOwner-user:D:\\\\Latex;}"));
 
         assertEquals("\\Literature\\", result.getMetaData().getDefaultFileDirectory().get());
         assertEquals("D:\\Documents", result.getMetaData().getUserFileDirectory("defaultOwner-user").get());
+        assertEquals("D:\\Latex", result.getMetaData().getLaTexFileDirectory("defaultOwner-user").get().toString());
     }
 
     @Test
diff --git a/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java b/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
index 765f93ddcfe..080b2594e69 100644
--- a/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
+++ b/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
@@ -17,6 +17,7 @@
 import org.jabref.model.groups.GroupHierarchyType;
 import org.jabref.model.groups.GroupTreeNode;
 import org.jabref.model.groups.TexGroup;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -28,17 +29,19 @@
 
 public class GroupsParserTest {
     private FileUpdateMonitor fileMonitor;
+    private MetaData metaData;
 
     @BeforeEach
     public void setUp() throws Exception {
         fileMonitor = new DummyFileUpdateMonitor();
+        metaData = new MetaData();
     }
 
     @Test
     // For https://github.com/JabRef/jabref/issues/1681
     public void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exception {
         ExplicitGroup expected = new ExplicitGroup("B{\\\"{o}}hmer", GroupHierarchyType.INDEPENDENT, ',');
-        AbstractGroup parsed = GroupsParser.fromString("ExplicitGroup:B{\\\\\"{o}}hmer;0;", ',', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("ExplicitGroup:B{\\\\\"{o}}hmer;0;", ',', fileMonitor, metaData);
 
         assertEquals(expected, parsed);
     }
@@ -46,20 +49,20 @@ public void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exc
     @Test
     public void keywordDelimiterThatNeedsToBeEscaped() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("group1", GroupHierarchyType.INDEPENDENT, "keywords", ';', '>');
-        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;\\;;>;1;;;;;", ';', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;\\;;>;1;;;;;", ';', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
     public void hierarchicalDelimiterThatNeedsToBeEscaped() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("group1", GroupHierarchyType.INDEPENDENT, "keywords", ',', ';');
-        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;,;\\;;1;;;;;", ';', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;,;\\;;1;;;;;", ';', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
     public void fromStringThrowsParseExceptionForNotEscapedGroupName() throws Exception {
-        assertThrows(ParseException.class, () -> GroupsParser.fromString("ExplicitGroup:slit\\\\;0\\;mertsch_slit2_2007\\;;", ',', fileMonitor));
+        assertThrows(ParseException.class, () -> GroupsParser.fromString("ExplicitGroup:slit\\\\;0\\;mertsch_slit2_2007\\;;", ',', fileMonitor, metaData));
     }
 
     @Test
@@ -85,7 +88,7 @@ public void testImportSubGroups() throws Exception {
         AbstractGroup thirdSubGrpLvl1 = new ExplicitGroup("3", GroupHierarchyType.INDEPENDENT, ',');
         rootNode.addSubgroup(thirdSubGrpLvl1);
 
-        GroupTreeNode parsedNode = GroupsParser.importGroups(orderedData, ',', fileMonitor);
+        GroupTreeNode parsedNode = GroupsParser.importGroups(orderedData, ',', fileMonitor, metaData);
         assertEquals(rootNode.getChildren(), parsedNode.getChildren());
     }
 
@@ -96,7 +99,7 @@ public void fromStringParsesExplicitGroupWithIconAndDescription() throws Excepti
         expected.setExpanded(true);
         expected.setColor(Color.ALICEBLUE);
         expected.setDescription("test description");
-        AbstractGroup parsed = GroupsParser.fromString("StaticGroup:myExplicitGroup;0;1;0xf0f8ffff;test icon;test description;", ',', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("StaticGroup:myExplicitGroup;0;1;0xf0f8ffff;test icon;test description;", ',', fileMonitor, metaData);
 
         assertEquals(expected, parsed);
     }
@@ -104,26 +107,26 @@ public void fromStringParsesExplicitGroupWithIconAndDescription() throws Excepti
     @Test
     public void fromStringParsesAutomaticKeywordGroup() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "keywords", ',', '>');
-        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:myAutomaticGroup;0;keywords;,;>;1;;;;", ',', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:myAutomaticGroup;0;keywords;,;>;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
     public void fromStringParsesAutomaticPersonGroup() throws Exception {
         AutomaticPersonsGroup expected = new AutomaticPersonsGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "authors");
-        AbstractGroup parsed = GroupsParser.fromString("AutomaticPersonsGroup:myAutomaticGroup;0;authors;1;;;;", ',', fileMonitor);
+        AbstractGroup parsed = GroupsParser.fromString("AutomaticPersonsGroup:myAutomaticGroup;0;authors;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
     public void fromStringParsesTexGroup() throws Exception {
-        TexGroup expected = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), fileMonitor);
-        AbstractGroup parsed = GroupsParser.fromString("TexGroup:myTexGroup;0;path/To/File;1;;;;", ',', fileMonitor);
+        TexGroup expected = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+        AbstractGroup parsed = GroupsParser.fromString("TexGroup:myTexGroup;0;path/To/File;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
     public void fromStringUnknownGroupThrowsException() throws Exception {
-        assertThrows(ParseException.class, () -> GroupsParser.fromString("0 UnknownGroup:myUnknownGroup;0;;1;;;;", ',', fileMonitor));
+        assertThrows(ParseException.class, () -> GroupsParser.fromString("0 UnknownGroup:myUnknownGroup;0;;1;;;;", ',', fileMonitor, metaData));
     }
 }
diff --git a/src/test/java/org/jabref/model/groups/TexGroupTest.java b/src/test/java/org/jabref/model/groups/TexGroupTest.java
index 3d869bee22f..e2408b08308 100644
--- a/src/test/java/org/jabref/model/groups/TexGroupTest.java
+++ b/src/test/java/org/jabref/model/groups/TexGroupTest.java
@@ -6,19 +6,29 @@
 import org.jabref.logic.auxparser.DefaultAuxParser;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
+import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class TexGroupTest {
 
+    private MetaData metaData;
+
+    @BeforeEach
+    public void setUp() throws Exception {
+        metaData = new MetaData();
+    }
+
     @Test
     public void containsReturnsTrueForEntryInAux() throws Exception {
         Path auxFile = Paths.get(TexGroupTest.class.getResource("paper.aux").toURI());
-        TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor());
+        TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), metaData);
         BibEntry inAux = new BibEntry();
         inAux.setCiteKey("Darwin1888");
 
@@ -28,10 +38,20 @@ public void containsReturnsTrueForEntryInAux() throws Exception {
     @Test
     public void containsReturnsTrueForEntryNotInAux() throws Exception {
         Path auxFile = Paths.get(TexGroupTest.class.getResource("paper.aux").toURI());
-        TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor());
+        TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), metaData);
         BibEntry notInAux = new BibEntry();
         notInAux.setCiteKey("NotInAux2017");
 
         assertFalse(group.contains(notInAux));
     }
+
+    @Test
+    public void getFilePathReturnsRelativePath() throws Exception {
+        Path auxFile = Paths.get(TexGroupTest.class.getResource("paper.aux").toURI());
+        String user = "Darwin";
+        metaData.setLaTexFileDirectory(user, auxFile.getParent());
+        TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), metaData, user);
+
+        assertEquals("paper.aux", group.getFilePath().toString());
+    }
 }

From 40600b35420e688ee5d5758224717b484ad34f84 Mon Sep 17 00:00:00 2001
From: Yash  Kothari <yashkothari199767@gmail.com>
Date: Sat, 30 Mar 2019 14:35:56 +0530
Subject: [PATCH 26/61] Select the first tab which matches the search query in
 preferences (#4825)

window

After every search clear the selection of tabs and select the first
tab in the tabsList.

Fixes #4824
---
 .../java/org/jabref/gui/preferences/PreferencesDialog.java    | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
index a64fa630780..437d26cbdf1 100644
--- a/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
+++ b/src/main/java/org/jabref/gui/preferences/PreferencesDialog.java
@@ -122,6 +122,8 @@ private void construct() {
                 ScrollPane preferencePaneContainer = new ScrollPane(tab.getBuilder());
                 preferencePaneContainer.getStyleClass().add("preferencePaneContainer");
                 container.setCenter(preferencePaneContainer);
+            } else {
+                container.setCenter(null);
             }
         });
         tabsList.getSelectionModel().selectFirst();
@@ -136,6 +138,8 @@ private void construct() {
         tabsList.itemsProperty().bindBidirectional(searchHandler.filteredPreferenceTabsProperty());
         searchBox.textProperty().addListener((observable, previousText, newText) -> {
             searchHandler.filterTabs(newText.toLowerCase(Locale.ROOT));
+            tabsList.getSelectionModel().clearSelection();
+            tabsList.getSelectionModel().selectFirst();
         });
 
         VBox buttonContainer = new VBox();

From df04e02255ce07175b878eed25df3947085c1566 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 1 Apr 2019 08:23:25 +0200
Subject: [PATCH 27/61] Bump checkstyle from 8.18 to 8.19 (#4834)

Bumps [checkstyle](https://github.com/checkstyle/checkstyle) from 8.18 to 8.19.
- [Release notes](https://github.com/checkstyle/checkstyle/releases)
- [Commits](https://github.com/checkstyle/checkstyle/compare/checkstyle-8.18...checkstyle-8.19)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9673626d496..a40b34db6e9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -177,7 +177,7 @@ dependencies {
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.18'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.19'
 }
 
 jacoco {

From f51b97291a8bdabba6c1fabb75a4afc6f55c919a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 1 Apr 2019 08:26:19 +0200
Subject: [PATCH 28/61] Bump archunit-junit5-engine from 0.10.1 to 0.10.2
 (#4832)

Bumps [archunit-junit5-engine](https://github.com/TNG/ArchUnit) from 0.10.1 to 0.10.2.
- [Release notes](https://github.com/TNG/ArchUnit/releases)
- [Commits](https://github.com/TNG/ArchUnit/compare/v0.10.1...0.10.2)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index a40b34db6e9..a693f117e9e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -172,7 +172,7 @@ dependencies {
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.1'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.2'
     testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.1'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"

From 85e684b5e6c04c8f47834b3c0a960a9c53d00a3c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 1 Apr 2019 08:47:11 +0200
Subject: [PATCH 29/61] Bump archunit-junit5-api from 0.10.1 to 0.10.2 (#4833)

Bumps [archunit-junit5-api](https://github.com/TNG/ArchUnit) from 0.10.1 to 0.10.2.
- [Release notes](https://github.com/TNG/ArchUnit/releases)
- [Commits](https://github.com/TNG/ArchUnit/compare/v0.10.1...0.10.2)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index a693f117e9e..261a39e8223 100644
--- a/build.gradle
+++ b/build.gradle
@@ -173,7 +173,7 @@ dependencies {
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
     testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.10.2'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.1'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.10.2'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 

From 05eaa64f409a722e54be102d869d09956f436063 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Mon, 1 Apr 2019 13:09:07 +0200
Subject: [PATCH 30/61] Convert AutoLinkFilesAction to JavaFX (#4822)

* Convert AutoLinkFilesAction to JavaFX

Fixes #4819.

* Convert a few more dialogs to JavaFX
---
 src/main/java/org/jabref/JabRefMain.java      |  12 +-
 .../org/jabref/cli/ArgumentProcessor.java     |   7 +-
 src/main/java/org/jabref/gui/JabRefFrame.java |  24 +--
 .../gui/actions/AutoLinkFilesAction.java      |  52 ------
 .../externalfiles/AutoLinkFilesAction.java    |  68 +++++++
 .../externalfiles/AutoSetFileLinksUtil.java   |  66 +++++--
 .../gui/externalfiles/AutoSetLinks.java       | 172 ------------------
 .../importer/ParserResultWarningDialog.java   |  17 +-
 .../actions/MergeReviewIntoCommentAction.java |   2 +-
 ...geReviewIntoCommentConfirmationDialog.java |  28 ++-
 .../gui/mergeentries/FetchAndMergeEntry.java  |   2 +-
 11 files changed, 153 insertions(+), 297 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/actions/AutoLinkFilesAction.java
 create mode 100644 src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java
 delete mode 100644 src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java

diff --git a/src/main/java/org/jabref/JabRefMain.java b/src/main/java/org/jabref/JabRefMain.java
index 66e624a002d..7c6f3d78f49 100644
--- a/src/main/java/org/jabref/JabRefMain.java
+++ b/src/main/java/org/jabref/JabRefMain.java
@@ -2,14 +2,13 @@
 
 import java.net.Authenticator;
 
-import javax.swing.JFrame;
-import javax.swing.JOptionPane;
-
 import javafx.application.Application;
 import javafx.application.Platform;
+import javafx.scene.control.Alert;
 import javafx.stage.Stage;
 
 import org.jabref.cli.ArgumentProcessor;
+import org.jabref.gui.FXDialog;
 import org.jabref.gui.remote.JabRefMessageHandler;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.l10n.Localization;
@@ -119,9 +118,10 @@ private static void ensureCorrectJavaVersion() {
                 versionError.append("\n");
                 versionError.append(Localization.lang("Note that currently, JabRef does not run with Java 9."));
             }
-            final JFrame frame = new JFrame();
-            JOptionPane.showMessageDialog(null, versionError, Localization.lang("Error"), JOptionPane.ERROR_MESSAGE);
-            frame.dispose();
+
+            FXDialog alert = new FXDialog(Alert.AlertType.ERROR, Localization.lang("Error"), true);
+            alert.setHeaderText(null);
+            alert.setContentText(versionError.toString());
 
             // We exit on Java 9 error since this will definitely not work
             if (java9Fail) {
diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
index f97a582daab..56a4de65bde 100644
--- a/src/main/java/org/jabref/cli/ArgumentProcessor.java
+++ b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -13,7 +13,9 @@
 
 import org.jabref.Globals;
 import org.jabref.JabRefException;
-import org.jabref.gui.externalfiles.AutoSetLinks;
+import org.jabref.gui.externalfiles.AutoSetFileLinksUtil;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.undo.NamedCompound;
 import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
 import org.jabref.logic.exporter.AtomicFileWriter;
 import org.jabref.logic.exporter.BibDatabaseWriter;
@@ -496,7 +498,8 @@ private void automaticallySetFileLinks(List<ParserResult> loaded) {
         for (ParserResult parserResult : loaded) {
             BibDatabase database = parserResult.getDatabase();
             LOGGER.info(Localization.lang("Automatically setting file links"));
-            AutoSetLinks.autoSetLinks(database.getEntries(), parserResult.getDatabaseContext());
+            AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(parserResult.getDatabaseContext(), Globals.prefs.getFilePreferences(), Globals.prefs.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
+            util.linkAssociatedFiles(database.getEntries(), new NamedCompound(""));
         }
     }
 
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 06ab62cb461..939a1aeb689 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -56,7 +56,6 @@
 import org.jabref.JabRefExecutorService;
 import org.jabref.gui.actions.ActionFactory;
 import org.jabref.gui.actions.Actions;
-import org.jabref.gui.actions.AutoLinkFilesAction;
 import org.jabref.gui.actions.BibtexKeyPatternAction;
 import org.jabref.gui.actions.ConnectToSharedDatabaseCommand;
 import org.jabref.gui.actions.CopyFilesAction;
@@ -87,6 +86,7 @@
 import org.jabref.gui.exporter.ExportToClipboardAction;
 import org.jabref.gui.exporter.SaveAllAction;
 import org.jabref.gui.exporter.SaveDatabaseAction;
+import org.jabref.gui.externalfiles.AutoLinkFilesAction;
 import org.jabref.gui.externalfiles.FindUnlinkedFilesAction;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.help.AboutAction;
@@ -112,7 +112,6 @@
 import org.jabref.logic.autosaveandbackup.BackupManager;
 import org.jabref.logic.importer.IdFetcher;
 import org.jabref.logic.importer.OpenDatabase;
-import org.jabref.logic.importer.OutputPrinter;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.l10n.Localization;
@@ -147,7 +146,7 @@
 /**
  * The main window of the application.
  */
-public class JabRefFrame extends BorderPane implements OutputPrinter {
+public class JabRefFrame extends BorderPane {
 
     // Frame titles.
     public static final String FRAME_TITLE = "JabRef";
@@ -819,7 +818,7 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction())
+                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs))
         );
 
         PushToApplicationButton pushToExternal = new PushToApplicationButton(this, pushApplications.getApplications());
@@ -1249,17 +1248,6 @@ private boolean isExistURLorDOI(List<BibEntry> selectEntryList) {
         return false;
     }
 
-    @Override
-    public void showMessage(String message, String title, int msgType) {
-        JOptionPane.showMessageDialog(null, message, title, msgType);
-    }
-
-    @Override
-    public void setStatus(String s) {
-        output(s);
-    }
-
-    @Override
     public void showMessage(String message) {
         JOptionPane.showMessageDialog(null, message);
     }
@@ -1438,7 +1426,7 @@ private void setDefaultTableFontSize() {
         for (BasePanel basePanel : getBasePanelList()) {
             basePanel.updateTableFont();
         }
-        setStatus(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
+        dialogService.notify(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
     }
 
     private void increaseTableFontSize() {
@@ -1446,7 +1434,7 @@ private void increaseTableFontSize() {
         for (BasePanel basePanel : getBasePanelList()) {
             basePanel.updateTableFont();
         }
-        setStatus(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
+        dialogService.notify(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
     }
 
     private void decreaseTableFontSize() {
@@ -1458,7 +1446,7 @@ private void decreaseTableFontSize() {
         for (BasePanel basePanel : getBasePanelList()) {
             basePanel.updateTableFont();
         }
-        setStatus(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
+        dialogService.notify(Localization.lang("Table font size is %0", String.valueOf(GUIGlobals.currentFont.getSize())));
     }
 
     private class CloseDatabaseAction extends SimpleCommand {
diff --git a/src/main/java/org/jabref/gui/actions/AutoLinkFilesAction.java b/src/main/java/org/jabref/gui/actions/AutoLinkFilesAction.java
deleted file mode 100644
index 7b77c9f59b4..00000000000
--- a/src/main/java/org/jabref/gui/actions/AutoLinkFilesAction.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package org.jabref.gui.actions;
-
-import java.util.List;
-
-import javax.swing.JDialog;
-import javax.swing.JFrame;
-
-import org.jabref.JabRefExecutorService;
-import org.jabref.JabRefGUI;
-import org.jabref.gui.externalfiles.AutoSetLinks;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.entry.BibEntry;
-
-/**
- * This Action may only be used in a menu or button.
- * Never in the entry editor. FileListEditor and EntryEditor have other ways to update the file links
- */
-public class AutoLinkFilesAction extends SimpleCommand {
-
-    public AutoLinkFilesAction() {
-
-    }
-
-    @Override
-    public void execute() {
-        List<BibEntry> entries = JabRefGUI.getMainFrame().getCurrentBasePanel().getSelectedEntries();
-        if (entries.isEmpty()) {
-            JabRefGUI.getMainFrame().getCurrentBasePanel()
-                    .output(Localization.lang("This operation requires one or more entries to be selected."));
-            return;
-        }
-        JDialog diag = new JDialog((JFrame) null, true);
-        final NamedCompound nc = new NamedCompound(Localization.lang("Automatically set file links"));
-        Runnable runnable = AutoSetLinks.autoSetLinks(entries, nc, null,
-                JabRefGUI.getMainFrame().getCurrentBasePanel().getBibDatabaseContext(), e -> {
-                    if (e.getID() > 0) {
-                        // entry has been updated in Util.autoSetLinks, only treat nc and status message
-                        if (nc.hasEdits()) {
-                            nc.end();
-                            JabRefGUI.getMainFrame().getCurrentBasePanel().getUndoManager().addEdit(nc);
-                            JabRefGUI.getMainFrame().getCurrentBasePanel().markBaseChanged();
-                        }
-                        JabRefGUI.getMainFrame().output(Localization.lang("Finished automatically setting external links."));
-                    } else {
-                        JabRefGUI.getMainFrame().output(Localization.lang("Finished automatically setting external links.") + " "
-                                + Localization.lang("No files found."));
-                    }
-                } , diag);
-        JabRefExecutorService.INSTANCE.execute(runnable);
-    }
-}
diff --git a/src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java b/src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java
new file mode 100644
index 00000000000..967243e840b
--- /dev/null
+++ b/src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java
@@ -0,0 +1,68 @@
+package org.jabref.gui.externalfiles;
+
+import java.util.List;
+
+import javafx.concurrent.Task;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.preferences.JabRefPreferences;
+
+/**
+ * This Action may only be used in a menu or button.
+ * Never in the entry editor. FileListEditor and EntryEditor have other ways to update the file links
+ */
+public class AutoLinkFilesAction extends SimpleCommand {
+
+    private final DialogService dialogService;
+    private final JabRefFrame frame;
+    private final JabRefPreferences preferences;
+
+    public AutoLinkFilesAction(JabRefFrame frame, JabRefPreferences preferences) {
+        this.frame = frame;
+        this.dialogService = frame.getDialogService();
+        this.preferences = preferences;
+    }
+
+    @Override
+    public void execute() {
+        List<BibEntry> entries = frame.getCurrentBasePanel().getSelectedEntries();
+        if (entries.isEmpty()) {
+            dialogService.notify(Localization.lang("This operation requires one or more entries to be selected."));
+            return;
+        }
+
+        final NamedCompound nc = new NamedCompound(Localization.lang("Automatically set file links"));
+        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(frame.getCurrentBasePanel().getBibDatabaseContext(), preferences.getFilePreferences(), preferences.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
+        Task<List<BibEntry>> linkFilesTask = new Task<List<BibEntry>>() {
+            @Override
+            protected List<BibEntry> call() {
+                return util.linkAssociatedFiles(entries, nc);
+            }
+
+            @Override
+            protected void succeeded() {
+                if (!getValue().isEmpty()) {
+                    if (nc.hasEdits()) {
+                        nc.end();
+                        frame.getCurrentBasePanel().getUndoManager().addEdit(nc);
+                    }
+                    dialogService.notify(Localization.lang("Finished automatically setting external links."));
+                } else {
+                    dialogService.notify(Localization.lang("Finished automatically setting external links.") + " " + Localization.lang("No files found."));
+                }
+            }
+        };
+
+        dialogService.showProgressDialogAndWait(
+                Localization.lang("Automatically setting file links"),
+                Localization.lang("Searching for files"),
+                linkFilesTask
+        );
+    }
+}
diff --git a/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java b/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java
index f1f07088a16..284eba0f689 100644
--- a/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java
+++ b/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java
@@ -11,12 +11,17 @@
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.externalfiletype.UnknownExternalFileType;
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.gui.undo.UndoableFieldChange;
+import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.util.io.AutoLinkPreferences;
 import org.jabref.logic.util.io.FileFinder;
 import org.jabref.logic.util.io.FileFinders;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.FieldName;
+import org.jabref.model.entry.FileFieldWriter;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.metadata.FilePreferences;
 import org.jabref.model.util.FileHelper;
@@ -26,7 +31,7 @@
 
 public class AutoSetFileLinksUtil {
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(AutoSetLinks.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(AutoSetFileLinksUtil.class);
     private List<Path> directories;
     private AutoLinkPreferences autoLinkPreferences;
     private ExternalFileTypes externalFileTypes;
@@ -35,12 +40,44 @@ public AutoSetFileLinksUtil(BibDatabaseContext databaseContext, FilePreferences
         this(databaseContext.getFileDirectoriesAsPaths(filePreferences), autoLinkPreferences, externalFileTypes);
     }
 
-    public AutoSetFileLinksUtil(List<Path> directories, AutoLinkPreferences autoLinkPreferences, ExternalFileTypes externalFileTypes) {
+    private AutoSetFileLinksUtil(List<Path> directories, AutoLinkPreferences autoLinkPreferences, ExternalFileTypes externalFileTypes) {
         this.directories = directories;
         this.autoLinkPreferences = autoLinkPreferences;
         this.externalFileTypes = externalFileTypes;
     }
 
+    public List<BibEntry> linkAssociatedFiles(List<BibEntry> entries, NamedCompound ce) {
+        List<BibEntry> changedEntries = new ArrayList<>();
+        for (BibEntry entry : entries) {
+
+            List<LinkedFile> linkedFiles = new ArrayList<>();
+            try {
+                linkedFiles = findAssociatedNotLinkedFiles(entry);
+            } catch (IOException e) {
+                LOGGER.error("Problem finding files", e);
+            }
+
+            if (ce != null) {
+                for (LinkedFile linkedFile : linkedFiles) {
+                    // store undo information
+                    String newVal = FileFieldWriter.getStringRepresentation(linkedFile);
+
+                    String oldVal = entry.getField(FieldName.FILE).orElse(null);
+
+                    UndoableFieldChange fieldChange = new UndoableFieldChange(entry, FieldName.FILE, oldVal, newVal);
+                    ce.addEdit(fieldChange);
+
+                    DefaultTaskExecutor.runInJavaFXThread(() -> {
+                        entry.addFile(linkedFile);
+                    });
+                }
+
+                changedEntries.add(entry);
+            }
+        }
+        return changedEntries;
+    }
+
     public List<LinkedFile> findAssociatedNotLinkedFiles(BibEntry entry) throws IOException {
         List<LinkedFile> linkedFiles = new ArrayList<>();
 
@@ -53,22 +90,23 @@ public List<LinkedFile> findAssociatedNotLinkedFiles(BibEntry entry) throws IOEx
         // Collect the found files that are not yet linked
         for (Path foundFile : result) {
             boolean fileAlreadyLinked = entry.getFiles().stream()
-                    .map(file -> file.findIn(directories))
-                    .anyMatch(file -> {
-                        try {
-                            return file.isPresent() && Files.isSameFile(file.get(), foundFile);
-                        } catch (IOException e) {
-                            LOGGER.error("Problem with isSameFile", e);
-                        }
-                        return false;
-                    });
+                                             .map(file -> file.findIn(directories))
+                                             .anyMatch(file -> {
+                                                 try {
+                                                     return file.isPresent() && Files.isSameFile(file.get(), foundFile);
+                                                 } catch (IOException e) {
+                                                     LOGGER.error("Problem with isSameFile", e);
+                                                 }
+                                                 return false;
+                                             });
+
             if (!fileAlreadyLinked) {
                 Optional<ExternalFileType> type = FileHelper.getFileExtension(foundFile)
-                        .map(externalFileTypes::getExternalFileTypeByExt)
-                        .orElse(Optional.of(new UnknownExternalFileType("")));
+                                                            .map(externalFileTypes::getExternalFileTypeByExt)
+                                                            .orElse(Optional.of(new UnknownExternalFileType("")));
 
                 String strType = type.isPresent() ? type.get().getName() : "";
-                String relativeFilePath = FileUtil.relativize(foundFile, directories).toString();
+                Path relativeFilePath = FileUtil.relativize(foundFile, directories);
                 LinkedFile linkedFile = new LinkedFile("", relativeFilePath, strType);
                 linkedFiles.add(linkedFile);
             }
diff --git a/src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java b/src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java
deleted file mode 100644
index d874493a98d..00000000000
--- a/src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java
+++ /dev/null
@@ -1,172 +0,0 @@
-package org.jabref.gui.externalfiles;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-import java.util.Set;
-
-import javax.swing.BorderFactory;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JProgressBar;
-import javax.swing.SwingConstants;
-import javax.swing.SwingUtilities;
-
-import org.jabref.Globals;
-import org.jabref.gui.externalfiletype.ExternalFileType;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.undo.NamedCompound;
-import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FieldName;
-import org.jabref.model.entry.FileFieldWriter;
-import org.jabref.model.entry.LinkedFile;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class AutoSetLinks {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(AutoSetLinks.class);
-
-    private AutoSetLinks() {
-    }
-
-    /**
-     * Shortcut method if links are set without using the GUI
-     *
-     * @param entries  the entries for which links should be set
-     * @param databaseContext the database for which links are set
-     */
-    public static void autoSetLinks(List<BibEntry> entries, BibDatabaseContext databaseContext) {
-        autoSetLinks(entries, null, null, databaseContext, null, null);
-    }
-
-    /**
-     * Automatically add links for this set of entries, based on the globally stored list of external file types. The
-     * entries are modified, and corresponding UndoEdit elements added to the NamedCompound given as argument.
-     * Furthermore, all entries which are modified are added to the Set of entries given as an argument.
-     * <p>
-     * The entries' bibtex keys must have been set - entries lacking key are ignored. The operation is done in a new
-     * thread, which is returned for the caller to wait for if needed.
-     *
-     * @param entries          A collection of BibEntry objects to find links for.
-     * @param ce               A NamedCompound to add UndoEdit elements to.
-     * @param changedEntries   MODIFIED, optional. A Set of BibEntry objects to which all modified entries is added.
-
-     * @param databaseContext  The database providing the relevant file directory, if any.
-     * @param callback         An ActionListener that is notified (on the event dispatch thread) when the search is finished.
-     *                         The ActionEvent has id=0 if no new links were added, and id=1 if one or more links were added. This
-     *                         parameter can be null, which means that no callback will be notified.
-     * @param diag             An instantiated modal JDialog which will be used to display the progress of the automatically setting. This
-     *                         parameter can be null, which means that no progress update will be shown.
-     * @return the thread performing the automatically setting
-     */
-    public static Runnable autoSetLinks(final List<BibEntry> entries, final NamedCompound ce,
-            final Set<BibEntry> changedEntries,
-            final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
-        final Collection<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
-        if (diag != null) {
-            final JProgressBar prog = new JProgressBar(SwingConstants.HORIZONTAL, 0, types.size() - 1);
-            final JLabel label = new JLabel(Localization.lang("Searching for files"));
-            prog.setIndeterminate(true);
-            prog.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
-            diag.setTitle(Localization.lang("Automatically setting file links"));
-            diag.getContentPane().add(prog, BorderLayout.CENTER);
-            diag.getContentPane().add(label, BorderLayout.SOUTH);
-
-            diag.pack();
-            diag.setLocationRelativeTo(diag.getParent());
-        }
-
-        Runnable r = () -> {
-            boolean foundAny = false;
-            AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, Globals.prefs.getFilePreferences(), Globals.prefs.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
-
-            for (BibEntry entry : entries) {
-
-                List<LinkedFile> linkedFiles = new ArrayList<>();
-                try {
-                    linkedFiles = util.findAssociatedNotLinkedFiles(entry);
-                } catch (IOException e) {
-                    LOGGER.error("Problem finding files", e);
-                }
-
-                if (ce != null) {
-                    for (LinkedFile linkedFile : linkedFiles) {
-                        // store undo information
-                        String newVal = FileFieldWriter.getStringRepresentation(linkedFile);
-
-                        String oldVal = entry.getField(FieldName.FILE).orElse(null);
-
-                        UndoableFieldChange fieldChange = new UndoableFieldChange(entry, FieldName.FILE, oldVal, newVal);
-                        ce.addEdit(fieldChange);
-
-                        DefaultTaskExecutor.runInJavaFXThread(() -> {
-                            entry.addFile(linkedFile);
-                        });
-                        foundAny = true;
-                    }
-
-                    if (changedEntries != null) {
-                        changedEntries.add(entry);
-                    }
-                }
-
-            }
-
-            final int id = foundAny ? 1 : 0;
-            SwingUtilities.invokeLater(() -> {
-
-                if (diag != null) {
-                    diag.dispose();
-                }
-                if (callback != null) {
-                    callback.actionPerformed(new ActionEvent(AutoSetLinks.class, id, ""));
-                }
-
-            });
-
-        };
-
-        SwingUtilities.invokeLater(() -> {
-            // show dialog which will be hidden when the task is done
-            if (diag != null) {
-                diag.setVisible(true);
-            }
-        });
-
-        return r;
-    }
-
-    /**
-     * Automatically add links for this entry to the table model given as an argument, based on the globally stored list
-     * of external file types. The entry itself is not modified. The entry's bibtex key must have been set.
-     *
-     * @param entry            The BibEntry to find links for.
-
-     * @param databaseContext  The database providing the relevant file directory, if any.
-     * @param callback         An ActionListener that is notified (on the event dispatch thread) when the search is finished.
-     *                         The ActionEvent has id=0 if no new links were added, and id=1 if one or more links were added. This
-     *                         parameter can be null, which means that no callback will be notified. The passed ActionEvent is
-     *                         constructed with (this, id, ""), where id is 1 if something has been done and 0 if nothing has been
-     *                         done.
-     * @param diag             An instantiated modal JDialog which will be used to display the progress of the automatically setting. This
-     *                         parameter can be null, which means that no progress update will be shown.
-     * @return the runnable able to perform the automatically setting
-     */
-    public static Runnable autoSetLinks(final BibEntry entry,
-            final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
-        return autoSetLinks(Collections.singletonList(entry), null, null, databaseContext, callback,
-                diag);
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/importer/ParserResultWarningDialog.java b/src/main/java/org/jabref/gui/importer/ParserResultWarningDialog.java
index 45dbf2fc9e7..827f88f51de 100644
--- a/src/main/java/org/jabref/gui/importer/ParserResultWarningDialog.java
+++ b/src/main/java/org/jabref/gui/importer/ParserResultWarningDialog.java
@@ -1,13 +1,8 @@
 package org.jabref.gui.importer;
 
-import java.awt.Dimension;
 import java.util.List;
 import java.util.Objects;
 
-import javax.swing.JOptionPane;
-import javax.swing.JScrollPane;
-import javax.swing.JTextArea;
-
 import org.jabref.gui.JabRefFrame;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
@@ -71,17 +66,7 @@ public static void showParserResultWarningDialog(final ParserResult parserResult
             dialogTitle = Localization.lang("Warnings") + " (" + parserResult.getFile().get().getName() + ")";
         }
 
-        // Create JTextArea with JScrollPane
-        final JTextArea textArea = new JTextArea(dialogContent.toString());
-        final JScrollPane scrollPane = new JScrollPane(textArea) {
-
-            @Override
-            public Dimension getPreferredSize() {
-                return new Dimension(800, Math.min(Math.max(100, warnings.size() * 15), 400)); // Guess a suitable height between 100 and 400
-            }
-        };
-
         // Show dialog
-        JOptionPane.showMessageDialog(null, scrollPane, dialogTitle, JOptionPane.WARNING_MESSAGE);
+        jabRefFrame.getDialogService().showWarningDialogAndWait(dialogTitle, dialogContent.toString());
     }
 }
diff --git a/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentAction.java b/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentAction.java
index 2a76c406f62..3196f1c46aa 100644
--- a/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentAction.java
+++ b/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentAction.java
@@ -20,7 +20,7 @@ public void performAction(BasePanel basePanel, ParserResult parserResult) {
 
         migration.performMigration(parserResult);
         List<BibEntry> conflicts = MergeReviewIntoCommentMigration.collectConflicts(parserResult);
-        if (!conflicts.isEmpty() && new MergeReviewIntoCommentConfirmationDialog(basePanel).askUserForMerge(conflicts)) {
+        if (!conflicts.isEmpty() && new MergeReviewIntoCommentConfirmationDialog(basePanel.frame().getDialogService()).askUserForMerge(conflicts)) {
             migration.performConflictingMigration(parserResult);
         }
     }
diff --git a/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentConfirmationDialog.java b/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentConfirmationDialog.java
index 2f789560771..74889ba5462 100644
--- a/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentConfirmationDialog.java
+++ b/src/main/java/org/jabref/gui/importer/actions/MergeReviewIntoCommentConfirmationDialog.java
@@ -4,18 +4,16 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import javax.swing.JOptionPane;
-
-import org.jabref.gui.BasePanel;
+import org.jabref.gui.DialogService;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 
 public class MergeReviewIntoCommentConfirmationDialog {
 
-    private final BasePanel panel;
+    private final DialogService dialogService;
 
-    public MergeReviewIntoCommentConfirmationDialog(BasePanel panel) {
-        this.panel = panel;
+    public MergeReviewIntoCommentConfirmationDialog(DialogService dialogService) {
+        this.dialogService = dialogService;
     }
 
     public boolean askUserForMerge(List<BibEntry> conflicts) {
@@ -25,15 +23,15 @@ public boolean askUserForMerge(List<BibEntry> conflicts) {
                 .map(Optional::get)
                 .collect(Collectors.joining(",\n"));
 
-        String[] options = {Localization.lang("Merge fields")};
-        int answer = JOptionPane.showOptionDialog(
-                null,
-                bibKeys + " " +
-                        Localization.lang("has/have both a 'Comment' and a 'Review' field.") + "\n" +
-                        Localization.lang("Since the 'Review' field was deprecated in JabRef 4.2, these two fields are about to be merged into the 'Comment' field.") + "\n" +
-                        Localization.lang("The conflicting fields of these entries will be merged into the 'Comment' field."),
-                Localization.lang("Review Field Migration"), JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE, null, options, options[0]);
+        String content = bibKeys + " " +
+                Localization.lang("has/have both a 'Comment' and a 'Review' field.") + "\n" +
+                Localization.lang("Since the 'Review' field was deprecated in JabRef 4.2, these two fields are about to be merged into the 'Comment' field.") + "\n" +
+                Localization.lang("The conflicting fields of these entries will be merged into the 'Comment' field.");
 
-        return 0 == answer;
+        return dialogService.showConfirmationDialogAndWait(
+                Localization.lang("Review Field Migration"),
+                content,
+                Localization.lang("Merge fields")
+        );
     }
 }
diff --git a/src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java b/src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java
index cd7be54acc3..ff87b3ddf2c 100644
--- a/src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java
+++ b/src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java
@@ -65,7 +65,7 @@ public void fetchAndMerge(BibEntry entry, List<String> fields) {
                                       if (fetchedEntry.isPresent()) {
                                           showMergeDialog(entry, fetchedEntry.get(), fetcher.get());
                                       } else {
-                                          panel.frame().setStatus(Localization.lang("Cannot get info based on given %0: %1", type, fieldContent.get()));
+                                          dialogService.notify(Localization.lang("Cannot get info based on given %0: %1", type, fieldContent.get()));
                                       }
                                   })
                                   .onFailure(exception -> {

From 1c1a6a42ca7fbd77905d6e06819bd6209d4aa7ee Mon Sep 17 00:00:00 2001
From: Johannes Manner <johannes.manner@web.de>
Date: Tue, 2 Apr 2019 22:45:03 +0200
Subject: [PATCH 31/61] All buttons in custom dialogs react on enter (#4835)

---
 src/main/java/org/jabref/gui/util/BaseDialog.java | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/main/java/org/jabref/gui/util/BaseDialog.java b/src/main/java/org/jabref/gui/util/BaseDialog.java
index 6cf9a1faf5b..921be10e748 100644
--- a/src/main/java/org/jabref/gui/util/BaseDialog.java
+++ b/src/main/java/org/jabref/gui/util/BaseDialog.java
@@ -6,6 +6,7 @@
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.Dialog;
 import javafx.scene.image.Image;
+import javafx.scene.input.KeyCode;
 import javafx.stage.Stage;
 
 import org.jabref.Globals;
@@ -23,6 +24,14 @@ protected BaseDialog() {
             } else if (keyBindingRepository.checkKeyCombinationEquality(KeyBinding.DEFAULT_DIALOG_ACTION, event)) {
                 getDefaultButton().ifPresent(Button::fire);
             }
+
+            // all buttons in base dialogs react on enter
+            if (event.getCode() == KeyCode.ENTER) {
+                if (event.getTarget() instanceof Button) {
+                    ((Button) event.getTarget()).fire();
+                    event.consume();
+                }
+            }
         });
 
         setDialogIcon(IconTheme.getJabRefImageFX());

From 3ed41efdcbe741793329a2954cea01a8c4934ceb Mon Sep 17 00:00:00 2001
From: Johannes Manner <johannes.manner@web.de>
Date: Tue, 2 Apr 2019 23:12:16 +0200
Subject: [PATCH 32/61] Adds a delay to the group expansion (#4838)

* Adds a delay to the group expansion

* Also collapses the item after 1 second

* Renamed handler class and method signature
---
 .../org/jabref/gui/groups/GroupTreeView.java  | 29 ++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/groups/GroupTreeView.java b/src/main/java/org/jabref/gui/groups/GroupTreeView.java
index 4dbbf152859..abc6e9fb460 100644
--- a/src/main/java/org/jabref/gui/groups/GroupTreeView.java
+++ b/src/main/java/org/jabref/gui/groups/GroupTreeView.java
@@ -71,6 +71,8 @@ public class GroupTreeView {
     private GroupTreeViewModel viewModel;
     private CustomLocalDragboard localDragboard;
 
+    private DragExpansionHandler dragExpansionHandler;
+
     private static void removePseudoClasses(TreeTableRow<GroupNodeViewModel> row, PseudoClass... pseudoClasses) {
         for (PseudoClass pseudoClass : pseudoClasses) {
             row.pseudoClassStateChanged(pseudoClass, false);
@@ -84,6 +86,7 @@ public void initialize() {
 
         // Set-up groups tree
         groupTree.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
+        dragExpansionHandler = new DragExpansionHandler();
 
         // Set-up bindings
         Consumer<ObservableList<GroupNodeViewModel>> updateSelectedGroups =
@@ -220,7 +223,7 @@ public void initialize() {
                     event.acceptTransferModes(TransferMode.MOVE, TransferMode.LINK);
 
                     //expand node and all children on drag over
-                    row.getTreeItem().setExpanded(true);
+                    dragExpansionHandler.expandGroup(row.getTreeItem());
 
                     removePseudoClasses(row, dragOverBottom, dragOverCenter, dragOverTop);
                     switch (getDroppingMouseLocation(row, event)) {
@@ -399,4 +402,28 @@ private DroppingMouseLocation getDroppingMouseLocation(TreeTableRow<GroupNodeVie
             return DroppingMouseLocation.CENTER;
         }
     }
+
+    private class DragExpansionHandler {
+        private static final long DRAG_TIME_BEFORE_EXPANDING_MS = 1000;
+        private TreeItem<GroupNodeViewModel> draggedItem;
+        private long dragStarted;
+
+        public void expandGroup(TreeItem<GroupNodeViewModel> treeItem) {
+            if (!treeItem.equals(draggedItem)) {
+                this.draggedItem = treeItem;
+                this.dragStarted = System.currentTimeMillis();
+                this.draggedItem.setExpanded(this.draggedItem.isExpanded());
+                return;
+            }
+
+            if (System.currentTimeMillis() - this.dragStarted > DRAG_TIME_BEFORE_EXPANDING_MS) {
+                // expand or collapse the tree item and reset the time
+                this.dragStarted = System.currentTimeMillis();
+                this.draggedItem.setExpanded(!this.draggedItem.isExpanded());
+            } else {
+                // leave the expansion state of the tree item as it is
+                this.draggedItem.setExpanded(this.draggedItem.isExpanded());
+            }
+        }
+    }
 }

From 54892f2ed6e2af249da48e367ceed116c4eeb728 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 2 Apr 2019 23:18:31 +0200
Subject: [PATCH 33/61] Remove global search feature (#4694)

* Remove global search feature

* Remove unused code
---
 CHANGELOG.md                                  |   2 +-
 src/main/java/org/jabref/gui/JabRefFrame.java |  17 +-
 .../java/org/jabref/gui/icon/IconTheme.java   |   2 -
 .../org/jabref/gui/keyboard/KeyBinding.java   |   1 -
 .../jabref/gui/search/GlobalSearchBar.java    | 124 +---
 .../jabref/gui/search/GlobalSearchWorker.java |  68 --
 .../jabref/gui/search/SearchResultFrame.java  | 650 ------------------
 .../jabref/preferences/SearchPreferences.java |  11 -
 src/main/resources/l10n/JabRef_en.properties  |   7 -
 9 files changed, 10 insertions(+), 872 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/search/GlobalSearchWorker.java
 delete mode 100644 src/main/java/org/jabref/gui/search/SearchResultFrame.java

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a64512c0723..564d782c9da 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -109,6 +109,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ### Removed
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.
 - The number column was removed.
+- We removed the global search feature.
 - We removed the coloring of cells in the maintable according to whether the field is optional/required.
 - We removed the feature to find and resolve duplicate BibTeX keys (as this use case is already covered by the integrity check).
 - We removed a few commands from the right-click menu that are not needed often and thus don't need to be placed that prominently:
@@ -146,7 +147,6 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 
-
 
 
 ## Older versions
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 939a1aeb689..d32b48dd30f 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -130,7 +130,6 @@
 import org.jabref.model.entry.specialfields.SpecialField;
 import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.LastFocusedTabPreferences;
-import org.jabref.preferences.SearchPreferences;
 
 import com.google.common.eventbus.Subscribe;
 import com.jfoenix.controls.JFXSnackbar;
@@ -270,16 +269,14 @@ private void init() {
             // Poor-mans binding to global state
             // We need to invoke this in the JavaFX thread as all the listeners sit there
             Platform.runLater(() -> Globals.stateManager.activeDatabaseProperty().setValue(Optional.of(currentBasePanel.getBibDatabaseContext())));
-            if (new SearchPreferences(Globals.prefs).isGlobalSearch()) {
-                globalSearchBar.performSearch();
-            } else {
-                String content = "";
-                Optional<SearchQuery> currentSearchQuery = currentBasePanel.getCurrentSearchQuery();
-                if (currentSearchQuery.isPresent()) {
-                    content = currentSearchQuery.get().getQuery();
-                }
-                globalSearchBar.setSearchTerm(content);
+
+            // Update search query
+            String content = "";
+            Optional<SearchQuery> currentSearchQuery = currentBasePanel.getCurrentSearchQuery();
+            if (currentSearchQuery.isPresent()) {
+                content = currentSearchQuery.get().getQuery();
             }
+            globalSearchBar.setSearchTerm(content);
 
             currentBasePanel.getPreviewPanel().updateLayout(Globals.prefs.getPreviewPreferences());
 
diff --git a/src/main/java/org/jabref/gui/icon/IconTheme.java b/src/main/java/org/jabref/gui/icon/IconTheme.java
index fbb97842ecf..e24a8e5d80a 100644
--- a/src/main/java/org/jabref/gui/icon/IconTheme.java
+++ b/src/main/java/org/jabref/gui/icon/IconTheme.java
@@ -283,7 +283,6 @@ public enum JabRefIcons implements JabRefIcon {
         SUCCESS(MaterialDesignIcon.CHECK_CIRCLE),
         WARNING(MaterialDesignIcon.ALERT),
         ERROR(MaterialDesignIcon.ALERT_CIRCLE),
-        OPEN_IN_NEW_WINDOW(MaterialDesignIcon.OPEN_IN_NEW), /*css: open-in-new */
         CASE_SENSITIVE(MaterialDesignIcon.ALPHABETICAL), /* css: mdi-alphabetical */
         REG_EX(MaterialDesignIcon.REGEX), /*css: mdi-regex */
         CONSOLE(MaterialDesignIcon.CONSOLE), /*css: console */
@@ -291,7 +290,6 @@ public enum JabRefIcons implements JabRefIcon {
         FACEBOOK(MaterialDesignIcon.FACEBOOK), /* css: facebook */
         TWITTER(MaterialDesignIcon.TWITTER), /* css: twitter */
         BLOG(MaterialDesignIcon.RSS), /* css: rss */
-        GLOBAL_SEARCH(MaterialDesignIcon.EARTH), /* css: earth */
         DATE_PICKER(MaterialDesignIcon.CALENDAR), /* css: calendar */
         DEFAULT_GROUP_ICON_COLORED(MaterialDesignIcon.PLAY),
         DEFAULT_GROUP_ICON(MaterialDesignIcon.LABEL_OUTLINE),
diff --git a/src/main/java/org/jabref/gui/keyboard/KeyBinding.java b/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
index b1b2cbbb4b5..43c55b7d444 100644
--- a/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
+++ b/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
@@ -40,7 +40,6 @@ public enum KeyBinding {
     FILE_LIST_EDITOR_MOVE_ENTRY_UP("File list editor, move entry up", Localization.lang("File list editor, move entry up"), "ctrl+UP", KeyBindingCategory.VIEW),
     FIND_UNLINKED_FILES("Find unlinked files", Localization.lang("Find unlinked files"), "shift+F7", KeyBindingCategory.QUALITY),
     FOCUS_ENTRY_TABLE("Focus entry table", Localization.lang("Focus entry table"), "alt+1", KeyBindingCategory.VIEW),
-    GLOBAL_SEARCH("Search globally", Localization.lang("Search globally"), "ctrl+shift+F", KeyBindingCategory.SEARCH),
     HELP("Help", Localization.lang("Help"), "F1", KeyBindingCategory.FILE),
     IMPORT_INTO_CURRENT_DATABASE("Import into current library", Localization.lang("Import into current library"), "ctrl+I", KeyBindingCategory.FILE),
     IMPORT_INTO_NEW_DATABASE("Import into new library", Localization.lang("Import into new library"), "ctrl+alt+I", KeyBindingCategory.FILE),
diff --git a/src/main/java/org/jabref/gui/search/GlobalSearchBar.java b/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
index 3f18ba400c6..8426b3fb290 100644
--- a/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
+++ b/src/main/java/org/jabref/gui/search/GlobalSearchBar.java
@@ -1,7 +1,6 @@
 package org.jabref.gui.search;
 
 import java.lang.reflect.Field;
-import java.nio.file.Path;
 import java.util.Objects;
 import java.util.Optional;
 
@@ -11,14 +10,12 @@
 import javafx.beans.binding.Bindings;
 import javafx.css.PseudoClass;
 import javafx.event.Event;
-import javafx.geometry.Orientation;
 import javafx.geometry.Pos;
 import javafx.scene.Node;
 import javafx.scene.control.Button;
 import javafx.scene.control.ContentDisplay;
 import javafx.scene.control.Label;
 import javafx.scene.control.ListView;
-import javafx.scene.control.Separator;
 import javafx.scene.control.Skin;
 import javafx.scene.control.TextField;
 import javafx.scene.control.ToggleButton;
@@ -35,7 +32,6 @@
 
 import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
-import org.jabref.gui.GUIGlobals;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.autocompleter.AppendPersonNamesStrategy;
 import org.jabref.gui.autocompleter.AutoCompleteFirstNameMode;
@@ -74,23 +70,13 @@ public class GlobalSearchBar extends HBox {
     private final TextField searchField = SearchTextField.create();
     private final ToggleButton caseSensitive;
     private final ToggleButton regularExp;
-    private final ToggleButton globalSearch;
     private final Button searchModeButton = new Button();
     private final Label currentResults = new Label("");
     private final SearchQueryHighlightObservable searchQueryHighlightObservable = new SearchQueryHighlightObservable();
-    private final Button openCurrentResultsInDialog = IconTheme.JabRefIcons.OPEN_IN_NEW_WINDOW.asButton();
     private SearchWorker searchWorker;
-    private GlobalSearchWorker globalSearchWorker;
-
-    private SearchResultFrame searchResultFrame;
 
     private SearchDisplayMode searchDisplayMode;
 
-    /**
-     * if this flag is set the searchbar won't be selected after the next search
-     */
-    private boolean dontSelectSearchBar;
-
     public GlobalSearchBar(JabRefFrame frame) {
         super();
         this.frame = Objects.requireNonNull(frame);
@@ -100,22 +86,11 @@ public GlobalSearchBar(JabRefFrame frame) {
         // fits the standard "found x entries"-message thus hinders the searchbar to jump around while searching if the frame width is too small
         currentResults.setPrefWidth(150);
 
-        globalSearch = IconTheme.JabRefIcons.GLOBAL_SEARCH.asToggleButton();
-        globalSearch.setSelected(searchPreferences.isGlobalSearch());
-        globalSearch.setTooltip(new Tooltip(Localization.lang("Search in all open libraries")));
-
-
         KeyBindingRepository keyBindingRepository = Globals.getKeyPrefs();
         searchField.addEventFilter(KeyEvent.KEY_PRESSED, event -> {
             Optional<KeyBinding> keyBinding = keyBindingRepository.mapToKeyBinding(event);
             if (keyBinding.isPresent()) {
-                if (keyBinding.get().equals(KeyBinding.GLOBAL_SEARCH)) {
-                    globalSearch.setSelected(true);
-                    searchPreferences.setGlobalSearch(globalSearch.isSelected());
-                    updateOpenCurrentResultsTooltip(globalSearch.isSelected());
-                    focus();
-                    event.consume();
-                } else if (keyBinding.get().equals(KeyBinding.CLOSE)) {
+                if (keyBinding.get().equals(KeyBinding.CLOSE)) {
                     // Clear search and select first entry, if available
                     clearSearch();
                     frame.getCurrentBasePanel().getMainTable().getSelectionModel().selectFirst();
@@ -124,22 +99,6 @@ public GlobalSearchBar(JabRefFrame frame) {
             }
         });
 
-        globalSearch.setOnAction(event -> {
-            searchPreferences.setGlobalSearch(globalSearch.isSelected());
-            updateOpenCurrentResultsTooltip(globalSearch.isSelected());
-        });
-
-        //openCurrentResultsInDialog.setDisabledIcon(IconTheme.JabRefIcons.OPEN_IN_NEW_WINDOW.disabled().getSmallIcon());
-        openCurrentResultsInDialog.setOnAction(event -> {
-            if (globalSearch.isSelected()) {
-                performGlobalSearch();
-            } else {
-                openLocalFindingsInExternalPanel();
-            }
-        });
-        openCurrentResultsInDialog.setDisable(true);
-        updateOpenCurrentResultsTooltip(globalSearch.isSelected());
-
         regularExp = IconTheme.JabRefIcons.REG_EX.asToggleButton();
         regularExp.setSelected(searchPreferences.isRegularExpression());
         regularExp.setTooltip(new Tooltip(Localization.lang("regular expression")));
@@ -193,64 +152,6 @@ public GlobalSearchBar(JabRefFrame frame) {
         this.setAlignment(Pos.CENTER_LEFT);
     }
 
-    private void performGlobalSearch() {
-        BasePanel currentBasePanel = frame.getCurrentBasePanel();
-        if ((currentBasePanel == null) || validateSearchResultFrame(true)) {
-            return;
-        }
-
-        if (globalSearchWorker != null) {
-            globalSearchWorker.cancel(true);
-        }
-
-        if (searchField.getText().isEmpty()) {
-            focus();
-            return;
-        }
-
-        globalSearchWorker = new GlobalSearchWorker(currentBasePanel.frame(), getSearchQuery());
-        globalSearchWorker.execute();
-    }
-
-    private void openLocalFindingsInExternalPanel() {
-        BasePanel currentBasePanel = frame.getCurrentBasePanel();
-        if ((currentBasePanel == null) || validateSearchResultFrame(false)) {
-            return;
-        }
-
-        if (searchField.getText().isEmpty()) {
-            focus();
-            return;
-        }
-
-        SearchResultFrame searchDialog = new SearchResultFrame(
-                currentBasePanel.frame(),
-                Localization.lang("Search results in library %0 for %1",
-                        currentBasePanel.getBibDatabaseContext()
-                                        .getDatabasePath()
-                                        .map(Path::getFileName)
-                                        .map(Path::toString)
-                                        .orElse(GUIGlobals.UNTITLED_TITLE),
-                        this.getSearchQuery().localize()), getSearchQuery(), false);
-        searchDialog.addEntries(currentBasePanel.getDatabase().getEntries(), currentBasePanel);
-        searchDialog.selectFirstEntry();
-        searchDialog.setVisible(true);
-    }
-
-    private boolean validateSearchResultFrame(boolean globalSearch) {
-        if (searchResultFrame != null) {
-            if ((searchResultFrame.isGlobalSearch() == globalSearch) && isStillValidQuery(searchResultFrame.getSearchQuery())) {
-                searchResultFrame.focus();
-                return true;
-            } else {
-                searchResultFrame.dispose();
-                return false;
-            }
-        }
-
-        return false;
-    }
-
     private void toggleSearchModeAndSearch() {
         int nextSearchMode = (searchDisplayMode.ordinal() + 1) % SearchDisplayMode.values().length;
         searchDisplayMode = SearchDisplayMode.values()[nextSearchMode];
@@ -288,7 +189,6 @@ private void clearSearch() {
         currentResults.setText("");
         searchField.setText("");
         searchQueryHighlightObservable.reset();
-        openCurrentResultsInDialog.setDisable(true);
 
         Globals.stateManager.clearSearchQuery();
     }
@@ -331,7 +231,6 @@ private void informUserAboutInvalidSearchQuery() {
 
         String illegalSearch = Localization.lang("Search failed: illegal search expression");
         currentResults.setText(illegalSearch);
-        openCurrentResultsInDialog.setDisable(true);
     }
 
     public void setAutoCompleter(AutoCompleteSuggestionProvider<Author> searchCompleter) {
@@ -364,12 +263,6 @@ public SearchQueryHighlightObservable getSearchQueryHighlightObservable() {
         return searchQueryHighlightObservable;
     }
 
-    public boolean isStillValidQuery(SearchQuery query) {
-        return query.getQuery().equals(this.searchField.getText())
-                && (query.isRegularExpression() == regularExp.isSelected())
-                && (query.isCaseSensitive() == caseSensitive.isSelected());
-    }
-
     private SearchQuery getSearchQuery() {
         SearchQuery searchQuery = new SearchQuery(this.searchField.getText(), this.caseSensitive.isSelected(), this.regularExp.isSelected());
         this.frame.getCurrentBasePanel().setCurrentSearchQuery(searchQuery);
@@ -396,11 +289,6 @@ public void updateResults(int matched, TextFlow description, boolean grammarBase
         tooltip.setGraphic(description);
         tooltip.setMaxHeight(10);
         searchField.setTooltip(tooltip);
-        openCurrentResultsInDialog.setDisable(false);
-    }
-
-    public void setSearchResultFrame(SearchResultFrame searchResultFrame) {
-        this.searchResultFrame = searchResultFrame;
     }
 
     public void setSearchTerm(String searchTerm) {
@@ -411,14 +299,6 @@ public void setSearchTerm(String searchTerm) {
         DefaultTaskExecutor.runInJavaFXThread(() -> searchField.setText(searchTerm));
     }
 
-    private void updateOpenCurrentResultsTooltip(boolean globalSearchEnabled) {
-        if (globalSearchEnabled) {
-            openCurrentResultsInDialog.setTooltip(new Tooltip(Localization.lang("Show global search results in a window")));
-        } else {
-            openCurrentResultsInDialog.setTooltip(new Tooltip(Localization.lang("Show search results in a window")));
-        }
-    }
-
     private class SearchPopupSkin<T> implements Skin<AutoCompletePopup<T>> {
 
         private final AutoCompletePopup<T> control;
@@ -436,7 +316,7 @@ public SearchPopupSkin(AutoCompletePopup<T> control) {
             this.suggestionList.maxWidthProperty().bind(control.maxWidthProperty());
             this.suggestionList.minWidthProperty().bind(control.minWidthProperty());
 
-            ToolBar toolBar = new ToolBar(openCurrentResultsInDialog, new Separator(Orientation.VERTICAL), globalSearch, regularExp, caseSensitive, searchModeButton);
+            ToolBar toolBar = new ToolBar(regularExp, caseSensitive, searchModeButton);
 
             this.container = new BorderPane();
             this.container.setCenter(suggestionList);
diff --git a/src/main/java/org/jabref/gui/search/GlobalSearchWorker.java b/src/main/java/org/jabref/gui/search/GlobalSearchWorker.java
deleted file mode 100644
index bdbd6fe4bba..00000000000
--- a/src/main/java/org/jabref/gui/search/GlobalSearchWorker.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package org.jabref.gui.search;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.concurrent.ExecutionException;
-import java.util.stream.Collectors;
-
-import javax.swing.SwingWorker;
-
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.search.SearchQuery;
-import org.jabref.model.entry.BibEntry;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-class GlobalSearchWorker extends SwingWorker<Map<BasePanel, List<BibEntry>>, Void> {
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(GlobalSearchWorker.class);
-
-    private final JabRefFrame frame;
-    private final SearchQuery searchQuery;
-    private final SearchResultFrame dialog;
-
-    public GlobalSearchWorker(JabRefFrame frame, SearchQuery query) {
-        this.frame = Objects.requireNonNull(frame);
-        this.searchQuery = Objects.requireNonNull(query);
-
-        dialog = new SearchResultFrame(frame,
-                Localization.lang("Search results in all libraries for %0",
-                        this.searchQuery.localize()),
-                searchQuery, true);
-        frame.getGlobalSearchBar().setSearchResultFrame(dialog);
-    }
-
-    @Override
-    protected Map<BasePanel, List<BibEntry>> doInBackground() throws Exception {
-        Map<BasePanel, List<BibEntry>> matches = new HashMap<>();
-        for (BasePanel basePanel : frame.getBasePanelList()) {
-            matches.put(basePanel, basePanel.getDatabase().getEntries().parallelStream()
-                    .filter(searchQuery::isMatch)
-                    .collect(Collectors.toList()));
-        }
-        return matches;
-    }
-
-    @Override
-    protected void done() {
-        if (isCancelled()) {
-            return;
-        }
-
-        try {
-            for (Map.Entry<BasePanel, List<BibEntry>> match : get().entrySet()) {
-                dialog.addEntries(match.getValue(), match.getKey());
-            }
-            dialog.selectFirstEntry();
-            dialog.setVisible(true);
-        } catch (InterruptedException | ExecutionException e) {
-            LOGGER.error("something went wrong during the search", e);
-        }
-    }
-
-}
diff --git a/src/main/java/org/jabref/gui/search/SearchResultFrame.java b/src/main/java/org/jabref/gui/search/SearchResultFrame.java
deleted file mode 100644
index 376de69855e..00000000000
--- a/src/main/java/org/jabref/gui/search/SearchResultFrame.java
+++ /dev/null
@@ -1,650 +0,0 @@
-package org.jabref.gui.search;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ComponentAdapter;
-import java.awt.event.ComponentEvent;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.IOException;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.Optional;
-
-import javax.swing.AbstractAction;
-import javax.swing.ActionMap;
-import javax.swing.InputMap;
-import javax.swing.JComponent;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JPopupMenu;
-import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
-import javax.swing.JTable;
-import javax.swing.KeyStroke;
-import javax.swing.table.TableColumnModel;
-
-import javafx.embed.swing.JFXPanel;
-import javafx.scene.Scene;
-
-import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.GUIGlobals;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.PreviewPanel;
-import org.jabref.gui.customjfx.CustomJFXPanel;
-import org.jabref.gui.desktop.JabRefDesktop;
-import org.jabref.gui.externalfiletype.ExternalFileMenuItem;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
-import org.jabref.gui.filelist.FileListEntry;
-import org.jabref.gui.filelist.FileListTableModel;
-import org.jabref.gui.icon.IconTheme;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.gui.maintable.MainTableNameFormatter;
-import org.jabref.gui.renderer.GeneralRenderer;
-import org.jabref.gui.util.comparator.IconComparator;
-import org.jabref.logic.bibtex.comparator.EntryComparator;
-import org.jabref.logic.bibtex.comparator.FieldComparator;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.search.SearchQuery;
-import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FieldName;
-import org.jabref.model.entry.FieldProperty;
-import org.jabref.model.entry.InternalBibtexFields;
-import org.jabref.model.strings.StringUtil;
-import org.jabref.preferences.SearchPreferences;
-
-import ca.odell.glazedlists.BasicEventList;
-import ca.odell.glazedlists.EventList;
-import ca.odell.glazedlists.SortedList;
-import ca.odell.glazedlists.event.ListEvent;
-import ca.odell.glazedlists.event.ListEventListener;
-import ca.odell.glazedlists.gui.AbstractTableComparatorChooser;
-import ca.odell.glazedlists.gui.AdvancedTableFormat;
-import ca.odell.glazedlists.swing.DefaultEventSelectionModel;
-import ca.odell.glazedlists.swing.DefaultEventTableModel;
-import ca.odell.glazedlists.swing.GlazedListsSwing;
-import ca.odell.glazedlists.swing.TableComparatorChooser;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * Dialog to display search results, potentially from more than one BasePanel, with
- * possibility to preview and to locate each entry in the main window.
- */
-public class SearchResultFrame {
-
-    private static final String[] FIELDS = new String[] {FieldName.AUTHOR, FieldName.TITLE, FieldName.YEAR, FieldName.JOURNAL};
-    private static final int DATABASE_COL = 0;
-    private static final int FILE_COL = 1;
-    private static final int URL_COL = 2;
-    private static final int PAD = 3;
-
-    private static final Logger LOGGER = LoggerFactory.getLogger(SearchResultFrame.class);
-
-    private final JabRefFrame frame;
-    private JFrame searchResultFrame;
-    private final JLabel fileLabel = new JLabel(IconTheme.JabRefIcons.FILE.getSmallIcon());
-    private final JLabel urlLabel = new JLabel(IconTheme.JabRefIcons.WWW.getSmallIcon());
-
-    private final JSplitPane contentPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
-
-    private final EventList<BibEntry> entries = new BasicEventList<>();
-
-    private final Map<BibEntry, BasePanel> entryHome = new HashMap<>();
-    private DefaultEventTableModel<BibEntry> model;
-
-    private SortedList<BibEntry> sortedEntries;
-    private JTable entryTable;
-    private PreviewPanel preview;
-
-    private final SearchQuery searchQuery;
-    private final boolean globalSearch;
-
-    public SearchResultFrame(JabRefFrame frame, String title, SearchQuery searchQuery, boolean globalSearch) {
-        this.frame = Objects.requireNonNull(frame);
-        this.searchQuery = searchQuery;
-        this.globalSearch = globalSearch;
-        frame.getGlobalSearchBar().setSearchResultFrame(this);
-        init(Objects.requireNonNull(title));
-    }
-
-    private void init(String title) {
-        searchResultFrame = new JFrame();
-        searchResultFrame.setTitle(title);
-        searchResultFrame.setIconImages(IconTheme.getLogoSet());
-
-        preview = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), frame.getDialogService(), ExternalFileTypes.getInstance());
-
-        sortedEntries = new SortedList<>(entries, new EntryComparator(false, true, FieldName.AUTHOR));
-        model = (DefaultEventTableModel<BibEntry>) GlazedListsSwing.eventTableModelWithThreadProxyList(sortedEntries,
-                                                                                                       new EntryTableFormat());
-        entryTable = new JTable(model);
-
-        GeneralRenderer renderer = new GeneralRenderer(Color.white);
-        entryTable.setDefaultRenderer(JLabel.class, renderer);
-        entryTable.setDefaultRenderer(String.class, renderer);
-        setWidths();
-        TableComparatorChooser<BibEntry> tableSorter = TableComparatorChooser.install(entryTable, sortedEntries,
-                                                                                      AbstractTableComparatorChooser.MULTIPLE_COLUMN_KEYBOARD);
-        setupComparatorChooser(tableSorter);
-        JScrollPane sp = new JScrollPane(entryTable);
-
-        final DefaultEventSelectionModel<BibEntry> selectionModel = (DefaultEventSelectionModel<BibEntry>) GlazedListsSwing
-                                                                                                                           .eventSelectionModelWithThreadProxyList(sortedEntries);
-        entryTable.setSelectionModel(selectionModel);
-        selectionModel.getSelected().addListEventListener(new EntrySelectionListener());
-        entryTable.addMouseListener(new TableClickListener());
-
-        contentPane.setTopComponent(sp);
-
-        JFXPanel container = CustomJFXPanel.wrap(new Scene(preview));
-        contentPane.setBottomComponent(container);
-
-        // Key bindings:
-        AbstractAction closeAction = new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                dispose();
-            }
-        };
-
-        ActionMap actionMap = contentPane.getActionMap();
-        InputMap inputMap = contentPane.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-        inputMap.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE), "close");
-        inputMap.put(Globals.getKeyPrefs().getKey(KeyBinding.CLOSE_DATABASE), "close");
-        actionMap.put("close", closeAction);
-
-        actionMap = entryTable.getActionMap();
-        inputMap = entryTable.getInputMap();
-        //Override 'selectNextColumnCell' and 'selectPreviousColumnCell' to move rows instead of cells on TAB
-        actionMap.put("selectNextColumnCell", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                selectNextEntry();
-            }
-        });
-        actionMap.put("selectPreviousColumnCell", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                selectPreviousEntry();
-            }
-        });
-        actionMap.put("selectNextRow", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                selectNextEntry();
-            }
-        });
-        actionMap.put("selectPreviousRow", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                selectPreviousEntry();
-            }
-        });
-
-        String selectFirst = "selectFirst";
-        inputMap.put(Globals.getKeyPrefs().getKey(KeyBinding.SELECT_FIRST_ENTRY), selectFirst);
-        actionMap.put(selectFirst, new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent event) {
-                selectFirstEntry();
-            }
-        });
-
-        String selectLast = "selectLast";
-        inputMap.put(Globals.getKeyPrefs().getKey(KeyBinding.SELECT_LAST_ENTRY), selectLast);
-        actionMap.put(selectLast, new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent event) {
-                selectLastEntry();
-            }
-        });
-
-        actionMap.put("copy", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                if (!selectionModel.getSelected().isEmpty()) {
-                    List<BibEntry> bes = selectionModel.getSelected();
-                    try {
-                        Globals.clipboardManager.setContent(bes);
-                    } catch (IOException e1) {
-                        LOGGER.error("Error while serializing entries for clipboard", e1);
-                    }
-                    frame.output(Localization.lang("Copied") + ' ' + (bes.size() > 1 ? bes.size() + " "
-                            + Localization.lang("entries")
-                            : "1 " + Localization.lang("entry") + '.'));
-                }
-            }
-        });
-
-        // override standard enter-action; enter opens the selected entry
-        entryTable.getInputMap(JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT).put(KeyStroke.getKeyStroke(KeyEvent.VK_ENTER, 0), "Enter");
-        actionMap.put("Enter", new AbstractAction() {
-
-            @Override
-            public void actionPerformed(ActionEvent ae) {
-                BibEntry entry = sortedEntries.get(entryTable.getSelectedRow());
-                selectEntryInBasePanel(entry);
-            }
-        });
-
-        searchResultFrame.addWindowListener(new WindowAdapter() {
-
-            @Override
-            public void windowOpened(WindowEvent e) {
-                contentPane.setDividerLocation(0.5f);
-            }
-
-            @Override
-            public void windowClosing(WindowEvent event) {
-                dispose();
-            }
-        });
-
-        searchResultFrame.getContentPane().add(contentPane, BorderLayout.CENTER);
-
-        // Remember and default to last size:
-        SearchPreferences searchPreferences = new SearchPreferences(Globals.prefs);
-        searchResultFrame.setSize(searchPreferences.getSeachDialogWidth(), searchPreferences.getSeachDialogHeight());
-        searchResultFrame.setLocation(searchPreferences.getSearchDialogPosX(), searchPreferences.getSearchDialogPosY());
-
-        searchResultFrame.addComponentListener(new ComponentAdapter() {
-
-            @Override
-            public void componentResized(ComponentEvent e) {
-                new SearchPreferences(Globals.prefs)
-                        .setSearchDialogWidth(searchResultFrame.getSize().width)
-                        .setSearchDialogHeight(searchResultFrame.getSize().height);
-            }
-
-            @Override
-            public void componentMoved(ComponentEvent e) {
-                new SearchPreferences(Globals.prefs)
-                                                    .setSearchDialogPosX(searchResultFrame.getLocation().x)
-                                                    .setSearchDialogPosY(searchResultFrame.getLocation().y);
-            }
-        });
-    }
-
-    /**
-     * Control the visibility of the dialog.
-     * @param visible true to show dialog, false to hide.
-     */
-    public void setVisible(boolean visible) {
-        searchResultFrame.setVisible(visible);
-    }
-
-    public void selectFirstEntry() {
-        selectEntry(0);
-    }
-
-    public void selectLastEntry() {
-        selectEntry(entryTable.getRowCount() - 1);
-    }
-
-    public void selectPreviousEntry() {
-        selectEntry(((entryTable.getSelectedRow() - 1) + entryTable.getRowCount()) % entryTable.getRowCount());
-    }
-
-    public void selectNextEntry() {
-        selectEntry((entryTable.getSelectedRow() + 1) % entryTable.getRowCount());
-    }
-
-    public void selectEntry(int index) {
-        if ((index >= 0) && (index < entryTable.getRowCount())) {
-            entryTable.changeSelection(index, 0, false, false);
-        } else {
-            contentPane.setDividerLocation(1.0f);
-        }
-    }
-
-    /**
-     * Set up the comparators for each column, so the user can modify sort order
-     * by clicking the column labels.
-     * @param comparatorChooser The comparator chooser controlling the sort order.
-     */
-    private void setupComparatorChooser(TableComparatorChooser<BibEntry> comparatorChooser) {
-        List<Comparator> comparators;
-        // Icon columns:
-        for (int i = 0; i < PAD; i++) {
-            comparators = comparatorChooser.getComparatorsForColumn(i);
-            comparators.clear();
-            if (i == FILE_COL) {
-                comparators.add(new IconComparator(Collections.singletonList(FieldName.FILE)));
-            } else if (i == URL_COL) {
-                comparators.add(new IconComparator(Collections.singletonList(FieldName.URL)));
-            } else if (i == DATABASE_COL) {
-                comparators.add((entry1, entry2) -> {
-                    String databaseTitle1 = entryHome.get(entry1).getTabTitle();
-                    String databaseTitle2 = entryHome.get(entry2).getTabTitle();
-                    return databaseTitle1.compareTo(databaseTitle2);
-                });
-            }
-
-        }
-        // Remaining columns:
-        for (int i = PAD; i < (PAD + FIELDS.length); i++) {
-            comparators = comparatorChooser.getComparatorsForColumn(i);
-            comparators.clear();
-            comparators.add(new FieldComparator(FIELDS[i - PAD]));
-        }
-
-        sortedEntries.getReadWriteLock().writeLock().lock();
-        comparatorChooser.appendComparator(PAD, 0, false);
-        sortedEntries.getReadWriteLock().writeLock().unlock();
-
-    }
-
-    /**
-     * Set column widths according to which field is shown, and lock icon columns
-     * to a suitable width.
-     */
-    private void setWidths() {
-        TableColumnModel cm = entryTable.getColumnModel();
-        for (int i = 0; i < (PAD + FIELDS.length); i++) {
-            switch (i) {
-                case FILE_COL:
-                case URL_COL:
-                    cm.getColumn(i).setPreferredWidth(GUIGlobals.WIDTH_ICON_COL);
-                    cm.getColumn(i).setMinWidth(GUIGlobals.WIDTH_ICON_COL);
-                    cm.getColumn(i).setMaxWidth(GUIGlobals.WIDTH_ICON_COL);
-                    break;
-                case DATABASE_COL: {
-                    Double width = InternalBibtexFields.getFieldLength(FieldName.AUTHOR);
-                    cm.getColumn(i).setPreferredWidth(width.intValue());
-                    break;
-                }
-                default: {
-                    Double width = InternalBibtexFields.getFieldLength(FIELDS[i - PAD]);
-                    cm.getColumn(i).setPreferredWidth(width.intValue());
-                    break;
-                }
-            }
-        }
-    }
-
-    /**
-     * Add a list of entries to the table.
-     * @param newEntries The list of entries.
-     * @param panel A reference to the BasePanel where the entries belong.
-     */
-    public void addEntries(List<BibEntry> newEntries, BasePanel panel) {
-        for (BibEntry entry : newEntries) {
-            addEntry(entry, panel);
-        }
-    }
-
-    /**
-     * Add a single entry to the table.
-     * @param entry The entry to add.
-     * @param panel A reference to the BasePanel where the entry belongs.
-     */
-    private void addEntry(BibEntry entry, BasePanel panel) {
-        entries.add(entry);
-        entryHome.put(entry, panel);
-
-        if ((preview.getEntry() == null) || !preview.getBasePanel().isPresent()) {
-            preview.setEntry(entry);
-            preview.setBasePanel(panel);
-            preview.setDatabaseContext(panel.getBibDatabaseContext());
-        }
-    }
-
-    private void selectEntryInBasePanel(BibEntry entry) {
-        BasePanel basePanel = entryHome.get(entry);
-        frame.showBasePanel(basePanel);
-        basePanel.requestFocus();
-        basePanel.clearAndSelect(entry);
-    }
-
-    public void dispose() {
-        frame.getGlobalSearchBar().setSearchResultFrame(null);
-        searchResultFrame.dispose();
-        frame.getGlobalSearchBar().focus();
-    }
-
-    public void focus() {
-        entryTable.requestFocus();
-    }
-
-    public SearchQuery getSearchQuery() {
-        return searchQuery;
-    }
-
-    public boolean isGlobalSearch() {
-        return globalSearch;
-    }
-
-    /**
-     * Mouse listener for the entry table. Processes icon clicks to open external
-     * files or urls, as well as the opening of the context menu.
-     */
-    class TableClickListener extends MouseAdapter {
-
-        @Override
-        public void mouseReleased(MouseEvent e) {
-            if (e.isPopupTrigger()) {
-                processPopupTrigger(e);
-            }
-        }
-
-        @Override
-        public void mousePressed(MouseEvent e) {
-            if (e.isPopupTrigger()) {
-                processPopupTrigger(e);
-                return;
-            }
-
-            // First find the row on which the user has clicked.
-            final int row = entryTable.rowAtPoint(e.getPoint());
-
-            // A double click on an entry should highlight the entry in its BasePanel:
-            if (e.getClickCount() == 2) {
-                selectEntryInBasePanel(model.getElementAt(row));
-            }
-        }
-
-        @Override
-        public void mouseClicked(MouseEvent e) {
-            if (e.isPopupTrigger()) {
-                processPopupTrigger(e);
-                return;
-            }
-            //if (e.)
-            final int col = entryTable.columnAtPoint(e.getPoint());
-            final int row = entryTable.rowAtPoint(e.getPoint());
-            if (col < PAD) {
-                BibEntry entry = sortedEntries.get(row);
-                BasePanel p = entryHome.get(entry);
-                switch (col) {
-                case FILE_COL:
-                    if (entry.hasField(FieldName.FILE)) {
-                        FileListTableModel tableModel = new FileListTableModel();
-                        entry.getField(FieldName.FILE).ifPresent(tableModel::setContent);
-                        if (tableModel.getRowCount() == 0) {
-                            return;
-                        }
-                        FileListEntry fl = tableModel.getEntry(0);
-                            (new ExternalFileMenuItem(frame, "", fl.getLink(), null,
-                                p.getBibDatabaseContext(), fl.getType())).actionPerformed(null);
-                    }
-                    break;
-                case URL_COL:
-                    entry.getField(FieldName.URL).ifPresent(link -> { try {
-                        JabRefDesktop.openExternalViewer(p.getBibDatabaseContext(), link, FieldName.URL);
-                    } catch (IOException ex) {
-                            LOGGER.warn("Could not open viewer", ex);
-                        }
-                    });
-                    break;
-                default:
-                    break;
-                }
-            }
-        }
-
-        /**
-         * If the user has signalled the opening of a context menu, the event
-         * gets redirected to this method. Here we open a file link menu if the
-         * user is pointing at a file link icon. Otherwise a general context
-         * menu should be shown.
-         * @param e The triggering mouse event.
-         */
-        public void processPopupTrigger(MouseEvent e) {
-            BibEntry entry = sortedEntries.get(entryTable.rowAtPoint(e.getPoint()));
-            BasePanel p = entryHome.get(entry);
-            int col = entryTable.columnAtPoint(e.getPoint());
-            JPopupMenu menu = new JPopupMenu();
-            int count = 0;
-
-            if (col == FILE_COL) {
-                // We use a FileListTableModel to parse the field content:
-                FileListTableModel fileList = new FileListTableModel();
-                entry.getField(FieldName.FILE).ifPresent(fileList::setContent);
-                // If there are one or more links, open the first one:
-                for (int i = 0; i < fileList.getRowCount(); i++) {
-                    FileListEntry flEntry = fileList.getEntry(i);
-                    String description = flEntry.getDescription();
-                    if ((description == null) || (description.trim().isEmpty())) {
-                        description = flEntry.getLink();
-                    }
-                    menu.add(new ExternalFileMenuItem(p.frame(), description, flEntry.getLink(),
-                                                      flEntry.getType().get().getIcon().getSmallIcon(), p.getBibDatabaseContext(), flEntry.getType()));
-                    count++;
-                }
-
-            }
-
-            if (count > 0) {
-                menu.show(entryTable, e.getX(), e.getY());
-            }
-        }
-    }
-
-    /**
-     * The listener for the Glazed list monitoring the current selection.
-     * When selection changes, we need to update the preview panel.
-     */
-    private class EntrySelectionListener implements ListEventListener<BibEntry> {
-
-        @Override
-        public void listChanged(ListEvent<BibEntry> listEvent) {
-            if (listEvent.getSourceList().size() == 1) {
-                BibEntry entry = listEvent.getSourceList().get(0);
-                // Find out which BasePanel the selected entry belongs to:
-                BasePanel basePanel = entryHome.get(entry);
-                // Update the preview's database context:
-                preview.setDatabaseContext(basePanel.getBibDatabaseContext());
-                // Update the preview's entry:
-                preview.setEntry(entry);
-                preview.setBasePanel(entryHome.get(entry));
-                preview.setDatabaseContext(entryHome.get(entry).getBibDatabaseContext());
-                contentPane.setDividerLocation(0.5f);
-            }
-        }
-    }
-
-    /**
-     * TableFormat for the table shown in the dialog. Handles the display of entry
-     * fields and icons for linked files and urls.
-     */
-    private class EntryTableFormat implements AdvancedTableFormat<BibEntry> {
-
-        @Override
-        public int getColumnCount() {
-            return PAD + FIELDS.length;
-        }
-
-        @Override
-        public String getColumnName(int column) {
-            if (column >= PAD) {
-                return StringUtil.capitalizeFirst(FIELDS[column - PAD]);
-            } else if (column == DATABASE_COL) {
-                return Localization.lang("Library");
-            } else {
-                return "";
-            }
-        }
-
-        @Override
-        public Object getColumnValue(BibEntry entry, int column) {
-            if (column < PAD) {
-                switch (column) {
-                    case DATABASE_COL:
-                        return entryHome.get(entry).getTabTitle();
-                    case FILE_COL:
-                        if (entry.hasField(FieldName.FILE)) {
-                            FileListTableModel tmpModel = new FileListTableModel();
-                            entry.getField(FieldName.FILE).ifPresent(tmpModel::setContent);
-                            fileLabel.setToolTipText(tmpModel.getToolTipHTMLRepresentation());
-                            if (tmpModel.getRowCount() > 0) {
-                                if (tmpModel.getEntry(0).getType().isPresent()) {
-                                    fileLabel.setIcon(tmpModel.getEntry(0).getType().get().getIcon().getSmallIcon());
-                                } else {
-                                    fileLabel.setIcon(IconTheme.JabRefIcons.FILE.getSmallIcon());
-                                }
-                            }
-                            return fileLabel;
-                        } else {
-                            return null;
-                        }
-                    case URL_COL: {
-                        Optional<String> urlField = entry.getField(FieldName.URL);
-                        if (urlField.isPresent()) {
-                            urlLabel.setToolTipText(urlField.get());
-                            return urlLabel;
-                        }
-                        return null;
-                    }
-                    default:
-                        return null;
-                }
-            } else {
-                String field = FIELDS[column - PAD];
-                String fieldContent = entry.getLatexFreeField(field).orElse("");
-
-                if (InternalBibtexFields.getFieldProperties(field).contains(FieldProperty.PERSON_NAMES)) {
-                    // For name fields, tap into a MainTableFormat instance and use
-                    // the same name formatting as is used in the entry table:
-                    return MainTableNameFormatter.formatName(fieldContent);
-                }
-                return fieldContent;
-            }
-        }
-
-        @Override
-        public Class<?> getColumnClass(int i) {
-            switch (i) {
-                case FILE_COL:
-                case URL_COL:
-                    return JLabel.class;
-                default:
-                    return String.class;
-            }
-        }
-
-        @Override
-        public Comparator<?> getColumnComparator(int i) {
-            return null;
-        }
-    }
-
-}
diff --git a/src/main/java/org/jabref/preferences/SearchPreferences.java b/src/main/java/org/jabref/preferences/SearchPreferences.java
index 53452b5d639..78c1ba8aff8 100644
--- a/src/main/java/org/jabref/preferences/SearchPreferences.java
+++ b/src/main/java/org/jabref/preferences/SearchPreferences.java
@@ -7,7 +7,6 @@
 
 public class SearchPreferences {
 
-    private static final String SEARCH_GLOBAL = "searchGlobal";
     private static final String SEARCH_DISPLAY_MODE = "searchDisplayMode";
     private static final String SEARCH_CASE_SENSITIVE = "caseSensitiveSearch";
     private static final String SEARCH_REG_EXP = "regExpSearch";
@@ -25,7 +24,6 @@ public SearchPreferences(JabRefPreferences preferences) {
     }
 
     public static void putDefaults(Map<String, Object> defaults) {
-        defaults.put(SEARCH_GLOBAL, Boolean.FALSE);
         defaults.put(SEARCH_DISPLAY_MODE, SearchDisplayMode.FILTER.toString());
         defaults.put(SEARCH_CASE_SENSITIVE, Boolean.FALSE);
         defaults.put(SEARCH_REG_EXP, Boolean.FALSE);
@@ -36,15 +34,6 @@ public static void putDefaults(Map<String, Object> defaults) {
         defaults.put(SEARCH_DIALOG_POS_Y, 0);
     }
 
-    public boolean isGlobalSearch() {
-        return preferences.getBoolean(SEARCH_GLOBAL);
-    }
-
-    public SearchPreferences setGlobalSearch(boolean isGlobalSearch) {
-        preferences.putBoolean(SEARCH_GLOBAL, isGlobalSearch);
-        return this;
-    }
-
     public SearchDisplayMode getSearchMode() {
         try {
             return SearchDisplayMode.valueOf(preferences.get(SEARCH_DISPLAY_MODE));
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 0258d204ee7..7893e31e5d1 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1039,9 +1039,6 @@ Could\ not\ find\ file\ '%0'.=Could not find file '%0'.
 Number\ of\ entries\ successfully\ imported=Number of entries successfully imported
 Error\ while\ fetching\ from\ %0=Error while fetching from %0
 
-Show\ search\ results\ in\ a\ window=Show search results in a window
-Show\ global\ search\ results\ in\ a\ window=Show global search results in a window
-Search\ in\ all\ open\ libraries=Search in all open libraries
 Refuse\ to\ save\ the\ library\ before\ external\ changes\ have\ been\ reviewed.=Refuse to save the library before external changes have been reviewed.
 Library\ protection=Library protection
 Unable\ to\ save\ library=Unable to save library
@@ -1438,10 +1435,6 @@ capital\ letters\ are\ not\ masked\ using\ curly\ brackets\ {}=capital letters a
 should\ contain\ a\ four\ digit\ number=should contain a four digit number
 should\ contain\ a\ valid\ page\ number\ range=should contain a valid page number range
 Search\ %0=Search %0
-
-Search\ results\ in\ all\ libraries\ for\ %0=Search results in all libraries for %0
-Search\ results\ in\ library\ %0\ for\ %1=Search results in library %0 for %1
-Search\ globally=Search globally
 No\ results\ found.=No results found.
 Found\ %0\ results.=Found %0 results.
 plain\ text=plain text

From 47772fd8ceffbe8eefac78bf680032cdf0bd72bc Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 2 Apr 2019 23:33:56 +0200
Subject: [PATCH 34/61] Fix parser exception when loading tex-groups with
 non-existing file (#4839)

* Fix #4735. Catch file not found exception and handle non existing aux files gracefully.

* Fix build

* Fix checkstyle
---
 CHANGELOG.md                                  |  1 +
 .../org/jabref/gui/groups/GroupDialog.java    |  4 +--
 .../logic/auxparser/DefaultAuxParser.java     |  2 +-
 .../logic/importer/util/GroupsParser.java     | 19 +++++++++--
 .../org/jabref/model/groups/TexGroup.java     | 17 +++++++---
 .../logic/exporter/GroupSerializerTest.java   | 32 +++++++++----------
 .../logic/importer/util/GroupsParserTest.java | 26 +++++++--------
 7 files changed, 62 insertions(+), 39 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 564d782c9da..60394941469 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -74,6 +74,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where selecting a group messed up the focus of the main table / entry editor. https://github.com/JabRef/jabref/issues/3367
 - We fixed an issue where composite author names were sorted incorrectly. https://github.com/JabRef/jabref/issues/2828
 - We fixed an issue where commands followed by `-` didn't work. [#3805](https://github.com/JabRef/jabref/issues/3805)
+- We fixed an issue where a non-existing aux file in a group made it impossible to open the library. [#4735](https://github.com/JabRef/jabref/issues/4735)
 - We fixed an issue where some journal names were wrongly marked as abbreviated. [#4115](https://github.com/JabRef/jabref/issues/4115)
 - We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
 - We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
index 2285db635ac..b40755e97e4 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDialog.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -335,7 +335,7 @@ groupName, getContext(),
                                     autoGroupPersonsField.getText().trim());
                         }
                     } else if (texRadioButton.isSelected()) {
-                        resultingGroup = new TexGroup(groupName, getContext(),
+                        resultingGroup = TexGroup.create(groupName, getContext(),
                                                       Paths.get(texGroupFilePath.getText().trim()), new DefaultAuxParser(new BibDatabase()), Globals.getFileUpdateMonitor(), basePanel.getBibDatabaseContext().getMetaData());
                     }
 
@@ -466,7 +466,7 @@ private VBox createOptionsTexGroup() {
         texGroupBrowseButton.setOnAction((ActionEvent e) -> openBrowseDialog());
         texGroupHBox.getChildren().add(texGroupFilePath);
         texGroupHBox.getChildren().add(texGroupBrowseButton);
-        texGroupHBox.setHgrow(texGroupFilePath, Priority.ALWAYS);
+        HBox.setHgrow(texGroupFilePath, Priority.ALWAYS);
         texPanel.getChildren().add(texGroupHBox);
         return texPanel;
     }
diff --git a/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java b/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java
index f8579ac68b9..054230c730b 100644
--- a/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java
+++ b/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java
@@ -77,7 +77,7 @@ private AuxParserResult parseAuxFile(Path auxFile) {
                     matchNestedAux(auxFile, result, fileList, line);
                 }
             } catch (FileNotFoundException e) {
-                LOGGER.info("Cannot locate input file", e);
+                LOGGER.warn("Cannot locate input file", e);
             } catch (IOException e) {
                 LOGGER.warn("Problem opening file", e);
             }
diff --git a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
index 4c9365b0dd8..f7f8dc27cdb 100644
--- a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
+++ b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
@@ -28,11 +28,15 @@
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileUpdateMonitor;
 
+import org.slf4j.LoggerFactory;
+
 /**
  * Converts string representation of groups to a parsed {@link GroupTreeNode}.
  */
 public class GroupsParser {
 
+    private static final org.slf4j.Logger LOGGER = LoggerFactory.getLogger(GroupsParser.class);
+
     private GroupsParser() {
     }
 
@@ -123,9 +127,18 @@ private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor
         GroupHierarchyType context = GroupHierarchyType.getByNumberOrDefault(Integer.parseInt(tok.nextToken()));
         try {
             Path path = Paths.get(tok.nextToken());
-            TexGroup newGroup = new TexGroup(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
-            addGroupDetails(tok, newGroup);
-            return newGroup;
+            try {
+                TexGroup newGroup = TexGroup.create(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+                addGroupDetails(tok, newGroup);
+                return newGroup;
+            } catch (IOException ex) {
+                // Problem accessing file -> create without file monitoring
+                LOGGER.warn("Could not access file " + path + ". The group " + name + " will not reflect changes to the aux file.", ex);
+
+                TexGroup newGroup = TexGroup.createWithoutFileMonitoring(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+                addGroupDetails(tok, newGroup);
+                return newGroup;
+            }
         } catch (InvalidPathException | IOException ex) {
             throw new ParseException(ex);
         }
diff --git a/src/main/java/org/jabref/model/groups/TexGroup.java b/src/main/java/org/jabref/model/groups/TexGroup.java
index ab350c486d5..b56e92dafff 100644
--- a/src/main/java/org/jabref/model/groups/TexGroup.java
+++ b/src/main/java/org/jabref/model/groups/TexGroup.java
@@ -30,20 +30,29 @@ public class TexGroup extends AbstractGroup implements FileUpdateListener {
     private final MetaData metaData;
     private String user;
 
-    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData, String user) throws IOException {
+    TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData, String user) {
         super(name, context);
         this.metaData = metaData;
         this.user = user;
         this.filePath = expandPath(Objects.requireNonNull(filePath));
         this.auxParser = auxParser;
         this.fileMonitor = fileMonitor;
-        fileMonitor.addListenerForFile(this.filePath, this);
     }
 
-    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+    TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
         this(name, context, filePath, auxParser, fileMonitor, metaData, System.getProperty("user.name") + '-' + InetAddress.getLocalHost().getHostName());
     }
 
+    public static TexGroup create(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+        TexGroup group = new TexGroup(name, context, filePath, auxParser, fileMonitor, metaData);
+        fileMonitor.addListenerForFile(filePath, group);
+        return group;
+    }
+
+    public static TexGroup createWithoutFileMonitoring(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+        return new TexGroup(name, context, filePath, auxParser, fileMonitor, metaData);
+    }
+    
     @Override
     public boolean contains(BibEntry entry) {
         if (keysUsedInAux == null) {
@@ -124,7 +133,7 @@ private List<Path> getFileDirectoriesAsPaths() {
         List<Path> fileDirs = new ArrayList<>();
 
         metaData.getLaTexFileDirectory(user)
-                .ifPresent(laTexFileDirectory -> fileDirs.add(laTexFileDirectory));
+                .ifPresent(fileDirs::add);
 
         return fileDirs;
     }
diff --git a/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java b/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
index b8625babeb4..26c7c61b0f2 100644
--- a/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
+++ b/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
@@ -30,31 +30,31 @@
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
-public class GroupSerializerTest {
+class GroupSerializerTest {
 
     private GroupSerializer groupSerializer;
 
     @BeforeEach
-    public void setUp() throws Exception {
+    void setUp() throws Exception {
         groupSerializer = new GroupSerializer();
     }
 
     @Test
-    public void serializeSingleAllEntriesGroup() {
+    void serializeSingleAllEntriesGroup() {
         AllEntriesGroup group = new AllEntriesGroup("");
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 AllEntriesGroup:"), serialization);
     }
 
     @Test
-    public void serializeSingleExplicitGroup() {
+    void serializeSingleExplicitGroup() {
         ExplicitGroup group = new ExplicitGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, ',');
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 StaticGroup:myExplicitGroup;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleExplicitGroupWithIconAndDescription() {
+    void serializeSingleExplicitGroupWithIconAndDescription() {
         ExplicitGroup group = new ExplicitGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, ',');
         group.setIconName("test icon");
         group.setExpanded(true);
@@ -66,63 +66,63 @@ public void serializeSingleExplicitGroupWithIconAndDescription() {
 
     @Test
     // For https://github.com/JabRef/jabref/issues/1681
-    public void serializeSingleExplicitGroupWithEscapedSlash() {
+    void serializeSingleExplicitGroupWithEscapedSlash() {
         ExplicitGroup group = new ExplicitGroup("B{\\\"{o}}hmer", GroupHierarchyType.INDEPENDENT, ',');
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 StaticGroup:B{\\\\\"{o}}hmer;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleSimpleKeywordGroup() {
+    void serializeSingleSimpleKeywordGroup() {
         WordKeywordGroup group = new WordKeywordGroup("name", GroupHierarchyType.INDEPENDENT, "keywords", "test", false, ',', false);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 KeywordGroup:name;0;keywords;test;0;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleRegexKeywordGroup() {
+    void serializeSingleRegexKeywordGroup() {
         KeywordGroup group = new RegexKeywordGroup("myExplicitGroup", GroupHierarchyType.REFINING, "author", "asdf", false);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 KeywordGroup:myExplicitGroup;1;author;asdf;0;1;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleSearchGroup() {
+    void serializeSingleSearchGroup() {
         SearchGroup group = new SearchGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, "author=harrer", true, true);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 SearchGroup:myExplicitGroup;0;author=harrer;1;1;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleSearchGroupWithRegex() {
+    void serializeSingleSearchGroupWithRegex() {
         SearchGroup group = new SearchGroup("myExplicitGroup", GroupHierarchyType.INCLUDING, "author=\"harrer\"", true, false);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 SearchGroup:myExplicitGroup;2;author=\"harrer\";1;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleAutomaticKeywordGroup() {
+    void serializeSingleAutomaticKeywordGroup() {
         AutomaticGroup group = new AutomaticKeywordGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "keywords", ',', '>');
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 AutomaticKeywordGroup:myAutomaticGroup;0;keywords;,;>;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleAutomaticPersonGroup() {
+    void serializeSingleAutomaticPersonGroup() {
         AutomaticPersonsGroup group = new AutomaticPersonsGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "authors");
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 AutomaticPersonsGroup:myAutomaticGroup;0;authors;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleTexGroup() throws Exception {
-        TexGroup group = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), new MetaData());
+    void serializeSingleTexGroup() throws Exception {
+        TexGroup group = TexGroup.createWithoutFileMonitoring("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), new MetaData());
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 TexGroup:myTexGroup;0;path/To/File;1;;;;"), serialization);
     }
 
     @Test
-    public void getTreeAsStringInSimpleTree() throws Exception {
+    void getTreeAsStringInSimpleTree() throws Exception {
         GroupTreeNode root = GroupTreeNodeTest.getRoot();
         GroupTreeNodeTest.getNodeInSimpleTree(root);
 
@@ -136,7 +136,7 @@ public void getTreeAsStringInSimpleTree() throws Exception {
     }
 
     @Test
-    public void getTreeAsStringInComplexTree() throws Exception {
+    void getTreeAsStringInComplexTree() throws Exception {
         GroupTreeNode root = GroupTreeNodeTest.getRoot();
         GroupTreeNodeTest.getNodeInComplexTree(root);
 
diff --git a/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java b/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
index 080b2594e69..640644dec0d 100644
--- a/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
+++ b/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
@@ -27,19 +27,19 @@
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
-public class GroupsParserTest {
+class GroupsParserTest {
     private FileUpdateMonitor fileMonitor;
     private MetaData metaData;
 
     @BeforeEach
-    public void setUp() throws Exception {
+    void setUp() throws Exception {
         fileMonitor = new DummyFileUpdateMonitor();
         metaData = new MetaData();
     }
 
     @Test
     // For https://github.com/JabRef/jabref/issues/1681
-    public void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exception {
+    void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exception {
         ExplicitGroup expected = new ExplicitGroup("B{\\\"{o}}hmer", GroupHierarchyType.INDEPENDENT, ',');
         AbstractGroup parsed = GroupsParser.fromString("ExplicitGroup:B{\\\\\"{o}}hmer;0;", ',', fileMonitor, metaData);
 
@@ -47,26 +47,26 @@ public void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exc
     }
 
     @Test
-    public void keywordDelimiterThatNeedsToBeEscaped() throws Exception {
+    void keywordDelimiterThatNeedsToBeEscaped() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("group1", GroupHierarchyType.INDEPENDENT, "keywords", ';', '>');
         AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;\\;;>;1;;;;;", ';', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void hierarchicalDelimiterThatNeedsToBeEscaped() throws Exception {
+    void hierarchicalDelimiterThatNeedsToBeEscaped() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("group1", GroupHierarchyType.INDEPENDENT, "keywords", ',', ';');
         AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;,;\\;;1;;;;;", ';', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringThrowsParseExceptionForNotEscapedGroupName() throws Exception {
+    void fromStringThrowsParseExceptionForNotEscapedGroupName() throws Exception {
         assertThrows(ParseException.class, () -> GroupsParser.fromString("ExplicitGroup:slit\\\\;0\\;mertsch_slit2_2007\\;;", ',', fileMonitor, metaData));
     }
 
     @Test
-    public void testImportSubGroups() throws Exception {
+    void testImportSubGroups() throws Exception {
 
         List<String> orderedData = Arrays.asList("0 AllEntriesGroup:", "1 ExplicitGroup:1;0;",
                 "2 ExplicitGroup:2;0;", "0 ExplicitGroup:3;0;");
@@ -93,7 +93,7 @@ public void testImportSubGroups() throws Exception {
     }
 
     @Test
-    public void fromStringParsesExplicitGroupWithIconAndDescription() throws Exception {
+    void fromStringParsesExplicitGroupWithIconAndDescription() throws Exception {
         ExplicitGroup expected = new ExplicitGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, ',');
         expected.setIconName("test icon");
         expected.setExpanded(true);
@@ -105,28 +105,28 @@ public void fromStringParsesExplicitGroupWithIconAndDescription() throws Excepti
     }
 
     @Test
-    public void fromStringParsesAutomaticKeywordGroup() throws Exception {
+    void fromStringParsesAutomaticKeywordGroup() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "keywords", ',', '>');
         AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:myAutomaticGroup;0;keywords;,;>;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringParsesAutomaticPersonGroup() throws Exception {
+    void fromStringParsesAutomaticPersonGroup() throws Exception {
         AutomaticPersonsGroup expected = new AutomaticPersonsGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "authors");
         AbstractGroup parsed = GroupsParser.fromString("AutomaticPersonsGroup:myAutomaticGroup;0;authors;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringParsesTexGroup() throws Exception {
-        TexGroup expected = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+    void fromStringParsesTexGroup() throws Exception {
+        TexGroup expected = TexGroup.createWithoutFileMonitoring("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
         AbstractGroup parsed = GroupsParser.fromString("TexGroup:myTexGroup;0;path/To/File;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringUnknownGroupThrowsException() throws Exception {
+    void fromStringUnknownGroupThrowsException() throws Exception {
         assertThrows(ParseException.class, () -> GroupsParser.fromString("0 UnknownGroup:myUnknownGroup;0;;1;;;;", ',', fileMonitor, metaData));
     }
 }

From a273eb1fa13317d4091a767849c40e9495de2b7e Mon Sep 17 00:00:00 2001
From: Robin <robin.lichtenthaeler@web.de>
Date: Wed, 3 Apr 2019 11:19:03 +0200
Subject: [PATCH 35/61] Enhanced message log (#4815)

* refactored JabRefFrame.output and FXDialogService.notify to only use FXDialogService.notify

* added logging to notifications and fixed problem with logger in JabRefGUI

* moved copying of logevents to GuiAppender

* directly use dialogService in BasePanel

* changed constructor to avoid NPE

* refactored code so that DialogService.notify does not need DefaultTaskExecutor.runInJavaFXThread

* replaced old swing dialog

* replaced another swing dialog
---
 src/main/java/org/jabref/gui/BasePanel.java   | 23 +++++----
 .../java/org/jabref/gui/FXDialogService.java  | 21 ++++++++-
 src/main/java/org/jabref/gui/JabRefFrame.java | 23 ++-------
 .../org/jabref/gui/actions/CleanupAction.java |  4 +-
 .../actions/CopyBibTeXKeyAndLinkAction.java   |  6 +--
 .../jabref/gui/actions/CopyDoiUrlAction.java  |  4 +-
 .../gui/actions/GenerateBibtexKeyAction.java  |  4 +-
 .../gui/actions/LookupIdentifierAction.java   | 13 +++--
 .../jabref/gui/actions/NewDatabaseAction.java |  2 +-
 .../jabref/gui/actions/WriteXMPAction.java    |  4 +-
 .../org/jabref/gui/desktop/JabRefDesktop.java | 20 +++-----
 .../jabref/gui/exporter/ExportCommand.java    |  4 +-
 .../gui/exporter/ExportToClipboardAction.java |  4 +-
 .../gui/exporter/SaveDatabaseAction.java      |  6 +--
 .../gui/externalfiles/FindFullTextAction.java | 27 ++++-------
 .../ExternalFileMenuItem.java                 |  4 +-
 .../jabref/gui/filelist/AttachFileAction.java |  2 +-
 .../org/jabref/gui/importer/ImportAction.java |  5 +-
 .../actions/AppendDatabaseAction.java         | 47 +++++++++----------
 .../importer/actions/OpenDatabaseAction.java  |  8 ++--
 .../fetcher/WebSearchPaneViewModel.java       |  4 +-
 .../jabref/gui/journals/AbbreviateAction.java |  3 +-
 .../gui/journals/UnabbreviateAction.java      |  3 +-
 .../org/jabref/gui/logging/GuiAppender.java   |  6 ++-
 .../gui/shared/SharedDatabaseUIManager.java   | 11 ++---
 .../gui/specialfields/SpecialFieldAction.java |  2 +-
 .../jabref/gui/worker/SendAsEMailAction.java  |  4 +-
 .../org/jabref/logic/logging/LogMessages.java |  6 +--
 28 files changed, 126 insertions(+), 144 deletions(-)

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index 2ccfcdcc927..c6501ec7da9 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -250,7 +250,7 @@ public JabRefFrame frame() {
     }
 
     public void output(String s) {
-        frame.output(s);
+        dialogService.notify(s);
     }
 
     private void setupActions() {
@@ -441,7 +441,7 @@ private void delete(boolean cut, List<BibEntry> entries) {
         getUndoManager().addEdit(compound);
 
         markBaseChanged();
-        frame.output(formatOutputMessage(cut ? Localization.lang("Cut") : Localization.lang("Deleted"), entries.size()));
+        this.output(formatOutputMessage(cut ? Localization.lang("Cut") : Localization.lang("Deleted"), entries.size()));
 
         // prevent the main table from loosing focus
         mainTable.requestFocus();
@@ -569,13 +569,12 @@ private void copyKeyAndTitle() {
     }
 
     private void openExternalFile() {
+        final List<BibEntry> selectedEntries = mainTable.getSelectedEntries();
+        if (selectedEntries.size() != 1) {
+            output(Localization.lang("This operation requires exactly one item to be selected."));
+            return;
+        }
         JabRefExecutorService.INSTANCE.execute(() -> {
-            final List<BibEntry> selectedEntries = mainTable.getSelectedEntries();
-            if (selectedEntries.size() != 1) {
-                output(Localization.lang("This operation requires exactly one item to be selected."));
-                return;
-            }
-
             final BibEntry entry = selectedEntries.get(0);
             if (!entry.hasField(FieldName.FILE)) {
                 // no bibtex field
@@ -1292,10 +1291,10 @@ public void action() {
             try {
                 getUndoManager().undo();
                 markBaseChanged();
-                frame.output(Localization.lang("Undo"));
+                output(Localization.lang("Undo"));
             } catch (CannotUndoException ex) {
                 LOGGER.warn("Nothing to undo", ex);
-                frame.output(Localization.lang("Nothing to undo") + '.');
+                output(Localization.lang("Nothing to undo") + '.');
             }
 
             markChangedOrUnChanged();
@@ -1363,9 +1362,9 @@ public void action() {
             try {
                 getUndoManager().redo();
                 markBaseChanged();
-                frame.output(Localization.lang("Redo"));
+                output(Localization.lang("Redo"));
             } catch (CannotRedoException ex) {
-                frame.output(Localization.lang("Nothing to redo") + '.');
+                output(Localization.lang("Nothing to redo") + '.');
             }
 
             markChangedOrUnChanged();
diff --git a/src/main/java/org/jabref/gui/FXDialogService.java b/src/main/java/org/jabref/gui/FXDialogService.java
index f3edaba275a..2fe537a30a1 100644
--- a/src/main/java/org/jabref/gui/FXDialogService.java
+++ b/src/main/java/org/jabref/gui/FXDialogService.java
@@ -24,21 +24,27 @@
 import javafx.scene.control.ChoiceDialog;
 import javafx.scene.control.DialogPane;
 import javafx.scene.control.TextInputDialog;
+import javafx.scene.layout.Pane;
 import javafx.scene.layout.Region;
 import javafx.stage.DirectoryChooser;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 import javafx.stage.Window;
+import javafx.util.Duration;
 
-import org.jabref.JabRefGUI;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.gui.util.ZipFileChooser;
 import org.jabref.logic.l10n.Localization;
 
+import com.jfoenix.controls.JFXSnackbar;
+import com.jfoenix.controls.JFXSnackbar.SnackbarEvent;
+import com.jfoenix.controls.JFXSnackbarLayout;
 import org.controlsfx.dialog.ExceptionDialog;
 import org.controlsfx.dialog.ProgressDialog;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * This class provides methods to create default
@@ -51,7 +57,11 @@
  */
 public class FXDialogService implements DialogService {
 
+    private static final Duration TOAST_MESSAGE_DISPLAY_TIME = Duration.millis(3000);
+    private static final Logger LOGGER = LoggerFactory.getLogger(FXDialogService.class);
+
     private final Window mainWindow;
+    private final JFXSnackbar statusLine;
 
     /**
      * @deprecated try not to initialize a new dialog service but reuse the one constructed in {@link org.jabref.gui.JabRefFrame}.
@@ -63,6 +73,12 @@ public FXDialogService() {
 
     public FXDialogService(Window mainWindow) {
         this.mainWindow = mainWindow;
+        this.statusLine = new JFXSnackbar();
+    }
+
+    public FXDialogService(Window mainWindow, Pane mainPane) {
+        this.mainWindow = mainWindow;
+        this.statusLine = new JFXSnackbar(mainPane);
     }
 
     private static FXDialog createDialog(AlertType type, String title, String content) {
@@ -253,7 +269,8 @@ public <V> void showProgressDialogAndWait(String title, String content, Task<V>
 
     @Override
     public void notify(String message) {
-        JabRefGUI.getMainFrame().output(message);
+        LOGGER.info(message);
+        statusLine.fireEvent(new SnackbarEvent(new JFXSnackbarLayout(message), TOAST_MESSAGE_DISPLAY_TIME, null));
     }
 
     @Override
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index d32b48dd30f..71e75d1c54d 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -50,7 +50,6 @@
 import javafx.scene.layout.Pane;
 import javafx.scene.layout.Priority;
 import javafx.stage.Stage;
-import javafx.util.Duration;
 
 import org.jabref.Globals;
 import org.jabref.JabRefExecutorService;
@@ -132,9 +131,6 @@
 import org.jabref.preferences.LastFocusedTabPreferences;
 
 import com.google.common.eventbus.Subscribe;
-import com.jfoenix.controls.JFXSnackbar;
-import com.jfoenix.controls.JFXSnackbar.SnackbarEvent;
-import com.jfoenix.controls.JFXSnackbarLayout;
 import org.eclipse.fx.ui.controls.tabpane.DndTabPane;
 import org.eclipse.fx.ui.controls.tabpane.DndTabPaneFactory;
 import org.fxmisc.easybind.EasyBind;
@@ -151,12 +147,11 @@ public class JabRefFrame extends BorderPane {
     public static final String FRAME_TITLE = "JabRef";
 
     private static final Logger LOGGER = LoggerFactory.getLogger(JabRefFrame.class);
-    private static final Duration TOAST_MESSAGE_DISPLAY_TIME = Duration.millis(3000);
 
     private final SplitPane splitPane = new SplitPane();
     private final JabRefPreferences prefs = Globals.prefs;
     private final GlobalSearchBar globalSearchBar = new GlobalSearchBar(this);
-    private final JFXSnackbar statusLine = new JFXSnackbar(this);
+
     private final ProgressBar progressBar = new ProgressBar();
     private final FileHistoryMenu fileHistory = new FileHistoryMenu(prefs, this);
 
@@ -182,7 +177,7 @@ public class JabRefFrame extends BorderPane {
 
     public JabRefFrame(Stage mainStage) {
         this.mainStage = mainStage;
-        this.dialogService = new FXDialogService(mainStage);
+        this.dialogService = new FXDialogService(mainStage, this);
         init();
     }
 
@@ -962,16 +957,6 @@ public void addParserResult(ParserResult pr, boolean focusPanel) {
         }
     }
 
-    /**
-     * Displays the given message at the bottom of the main frame
-     *
-     * @deprecated use {@link DialogService#notify(String)} instead. However, do not remove this method, it's called from the dialogService
-     */
-    @Deprecated
-    public void output(final String message) {
-        DefaultTaskExecutor.runInJavaFXThread(() -> statusLine.fireEvent(new SnackbarEvent(new JFXSnackbarLayout(message), TOAST_MESSAGE_DISPLAY_TIME, null)));
-    }
-
     private void initActions() {
         /*
         openDatabaseOnlyActions.clear();
@@ -1279,7 +1264,7 @@ private boolean confirmClose(BasePanel panel) {
                     return true;
                 }
                 // The action was either canceled or unsuccessful.
-                output(Localization.lang("Unable to save library"));
+                dialogService.notify(Localization.lang("Unable to save library"));
             } catch (Throwable ex) {
                 LOGGER.error("A problem occurred when trying to save the file", ex);
                 dialogService.showErrorDialogAndWait(Localization.lang("Save library"), Localization.lang("Could not save file."), ex);
@@ -1321,7 +1306,7 @@ private void removeTab(BasePanel panel) {
             panel.cleanUp();
             tabbedPane.getTabs().remove(getTab(panel));
             setWindowTitle();
-            output(Localization.lang("Closed library") + '.');
+            dialogService.notify(Localization.lang("Closed library") + '.');
             // update tab titles
             updateAllTabTitles();
         });
diff --git a/src/main/java/org/jabref/gui/actions/CleanupAction.java b/src/main/java/org/jabref/gui/actions/CleanupAction.java
index f2251d45616..d79a8a62c4f 100644
--- a/src/main/java/org/jabref/gui/actions/CleanupAction.java
+++ b/src/main/java/org/jabref/gui/actions/CleanupAction.java
@@ -71,7 +71,7 @@ public void init() {
             isCanceled = true;
             return;
         }
-        panel.output(Localization.lang("Doing a cleanup for %0 entries...",
+        dialogService.notify(Localization.lang("Doing a cleanup for %0 entries...",
                 Integer.toString(panel.getSelectedEntries().size())));
     }
 
@@ -115,7 +115,7 @@ private void showResults() {
                 message = Localization.lang("%0 entries needed a clean up", Integer.toString(modifiedEntriesCount));
                 break;
         }
-        panel.output(message);
+        dialogService.notify(message);
     }
 
     private void cleanup(CleanupPreset cleanupPreset) {
diff --git a/src/main/java/org/jabref/gui/actions/CopyBibTeXKeyAndLinkAction.java b/src/main/java/org/jabref/gui/actions/CopyBibTeXKeyAndLinkAction.java
index 6f55af1e27b..49c8a5f46ec 100644
--- a/src/main/java/org/jabref/gui/actions/CopyBibTeXKeyAndLinkAction.java
+++ b/src/main/java/org/jabref/gui/actions/CopyBibTeXKeyAndLinkAction.java
@@ -36,7 +36,7 @@ public void action() throws Exception {
             List<BibEntry> entriesWithKey = entries.stream().filter(BibEntry::hasCiteKey).collect(Collectors.toList());
 
             if (entriesWithKey.isEmpty()) {
-                JabRefGUI.getMainFrame().output(Localization.lang("None of the selected entries have BibTeX keys."));
+                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("None of the selected entries have BibTeX keys."));
                 return;
             }
 
@@ -53,9 +53,9 @@ public void action() throws Exception {
             int toCopy = entries.size();
             if (copied == toCopy) {
                 // All entries had keys.
-                JabRefGUI.getMainFrame().output((entries.size() > 1 ? Localization.lang("Copied keys") : Localization.lang("Copied key")) + '.');
+                JabRefGUI.getMainFrame().getDialogService().notify((entries.size() > 1 ? Localization.lang("Copied keys") : Localization.lang("Copied key")) + '.');
             } else {
-                JabRefGUI.getMainFrame().output(Localization.lang("Warning: %0 out of %1 entries have undefined BibTeX key.",
+                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Warning: %0 out of %1 entries have undefined BibTeX key.",
                         Long.toString(toCopy - copied), Integer.toString(toCopy)));
             }
         }
diff --git a/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java b/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
index 51adf9ba8b3..e541cd58d5a 100644
--- a/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
+++ b/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
@@ -27,9 +27,9 @@ public void execute() {
         Optional<String> urlOptional = DOI.parse(identifier).map(DOI::getURIAsASCIIString);
         if (urlOptional.isPresent()) {
             Globals.clipboardManager.setContent(urlOptional.get());
-            JabRefGUI.getMainFrame().output(Localization.lang("The link has been copied to the clipboard."));
+            JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("The link has been copied to the clipboard."));
         } else {
-            JabRefGUI.getMainFrame().output(Localization.lang("Invalid DOI: '%0'.", identifier));
+            JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Invalid DOI: '%0'.", identifier));
         }
     }
 }
diff --git a/src/main/java/org/jabref/gui/actions/GenerateBibtexKeyAction.java b/src/main/java/org/jabref/gui/actions/GenerateBibtexKeyAction.java
index 90b61800215..744db49711c 100644
--- a/src/main/java/org/jabref/gui/actions/GenerateBibtexKeyAction.java
+++ b/src/main/java/org/jabref/gui/actions/GenerateBibtexKeyAction.java
@@ -33,7 +33,7 @@ public void init() {
                                                    Localization.lang("First select the entries you want keys to be generated for."));
             return;
         }
-        basePanel.output(formatOutputMessage(Localization.lang("Generating BibTeX key for"), entries.size()));
+        dialogService.notify(formatOutputMessage(Localization.lang("Generating BibTeX key for"), entries.size()));
     }
 
     public static boolean confirmOverwriteKeys(DialogService dialogService) {
@@ -87,7 +87,7 @@ private void generateKeys() {
         }
 
         basePanel.markBaseChanged();
-        basePanel.output(formatOutputMessage(Localization.lang("Generated BibTeX key for"), entries.size()));
+        dialogService.notify(formatOutputMessage(Localization.lang("Generated BibTeX key for"), entries.size()));
     }
 
     private String formatOutputMessage(String start, int count) {
diff --git a/src/main/java/org/jabref/gui/actions/LookupIdentifierAction.java b/src/main/java/org/jabref/gui/actions/LookupIdentifierAction.java
index f1f6e6f0846..a2d6c7372d9 100644
--- a/src/main/java/org/jabref/gui/actions/LookupIdentifierAction.java
+++ b/src/main/java/org/jabref/gui/actions/LookupIdentifierAction.java
@@ -12,6 +12,7 @@
 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.importer.FetcherException;
 import org.jabref.logic.importer.IdFetcher;
 import org.jabref.logic.l10n.Localization;
@@ -39,7 +40,7 @@ public LookupIdentifierAction(JabRefFrame frame, IdFetcher<T> fetcher) {
     public void execute() {
         try {
             BackgroundTask.wrap(this::lookupIdentifiers)
-                          .onSuccess(frame::output)
+                          .onSuccess(frame.getDialogService()::notify)
                           .executeWith(Globals.TASK_EXECUTOR);
         } catch (Exception e) {
             LOGGER.error("Problem running ID Worker", e);
@@ -84,8 +85,9 @@ private String lookupIdentifiers() {
         int foundCount = 0;
         for (BibEntry bibEntry : bibEntries) {
             count++;
-            frame.output(Localization.lang("Looking up %0... - entry %1 out of %2 - found %3",
-                    fetcher.getIdentifierName(), Integer.toString(count), totalCount, Integer.toString(foundCount)));
+            final String statusMessage = Localization.lang("Looking up %0... - entry %1 out of %2 - found %3",
+                    fetcher.getIdentifierName(), Integer.toString(count), totalCount, Integer.toString(foundCount));
+            DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().notify(statusMessage));
             Optional<T> identifier = Optional.empty();
             try {
                 identifier = fetcher.findIdentifier(bibEntry);
@@ -97,8 +99,9 @@ private String lookupIdentifiers() {
                 if (fieldChange.isPresent()) {
                     namedCompound.addEdit(new UndoableFieldChange(fieldChange.get()));
                     foundCount++;
-                    frame.output(Localization.lang("Looking up %0... - entry %1 out of %2 - found %3",
-                            Integer.toString(count), totalCount, Integer.toString(foundCount)));
+                    final String nextStatusMessage = Localization.lang("Looking up %0... - entry %1 out of %2 - found %3",
+                            fetcher.getIdentifierName(), Integer.toString(count), totalCount, Integer.toString(foundCount));
+                    DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().notify(nextStatusMessage));
                 }
             }
         }
diff --git a/src/main/java/org/jabref/gui/actions/NewDatabaseAction.java b/src/main/java/org/jabref/gui/actions/NewDatabaseAction.java
index 90b2f8ced30..e00604e3a1b 100644
--- a/src/main/java/org/jabref/gui/actions/NewDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/actions/NewDatabaseAction.java
@@ -24,6 +24,6 @@ public void execute() {
         BibDatabaseContext bibDatabaseContext = new BibDatabaseContext(new Defaults(BibDatabaseMode.BIBTEX));
         bibDatabaseContext.setMode(mode);
         jabRefFrame.addTab(bibDatabaseContext, true);
-        jabRefFrame.output(Localization.lang("New %0 library created.", mode.getFormattedName()));
+        jabRefFrame.getDialogService().notify(Localization.lang("New %0 library created.", mode.getFormattedName()));
     }
 }
diff --git a/src/main/java/org/jabref/gui/actions/WriteXMPAction.java b/src/main/java/org/jabref/gui/actions/WriteXMPAction.java
index de4face8b53..67a1217a113 100644
--- a/src/main/java/org/jabref/gui/actions/WriteXMPAction.java
+++ b/src/main/java/org/jabref/gui/actions/WriteXMPAction.java
@@ -92,7 +92,7 @@ public void init() {
         }
         optionsDialog.open();
 
-        basePanel.output(Localization.lang("Writing XMP-metadata..."));
+        dialogService.notify(Localization.lang("Writing XMP-metadata..."));
     }
 
     private void writeXMP() {
@@ -162,7 +162,7 @@ private void writeXMP() {
             return;
         }
 
-        basePanel.output(Localization.lang("Finished writing XMP for %0 file (%1 skipped, %2 errors).",
+        dialogService.notify(Localization.lang("Finished writing XMP for %0 file (%1 skipped, %2 errors).",
                 String.valueOf(entriesChanged), String.valueOf(skipped), String.valueOf(errors)));
     }
 
diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
index aa7f9dd22fc..fbd9478789b 100644
--- a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
+++ b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -10,8 +10,6 @@
 import java.util.Optional;
 import java.util.regex.Pattern;
 
-import javax.swing.JOptionPane;
-
 import org.jabref.Globals;
 import org.jabref.JabRefGUI;
 import org.jabref.gui.desktop.os.DefaultDesktop;
@@ -201,12 +199,8 @@ public static void openBrowserShowPopup(String url) {
             String couldNotOpenBrowser = Localization.lang("Could not open browser.");
             String openManually = Localization.lang("Please open %0 manually.", url);
             String copiedToClipboard = Localization.lang("The link has been copied to the clipboard.");
-            JabRefGUI.getMainFrame().output(couldNotOpenBrowser);
-            JOptionPane.showMessageDialog(null,
-                                          couldNotOpenBrowser + "\n" + openManually + "\n" +
-                                                copiedToClipboard,
-                                          couldNotOpenBrowser,
-                                          JOptionPane.ERROR_MESSAGE);
+            JabRefGUI.getMainFrame().getDialogService().notify(couldNotOpenBrowser);
+            JabRefGUI.getMainFrame().getDialogService().showErrorDialogAndWait(couldNotOpenBrowser, couldNotOpenBrowser + "\n" + openManually + "\n" + copiedToClipboard);
         }
     }
 
@@ -239,7 +233,7 @@ public static void openConsole(File file) throws IOException {
                 // replace the placeholder if used
                 String commandLoggingText = command.replace("%DIR", absolutePath);
 
-                JabRefGUI.getMainFrame().output(Localization.lang("Executing command \"%0\"...", commandLoggingText));
+                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", commandLoggingText));
                 LOGGER.info("Executing command \"" + commandLoggingText + "\"...");
 
                 try {
@@ -247,11 +241,9 @@ public static void openConsole(File file) throws IOException {
                 } catch (IOException exception) {
                     LOGGER.error("Open console", exception);
 
-                    JOptionPane.showMessageDialog(null,
-                                                  Localization.lang("Error occured while executing the command \"%0\".", commandLoggingText),
-                                                  Localization.lang("Open console") + " - " + Localization.lang("Error"),
-                                                  JOptionPane.ERROR_MESSAGE);
-                    JabRefGUI.getMainFrame().output(null);
+                    JabRefGUI.getMainFrame().getDialogService().showErrorDialogAndWait(
+                            Localization.lang("Open console") + " - " + Localization.lang("Error",
+                            Localization.lang("Error occured while executing the command \"%0\".", commandLoggingText)));
                 }
             }
         }
diff --git a/src/main/java/org/jabref/gui/exporter/ExportCommand.java b/src/main/java/org/jabref/gui/exporter/ExportCommand.java
index 36bb095a027..77b3a8430de 100644
--- a/src/main/java/org/jabref/gui/exporter/ExportCommand.java
+++ b/src/main/java/org/jabref/gui/exporter/ExportCommand.java
@@ -113,14 +113,14 @@ private void export(Path file, FileChooser.ExtensionFilter selectedExtensionFilt
                             finEntries);
                     return null; // can not use BackgroundTask.wrap(Runnable) because Runnable.run() can't throw Exceptions
                 })
-                .onSuccess(x -> frame.output(Localization.lang("%0 export successful", format.getName())))
+                .onSuccess(x -> frame.getDialogService().notify(Localization.lang("%0 export successful", format.getName())))
                 .onFailure(this::handleError)
                 .executeWith(Globals.TASK_EXECUTOR);
     }
 
     private void handleError(Exception ex) {
         LOGGER.warn("Problem exporting", ex);
-        frame.output(Localization.lang("Could not save file."));
+        frame.getDialogService().notify(Localization.lang("Could not save file."));
         // Need to warn the user that saving failed!
         frame.getDialogService().showErrorDialogAndWait(Localization.lang("Save library"), Localization.lang("Could not save file."), ex);
     }
diff --git a/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java b/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
index 2148a0146c0..122b5baf610 100644
--- a/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
+++ b/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
@@ -53,7 +53,7 @@ public void execute() {
         }
 
         if (panel.getSelectedEntries().isEmpty()) {
-            panel.output(Localization.lang("This operation requires one or more entries to be selected."));
+            dialogService.notify(Localization.lang("This operation requires one or more entries to be selected."));
             return;
         }
 
@@ -123,7 +123,7 @@ private void setContentToClipboard(String content) {
         clipboardContent.putRtf(content);
         Globals.clipboardManager.setContent(clipboardContent);
 
-        panel.output(Localization.lang("Entries exported to clipboard") + ": " + entries.size());
+        dialogService.notify(Localization.lang("Entries exported to clipboard") + ": " + entries.size());
 
     }
 
diff --git a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
index b743b7fa199..db4a591b1ec 100644
--- a/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java
@@ -140,7 +140,7 @@ private boolean doSave() {
                 // Reset title of tab
                 frame.setTabTitle(panel, panel.getTabTitle(),
                                   panel.getBibDatabaseContext().getDatabaseFile().get().getAbsolutePath());
-                frame.output(Localization.lang("Saved library") + " '"
+                frame.getDialogService().notify(Localization.lang("Saved library") + " '"
                              + panel.getBibDatabaseContext().getDatabaseFile().get().getPath() + "'.");
                 frame.setWindowTitle();
                 frame.updateAllTabTitles();
@@ -158,7 +158,7 @@ private boolean doSave() {
 
     public boolean save() {
         if (panel.getBibDatabaseContext().getDatabasePath().isPresent()) {
-            panel.frame().output(Localization.lang("Saving library") + "...");
+            panel.frame().getDialogService().notify(Localization.lang("Saving library") + "...");
             panel.setSaving(true);
             return doSave();
         } else {
@@ -240,7 +240,7 @@ public void saveSelectedAsPlain() {
             try {
                 saveDatabase(path, true, prefs.getDefaultEncoding(), SavePreferences.DatabaseSaveType.PLAIN_BIBTEX);
                 frame.getFileHistory().newFile(path);
-                frame.output(Localization.lang("Saved selected to '%0'.", path.toString()));
+                frame.getDialogService().notify(Localization.lang("Saved selected to '%0'.", path.toString()));
             } catch (SaveException ex) {
                 LOGGER.error("A problem occurred when trying to save the file", ex);
                 frame.getDialogService().showErrorDialogAndWait(Localization.lang("Save library"), Localization.lang("Could not save file."), ex);
diff --git a/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java b/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
index 3874a503d16..adb6affcc4c 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
@@ -2,8 +2,6 @@
 
 import java.net.URL;
 import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 import java.util.concurrent.ConcurrentHashMap;
@@ -42,12 +40,6 @@ public FindFullTextAction(BasePanel basePanel) {
 
     @Override
     public void execute() {
-        BackgroundTask.wrap(this::findFullTexts)
-                      .onSuccess(this::downloadFullTexts)
-                      .executeWith(Globals.TASK_EXECUTOR);
-    }
-
-    private Map<Optional<URL>, BibEntry> findFullTexts() {
         if (!basePanel.getSelectedEntries().isEmpty()) {
             basePanel.output(Localization.lang("Looking for full text document..."));
         } else {
@@ -68,21 +60,24 @@ private Map<Optional<URL>, BibEntry> findFullTexts() {
 
             if (!confirmDownload) {
                 basePanel.output(Localization.lang("Operation canceled."));
-                return null;
+                return;
             }
         }
+        BackgroundTask.wrap(this::findFullTexts)
+                      .onSuccess(this::downloadFullTexts)
+                      .executeWith(Globals.TASK_EXECUTOR);
+    }
 
+    private Map<Optional<URL>, BibEntry> findFullTexts() {
         Map<Optional<URL>, BibEntry> downloads = new ConcurrentHashMap<>();
         for (BibEntry entry : basePanel.getSelectedEntries()) {
             FulltextFetchers fetchers = new FulltextFetchers(Globals.prefs.getImportFormatPreferences());
             downloads.put(fetchers.findFullTextPDF(entry), entry);
         }
-
         return downloads;
     }
 
     private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
-        List<Optional<URL>> finishedTasks = new ArrayList<>();
         for (Map.Entry<Optional<URL>, BibEntry> download : downloads.entrySet()) {
             BibEntry entry = download.getValue();
             Optional<URL> result = download.getKey();
@@ -94,20 +89,15 @@ private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
                     dialogService.showErrorDialogAndWait(Localization.lang("Directory not found"),
                             Localization.lang("Main file directory not set!") + " " + Localization.lang("Preferences")
                                     + " -> " + Localization.lang("File"));
-
                     return;
                 }
-
-                //Download full text
+                //Download and link full text
                 addLinkedFileFromURL(result.get(), entry);
+
             } else {
                 dialogService.notify(Localization.lang("No full text document found for entry %0.",
                         entry.getCiteKeyOptional().orElse(Localization.lang("undefined"))));
             }
-            finishedTasks.add(result);
-        }
-        for (Optional<URL> result : finishedTasks) {
-            downloads.remove(result);
         }
     }
 
@@ -119,7 +109,6 @@ private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
      * @param entry the entry "value"
      */
     private void addLinkedFileFromURL(URL url, BibEntry entry) {
-
         LinkedFile newLinkedFile = new LinkedFile(url, "");
 
         if (!entry.getFiles().contains(newLinkedFile)) {
diff --git a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileMenuItem.java b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileMenuItem.java
index a2ebcb02dae..e204ca6b761 100644
--- a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileMenuItem.java
+++ b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileMenuItem.java
@@ -58,12 +58,12 @@ public void actionPerformed(ActionEvent e) {
         boolean success = openLink();
         if (!success) {
             List<Path> searchedDirs = databaseContext.getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
-            frame.output(Localization.lang("Unable to open %0", link) + " " + Arrays.toString(searchedDirs.toArray()));
+            frame.getDialogService().notify(Localization.lang("Unable to open %0", link) + " " + Arrays.toString(searchedDirs.toArray()));
         }
     }
 
     private boolean openLink() {
-        frame.output(Localization.lang("External viewer called") + ".");
+        frame.getDialogService().notify(Localization.lang("External viewer called") + ".");
         try {
             Optional<ExternalFileType> type = fileType;
             if (!this.fileType.isPresent()) {
diff --git a/src/main/java/org/jabref/gui/filelist/AttachFileAction.java b/src/main/java/org/jabref/gui/filelist/AttachFileAction.java
index c36318ea60e..8ff43c37060 100644
--- a/src/main/java/org/jabref/gui/filelist/AttachFileAction.java
+++ b/src/main/java/org/jabref/gui/filelist/AttachFileAction.java
@@ -28,7 +28,7 @@ public AttachFileAction(BasePanel panel, DialogService dialogService) {
     @Override
     public void execute() {
         if (panel.getSelectedEntries().size() != 1) {
-            panel.output(Localization.lang("This operation requires exactly one item to be selected."));
+            dialogService.notify(Localization.lang("This operation requires exactly one item to be selected."));
             return;
         }
         BibEntry entry = panel.getSelectedEntries().get(0);
diff --git a/src/main/java/org/jabref/gui/importer/ImportAction.java b/src/main/java/org/jabref/gui/importer/ImportAction.java
index 99fa2b36f33..7a945fef1f8 100644
--- a/src/main/java/org/jabref/gui/importer/ImportAction.java
+++ b/src/main/java/org/jabref/gui/importer/ImportAction.java
@@ -15,6 +15,7 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.importer.ImportException;
 import org.jabref.logic.importer.ImportFormatReader;
@@ -95,11 +96,11 @@ private List<ImportFormatReader.UnknownFormatImport> doImport(List<Path> files)
             try {
                 if (!importer.isPresent()) {
                     // Unknown format:
-                    frame.output(Localization.lang("Importing in unknown format") + "...");
+                    DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().notify(Localization.lang("Importing in unknown format") + "..."));
                     // This import method never throws an IOException:
                     imports.add(Globals.IMPORT_FORMAT_READER.importUnknownFormat(filename, Globals.getFileUpdateMonitor()));
                 } else {
-                    frame.output(Localization.lang("Importing in %0 format", importer.get().getName()) + "...");
+                    DefaultTaskExecutor.runInJavaFXThread(() -> frame.getDialogService().notify(Localization.lang("Importing in %0 format", importer.get().getName()) + "..."));
                     // Specific importer:
                     ParserResult pr = importer.get().importDatabase(filename, Globals.prefs.getDefaultEncoding());
                     imports.add(new ImportFormatReader.UnknownFormatImport(importer.get().getName(), pr));
diff --git a/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java b/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java
index 5231d0edede..a5f190f5de5 100644
--- a/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/importer/actions/AppendDatabaseAction.java
@@ -9,7 +9,6 @@
 import javax.swing.undo.CompoundEdit;
 
 import org.jabref.Globals;
-import org.jabref.JabRefExecutorService;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
@@ -18,6 +17,7 @@
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableInsertEntry;
 import org.jabref.gui.undo.UndoableInsertString;
+import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.importer.OpenDatabase;
 import org.jabref.logic.importer.ParserResult;
@@ -159,32 +159,31 @@ public void action() {
             }
             filesToOpen.addAll(chosen);
 
-            // Run the actual open in a thread to prevent the program locking until the file is loaded.
-            JabRefExecutorService.INSTANCE.execute(
-                    () -> openIt(dialog.importEntries(), dialog.importStrings(), dialog.importGroups(), dialog.importSelectorWords()));
-        }
-    }
+            if (filesToOpen.isEmpty()) {
+                return;
+            }
 
-    private void openIt(boolean importEntries, boolean importStrings, boolean importGroups,
-                        boolean importSelectorWords) {
-        if (filesToOpen.isEmpty()) {
-            return;
-        }
-        for (Path file : filesToOpen) {
-            try {
-                Globals.prefs.put(JabRefPreferences.WORKING_DIRECTORY, file.getParent().toString());
-                // Should this be done _after_ we know it was successfully opened?
-                ParserResult parserResult = OpenDatabase.loadDatabase(file.toFile(),
-                        Globals.prefs.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
-                AppendDatabaseAction.mergeFromBibtex(panel, parserResult, importEntries, importStrings, importGroups,
-                        importSelectorWords);
-                panel.output(Localization.lang("Imported from library") + " '" + file + "'");
-            } catch (IOException | KeyCollisionException ex) {
-                LOGGER.warn("Could not open database", ex);
-
-                dialogService.showErrorDialogAndWait(Localization.lang("Open library"), ex);
+            for (Path file : filesToOpen) {
+                // Run the actual open in a thread to prevent the program locking until the file is loaded.
+                BackgroundTask.wrap(() -> openIt(file, dialog.importEntries(), dialog.importStrings(), dialog.importGroups(), dialog.importSelectorWords()))
+                              .onSuccess(fileName -> dialogService.notify(Localization.lang("Imported from library") + " '" + fileName + "'"))
+                              .onFailure(exception -> {
+                                  LOGGER.warn("Could not open database", exception);
+                                  dialogService.showErrorDialogAndWait(Localization.lang("Open library"), exception);})
+                              .executeWith(Globals.TASK_EXECUTOR);;
             }
         }
     }
 
+    private String openIt(Path file, boolean importEntries, boolean importStrings, boolean importGroups,
+                        boolean importSelectorWords) throws IOException, KeyCollisionException {
+            Globals.prefs.put(JabRefPreferences.WORKING_DIRECTORY, file.getParent().toString());
+            // Should this be done _after_ we know it was successfully opened?
+            ParserResult parserResult = OpenDatabase.loadDatabase(file.toFile(),
+                    Globals.prefs.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
+            AppendDatabaseAction.mergeFromBibtex(panel, parserResult, importEntries, importStrings, importGroups,
+                    importSelectorWords);
+            return file.toString();
+    }
+
 }
diff --git a/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java b/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
index 67bd022cbc0..b8be7090041 100644
--- a/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
+++ b/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
@@ -174,12 +174,12 @@ public void openFiles(List<Path> filesToOpen, boolean raisePanel) {
         // If no files are remaining to open, this could mean that a file was
         // already open. If so, we may have to raise the correct tab:
         else if (toRaise != null) {
-            frame.output(Localization.lang("File '%0' is already open.",
+            frame.getDialogService().notify(Localization.lang("File '%0' is already open.",
                     toRaise.getBibDatabaseContext().getDatabaseFile().get().getPath()));
             frame.showBasePanel(toRaise);
         }
 
-        frame.output(Localization.lang("Files opened") + ": " + (filesToOpen.size()));
+        frame.getDialogService().notify(Localization.lang("Files opened") + ": " + (filesToOpen.size()));
     }
 
     /**
@@ -190,7 +190,7 @@ private void openTheFile(Path file, boolean raisePanel) {
         if (Files.exists(file)) {
             Path fileToLoad = file.toAbsolutePath();
 
-            frame.output(Localization.lang("Opening") + ": '" + file + "'");
+            frame.getDialogService().notify(Localization.lang("Opening") + ": '" + file + "'");
 
             Globals.prefs.put(JabRefPreferences.WORKING_DIRECTORY, fileToLoad.getParent().toString());
 
@@ -239,7 +239,7 @@ private BasePanel addNewDatabase(ParserResult result, final Path file, boolean r
         }
 
         if (Objects.nonNull(file)) {
-            frame.output(Localization.lang("Opened library") + " '" + file.toString() + "' "
+            frame.getDialogService().notify(Localization.lang("Opened library") + " '" + file.toString() + "' "
                     + Localization.lang("with")
                     + " "
                     + database.getEntryCount() + " " + Localization.lang("entries") + ".");
diff --git a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java
index 77354393115..dba5c3352da 100644
--- a/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java
+++ b/src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java
@@ -84,12 +84,12 @@ public StringProperty queryProperty() {
 
     public void search() {
         if (StringUtil.isBlank(getQuery())) {
-            frame.output(Localization.lang("Please enter a search string"));
+            frame.getDialogService().notify(Localization.lang("Please enter a search string"));
             return;
         }
 
         if (frame.getCurrentBasePanel() == null) {
-            frame.output(Localization.lang("Please open or start a new library before searching"));
+            frame.getDialogService().notify(Localization.lang("Please open or start a new library before searching"));
             return;
         }
 
diff --git a/src/main/java/org/jabref/gui/journals/AbbreviateAction.java b/src/main/java/org/jabref/gui/journals/AbbreviateAction.java
index 283905fb435..734074c74fe 100644
--- a/src/main/java/org/jabref/gui/journals/AbbreviateAction.java
+++ b/src/main/java/org/jabref/gui/journals/AbbreviateAction.java
@@ -37,6 +37,7 @@ public AbbreviateAction(BasePanel panel, boolean iso) {
 
     @Override
     public void action() {
+        panel.output(Localization.lang("Abbreviating..."));
         BackgroundTask.wrap(this::abbreviate)
                       .onSuccess(panel::output)
                       .executeWith(Globals.TASK_EXECUTOR);
@@ -44,8 +45,6 @@ public void action() {
     }
 
     private String abbreviate() {
-        panel.output(Localization.lang("Abbreviating..."));
-
         List<BibEntry> entries = panel.getSelectedEntries();
         UndoableAbbreviator undoableAbbreviator = new UndoableAbbreviator(
                 Globals.journalAbbreviationLoader.getRepository(Globals.prefs.getJournalAbbreviationPreferences()),
diff --git a/src/main/java/org/jabref/gui/journals/UnabbreviateAction.java b/src/main/java/org/jabref/gui/journals/UnabbreviateAction.java
index 770c996856a..7980beabdc0 100644
--- a/src/main/java/org/jabref/gui/journals/UnabbreviateAction.java
+++ b/src/main/java/org/jabref/gui/journals/UnabbreviateAction.java
@@ -24,14 +24,13 @@ public UnabbreviateAction(BasePanel panel) {
 
     @Override
     public void action() {
+        panel.output(Localization.lang("Unabbreviating..."));
         BackgroundTask.wrap(this::unabbreviate)
                       .onSuccess(panel::output)
                       .executeWith(Globals.TASK_EXECUTOR);
     }
 
     private String unabbreviate() {
-        panel.output(Localization.lang("Unabbreviating..."));
-
         List<BibEntry> entries = panel.getSelectedEntries(); // never null
 
         UndoableUnabbreviator undoableAbbreviator = new UndoableUnabbreviator(Globals.journalAbbreviationLoader
diff --git a/src/main/java/org/jabref/gui/logging/GuiAppender.java b/src/main/java/org/jabref/gui/logging/GuiAppender.java
index d6a6f25ebd6..4d5956b94c5 100644
--- a/src/main/java/org/jabref/gui/logging/GuiAppender.java
+++ b/src/main/java/org/jabref/gui/logging/GuiAppender.java
@@ -13,6 +13,7 @@
 import org.apache.logging.log4j.core.config.plugins.PluginAttribute;
 import org.apache.logging.log4j.core.config.plugins.PluginElement;
 import org.apache.logging.log4j.core.config.plugins.PluginFactory;
+import org.apache.logging.log4j.core.impl.MutableLogEvent;
 import org.apache.logging.log4j.core.layout.PatternLayout;
 
 @Plugin(name = "GuiAppender", category = "Core", elementType = "appender", printObject = true)
@@ -44,6 +45,9 @@ public static GuiAppender createAppender(@PluginAttribute("name") String name,
      */
     @Override
     public void append(LogEvent event) {
-        DefaultTaskExecutor.runInJavaFXThread(() -> LogMessages.getInstance().add(event));
+        // We need to make a copy as instances of LogEvent are reused by log4j
+        MutableLogEvent copy = new MutableLogEvent();
+        copy.initFrom(event);
+        DefaultTaskExecutor.runInJavaFXThread(() -> LogMessages.getInstance().add(copy));
     }
 }
diff --git a/src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java b/src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java
index 219c157fc53..94bc02ddc5b 100644
--- a/src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java
+++ b/src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java
@@ -48,7 +48,7 @@ public SharedDatabaseUIManager(JabRefFrame jabRefFrame) {
     @Subscribe
     public void listen(ConnectionLostEvent connectionLostEvent) {
 
-        jabRefFrame.output(Localization.lang("Connection lost."));
+        jabRefFrame.getDialogService().notify(Localization.lang("Connection lost."));
 
         ButtonType reconnect = new ButtonType(Localization.lang("Reconnect"), ButtonData.YES);
         ButtonType workOffline = new ButtonType(Localization.lang("Work offline"), ButtonData.NO);
@@ -69,7 +69,7 @@ public void listen(ConnectionLostEvent connectionLostEvent) {
             } else if (answer.get().equals(workOffline)) {
                 connectionLostEvent.getBibDatabaseContext().convertToLocalDatabase();
                 jabRefFrame.refreshTitleAndTabs();
-                jabRefFrame.output(Localization.lang("Working offline."));
+                jabRefFrame.getDialogService().notify(Localization.lang("Working offline."));
             }
         } else {
             jabRefFrame.closeCurrentTab();
@@ -79,7 +79,7 @@ public void listen(ConnectionLostEvent connectionLostEvent) {
     @Subscribe
     public void listen(UpdateRefusedEvent updateRefusedEvent) {
 
-        jabRefFrame.output(Localization.lang("Update refused."));
+        jabRefFrame.getDialogService().notify(Localization.lang("Update refused."));
 
         new MergeSharedEntryDialog(jabRefFrame, dbmsSynchronizer, updateRefusedEvent.getLocalBibEntry(),
                                    updateRefusedEvent.getSharedBibEntry(),
@@ -107,7 +107,6 @@ public void listen(SharedEntryNotPresentEvent event) {
      * Opens a new shared database tab with the given {@link DBMSConnectionProperties}.
      *
      * @param dbmsConnectionProperties Connection data
-     * @param raiseTab If <code>true</code> the new tab gets selected.
      * @return BasePanel which also used by {@link SaveDatabaseAction}
      */
     public BasePanel openNewSharedDatabaseTab(DBMSConnectionProperties dbmsConnectionProperties)
@@ -121,7 +120,7 @@ public BasePanel openNewSharedDatabaseTab(DBMSConnectionProperties dbmsConnectio
         dbmsSynchronizer = bibDatabaseContext.getDBMSSynchronizer();
         dbmsSynchronizer.openSharedDatabase(new DBMSConnection(dbmsConnectionProperties));
         dbmsSynchronizer.registerListener(this);
-        jabRefFrame.output(Localization.lang("Connection to %0 server established.", dbmsConnectionProperties.getType().toString()));
+        jabRefFrame.getDialogService().notify(Localization.lang("Connection to %0 server established.", dbmsConnectionProperties.getType().toString()));
         return jabRefFrame.addTab(bibDatabaseContext, true);
     }
 
@@ -150,6 +149,6 @@ public void openSharedDatabaseFromParserResult(ParserResult parserResult)
         dbmsSynchronizer.openSharedDatabase(new DBMSConnection(dbmsConnectionProperties));
         dbmsSynchronizer.registerListener(this);
         parserResult.setDatabaseContext(bibDatabaseContext);
-        jabRefFrame.output(Localization.lang("Connection to %0 server established.", dbmsConnectionProperties.getType().toString()));
+        jabRefFrame.getDialogService().notify(Localization.lang("Connection to %0 server established.", dbmsConnectionProperties.getType().toString()));
     }
 }
diff --git a/src/main/java/org/jabref/gui/specialfields/SpecialFieldAction.java b/src/main/java/org/jabref/gui/specialfields/SpecialFieldAction.java
index 7c5f1f0e217..db486945462 100644
--- a/src/main/java/org/jabref/gui/specialfields/SpecialFieldAction.java
+++ b/src/main/java/org/jabref/gui/specialfields/SpecialFieldAction.java
@@ -70,7 +70,7 @@ public void action() {
                 } else {
                     outText = getTextDone(specialField, value, Integer.toString(bes.size()));
                 }
-                frame.output(outText);
+                frame.getDialogService().notify(outText);
             } else {
                 // if user does not change anything with his action, we do not do anything either
                 // even no output message
diff --git a/src/main/java/org/jabref/gui/worker/SendAsEMailAction.java b/src/main/java/org/jabref/gui/worker/SendAsEMailAction.java
index 51b85ba2784..ee8b7eace9a 100644
--- a/src/main/java/org/jabref/gui/worker/SendAsEMailAction.java
+++ b/src/main/java/org/jabref/gui/worker/SendAsEMailAction.java
@@ -46,11 +46,11 @@ public SendAsEMailAction(JabRefFrame frame) {
     @Override
     public void action() {
         BackgroundTask.wrap(this::sendEmail)
-                      .onSuccess(frame::output)
+                      .onSuccess(frame.getDialogService()::notify)
                       .onFailure(e -> {
                           String message = Localization.lang("Error creating email");
                           LOGGER.warn(message, e);
-                          frame.output(message);
+                          frame.getDialogService().notify(message);
                       })
                       .executeWith(Globals.TASK_EXECUTOR);
     }
diff --git a/src/main/java/org/jabref/logic/logging/LogMessages.java b/src/main/java/org/jabref/logic/logging/LogMessages.java
index 06f10f1c3eb..053252b6e1f 100644
--- a/src/main/java/org/jabref/logic/logging/LogMessages.java
+++ b/src/main/java/org/jabref/logic/logging/LogMessages.java
@@ -4,7 +4,6 @@
 import javafx.collections.ObservableList;
 
 import org.apache.logging.log4j.core.LogEvent;
-import org.apache.logging.log4j.core.impl.MutableLogEvent;
 
 /**
  * This class is used for storing and archiving all message output of JabRef as log events.
@@ -28,10 +27,7 @@ public ObservableList<LogEvent> getMessages() {
     }
 
     public void add(LogEvent event) {
-        // We need to make a copy as instances of LogEvent are reused by log4j
-        MutableLogEvent copy = new MutableLogEvent();
-        copy.initFrom(event);
-        messages.add(copy);
+        messages.add(event);
     }
 
     public void clear() {

From 8095f46a6e21fa98c7445f2a77f707a679a41a3c Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Thu, 4 Apr 2019 12:48:59 +0200
Subject: [PATCH 36/61] Fix custom name formatters (#4848)

Fixes #3531.
---
 CHANGELOG.md                                  |  1 +
 .../org/jabref/logic/layout/LayoutEntry.java  | 30 ++++++-------------
 .../logic/layout/format/NameFormatter.java    |  1 -
 .../layout/format/NotFoundFormatter.java      |  2 --
 .../org/jabref/logic/layout/LayoutTest.java   | 16 +++++++++-
 5 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 60394941469..4ba983b0641 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -88,6 +88,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the default icon of a group was not colored correctly.
 - We fixed an issue where the first field in entry editor was not focused when adding a new entry. [#4024](https://github.com/JabRef/jabref/issues/4024)
 - We reworked the "Edit file" dialog to make it resizeable and improved the workflow for adding and editing files https://github.com/JabRef/jabref/issues/2970
+- We fixed an issue where custom name formatters were no longer found correctly. [#3531](https://github.com/JabRef/jabref/issues/3531)
 - We fixed an issue where the month was not shown in the preview https://github.com/JabRef/jabref/issues/3239.
 - Rewritten logic to detect a second jabref instance. [#4023](https://github.com/JabRef/jabref/issues/4023)
 - We fixed an issue where the "Convert to BibTeX-Cleanup" moved the content of the `file` field to the `pdf` field [#4120](https://github.com/JabRef/jabref/issues/4120)
diff --git a/src/main/java/org/jabref/logic/layout/LayoutEntry.java b/src/main/java/org/jabref/logic/layout/LayoutEntry.java
index 18927ef8cf5..cae756e3a22 100644
--- a/src/main/java/org/jabref/logic/layout/LayoutEntry.java
+++ b/src/main/java/org/jabref/logic/layout/LayoutEntry.java
@@ -391,8 +391,7 @@ private void doOptionField(String s) {
         }
     }
 
-    private LayoutFormatter getLayoutFormatterByName(String name) throws Exception {
-
+    private LayoutFormatter getLayoutFormatterByName(String name) {
         switch (name) {
             case "HTMLToLatexFormatter": // For backward compatibility
             case "HtmlToLatex":
@@ -481,8 +480,7 @@ private LayoutFormatter getLayoutFormatterByName(String name) throws Exception {
             case "Iso690NamesAuthors":
                 return new Iso690NamesAuthors();
             case "JournalAbbreviator":
-                return new JournalAbbreviator(prefs.getJournalAbbreviationLoader(),
-                        prefs.getJournalAbbreviationPreferences());
+                return new JournalAbbreviator(prefs.getJournalAbbreviationLoader(), prefs.getJournalAbbreviationPreferences());
             case "LastPage":
                 return new LastPage();
             case "FormatChars": // For backward compatibility
@@ -535,7 +533,7 @@ private LayoutFormatter getLayoutFormatterByName(String name) throws Exception {
             case "WrapFileLinks":
                 return new WrapFileLinks(prefs.getFileLinkPreferences());
             default:
-                return new NotFoundFormatter(name);
+                return null;
         }
     }
 
@@ -544,19 +542,13 @@ private LayoutFormatter getLayoutFormatterByName(String name) throws Exception {
      * string (in order of appearance).
      */
     private List<LayoutFormatter> getOptionalLayout(String formatterName) {
-
         List<List<String>> formatterStrings = parseMethodsCalls(formatterName);
-
         List<LayoutFormatter> results = new ArrayList<>(formatterStrings.size());
-
         Map<String, String> userNameFormatter = NameFormatter.getNameFormatters(prefs.getNameFormatterPreferences());
-
         for (List<String> strings : formatterStrings) {
-
             String nameFormatterName = strings.get(0).trim();
 
             // Check if this is a name formatter defined by this export filter:
-
             Optional<String> contents = prefs.getCustomExportNameFormatter(nameFormatterName);
             if (contents.isPresent()) {
                 NameFormatter nf = new NameFormatter();
@@ -566,22 +558,18 @@ private List<LayoutFormatter> getOptionalLayout(String formatterName) {
             }
 
             // Try to load from formatters in formatter folder
-            try {
-                LayoutFormatter f = getLayoutFormatterByName(nameFormatterName);
-                // If this formatter accepts an argument, check if we have one, and
-                // set it if so:
-                if ((f instanceof ParamLayoutFormatter) && (strings.size() >= 2)) {
-                    ((ParamLayoutFormatter) f).setArgument(strings.get(1));
+            LayoutFormatter formatter = getLayoutFormatterByName(nameFormatterName);
+            if (formatter != null) {
+                // If this formatter accepts an argument, check if we have one, and set it if so
+                if ((formatter instanceof ParamLayoutFormatter) && (strings.size() >= 2)) {
+                    ((ParamLayoutFormatter) formatter).setArgument(strings.get(1));
                 }
-                results.add(f);
+                results.add(formatter);
                 continue;
-            } catch (Exception ex) {
-                LOGGER.info("Problem with formatter", ex);
             }
 
             // Then check whether this is a user defined formatter
             String formatterParameter = userNameFormatter.get(nameFormatterName);
-
             if (formatterParameter != null) {
                 NameFormatter nf = new NameFormatter();
                 nf.setParameter(formatterParameter);
diff --git a/src/main/java/org/jabref/logic/layout/format/NameFormatter.java b/src/main/java/org/jabref/logic/layout/format/NameFormatter.java
index 8c70fad7ea2..e8830ad1c5b 100644
--- a/src/main/java/org/jabref/logic/layout/format/NameFormatter.java
+++ b/src/main/java/org/jabref/logic/layout/format/NameFormatter.java
@@ -124,7 +124,6 @@ private static String format(String toFormat, AuthorList al, String[] formats) {
     }
 
     public String format(String toFormat, String inParameters) {
-
         AuthorList al = AuthorList.parse(toFormat);
         String parameters;
 
diff --git a/src/main/java/org/jabref/logic/layout/format/NotFoundFormatter.java b/src/main/java/org/jabref/logic/layout/format/NotFoundFormatter.java
index 80596b88dcf..e53b71296d9 100644
--- a/src/main/java/org/jabref/logic/layout/format/NotFoundFormatter.java
+++ b/src/main/java/org/jabref/logic/layout/format/NotFoundFormatter.java
@@ -11,9 +11,7 @@ public class NotFoundFormatter implements LayoutFormatter {
 
     private final String notFound;
 
-
     public NotFoundFormatter(String notFound) {
-
         this.notFound = notFound;
     }
 
diff --git a/src/test/java/org/jabref/logic/layout/LayoutTest.java b/src/test/java/org/jabref/logic/layout/LayoutTest.java
index 06ec187f56b..34e04b157e3 100644
--- a/src/test/java/org/jabref/logic/layout/LayoutTest.java
+++ b/src/test/java/org/jabref/logic/layout/LayoutTest.java
@@ -6,6 +6,7 @@
 import java.util.Collections;
 
 import org.jabref.logic.layout.format.FileLinkPreferences;
+import org.jabref.logic.layout.format.NameFormatterPreferences;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.CustomEntryType;
@@ -98,8 +99,10 @@ void HTMLCharsWithDotlessIAndTiled() throws IOException {
                 layoutText);
     }
 
+    /**
+     * Test for http://discourse.jabref.org/t/the-wrapfilelinks-formatter/172 (the example in the help files)
+     */
     @Test
-        // Test for http://discourse.jabref.org/t/the-wrapfilelinks-formatter/172 (the example in the help files)
     void wrapFileLinksExpandFile() throws IOException {
         when(layoutFormatterPreferences.getFileLinkPreferences()).thenReturn(
                 new FileLinkPreferences(Collections.emptyList(), Collections.singletonList("src/test/resources/pdfs/")));
@@ -121,4 +124,15 @@ void expandCommandIfTerminatedByMinus() throws IOException {
 
         assertEquals("2-th ed.-", layoutText);
     }
+
+    @Test
+    void customNameFormatter() throws IOException {
+        when(layoutFormatterPreferences.getNameFormatterPreferences()).thenReturn(
+                new NameFormatterPreferences(Collections.singletonList("DCA"), Collections.singletonList("1@*@{ll}@@2@1..1@{ff}{ll}@2..2@ and {ff}{l}@@*@*@more")));
+        BibEntry entry = new BibEntry(BibtexEntryTypes.ARTICLE).withField("author", "Joe Doe and Mary Jane");
+
+        String layoutText = layout("\\begin{author}\\format[DCA]{\\author}\\end{author}", entry);
+
+        assertEquals("JoeDoe and MaryJ", layoutText);
+    }
 }

From 42d7b63f1de0615db0b2107a5c01f8c8f3666278 Mon Sep 17 00:00:00 2001
From: Atul Kaushik <atul.kaushikim@gmail.com>
Date: Thu, 4 Apr 2019 16:35:24 +0530
Subject: [PATCH 37/61] Improved and Added Documentation (#4803)

---
 src/main/java/org/jabref/JabRefException.java | 2 +-
 src/main/java/org/jabref/JabRefMain.java      | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/jabref/JabRefException.java b/src/main/java/org/jabref/JabRefException.java
index 0c312fc10df..a1dd034d89e 100644
--- a/src/main/java/org/jabref/JabRefException.java
+++ b/src/main/java/org/jabref/JabRefException.java
@@ -33,7 +33,7 @@ public JabRefException(Throwable cause) {
     @Override
     public String getLocalizedMessage() {
         if (localizedMessage == null) {
-            LOGGER.debug("No localized message exception message defined. Falling back to getMessage().");
+            LOGGER.debug("No localized exception message defined. Falling back to getMessage().");
             return getMessage();
         } else {
             return localizedMessage;
diff --git a/src/main/java/org/jabref/JabRefMain.java b/src/main/java/org/jabref/JabRefMain.java
index 7c6f3d78f49..62758e9c9f0 100644
--- a/src/main/java/org/jabref/JabRefMain.java
+++ b/src/main/java/org/jabref/JabRefMain.java
@@ -88,11 +88,11 @@ public void stop() {
     /**
      * Tests if we are running an acceptable Java and terminates JabRef when we are sure the version is not supported.
      * This test uses the requirements for the Java version as specified in <code>gradle.build</code>. It is possible to
-     * define a minimum version including the built number and to indicate whether Java 9 can be use (which it currently
+     * define a minimum version including the built number and to indicate whether Java 9 can be used (which it currently
      * can't). It tries to compare this version number to the version of the currently running JVM. The check is
      * optimistic and will rather return true even if we could not exactly determine the version.
      * <p>
-     * Note: Users with an very old version like 1.6 will not profit from this since class versions are incompatible and
+     * Note: Users with a very old version like 1.6 will not profit from this since class versions are incompatible and
      * JabRef won't even start. Currently, JabRef won't start with Java 9 either, but the warning that it cannot be used
      * with this version is helpful anyway to prevent users to update from an old 1.8 directly to version 9. Additionally,
      * we soon might have a JabRef that does start with Java 9 but is not perfectly compatible. Therefore, we should leave
@@ -163,7 +163,7 @@ private static void applyPreferences(JabRefPreferences preferences) {
         // Read list(s) of journal names and abbreviations
         Globals.journalAbbreviationLoader = new JournalAbbreviationLoader();
 
-        /* Build list of Import and Export formats */
+        // Build list of Import and Export formats
         Globals.IMPORT_FORMAT_READER.resetImportFormats(Globals.prefs.getImportFormatPreferences(),
                                                         Globals.prefs.getXMPPreferences(), Globals.getFileUpdateMonitor());
         EntryTypes.loadCustomEntryTypes(preferences.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
@@ -173,7 +173,7 @@ private static void applyPreferences(JabRefPreferences preferences) {
         // Initialize protected terms loader
         Globals.protectedTermsLoader = new ProtectedTermsLoader(Globals.prefs.getProtectedTermsPreferences());
 
-        // override used newline character with the one stored in the preferences
+        // Override used newline character with the one stored in the preferences
         // The preferences return the system newline character sequence as default
         OS.NEWLINE = Globals.prefs.get(JabRefPreferences.NEWLINE);
     }

From 7db6e7c4d85e075829d7de1a58d585d76d5da303 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2019 08:21:32 +0200
Subject: [PATCH 38/61] Bump mockito-core from 2.25.1 to 2.26.0 (#4849)

Bumps [mockito-core](https://github.com/mockito/mockito) from 2.25.1 to 2.26.0.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v2.25.1...v2.26.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 261a39e8223..c75f020e690 100644
--- a/build.gradle
+++ b/build.gradle
@@ -167,7 +167,7 @@ dependencies {
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
-    testCompile 'org.mockito:mockito-core:2.25.1'
+    testCompile 'org.mockito:mockito-core:2.26.0'
     testCompile 'com.github.tomakehurst:wiremock:2.22.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'

From ca504d90863557350dde381203ff3b79f556f325 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2019 08:22:00 +0200
Subject: [PATCH 39/61] Bump jurt from 5.4.2 to 6.2.2 (#4850)

Bumps jurt from 5.4.2 to 6.2.2.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index c75f020e690..684c9eae541 100644
--- a/build.gradle
+++ b/build.gradle
@@ -107,7 +107,7 @@ dependencies {
     compile 'commons-cli:commons-cli:1.4'
 
     compile "org.libreoffice:juh:5.4.2"
-    compile "org.libreoffice:jurt:5.4.2"
+    compile "org.libreoffice:jurt:6.2.2"
     compile "org.libreoffice:ridl:5.4.2"
     compile "org.libreoffice:unoil:5.4.2"
 

From 99cacc46f9ceb8fafa507ebc9b0efadfdeee4fb0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2019 08:22:22 +0200
Subject: [PATCH 40/61] Bump unoil from 5.4.2 to 6.2.2 (#4852)

Bumps unoil from 5.4.2 to 6.2.2.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 684c9eae541..30b4f47ccdd 100644
--- a/build.gradle
+++ b/build.gradle
@@ -109,7 +109,7 @@ dependencies {
     compile "org.libreoffice:juh:5.4.2"
     compile "org.libreoffice:jurt:6.2.2"
     compile "org.libreoffice:ridl:5.4.2"
-    compile "org.libreoffice:unoil:5.4.2"
+    compile "org.libreoffice:unoil:6.2.2"
 
     compile 'io.github.java-diff-utils:java-diff-utils:4.0'
     compile 'info.debatty:java-string-similarity:1.1.0'

From 44b74ea8b6764cc201af41293609bbec9e2658cd Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2019 14:23:23 +0200
Subject: [PATCH 41/61] Bump ridl from 5.4.2 to 6.2.2 (#4853)

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 30b4f47ccdd..3bd4bc0cd75 100644
--- a/build.gradle
+++ b/build.gradle
@@ -108,7 +108,7 @@ dependencies {
 
     compile "org.libreoffice:juh:5.4.2"
     compile "org.libreoffice:jurt:6.2.2"
-    compile "org.libreoffice:ridl:5.4.2"
+    compile "org.libreoffice:ridl:6.2.2"
     compile "org.libreoffice:unoil:6.2.2"
 
     compile 'io.github.java-diff-utils:java-diff-utils:4.0'

From 7f7d81ab3e79548f3054c9d94af4dff49d21fe39 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2019 14:24:06 +0200
Subject: [PATCH 42/61] Bump juh from 5.4.2 to 6.2.2 (#4851)

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 3bd4bc0cd75..8a6385b8e6e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -106,7 +106,7 @@ dependencies {
 
     compile 'commons-cli:commons-cli:1.4'
 
-    compile "org.libreoffice:juh:5.4.2"
+    compile "org.libreoffice:juh:6.2.2"
     compile "org.libreoffice:jurt:6.2.2"
     compile "org.libreoffice:ridl:6.2.2"
     compile "org.libreoffice:unoil:6.2.2"

From 17bfe91cd5a87f3c0f7299b86686bde0075b2fc4 Mon Sep 17 00:00:00 2001
From: Abraham Polk <abepolk@gmail.com>
Date: Fri, 5 Apr 2019 10:40:30 -0400
Subject: [PATCH 43/61] QuotedStringTokenizer now does not unquote (#4830)

* QuotedStringTokenizer now does not unquote

* Unquote to fix test failures

* Add javadoc to nextToken
---
 .../jabref/logic/importer/util/GroupsParser.java | 16 ++++++++--------
 .../util/strings/QuotedStringTokenizer.java      |  5 +++++
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
index f7f8dc27cdb..dd25ce3dc7a 100644
--- a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
+++ b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
@@ -169,8 +169,8 @@ private static AbstractGroup automaticKeywordGroupFromString(String string) {
         String name = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         GroupHierarchyType context = GroupHierarchyType.getByNumberOrDefault(Integer.parseInt(tok.nextToken()));
         String field = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
-        Character delimiter = tok.nextToken().charAt(0);
-        Character hierarchicalDelimiter = tok.nextToken().charAt(0);
+        Character delimiter = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR).charAt(0);
+        Character hierarchicalDelimiter = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR).charAt(0);
         AutomaticKeywordGroup newGroup = new AutomaticKeywordGroup(name, context, field, delimiter, hierarchicalDelimiter);
         addGroupDetails(tok, newGroup);
         return newGroup;
@@ -212,7 +212,7 @@ private static ExplicitGroup explicitGroupFromString(String input, Character key
         QuotedStringTokenizer tok = new QuotedStringTokenizer(input.substring(MetadataSerializationConfiguration.EXPLICIT_GROUP_ID.length()),
                 MetadataSerializationConfiguration.GROUP_UNIT_SEPARATOR, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
 
-        String name = tok.nextToken();
+        String name = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         try {
             int context = Integer.parseInt(tok.nextToken());
             ExplicitGroup newGroup = new ExplicitGroup(name, GroupHierarchyType.getByNumberOrDefault(context), keywordSeparator);
@@ -230,7 +230,7 @@ private static ExplicitGroup legacyExplicitGroupFromString(String input, Charact
         QuotedStringTokenizer tok = new QuotedStringTokenizer(input.substring(MetadataSerializationConfiguration.LEGACY_EXPLICIT_GROUP_ID.length()),
                 MetadataSerializationConfiguration.GROUP_UNIT_SEPARATOR, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
 
-        String name = tok.nextToken();
+        String name = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         try {
             int context = Integer.parseInt(tok.nextToken());
             ExplicitGroup newGroup = new ExplicitGroup(name, GroupHierarchyType.getByNumberOrDefault(context), keywordSeparator);
@@ -274,15 +274,15 @@ private static AbstractGroup searchGroupFromString(String s) {
         QuotedStringTokenizer tok = new QuotedStringTokenizer(s.substring(MetadataSerializationConfiguration.SEARCH_GROUP_ID.length()),
                 MetadataSerializationConfiguration.GROUP_UNIT_SEPARATOR, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
 
-        String name = tok.nextToken();
+        String name = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         int context = Integer.parseInt(tok.nextToken());
-        String expression = tok.nextToken();
+        String expression = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         boolean caseSensitive = Integer.parseInt(tok.nextToken()) == 1;
         boolean regExp = Integer.parseInt(tok.nextToken()) == 1;
         // version 0 contained 4 additional booleans to specify search
         // fields; these are ignored now, all fields are always searched
-        return new SearchGroup(StringUtil.unquote(name, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR),
-                GroupHierarchyType.getByNumberOrDefault(context), StringUtil.unquote(expression, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR), caseSensitive, regExp
+        return new SearchGroup(name,
+                GroupHierarchyType.getByNumberOrDefault(context), expression, caseSensitive, regExp
         );
     }
 
diff --git a/src/main/java/org/jabref/logic/util/strings/QuotedStringTokenizer.java b/src/main/java/org/jabref/logic/util/strings/QuotedStringTokenizer.java
index 720d6fe12e2..8c27e745dd4 100644
--- a/src/main/java/org/jabref/logic/util/strings/QuotedStringTokenizer.java
+++ b/src/main/java/org/jabref/logic/util/strings/QuotedStringTokenizer.java
@@ -34,6 +34,10 @@ public QuotedStringTokenizer(String content, String delimiters, char quoteCharac
         }
     }
 
+    /**
+     * @return the next token from the content string, ending at the next
+     * unquoted delimiter. Does not unquote the string itself.
+     */
     public String nextToken() {
         char c;
         StringBuilder stringBuilder = new StringBuilder();
@@ -41,6 +45,7 @@ public String nextToken() {
             c = content.charAt(index);
             if (c == quoteChar) { // next is quoted
                 ++index;
+                stringBuilder.append(c);
                 if (index < contentLength) {
                     stringBuilder.append(content.charAt(index));
                     // ignore for delimiter search!

From 38e162df42fddc6b317ea550d538591030b945a9 Mon Sep 17 00:00:00 2001
From: Robin <robin.lichtenthaeler@web.de>
Date: Fri, 5 Apr 2019 19:07:53 +0200
Subject: [PATCH 44/61] removed default constructor of FXDialogService (#4847)

* removed default constructor of FXDialogService

* Revert "removed default constructor of FXDialogService"

This reverts commit 4c964ca602a9e4b9081e8273e03277c068da2c4c.

* regained injection and splitted jabrefframe creation and init to hav dialogservice ready

* replaced JabRegGUI.mainFrame with mainFrame
---
 src/main/java/org/jabref/JabRefGUI.java       | 25 ++++++++-----------
 .../java/org/jabref/gui/DefaultInjector.java  |  3 ++-
 .../java/org/jabref/gui/FXDialogService.java  | 13 ----------
 src/main/java/org/jabref/gui/JabRefFrame.java |  3 +--
 .../gui/collab/EntryAddChangeViewModel.java   |  4 +--
 .../collab/EntryDeleteChangeViewModel.java    |  4 +--
 .../ExternalFileTypeEntryEditor.java          |  4 +--
 .../jabref/gui/entryeditor/SourceTabTest.java |  4 +--
 8 files changed, 22 insertions(+), 38 deletions(-)

diff --git a/src/main/java/org/jabref/JabRefGUI.java b/src/main/java/org/jabref/JabRefGUI.java
index 203dcf03386..66fe3694ffa 100644
--- a/src/main/java/org/jabref/JabRefGUI.java
+++ b/src/main/java/org/jabref/JabRefGUI.java
@@ -10,8 +10,6 @@
 import javafx.stage.Stage;
 
 import org.jabref.gui.BasePanel;
-import org.jabref.gui.DialogService;
-import org.jabref.gui.FXDialogService;
 import org.jabref.gui.GUIGlobals;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.dialogs.BackupUIManager;
@@ -43,14 +41,13 @@ public class JabRefGUI {
     private final boolean isBlank;
     private final List<ParserResult> failed = new ArrayList<>();
     private final List<ParserResult> toOpenTab = new ArrayList<>();
-    private final DialogService dialogService;
 
     private final String focusedFile;
 
     public JabRefGUI(Stage mainStage, List<ParserResult> argsDatabases, boolean isBlank) {
         this.bibDatabases = argsDatabases;
         this.isBlank = isBlank;
-        this.dialogService = new FXDialogService(mainStage);
+        mainFrame = new JabRefFrame(mainStage);
 
         // passed file (we take the first one) should be focused
         focusedFile = argsDatabases.stream()
@@ -60,7 +57,7 @@ public JabRefGUI(Stage mainStage, List<ParserResult> argsDatabases, boolean isBl
                                     .orElse(Globals.prefs.get(JabRefPreferences.LAST_FOCUSED));
 
         openWindow(mainStage);
-        new VersionWorker(Globals.BUILD_INFO.getVersion(), Globals.prefs.getVersionPreferences().getIgnoredVersion(), JabRefGUI.getMainFrame().getDialogService(), Globals.TASK_EXECUTOR)
+        new VersionWorker(Globals.BUILD_INFO.getVersion(), Globals.prefs.getVersionPreferences().getIgnoredVersion(), mainFrame.getDialogService(), Globals.TASK_EXECUTOR)
                 .checkForNewVersionAsync(false);
     }
 
@@ -75,7 +72,7 @@ private void openWindow(Stage mainStage) {
         GUIGlobals.init();
 
         LOGGER.debug("Initializing frame");
-        JabRefGUI.mainFrame = new JabRefFrame(mainStage);
+        mainFrame.init();
 
         // Add all bibDatabases databases to the frame:
         boolean first = false;
@@ -99,7 +96,7 @@ private void openWindow(Stage mainStage) {
                         pr.getDatabase().clearSharedDatabaseID();
 
                         LOGGER.error("Connection error", e);
-                        dialogService.showErrorDialogAndWait(
+                        mainFrame.getDialogService().showErrorDialogAndWait(
                                 Localization.lang("Connection error"),
                                 Localization.lang("A local copy will be opened."),
                                 e);
@@ -110,7 +107,7 @@ private void openWindow(Stage mainStage) {
                     // add them to the list
                     toOpenTab.add(pr);
                 } else {
-                    JabRefGUI.getMainFrame().addParserResult(pr, first);
+                    mainFrame.addParserResult(pr, first);
                     first = false;
                 }
             }
@@ -118,7 +115,7 @@ private void openWindow(Stage mainStage) {
 
         // finally add things to the currently opened tab
         for (ParserResult pr : toOpenTab) {
-            JabRefGUI.getMainFrame().addParserResult(pr, first);
+            mainFrame.addParserResult(pr, first);
             first = false;
         }
 
@@ -158,14 +155,14 @@ private void openWindow(Stage mainStage) {
             String message = Localization.lang("Error opening file '%0'.", pr.getFile().get().getName()) + "\n"
                     + pr.getErrorMessage();
 
-            dialogService.showErrorDialogAndWait(Localization.lang("Error opening file"), message);
+            mainFrame.getDialogService().showErrorDialogAndWait(Localization.lang("Error opening file"), message);
 
         }
 
         // Display warnings, if any
         int tabNumber = 0;
         for (ParserResult pr : bibDatabases) {
-            ParserResultWarningDialog.showParserResultWarningDialog(pr, JabRefGUI.getMainFrame(), tabNumber++);
+            ParserResultWarningDialog.showParserResultWarningDialog(pr, mainFrame, tabNumber++);
         }
 
         // After adding the databases, go through each and see if
@@ -177,9 +174,9 @@ private void openWindow(Stage mainStage) {
         // This is because importToOpen might have been used, which adds to
         // loadedDatabases, but not to getBasePanelCount()
 
-        for (int i = 0; (i < bibDatabases.size()) && (i < JabRefGUI.getMainFrame().getBasePanelCount()); i++) {
+        for (int i = 0; (i < bibDatabases.size()) && (i < mainFrame.getBasePanelCount()); i++) {
             ParserResult pr = bibDatabases.get(i);
-            BasePanel panel = JabRefGUI.getMainFrame().getBasePanelAt(i);
+            BasePanel panel = mainFrame.getBasePanelAt(i);
             OpenDatabaseAction.performPostOpenActions(panel, pr);
         }
 
@@ -209,7 +206,7 @@ private void openLastEditedDatabases() {
             }
 
             if (BackupManager.checkForBackupFile(dbFile.toPath())) {
-                BackupUIManager.showRestoreBackupDialog(dialogService, dbFile.toPath());
+                BackupUIManager.showRestoreBackupDialog(mainFrame.getDialogService(), dbFile.toPath());
             }
 
             ParserResult parsedDatabase = OpenDatabase.loadDatabase(fileName,
diff --git a/src/main/java/org/jabref/gui/DefaultInjector.java b/src/main/java/org/jabref/gui/DefaultInjector.java
index ee7c8c05839..ed9963b55c5 100644
--- a/src/main/java/org/jabref/gui/DefaultInjector.java
+++ b/src/main/java/org/jabref/gui/DefaultInjector.java
@@ -5,6 +5,7 @@
 import javax.swing.undo.UndoManager;
 
 import org.jabref.Globals;
+import org.jabref.JabRefGUI;
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
@@ -28,7 +29,7 @@ public class DefaultInjector implements PresenterFactory {
      */
     private static Object createDependency(Class<?> clazz) {
         if (clazz == DialogService.class) {
-            return new FXDialogService();
+            return JabRefGUI.getMainFrame().getDialogService();
         } else if (clazz == TaskExecutor.class) {
             return Globals.TASK_EXECUTOR;
         } else if (clazz == PreferencesService.class) {
diff --git a/src/main/java/org/jabref/gui/FXDialogService.java b/src/main/java/org/jabref/gui/FXDialogService.java
index 2fe537a30a1..579b4de8bdd 100644
--- a/src/main/java/org/jabref/gui/FXDialogService.java
+++ b/src/main/java/org/jabref/gui/FXDialogService.java
@@ -63,19 +63,6 @@ public class FXDialogService implements DialogService {
     private final Window mainWindow;
     private final JFXSnackbar statusLine;
 
-    /**
-     * @deprecated try not to initialize a new dialog service but reuse the one constructed in {@link org.jabref.gui.JabRefFrame}.
-     */
-    @Deprecated
-    public FXDialogService() {
-        this(null);
-    }
-
-    public FXDialogService(Window mainWindow) {
-        this.mainWindow = mainWindow;
-        this.statusLine = new JFXSnackbar();
-    }
-
     public FXDialogService(Window mainWindow, Pane mainPane) {
         this.mainWindow = mainWindow;
         this.statusLine = new JFXSnackbar(mainPane);
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 71e75d1c54d..8ec31a46d11 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -178,7 +178,6 @@ public class JabRefFrame extends BorderPane {
     public JabRefFrame(Stage mainStage) {
         this.mainStage = mainStage;
         this.dialogService = new FXDialogService(mainStage, this);
-        init();
     }
 
     /**
@@ -204,7 +203,7 @@ private static void setEnabled(List<Object> list, boolean enabled) {
         }
     }
 
-    private void init() {
+    public void init() {
         sidePaneManager = new SidePaneManager(Globals.prefs, this);
         sidePane = sidePaneManager.getPane();
 
diff --git a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
index c5849decfef..a84904534bb 100644
--- a/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryAddChangeViewModel.java
@@ -3,7 +3,7 @@
 import javafx.scene.Node;
 
 import org.jabref.Globals;
-import org.jabref.gui.FXDialogService;
+import org.jabref.JabRefGUI;
 import org.jabref.gui.PreviewPanel;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
@@ -29,7 +29,7 @@ public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
 
     @Override
     public Node description() {
-        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), JabRefGUI.getMainFrame().getDialogService(), ExternalFileTypes.getInstance());
         previewPanel.setEntry(diskEntry);
         return previewPanel;
     }
diff --git a/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
index e4b658036a0..3efe55cb530 100644
--- a/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
+++ b/src/main/java/org/jabref/gui/collab/EntryDeleteChangeViewModel.java
@@ -3,7 +3,7 @@
 import javafx.scene.Node;
 
 import org.jabref.Globals;
-import org.jabref.gui.FXDialogService;
+import org.jabref.JabRefGUI;
 import org.jabref.gui.PreviewPanel;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
@@ -46,7 +46,7 @@ public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
 
     @Override
     public Node description() {
-        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        PreviewPanel previewPanel = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), JabRefGUI.getMainFrame().getDialogService(), ExternalFileTypes.getInstance());
         previewPanel.setEntry(memEntry);
         return previewPanel;
     }
diff --git a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java
index e620e69e84b..676868ac898 100644
--- a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java
+++ b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypeEntryEditor.java
@@ -20,8 +20,8 @@
 import javax.swing.event.DocumentListener;
 
 import org.jabref.Globals;
+import org.jabref.JabRefGUI;
 import org.jabref.gui.DialogService;
-import org.jabref.gui.FXDialogService;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.FileDialogConfiguration;
@@ -62,7 +62,7 @@ public class ExternalFileTypeEntryEditor {
 
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
                 .withInitialDirectory(Paths.get(appDir)).build();
-        DialogService ds = new FXDialogService();
+        DialogService ds = JabRefGUI.getMainFrame().getDialogService();
 
         Optional<Path> path = DefaultTaskExecutor
                 .runInJavaFXThread(() -> ds.showFileOpenDialog(fileDialogConfiguration));
diff --git a/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java b/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java
index 51a27e3b70a..c3f50e3c853 100644
--- a/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java
+++ b/src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java
@@ -6,7 +6,7 @@
 import javafx.scene.control.TabPane;
 import javafx.stage.Stage;
 
-import org.jabref.gui.FXDialogService;
+import org.jabref.gui.DialogService;
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.logic.bibtex.LatexFieldFormatterPreferences;
 import org.jabref.logic.importer.ImportFormatPreferences;
@@ -38,7 +38,7 @@ public class SourceTabTest {
     public void onStart(Stage stage) {
         area = new CodeArea();
         area.appendText("some example\n text to go here\n across a couple of \n lines....");
-        sourceTab = new SourceTab(new BibDatabaseContext(), new CountingUndoManager(), new LatexFieldFormatterPreferences(), mock(ImportFormatPreferences.class), new DummyFileUpdateMonitor(), new FXDialogService());
+        sourceTab = new SourceTab(new BibDatabaseContext(), new CountingUndoManager(), new LatexFieldFormatterPreferences(), mock(ImportFormatPreferences.class), new DummyFileUpdateMonitor(), mock(DialogService.class));
         pane = new TabPane(
                 new Tab("main area", area),
                 new Tab("other tab", new Label("some text")),

From 8fb663e477cb357e1faf3491c180982d17451fcb Mon Sep 17 00:00:00 2001
From: Harinda Samarasekara <harindaburndown@gmail.com>
Date: Sun, 7 Apr 2019 20:11:46 +0530
Subject: [PATCH 45/61] Fixed group creation with default settings (#4801)

* Fix for the issue - #4783 Group creation not possible anymore with default settings

* Changed the position of the listeners and onaction replaced with changelistener

* Removed changelog entry

* Fix for issue 4783 - Simplified listeners in to lambdas

* Update GroupDialog.java
---
 src/main/java/org/jabref/gui/groups/GroupDialog.java | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
index b40755e97e4..9fc080c8749 100644
--- a/src/main/java/org/jabref/gui/groups/GroupDialog.java
+++ b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -351,6 +351,10 @@ groupName, getContext(),
             return null;
         });
 
+        nameField.textProperty().addListener((observable, oldValue, newValue) -> updateComponents());
+        keywordGroupSearchTerm.textProperty().addListener((observable, oldValue, newValue) -> updateComponents());
+        searchGroupSearchExpression.textProperty().addListener((observable, oldValue, newValue) -> updateComponents());
+
         EventHandler<ActionEvent> actionHandler = (ActionEvent e) -> updateComponents();
         nameField.setOnAction(actionHandler);
         descriptionField.setOnAction(actionHandler);

From e26d9ab9a7e47b2818c8eafd2e08de5808d6ce98 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Sun, 7 Apr 2019 20:35:26 +0200
Subject: [PATCH 46/61] Add author normalizer for medline import (#4863)

* Add author normalizer for medline import

Author names from medline lack the dot by Abbrevatieed authors
e.g. Lahiru S instead of Lahuri S.

Fix tests
Fixes #4345

* Add changelog entry
---
 CHANGELOG.md                                                | 2 ++
 .../org/jabref/logic/importer/fetcher/MedlineFetcher.java   | 2 ++
 .../jabref/logic/importer/fetcher/MedlineFetcherTest.java   | 6 +++---
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4ba983b0641..2d7c0f75166 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -61,6 +61,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
 - We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
 - We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
+- The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
+
 
 ### Fixed
 - We fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries [#3112](https://github.com/JabRef/jabref/issues/3112)
diff --git a/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java b/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java
index 0b8ace85d7d..7fbe0f809ac 100644
--- a/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java
+++ b/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java
@@ -21,6 +21,7 @@
 
 import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
 import org.jabref.logic.formatter.bibtexfields.NormalizeMonthFormatter;
+import org.jabref.logic.formatter.bibtexfields.NormalizeNamesFormatter;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedParserFetcher;
@@ -153,6 +154,7 @@ public void doPostCleanup(BibEntry entry) {
         new FieldFormatterCleanup("copyright", new ClearFormatter()).cleanup(entry);
 
         new FieldFormatterCleanup(FieldName.MONTH, new NormalizeMonthFormatter()).cleanup(entry);
+        new FieldFormatterCleanup(FieldName.AUTHOR, new NormalizeNamesFormatter()).cleanup(entry);
     }
 
     @Override
diff --git a/src/test/java/org/jabref/logic/importer/fetcher/MedlineFetcherTest.java b/src/test/java/org/jabref/logic/importer/fetcher/MedlineFetcherTest.java
index 54e7ac3944a..bbfa9a6ee8a 100644
--- a/src/test/java/org/jabref/logic/importer/fetcher/MedlineFetcherTest.java
+++ b/src/test/java/org/jabref/logic/importer/fetcher/MedlineFetcherTest.java
@@ -27,7 +27,7 @@ public void setUp() {
 
         entryWijedasa = new BibEntry();
         entryWijedasa.setType(BiblatexEntryTypes.ARTICLE);
-        entryWijedasa.setField("author", "Wijedasa, Lahiru S and Jauhiainen, Jyrki and Könönen, Mari and Lampela, Maija and Vasander, Harri and Leblanc, Marie-Claire and Evers, Stephanie and Smith, Thomas E L and Yule, Catherine M and Varkkey, Helena and Lupascu, Massimo and Parish, Faizal and Singleton, Ian and Clements, Gopalasamy R and Aziz, Sheema Abdul and Harrison, Mark E and Cheyne, Susan and Anshari, Gusti Z and Meijaard, Erik and Goldstein, Jenny E and Waldron, Susan and Hergoualc'h, Kristell and Dommain, Rene and Frolking, Steve and Evans, Christopher D and Posa, Mary Rose C and Glaser, Paul H and Suryadiputra, Nyoman and Lubis, Reza and Santika, Truly and Padfield, Rory and Kurnianto, Sofyan and Hadisiswoyo, Panut and Lim, Teck Wyn and Page, Susan E and Gauci, Vincent and Van Der Meer, Peter J and Buckland, Helen and Garnier, Fabien and Samuel, Marshall K and Choo, Liza Nuriati Lim Kim and O'Reilly, Patrick and Warren, Matthew and Suksuwan, Surin and Sumarga, Elham and Jain, Anuj and Laurance, William F and Couwenberg, John and Joosten, Hans and Vernimmen, Ronald and Hooijer, Aljosja and Malins, Chris and Cochrane, Mark A and Perumal, Balu and Siegert, Florian and Peh, Kelvin S-H and Comeau, Louis-Pierre and Verchot, Louis and Harvey, Charles F and Cobb, Alex and Jaafar, Zeehan and Wösten, Henk and Manuri, Solichin and Müller, Moritz and Giesen, Wim and Phelps, Jacob and Yong, Ding Li and Silvius, Marcel and Wedeux, Béatrice M M and Hoyt, Alison and Osaki, Mitsuru and Hirano, Takashi and Takahashi, Hidenori and Kohyama, Takashi S and Haraguchi, Akira and Nugroho, Nunung P and Coomes, David A and Quoi, Le Phat and Dohong, Alue and Gunawan, Haris and Gaveau, David L A and Langner, Andreas and Lim, Felix K S and Edwards, David P and Giam, Xingli and Van Der Werf, Guido and Carmenta, Rachel and Verwer, Caspar C and Gibson, Luke and Gandois, Laure and Graham, Laura Linda Bozena and Regalino, Jhanson and Wich, Serge A and Rieley, Jack and Kettridge, Nicholas and Brown, Chloe and Pirard, Romain and Moore, Sam and Capilla, B Ripoll and Ballhorn, Uwe and Ho, Hua Chew and Hoscilo, Agata and Lohberger, Sandra and Evans, Theodore A and Yulianti, Nina and Blackham, Grace and Onrizal and Husson, Simon and Murdiyarso, Daniel and Pangala, Sunita and Cole, Lydia E S and Tacconi, Luca and Segah, Hendrik and Tonoto, Prayoto and Lee, Janice S H and Schmilewski, Gerald and Wulffraat, Stephan and Putra, Erianto Indra and Cattau, Megan E and Clymo, R S and Morrison, Ross and Mujahid, Aazani and Miettinen, Jukka and Liew, Soo Chin and Valpola, Samu and Wilson, David and D'Arcy, Laura and Gerding, Michiel and Sundari, Siti and Thornton, Sara A and Kalisz, Barbara and Chapman, Stephen J and Su, Ahmad Suhaizi Mat and Basuki, Imam and Itoh, Masayuki and Traeholt, Carl and Sloan, Sean and Sayok, Alexander K and Andersen, Roxane");
+        entryWijedasa.setField("author", "Wijedasa, Lahiru S. and Jauhiainen, Jyrki and Könönen, Mari and Lampela, Maija and Vasander, Harri and Leblanc, Marie-Claire and Evers, Stephanie and Smith, Thomas E.  L. and Yule, Catherine M. and Varkkey, Helena and Lupascu, Massimo and Parish, Faizal and Singleton, Ian and Clements, Gopalasamy R. and Aziz, Sheema Abdul and Harrison, Mark E. and Cheyne, Susan and Anshari, Gusti Z. and Meijaard, Erik and Goldstein, Jenny E. and Waldron, Susan and Hergoualc'h, Kristell and Dommain, Rene and Frolking, Steve and Evans, Christopher D. and Posa, Mary Rose C. and Glaser, Paul H. and Suryadiputra, Nyoman and Lubis, Reza and Santika, Truly and Padfield, Rory and Kurnianto, Sofyan and Hadisiswoyo, Panut and Lim, Teck Wyn and Page, Susan E. and Gauci, Vincent and Van Der Meer, Peter J. and Buckland, Helen and Garnier, Fabien and Samuel, Marshall K. and Choo, Liza Nuriati Lim Kim and O'Reilly, Patrick and Warren, Matthew and Suksuwan, Surin and Sumarga, Elham and Jain, Anuj and Laurance, William F. and Couwenberg, John and Joosten, Hans and Vernimmen, Ronald and Hooijer, Aljosja and Malins, Chris and Cochrane, Mark A. and Perumal, Balu and Siegert, Florian and Peh, Kelvin S.-H. and Comeau, Louis-Pierre and Verchot, Louis and Harvey, Charles F. and Cobb, Alex and Jaafar, Zeehan and Wösten, Henk and Manuri, Solichin and Müller, Moritz and Giesen, Wim and Phelps, Jacob and Yong, Ding Li and Silvius, Marcel and Wedeux, Béatrice M.  M. and Hoyt, Alison and Osaki, Mitsuru and Hirano, Takashi and Takahashi, Hidenori and Kohyama, Takashi S. and Haraguchi, Akira and Nugroho, Nunung P. and Coomes, David A. and Quoi, Le Phat and Dohong, Alue and Gunawan, Haris and Gaveau, David L.  A. and Langner, Andreas and Lim, Felix K.  S. and Edwards, David P. and Giam, Xingli and Van Der Werf, Guido and Carmenta, Rachel and Verwer, Caspar C. and Gibson, Luke and Gandois, Laure and Graham, Laura Linda Bozena and Regalino, Jhanson and Wich, Serge A. and Rieley, Jack and Kettridge, Nicholas and Brown, Chloe and Pirard, Romain and Moore, Sam and Capilla, B.  Ripoll and Ballhorn, Uwe and Ho, Hua Chew and Hoscilo, Agata and Lohberger, Sandra and Evans, Theodore A. and Yulianti, Nina and Blackham, Grace and Onrizal and Husson, Simon and Murdiyarso, Daniel and Pangala, Sunita and Cole, Lydia E.  S. and Tacconi, Luca and Segah, Hendrik and Tonoto, Prayoto and Lee, Janice S.  H. and Schmilewski, Gerald and Wulffraat, Stephan and Putra, Erianto Indra and Cattau, Megan E. and Clymo, R.  S. and Morrison, Ross and Mujahid, Aazani and Miettinen, Jukka and Liew, Soo Chin and Valpola, Samu and Wilson, David and D'Arcy, Laura and Gerding, Michiel and Sundari, Siti and Thornton, Sara A. and Kalisz, Barbara and Chapman, Stephen J. and Su, Ahmad Suhaizi Mat and Basuki, Imam and Itoh, Masayuki and Traeholt, Carl and Sloan, Sean and Sayok, Alexander K. and Andersen, Roxane");
         entryWijedasa.setField("country", "England");
         entryWijedasa.setField("doi", "10.1111/gcb.13516");
         entryWijedasa.setField("issn", "1365-2486");
@@ -66,7 +66,7 @@ public void setUp() {
         entryEndharti.setField("pmid", "27670445");
         entryEndharti.setField("pubmodel", "Electronic");
         entryEndharti.setField("pubstatus", "epublish");
-        entryEndharti.setField("revised", "2017-02-20");
+        entryEndharti.setField("revised", "2018-11-13");
         entryEndharti.setField("volume", "16");
         entryEndharti.setField("year", "2016");
 
@@ -110,7 +110,7 @@ public void setUp() {
         bibEntrySari.setField("keywords", "Antibodies, Protozoan; Antibodies, Viral, immunology; Coinfection, epidemiology, immunology; Female; HIV Infections, epidemiology; HTLV-I Antibodies, immunology; HTLV-I Infections, epidemiology, immunology; HTLV-II Antibodies, immunology; HTLV-II Infections, epidemiology, immunology; Hepatitis Antibodies, immunology; Hepatitis B Antibodies, immunology; Hepatitis C Antibodies, immunology; Hepatitis Delta Virus, immunology; Hepatitis, Viral, Human, epidemiology, immunology; Humans; Immunoglobulin G, immunology; Immunoglobulin M, immunology; Indonesia, epidemiology; Male; Prisoners; Seroepidemiologic Studies; Toxoplasma, immunology; Toxoplasmosis, epidemiology, immunology");
         bibEntrySari.setField("month", "#nov#");
         bibEntrySari.setField("pubstatus", "ppublish");
-        bibEntrySari.setField("revised", "2016-02-12");
+        bibEntrySari.setField("revised", "2018-12-02");
         bibEntrySari.setField("nlm-id", "0266303");
         bibEntrySari.setField("owner", "NLM");
         bibEntrySari.setField("pages", "977--985");

From ec8ae8401f879ee1443c30e191b234ecc79c47d8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 8 Apr 2019 08:10:33 +0200
Subject: [PATCH 47/61] Bump junit-jupiter from 5.4.1 to 5.4.2 (#4867)

Bumps [junit-jupiter](https://github.com/junit-team/junit5) from 5.4.1 to 5.4.2.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/compare/r5.4.1...r5.4.2)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 8a6385b8e6e..38e6e502cb4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -161,7 +161,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.1'
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.1'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.1'
 

From 3d2d61d0ce3263b257f33d721623b512e748811d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 8 Apr 2019 08:10:58 +0200
Subject: [PATCH 48/61] Bump junit-platform-launcher from 1.4.1 to 1.4.2
 (#4865)

Bumps [junit-platform-launcher](https://github.com/junit-team/junit5) from 1.4.1 to 1.4.2.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](https://github.com/junit-team/junit5/commits)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 38e6e502cb4..8f63f2fdbe1 100644
--- a/build.gradle
+++ b/build.gradle
@@ -163,7 +163,7 @@ dependencies {
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.4.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.4.1'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.4.2'
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'

From 4d3ddf5c6e85fe46563922150203a306781bb7dd Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Mon, 8 Apr 2019 11:37:36 +0200
Subject: [PATCH 49/61] Bump junit-vintage-engine from 5.4.1 to 5.4.2 (#4866)

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 8f63f2fdbe1..b20bd600e17 100644
--- a/build.gradle
+++ b/build.gradle
@@ -162,7 +162,7 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.4.2'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.1'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.2'
     testCompile 'org.junit.platform:junit-platform-launcher:1.4.2'
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'

From fdb9fa5bcbf96ae30f1467c4a018370373718117 Mon Sep 17 00:00:00 2001
From: Kaique Komata <kaique.komata@usp.br>
Date: Mon, 8 Apr 2019 08:54:55 -0300
Subject: [PATCH 50/61] Fix IllegalArgumentException when ranking entries
 (#4779)

---
 CHANGELOG.md                                           |  1 +
 .../java/org/jabref/gui/actions/StandardActions.java   | 10 +++++-----
 src/main/resources/l10n/JabRef_en.properties           |  5 +++++
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2d7c0f75166..7a941e10ce1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -104,6 +104,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
+- We fixed an issue where ranking an entry would generate an IllegalArgumentException. [#4754](https://github.com/JabRef/jabref/issues/4754)
 - We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
 - We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 
diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
index 2c91ff5c4b5..eb4c6508955 100644
--- a/src/main/java/org/jabref/gui/actions/StandardActions.java
+++ b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -44,11 +44,11 @@ public enum StandardActions implements Action {
     QUALITY_ASSURED(Localization.lang("Toggle quality assured"), IconTheme.JabRefIcons.QUALITY_ASSURED),
     RANKING(Localization.lang("Rank"), IconTheme.JabRefIcons.RANKING),
     CLEAR_RANK(Localization.lang("Clear rank")),
-    RANK_1("", IconTheme.JabRefIcons.RANK1),
-    RANK_2("", IconTheme.JabRefIcons.RANK2),
-    RANK_3("", IconTheme.JabRefIcons.RANK3),
-    RANK_4("", IconTheme.JabRefIcons.RANK4),
-    RANK_5("", IconTheme.JabRefIcons.RANK5),
+    RANK_1(Localization.lang("Set rank to one"), IconTheme.JabRefIcons.RANK1),
+    RANK_2(Localization.lang("Set rank to two"), IconTheme.JabRefIcons.RANK2),
+    RANK_3(Localization.lang("Set rank to three"), IconTheme.JabRefIcons.RANK3),
+    RANK_4(Localization.lang("Set rank to four"), IconTheme.JabRefIcons.RANK4),
+    RANK_5(Localization.lang("Set rank to five"), IconTheme.JabRefIcons.RANK5),
     PRINTED(Localization.lang("Printed"), IconTheme.JabRefIcons.PRINTED),
     TOGGLE_PRINTED(Localization.lang("Toggle print status"), IconTheme.JabRefIcons.PRINTED),
     READ_STATUS(Localization.lang("Read status"), IconTheme.JabRefIcons.READ_STATUS),
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 7893e31e5d1..7398d8fc491 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2081,3 +2081,8 @@ Use\ selected\ document=Use selected document
 Accept\ changes=Accept changes
 Dismiss\ changes=Dismiss changes
 The\ library\ has\ been\ modified\ by\ another\ program.=The library has been modified by another program.
+Set\ rank\ to\ one=Set rank to one
+Set\ rank\ to\ two=Set rank to two
+Set\ rank\ to\ three=Set rank to three
+Set\ rank\ to\ four=Set rank to four
+Set\ rank\ to\ five=Set rank to five

From bb7b7213d7e0339491c066eb457c27b70fad0b16 Mon Sep 17 00:00:00 2001
From: Christoph <cschwentker@gmail.com>
Date: Mon, 8 Apr 2019 19:13:51 +0200
Subject: [PATCH 51/61] Remove deprecated awt apple extension (#4860)

---
 lib/AppleJavaExtensions.jar                   | Bin 25467 -> 0 bytes
 src/main/java/org/jabref/gui/JabRefFrame.java |  14 ---
 .../org/jabref/gui/OSXCompatibleToolbar.java  |  39 --------
 src/main/java/osx/macadapter/MacAdapter.java  |  83 ------------------
 4 files changed, 136 deletions(-)
 delete mode 100644 lib/AppleJavaExtensions.jar
 delete mode 100644 src/main/java/org/jabref/gui/OSXCompatibleToolbar.java
 delete mode 100644 src/main/java/osx/macadapter/MacAdapter.java

diff --git a/lib/AppleJavaExtensions.jar b/lib/AppleJavaExtensions.jar
deleted file mode 100644
index 6659a81c69fc189cf966dd79f5824b486c9c0281..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 25467
zcmce;by${L6E})<cS?76cXxM6cc-*8NOyNiN(e|ucY}g7NC--|3IgYG`|gcATY2B>
zob!EL*L~?9_x*d;`mI?rvu0+Ek}McFEC>iR2na=lo*>9Ce=s26AoAjB!t~M#5{x&)
zARtQrc@-Lj9Pn!INMyMI;B_0ogARE9c~xFmL0UpwRgFPj;#7WgL{65TVG2Q(o@RV>
z;*|>1H0y_t&ZDBJPIOXo<5KD%5s%2}&!Rk<vm#Z{WK~pMvuT8P#?Ii^qv_ld;St=T
z>FM1N5PYNM5u(u9@ZeybRWSHY6VBN@n?0KU8PLDS4h|TQiGv;E-$VZQ8-O|g^@fq7
zqpjHk?_u0~&&0vr#Ld~+%-;2ZPmu0?VrJz2(98Gn|9aW%>BIPl_wlV9{uvAOUyHbE
zAFjd)3Id`7V1e%5yT1%y%*w^l$koJ>Ov%~G!P&~ylflH+$i*dD)lTu968f`)g{mi-
zbEasUW1Pr~@@1u#Bya(pN#uz*71--9UTV-$<A2scy-ki0i<0QE@Iyad%0vlcfV^DG
z%5uqd$=S~FzTDkhR0M(Z$O?(#MtE&Rg{`jio+%2J(_L+oo#)L6$|+66k}i$R(yD4r
zClPyw1NJml{A$eiucSfxNTQ57a9IiiyG+;!uiGrRudV_tn)fH=3kKm#Y?crAcx$hW
zF6te_iC@k8eDi7OB666{wPT`srCSj_%bwZg;~l^Nr4Z-172y=m;#qY)ZZgREeR5Im
zLP!5>*a{*^S*&BrJG6Xi&J7Wd*0CFZB!*OQNt=a{sB$Ol*_%-&jy%OSdwXV6J3mU-
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diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 8ec31a46d11..214530e363e 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -118,7 +118,6 @@
 import org.jabref.logic.undo.AddUndoableActionEvent;
 import org.jabref.logic.undo.UndoChangeEvent;
 import org.jabref.logic.undo.UndoRedoEvent;
-import org.jabref.logic.util.OS;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -136,7 +135,6 @@
 import org.fxmisc.easybind.EasyBind;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import osx.macadapter.MacAdapter;
 
 /**
  * The main window of the application.
@@ -286,18 +284,6 @@ public void init() {
             currentBasePanel.getUndoManager().postUndoRedoEvent();
             currentBasePanel.getMainTable().requestFocus();
         });
-
-        //Note: The registration of Apple event is at the end of initialization, because
-        //if the events happen too early (ie when the window is not initialized yet), the
-        //opened (double-clicked) documents are not displayed.
-        if (OS.OS_X) {
-            try {
-                new MacAdapter().registerMacEvents(this);
-            } catch (Exception e) {
-                LOGGER.error("Could not interface with Mac OS X methods.", e);
-            }
-        }
-
         initShowTrackingNotification();
     }
 
diff --git a/src/main/java/org/jabref/gui/OSXCompatibleToolbar.java b/src/main/java/org/jabref/gui/OSXCompatibleToolbar.java
deleted file mode 100644
index f71c9e72af5..00000000000
--- a/src/main/java/org/jabref/gui/OSXCompatibleToolbar.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package org.jabref.gui;
-
-import java.awt.Component;
-
-import javax.swing.JButton;
-import javax.swing.JToolBar;
-
-import org.jabref.logic.util.OS;
-
-public class OSXCompatibleToolbar extends JToolBar {
-
-    public OSXCompatibleToolbar() {
-    }
-
-    public OSXCompatibleToolbar(int orientation) {
-        super(orientation);
-    }
-
-    public OSXCompatibleToolbar(String name) {
-        super(name);
-    }
-
-    public OSXCompatibleToolbar(String name, int orientation) {
-        super(name, orientation);
-    }
-
-    @Override
-    public Component add(Component a) {
-        if (a instanceof JButton) {
-            JButton button = (JButton) a;
-            if (OS.OS_X) {
-                button.putClientProperty("JButton.buttonType", "toolbar");
-            }
-        }
-
-        return super.add(a);
-    }
-
-}
diff --git a/src/main/java/osx/macadapter/MacAdapter.java b/src/main/java/osx/macadapter/MacAdapter.java
deleted file mode 100644
index 9c7938aa5f6..00000000000
--- a/src/main/java/osx/macadapter/MacAdapter.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package osx.macadapter;
-
-import java.io.File;
-import java.util.List;
-
-import org.jabref.gui.JabRefFrame;
-
-import com.apple.eawt.AboutHandler;
-import com.apple.eawt.AppEvent;
-import com.apple.eawt.AppEvent.AboutEvent;
-import com.apple.eawt.AppEvent.OpenFilesEvent;
-import com.apple.eawt.AppEvent.PreferencesEvent;
-import com.apple.eawt.AppEvent.QuitEvent;
-import com.apple.eawt.AppReOpenedListener;
-import com.apple.eawt.Application;
-import com.apple.eawt.OpenFilesHandler;
-import com.apple.eawt.PreferencesHandler;
-import com.apple.eawt.QuitHandler;
-import com.apple.eawt.QuitResponse;
-
-public class MacAdapter implements PreferencesHandler, AboutHandler, QuitHandler, OpenFilesHandler, AppReOpenedListener {
-
-    private JabRefFrame parentFrame;
-
-    public void registerMacEvents(JabRefFrame inputFrame) {
-        parentFrame = inputFrame;
-        Application.getApplication().setOpenFileHandler(this);
-        Application.getApplication().setAboutHandler(this);
-        Application.getApplication().setPreferencesHandler(this);
-        Application.getApplication().setQuitHandler(this);
-        Application.getApplication().addAppEventListener(this);
-    }
-
-    @Override
-    // The OSXAdapter calls this method when a ".bib" file has been double-clicked from the Finder.
-    public void openFiles(OpenFilesEvent event) {
-        if (parentFrame == null) {
-            return;
-        }
-
-        List<File> files = event.getFiles();
-
-        for (File file : files) {
-            parentFrame.openAction(file.getAbsolutePath());
-        }
-    }
-
-    @Override
-    public void handleQuitRequestWith(QuitEvent evt, QuitResponse resp) {
-        if (parentFrame == null) {
-            return;
-        }
-
-        if (parentFrame.quit()) {
-            resp.performQuit();
-        } else {
-            resp.cancelQuit();
-        }
-    }
-
-    @Override
-    public void handleAbout(AboutEvent arg0) {
-        if (parentFrame == null) {
-            return;
-        }
-
-        parentFrame.about();
-    }
-
-    @Override
-    public void handlePreferences(PreferencesEvent arg0) {
-        if (parentFrame == null) {
-            return;
-        }
-
-        //  parentFrame.showPreferencesDialog();
-    }
-
-    @Override
-    public void appReOpened(AppEvent.AppReOpenedEvent appReOpenedEvent) {
-        parentFrame.setVisible(true);
-    }
-}

From 856c170f2ed4b6eb72907c372e239c32e7fe13f6 Mon Sep 17 00:00:00 2001
From: Ali <alijakparov.kz@gmail.com>
Date: Tue, 9 Apr 2019 09:01:07 +0300
Subject: [PATCH 52/61] #4795 disable menu item if database not connected
 (#4828)

* #4795 disable menu item if database not connected

* resolve merge conflict

* resolve merge conflict

* resolve merge conflicts

* resolve check style

* fix import order

* resolve merge

* delete duplicate code

* change push to application implementation

* fix check style

* delete action

* put deprecated annotation on OldDatabaseCommandWrapper
---
 src/main/java/org/jabref/gui/JabRefFrame.java | 11 +--
 .../actions/OldDatabaseCommandWrapper.java    |  3 +
 .../gui/push/PushToApplicationAction.java     | 68 +++++++++++---
 .../gui/push/PushToApplicationButton.java     | 90 -------------------
 4 files changed, 63 insertions(+), 109 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/push/PushToApplicationButton.java

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
index 214530e363e..abc4abf83a2 100644
--- a/src/main/java/org/jabref/gui/JabRefFrame.java
+++ b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -100,7 +100,7 @@
 import org.jabref.gui.metadata.BibtexStringEditorAction;
 import org.jabref.gui.metadata.PreambleEditor;
 import org.jabref.gui.protectedterms.ManageProtectedTermsAction;
-import org.jabref.gui.push.PushToApplicationButton;
+import org.jabref.gui.push.PushToApplicationAction;
 import org.jabref.gui.push.PushToApplications;
 import org.jabref.gui.search.GlobalSearchBar;
 import org.jabref.gui.specialfields.SpecialFieldMenuItemFactory;
@@ -559,7 +559,8 @@ private Node createToolbar() {
         leftSide.setMinWidth(100);
         leftSide.prefWidthProperty().bind(sidePane.widthProperty());
         leftSide.maxWidthProperty().bind(sidePane.widthProperty());
-        PushToApplicationButton pushToExternal = new PushToApplicationButton(this, pushApplications.getApplications());
+
+        PushToApplicationAction pushToApplicationAction = new PushToApplicationAction(this, Globals.stateManager);
         HBox rightSide = new HBox(
                 factory.createIconButton(StandardActions.NEW_ARTICLE, new NewEntryAction(this, BiblatexEntryTypes.ARTICLE, dialogService, Globals.prefs)),
                 factory.createIconButton(StandardActions.DELETE_ENTRY, new OldDatabaseCommandWrapper(Actions.DELETE, this, Globals.stateManager)),
@@ -570,7 +571,7 @@ private Node createToolbar() {
                 factory.createIconButton(StandardActions.COPY, new OldDatabaseCommandWrapper(Actions.COPY, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.PASTE, new OldDatabaseCommandWrapper(Actions.PASTE, this, Globals.stateManager)),
                 new Separator(Orientation.VERTICAL),
-                factory.createIconButton(pushToExternal.getMenuAction(), pushToExternal),
+                factory.createIconButton(pushToApplicationAction.getActionInformation(), pushToApplicationAction),
                 factory.createIconButton(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, Globals.stateManager)),
                 factory.createIconButton(StandardActions.CLEANUP_ENTRIES, new OldDatabaseCommandWrapper(Actions.CLEANUP, this, Globals.stateManager)),
                 new Separator(Orientation.VERTICAL),
@@ -798,7 +799,7 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs))
         );
 
-        PushToApplicationButton pushToExternal = new PushToApplicationButton(this, pushApplications.getApplications());
+        final PushToApplicationAction pushToApplicationAction = new PushToApplicationAction(this, Globals.stateManager);
         tools.getItems().addAll(
                 factory.createMenuItem(StandardActions.NEW_SUB_LIBRARY_FROM_AUX, new NewSubLibraryAction(this)),
                 factory.createMenuItem(StandardActions.FIND_UNLINKED_FILES, new FindUnlinkedFilesAction(this)),
@@ -815,7 +816,7 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.GENERATE_CITE_KEYS, new OldDatabaseCommandWrapper(Actions.MAKE_KEY, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.REPLACE_ALL, new OldDatabaseCommandWrapper(Actions.REPLACE_ALL, this, Globals.stateManager)),
                 factory.createMenuItem(StandardActions.SEND_AS_EMAIL, new OldDatabaseCommandWrapper(Actions.SEND_AS_EMAIL, this, Globals.stateManager)),
-                factory.createMenuItem(pushToExternal.getMenuAction(), pushToExternal),
+                factory.createMenuItem(pushToApplicationAction.getActionInformation(), pushToApplicationAction),
 
                 factory.createSubMenu(StandardActions.ABBREVIATE,
                         factory.createMenuItem(StandardActions.ABBREVIATE_ISO, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_ISO, this, Globals.stateManager)),
diff --git a/src/main/java/org/jabref/gui/actions/OldDatabaseCommandWrapper.java b/src/main/java/org/jabref/gui/actions/OldDatabaseCommandWrapper.java
index a752da3ce9c..58a702e4190 100644
--- a/src/main/java/org/jabref/gui/actions/OldDatabaseCommandWrapper.java
+++ b/src/main/java/org/jabref/gui/actions/OldDatabaseCommandWrapper.java
@@ -14,7 +14,10 @@
 
 /**
  * A command that is only executable if a database is open.
+ * Deprecated use instead
+ * @see org.jabref.gui.actions.SimpleCommand
  */
+@Deprecated
 public class OldDatabaseCommandWrapper extends CommandBase {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(OldDatabaseCommandWrapper.class);
diff --git a/src/main/java/org/jabref/gui/push/PushToApplicationAction.java b/src/main/java/org/jabref/gui/push/PushToApplicationAction.java
index 468fb8b57dc..e514a8fec55 100644
--- a/src/main/java/org/jabref/gui/push/PushToApplicationAction.java
+++ b/src/main/java/org/jabref/gui/push/PushToApplicationAction.java
@@ -1,39 +1,79 @@
 package org.jabref.gui.push;
 
-import java.awt.event.ActionEvent;
 import java.util.List;
 import java.util.Optional;
 
-import javax.swing.AbstractAction;
-import javax.swing.Action;
 import javax.swing.SwingUtilities;
 
+import org.jabref.Globals;
 import org.jabref.JabRefExecutorService;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.Action;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.icon.JabRefIcon;
+import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.preferences.JabRefPreferences;
+
+import org.fxmisc.easybind.EasyBind;
 
 /**
  * An Action class representing the process of invoking a PushToApplication operation.
  */
-class PushToApplicationAction extends AbstractAction implements Runnable {
+public class PushToApplicationAction extends SimpleCommand implements Runnable {
 
-    private final PushToApplication operation;
-    private final JabRefFrame frame;
+    private PushToApplication operation;
+    private JabRefFrame frame;
     private BasePanel panel;
     private List<BibEntry> entries;
 
-    public PushToApplicationAction(JabRefFrame frame, PushToApplication operation) {
+    public PushToApplicationAction(final JabRefFrame frame, final StateManager stateManager) {
         this.frame = frame;
-        putValue(Action.SMALL_ICON, operation.getIcon());
-        putValue(Action.NAME, operation.getName());
-        putValue(Action.SHORT_DESCRIPTION, operation.getTooltip());
-        this.operation = operation;
+        this.operation = getLastUsedApplication(frame.getPushApplications().getApplications());
+        this.executable.bind(EasyBind.map(stateManager.activeDatabaseProperty(), Optional::isPresent));
+    }
+
+    private PushToApplication getLastUsedApplication(List<PushToApplication> pushActions) {
+        String appSelected = Globals.prefs.get(JabRefPreferences.PUSH_TO_APPLICATION);
+        for (PushToApplication application : pushActions) {
+            if (application.getApplicationName().equals(appSelected)) {
+                return application;
+            }
+        }
+
+        // Nothing found, pick first
+        return pushActions.get(0);
+    }
+
+    public Action getActionInformation() {
+        return new Action() {
+            @Override
+            public Optional<JabRefIcon> getIcon() {
+                return Optional.of(operation.getIcon());
+            }
+
+            @Override
+            public Optional<KeyBinding> getKeyBinding() {
+                return Optional.of(KeyBinding.PUSH_TO_APPLICATION);
+            }
+
+            @Override
+            public String getText() {
+                return Localization.lang("Push entries to external application (%0)", operation.getApplicationName());
+            }
+
+            @Override
+            public String getDescription() {
+                return "";
+            }
+        };
     }
 
     @Override
-    public void actionPerformed(ActionEvent e) {
+    public void execute() {
         panel = frame.getCurrentBasePanel();
 
         // Check if a BasePanel exists:
@@ -44,7 +84,7 @@ public void actionPerformed(ActionEvent e) {
         // Check if any entries are selected:
         entries = panel.getSelectedEntries();
         if (entries.isEmpty()) {
-            frame.getDialogService().showErrorDialogAndWait((String) getValue(Action.NAME),
+            frame.getDialogService().showErrorDialogAndWait(operation.getApplicationName(),
                     Localization.lang("This operation requires one or more entries to be selected."));
 
             return;
@@ -54,7 +94,7 @@ public void actionPerformed(ActionEvent e) {
         if (operation.requiresBibtexKeys()) {
             for (BibEntry entry : entries) {
                 if (!(entry.getCiteKeyOptional().isPresent()) || entry.getCiteKeyOptional().get().trim().isEmpty()) {
-                    frame.getDialogService().showErrorDialogAndWait((String) getValue(Action.NAME),
+                    frame.getDialogService().showErrorDialogAndWait(operation.getApplicationName(),
                             Localization.lang("This operation requires all selected entries to have BibTeX keys defined."));
 
                     return;
diff --git a/src/main/java/org/jabref/gui/push/PushToApplicationButton.java b/src/main/java/org/jabref/gui/push/PushToApplicationButton.java
deleted file mode 100644
index 5ab8fefd4aa..00000000000
--- a/src/main/java/org/jabref/gui/push/PushToApplicationButton.java
+++ /dev/null
@@ -1,90 +0,0 @@
-package org.jabref.gui.push;
-
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
-
-import org.jabref.Globals;
-import org.jabref.gui.JabRefFrame;
-import org.jabref.gui.actions.SimpleCommand;
-import org.jabref.gui.icon.JabRefIcon;
-import org.jabref.gui.keyboard.KeyBinding;
-import org.jabref.logic.l10n.Localization;
-import org.jabref.preferences.JabRefPreferences;
-
-/**
- * Customized UI component for pushing to external applications. Has a selection popup menu to change the selected
- * external application. This class implements the ActionListener interface. When actionPerformed() is invoked, the
- * currently selected PushToApplication is activated. The actionPerformed() method can be called with a null argument.
- */
-public class PushToApplicationButton extends SimpleCommand implements ActionListener {
-
-    private final JabRefFrame frame;
-    private final List<PushToApplication> pushActions;
-    private final PushToApplication toApp;
-    private final Map<PushToApplication, PushToApplicationAction> actions = new HashMap<>();
-
-    public PushToApplicationButton(JabRefFrame frame, List<PushToApplication> pushActions) {
-        this.frame = frame;
-        this.pushActions = pushActions;
-        // Set the last used external application
-        toApp = getLastUsedApplication();
-    }
-
-    private PushToApplication getLastUsedApplication() {
-        String appSelected = Globals.prefs.get(JabRefPreferences.PUSH_TO_APPLICATION);
-        for (PushToApplication application : pushActions) {
-            if (application.getApplicationName().equals(appSelected)) {
-                return application;
-            }
-        }
-
-        // Nothing found, pick first
-        return pushActions.get(0);
-    }
-
-    public org.jabref.gui.actions.Action getMenuAction() {
-        PushToApplication application = getLastUsedApplication();
-
-        return new org.jabref.gui.actions.Action() {
-            @Override
-            public Optional<JabRefIcon> getIcon() {
-                return Optional.of(application.getIcon());
-            }
-
-            @Override
-            public Optional<KeyBinding> getKeyBinding() {
-                return Optional.of(KeyBinding.PUSH_TO_APPLICATION);
-            }
-
-            @Override
-            public String getText() {
-                return Localization.lang("Push entries to external application (%0)", application.getApplicationName());
-            }
-
-            @Override
-            public String getDescription() {
-                return "";
-            }
-        };
-    }
-
-    @Override
-    public void actionPerformed(ActionEvent e) {
-        execute();
-    }
-
-    @Override
-    public void execute() {
-        // Lazy initialization of the push action:
-        PushToApplicationAction action = actions.get(toApp);
-        if (action == null) {
-            action = new PushToApplicationAction(frame, toApp);
-            actions.put(toApp, action);
-        }
-        action.actionPerformed(new ActionEvent(toApp, 0, "push"));
-    }
-}

From 0dd091f31b86b02dd9e44b4ac86aa204d4dec9ef Mon Sep 17 00:00:00 2001
From: Marco Konersmann <marco.konersmann@paluno.uni-due.de>
Date: Tue, 9 Apr 2019 15:36:38 +0200
Subject: [PATCH 53/61] Fix JabRef dying silently without enough inotify
 instances (#4875)

* Logs exceptions in file monitor as errors

An exception in the initialization of DefaultFileUpdateMonitor is now logged as error

* Describes fix for issue #4874
---
 CHANGELOG.md                                                    | 1 +
 src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7a941e10ce1..3ec7d2b519a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -65,6 +65,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 ### Fixed
+- We fixed an issue where JabRef died silently for the user without enough inotify instances [#4874](https://github.com/JabRef/jabref/issues/4847)
 - We fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries [#3112](https://github.com/JabRef/jabref/issues/3112)
 - We fixed an issue where custom exports could not be selected in the 'Export (selected) entries' dialog [#4013](https://github.com/JabRef/jabref/issues/4013)
 - Italic text is now rendered correctly. https://github.com/JabRef/jabref/issues/3356
diff --git a/src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java b/src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java
index 28de7285f3f..bdf0b51e2a6 100644
--- a/src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java
+++ b/src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java
@@ -59,7 +59,7 @@ public void run() {
                 Thread.yield();
             }
         } catch (Throwable e) {
-            LOGGER.debug("FileUpdateMonitor has been interrupted. Terminating...", e);
+            LOGGER.error("FileUpdateMonitor has been interrupted.", e);
         }
     }
 

From e1a01d2a6afd7498e3382f74b172d3b8c5e55293 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Thu, 11 Apr 2019 08:06:54 +0200
Subject: [PATCH 54/61] Bump java-string-similarity from 1.1.0 to 1.2.1 (#4878)

Bumps [java-string-similarity](https://github.com/tdebatty/java-string-similarity) from 1.1.0 to 1.2.1.
- [Release notes](https://github.com/tdebatty/java-string-similarity/releases)
- [Commits](https://github.com/tdebatty/java-string-similarity/compare/v1.1.0...v1.2.1)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index b20bd600e17..9b0ba62711c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -112,7 +112,7 @@ dependencies {
     compile "org.libreoffice:unoil:6.2.2"
 
     compile 'io.github.java-diff-utils:java-diff-utils:4.0'
-    compile 'info.debatty:java-string-similarity:1.1.0'
+    compile 'info.debatty:java-string-similarity:1.2.1'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'

From 6e062d9484e31f917c877d9e6fd72e5f62bcb7ff Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Thu, 11 Apr 2019 08:07:28 +0200
Subject: [PATCH 55/61] Bump mockito-core from 2.26.0 to 2.27.0 (#4879)

Bumps [mockito-core](https://github.com/mockito/mockito) from 2.26.0 to 2.27.0.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v2.26.0...v2.27.0)

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 9b0ba62711c..5154e337837 100644
--- a/build.gradle
+++ b/build.gradle
@@ -167,7 +167,7 @@ dependencies {
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
-    testCompile 'org.mockito:mockito-core:2.26.0'
+    testCompile 'org.mockito:mockito-core:2.27.0'
     testCompile 'com.github.tomakehurst:wiremock:2.22.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'

From f0e548935fdfe8d4b87e37df0d1eb16b2251500e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Sat, 13 Apr 2019 13:46:44 +0200
Subject: [PATCH 56/61] Bump xmpbox from 2.0.14 to 2.0.15 (#4883)

Bumps xmpbox from 2.0.14 to 2.0.15.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 5154e337837..55b978e8782 100644
--- a/build.gradle
+++ b/build.gradle
@@ -97,7 +97,7 @@ dependencies {
 
     compile 'org.apache.pdfbox:pdfbox:2.0.14'
     compile 'org.apache.pdfbox:fontbox:2.0.14'
-    compile 'org.apache.pdfbox:xmpbox:2.0.14'
+    compile 'org.apache.pdfbox:xmpbox:2.0.15'
 
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'
 

From d68bcb30f14a11dc7c54d965e3195669fdf8944c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Sat, 13 Apr 2019 13:46:58 +0200
Subject: [PATCH 57/61] Bump pdfbox from 2.0.14 to 2.0.15 (#4881)

Bumps pdfbox from 2.0.14 to 2.0.15.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 55b978e8782..8123dcd0a1d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -95,7 +95,7 @@ dependencies {
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    compile 'org.apache.pdfbox:pdfbox:2.0.14'
+    compile 'org.apache.pdfbox:pdfbox:2.0.15'
     compile 'org.apache.pdfbox:fontbox:2.0.14'
     compile 'org.apache.pdfbox:xmpbox:2.0.15'
 

From b7989072fd68fe472dd712e18cc72bed69da2247 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <dependabot[bot]@users.noreply.github.com>
Date: Sat, 13 Apr 2019 14:14:07 +0200
Subject: [PATCH 58/61] Bump fontbox from 2.0.14 to 2.0.15 (#4882)

Bumps fontbox from 2.0.14 to 2.0.15.

Signed-off-by: dependabot[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 8123dcd0a1d..277af5824b9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -96,7 +96,7 @@ dependencies {
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
     compile 'org.apache.pdfbox:pdfbox:2.0.15'
-    compile 'org.apache.pdfbox:fontbox:2.0.14'
+    compile 'org.apache.pdfbox:fontbox:2.0.15'
     compile 'org.apache.pdfbox:xmpbox:2.0.15'
 
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'

From 3d770b858f3a028cdfd9c37aac6c881b0b5fb738 Mon Sep 17 00:00:00 2001
From: Deepak Kumar <deepakkumar24196@gmail.com>
Date: Sat, 13 Apr 2019 21:20:23 +0530
Subject: [PATCH 59/61] Fix right clicking on any entry and selecting "Open
 folder" results in the NullPointer exception (#4797)

* Add an option in preference settings to set what action to be taken by JabRef when user clicks 'open folder' on a entry.

* Fix #4763 and add added required changes in CHANGELOG.md and JabRef_en.properties

* Refactor and Reformat code.

* Fix issue #4802, where option 'open terminal here' with custom command was passing wrong argument

* Fix failure of LocalizationConsistencyTest after code changes.
---
 .mailmap                                      |  3 +-
 CHANGELOG.md                                  |  4 +-
 .../org/jabref/gui/desktop/JabRefDesktop.java | 39 +++++++++++----
 .../java/org/jabref/gui/desktop/os/Linux.java | 19 ++++----
 .../jabref/gui/preferences/ExternalTab.java   | 48 +++++++++++++++++++
 .../jabref/preferences/JabRefPreferences.java |  6 +++
 src/main/resources/l10n/JabRef_en.properties  |  7 ++-
 7 files changed, 105 insertions(+), 21 deletions(-)

diff --git a/.mailmap b/.mailmap
index b8698d75865..3af3033fd28 100644
--- a/.mailmap
+++ b/.mailmap
@@ -142,4 +142,5 @@ Johannes Manner <johannes.manner@web.de>
 Dominik Traczyk <dominik646@gmail.com>
 Cerrianne Santos <cerrianne.santos@gmail.com>
 Stefan Scheffel <st155160@stud.uni-stuttgart.de>
-Stefan Gerzmann <steppery@gmx.de>
\ No newline at end of file
+Stefan Gerzmann <steppery@gmx.de>
+Deepak Kumar <deepakkumar24196@gmail.com>
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3ec7d2b519a..651ab6ab391 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -61,6 +61,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
 - We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
 - We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
+- We added an option in the settings to set the default action in JabRef when right clicking on any entry in any database and selecting "Open folder". [#4763](https://github.com/JabRef/jabref/issues/4763)
 - The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
 
 
@@ -105,13 +106,14 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
+- We fixed an issue where right clicking on any entry in any database and selecting "Open folder" results in the NullPointer exception. [#4763](https://github.com/JabRef/jabref/issues/4763)
+- We fixed an issue where option 'open terminal here' with custom command was passing wrong argument. [#4802](https://github.com/JabRef/jabref/issues/4802)
 - We fixed an issue where ranking an entry would generate an IllegalArgumentException. [#4754](https://github.com/JabRef/jabref/issues/4754)
 - We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
 - We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 
 
 
-
 ### Removed
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.
 - The number column was removed.
diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
index fbd9478789b..befd35ed0af 100644
--- a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
+++ b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -166,7 +166,33 @@ private static void openExternalFilePlatformIndependent(Optional<ExternalFileTyp
      * @throws IOException
      */
     public static void openFolderAndSelectFile(Path fileLink) throws IOException {
-        NATIVE_DESKTOP.openFolderAndSelectFile(fileLink);
+        if (fileLink == null) {
+            return;
+        }
+        boolean usingDefault = Globals.prefs.getBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION);
+
+        if (usingDefault) {
+            NATIVE_DESKTOP.openFolderAndSelectFile(fileLink);
+        } else {
+            String absolutePath = fileLink.toAbsolutePath().getParent().toString();
+            String command = Globals.prefs.get(JabRefPreferences.FILE_BROWSER_COMMAND);
+            if (!command.isEmpty()) {
+                command = command.replaceAll("\\s+", " "); // normalize white spaces
+
+                // replace the placeholder if used
+                command = command.replace("%DIR", absolutePath);
+                String[] subcommands = command.split(" ");
+
+                LOGGER.info("Executing command \"" + command + "\"...");
+
+                try {
+                    new ProcessBuilder(subcommands).start();
+                } catch (IOException exception) {
+                    LOGGER.error("Open File Browser", exception);
+                    JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Error occured while executing the command \"%0\".", command));
+                }
+            }
+        }
     }
 
     /**
@@ -228,22 +254,19 @@ public static void openConsole(File file) throws IOException {
 
             if (!command.isEmpty()) {
                 command = command.replaceAll("\\s+", " "); // normalize white spaces
-                String[] subcommands = command.split(" ");
+                command = command.replace("%DIR", absolutePath); // replace the placeholder if used
 
-                // replace the placeholder if used
-                String commandLoggingText = command.replace("%DIR", absolutePath);
+                String[] subcommands = command.split(" ");
 
+                LOGGER.info("Executing command \"" + command + "\"...");
                 JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", commandLoggingText));
-                LOGGER.info("Executing command \"" + commandLoggingText + "\"...");
 
                 try {
                     new ProcessBuilder(subcommands).start();
                 } catch (IOException exception) {
                     LOGGER.error("Open console", exception);
 
-                    JabRefGUI.getMainFrame().getDialogService().showErrorDialogAndWait(
-                            Localization.lang("Open console") + " - " + Localization.lang("Error",
-                            Localization.lang("Error occured while executing the command \"%0\".", commandLoggingText)));
+                    JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Error occured while executing the command \"%0\".", command));
                 }
             }
         }
diff --git a/src/main/java/org/jabref/gui/desktop/os/Linux.java b/src/main/java/org/jabref/gui/desktop/os/Linux.java
index 4f007e01ce9..dd45135a6b1 100644
--- a/src/main/java/org/jabref/gui/desktop/os/Linux.java
+++ b/src/main/java/org/jabref/gui/desktop/os/Linux.java
@@ -51,18 +51,18 @@ public void openFileWithApplication(String filePath, String application) throws
 
     @Override
     public void openFolderAndSelectFile(Path filePath) throws IOException {
-        String desktopSession = System.getenv("DESKTOP_SESSION").toLowerCase(Locale.ROOT);
+        String desktopSession = System.getenv("DESKTOP_SESSION");
 
-        String cmd;
+        String cmd = "xdg-open " + filePath.toAbsolutePath().getParent().toString(); //default command
 
-        if (desktopSession.contains("gnome")) {
-            cmd = "nautilus" + filePath.toString().replace(" ", "\\ ");
-        } else if (desktopSession.contains("kde")) {
-            cmd = "dolphin --select " + filePath.toString().replace(" ", "\\ ");
-        } else {
-            cmd = "xdg-open " + filePath.toAbsolutePath().getParent().toString();
+        if (desktopSession != null) {
+            desktopSession = desktopSession.toLowerCase(Locale.ROOT);
+            if (desktopSession.contains("gnome")) {
+                cmd = "nautilus" + filePath.toString().replace(" ", "\\ ");
+            } else if (desktopSession.contains("kde")) {
+                cmd = "dolphin --select " + filePath.toString().replace(" ", "\\ ");
+            }
         }
-
         Runtime.getRuntime().exec(cmd);
     }
 
@@ -73,7 +73,6 @@ public void openConsole(String absolutePath) throws IOException {
         BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));
 
         String emulatorName = reader.readLine();
-
         if (emulatorName != null) {
             emulatorName = emulatorName.substring(emulatorName.lastIndexOf(File.separator) + 1);
 
diff --git a/src/main/java/org/jabref/gui/preferences/ExternalTab.java b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
index e872abeadb4..8ce4dced4e7 100644
--- a/src/main/java/org/jabref/gui/preferences/ExternalTab.java
+++ b/src/main/java/org/jabref/gui/preferences/ExternalTab.java
@@ -20,6 +20,7 @@
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.OS;
+import org.jabref.model.strings.StringUtil;
 import org.jabref.preferences.JabRefPreferences;
 
 class ExternalTab implements PrefsTab {
@@ -38,6 +39,12 @@ class ExternalTab implements PrefsTab {
     private final RadioButton sumatraReader;
     private final TextField adobeAcrobatReaderPath;
     private final TextField sumatraReaderPath;
+
+    private final RadioButton defaultFileBrowser;
+    private final RadioButton executeFileBrowser;
+    private final TextField fileBrowserCommand;
+    private final Button fileBrowserButton;
+
     private final GridPane builder = new GridPane();
     private final DialogService dialogService;
     private final FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder().build();
@@ -59,11 +66,20 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
         sumatraReaderPath = new TextField();
         Button browseSumatraReader = new Button(Localization.lang("Browse"));
 
+        defaultFileBrowser = new RadioButton(Localization.lang("Use default file browser"));
+        executeFileBrowser = new RadioButton(Localization.lang("Execute Command"));
+        fileBrowserCommand = new TextField();
+        fileBrowserButton = new Button(Localization.lang("Browser"));
+
         Label commandDescription = new Label(Localization.lang("Note: Use the placeholder %0 for the location of the opened library file.", "%DIR"));
         defaultConsole.setOnAction(e -> updateExecuteConsoleButtonAndFieldEnabledState());
         executeConsole.setOnAction(e -> updateExecuteConsoleButtonAndFieldEnabledState());
         browseButton.setOnAction(e -> showConsoleChooser());
 
+        fileBrowserButton.disableProperty().bind(executeFileBrowser.selectedProperty().not());
+        fileBrowserCommand.disableProperty().bind(executeFileBrowser.selectedProperty().not());
+        fileBrowserButton.setOnAction(e -> showFileBrowserCommandChooser());
+
         browseAdobeAcrobatReader.setOnAction(e -> showAdobeChooser());
 
         GridPane consoleOptionPanel = new GridPane();
@@ -83,6 +99,17 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
         adobeAcrobatReader.setToggleGroup(pdfReaderGroup);
         pdfOptionPanel.add(browseAdobeAcrobatReader, 3, 1);
 
+        Label fileBrowserCommandDescription = new Label(Localization.lang("Note: Use the placeholder %0 for the location of the opened library file.", "%DIR"));
+        GridPane fileBrowserOptionPanel = new GridPane();
+        final ToggleGroup fileBrowserGroup = new ToggleGroup();
+        defaultFileBrowser.setToggleGroup(fileBrowserGroup);
+        executeFileBrowser.setToggleGroup(fileBrowserGroup);
+        fileBrowserOptionPanel.add(defaultFileBrowser, 1, 1);
+        fileBrowserOptionPanel.add(executeFileBrowser, 1, 2);
+        fileBrowserOptionPanel.add(fileBrowserCommand, 2, 2);
+        fileBrowserOptionPanel.add(fileBrowserButton, 3, 2);
+        fileBrowserOptionPanel.add(fileBrowserCommandDescription, 2, 3);
+
         if (OS.WINDOWS) {
             browseSumatraReader.setOnAction(e -> showSumatraChooser());
             pdfOptionPanel.add(sumatraReader, 1, 2);
@@ -133,6 +160,12 @@ public ExternalTab(JabRefFrame frame, PreferencesDialog prefsDiag, JabRefPrefere
 
         builder.add(pdfOptionPanel, 1, 13);
 
+        Label openFileBrowser = new Label(Localization.lang("Open File Browser"));
+        openFileBrowser.getStyleClass().add("sectionHeader");
+        builder.add(openFileBrowser,  1, 14);
+
+        builder.add(fileBrowserOptionPanel, 1, 15);
+
     }
 
     @Override
@@ -165,6 +198,10 @@ public void setValues() {
 
         consoleCommand.setText(Globals.prefs.get(JabRefPreferences.CONSOLE_COMMAND));
 
+        defaultFileBrowser.setSelected(Globals.prefs.getBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION));
+        executeFileBrowser.setSelected(!Globals.prefs.getBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION));
+        fileBrowserCommand.setText(Globals.prefs.get(JabRefPreferences.FILE_BROWSER_COMMAND));
+
         adobeAcrobatReaderPath.setText(Globals.prefs.get(JabRefPreferences.ADOBE_ACROBAT_COMMAND));
         if (OS.WINDOWS) {
             sumatraReaderPath.setText(Globals.prefs.get(JabRefPreferences.SUMATRA_PDF_COMMAND));
@@ -187,6 +224,13 @@ public void storeSettings() {
         prefs.putBoolean(JabRefPreferences.USE_DEFAULT_CONSOLE_APPLICATION, defaultConsole.isSelected());
         prefs.put(JabRefPreferences.CONSOLE_COMMAND, consoleCommand.getText());
         prefs.put(JabRefPreferences.ADOBE_ACROBAT_COMMAND, adobeAcrobatReaderPath.getText());
+
+        prefs.putBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION, defaultFileBrowser.isSelected());
+        if (StringUtil.isNotBlank(fileBrowserCommand.getText())) {
+            prefs.put(JabRefPreferences.FILE_BROWSER_COMMAND, fileBrowserCommand.getText());
+        } else {
+            prefs.putBoolean(JabRefPreferences.USE_DEFAULT_FILE_BROWSER_APPLICATION, true); //default if no command specified
+        }
         if (OS.WINDOWS) {
             prefs.put(JabRefPreferences.SUMATRA_PDF_COMMAND, sumatraReaderPath.getText());
         }
@@ -220,6 +264,10 @@ private void showSumatraChooser() {
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> sumatraReaderPath.setText(file.toAbsolutePath().toString()));
     }
 
+    private void showFileBrowserCommandChooser() {
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> fileBrowserCommand.setText(file.toAbsolutePath().toString()));
+    }
+
     private void readerSelected() {
         if (adobeAcrobatReader.isSelected()) {
             prefs.put(JabRefPreferences.USE_PDF_READER, adobeAcrobatReaderPath.getText());
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index 88eae71f20a..92b6fa622a0 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -244,6 +244,9 @@ public class JabRefPreferences implements PreferencesService {
     public static final String ADOBE_ACROBAT_COMMAND = "adobeAcrobatCommand";
     public static final String SUMATRA_PDF_COMMAND = "sumatraCommand";
     public static final String USE_PDF_READER = "usePDFReader";
+    public static final String USE_DEFAULT_FILE_BROWSER_APPLICATION = "userDefaultFileBrowserApplication";
+    public static final String FILE_BROWSER_COMMAND = "fileBrowserCommand";
+
     // Currently, it is not possible to specify defaults for specific entry types
     // When this should be made possible, the code to inspect is org.jabref.gui.preferences.BibtexKeyPatternPrefTab.storeSettings() -> LabelPattern keypatterns = getCiteKeyPattern(); etc
     public static final String DEFAULT_BIBTEX_KEY_PATTERN = "defaultBibtexKeyPattern";
@@ -729,16 +732,19 @@ private JabRefPreferences() {
         defaults.put(USE_UNIT_FORMATTER_ON_SEARCH, Boolean.TRUE);
 
         defaults.put(USE_DEFAULT_CONSOLE_APPLICATION, Boolean.TRUE);
+        defaults.put(USE_DEFAULT_FILE_BROWSER_APPLICATION, Boolean.TRUE);
         if (OS.WINDOWS) {
             defaults.put(CONSOLE_COMMAND, "C:\\Program Files\\ConEmu\\ConEmu64.exe /single /dir \"%DIR\"");
             defaults.put(ADOBE_ACROBAT_COMMAND, "C:\\Program Files (x86)\\Adobe\\Acrobat Reader DC\\Reader");
             defaults.put(SUMATRA_PDF_COMMAND, "C:\\Program Files\\SumatraPDF");
             defaults.put(USE_PDF_READER, ADOBE_ACROBAT_COMMAND);
+            defaults.put(FILE_BROWSER_COMMAND, "explorer.exe /select, \"%DIR\"");
         } else {
             defaults.put(CONSOLE_COMMAND, "");
             defaults.put(ADOBE_ACROBAT_COMMAND, "");
             defaults.put(SUMATRA_PDF_COMMAND, "");
             defaults.put(USE_PDF_READER, "");
+            defaults.put(FILE_BROWSER_COMMAND, "");
         }
 
         //versioncheck defaults
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 7398d8fc491..1d75fc2d918 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1689,7 +1689,6 @@ Open\ console=Open console
 Use\ default\ terminal\ emulator=Use default terminal emulator
 Execute\ command=Execute command
 Note\:\ Use\ the\ placeholder\ %0\ for\ the\ location\ of\ the\ opened\ library\ file.=Note: Use the placeholder %0 for the location of the opened library file.
-Executing\ command\ \"%0\"...=Executing command \"%0\"...
 Error\ occured\ while\ executing\ the\ command\ \"%0\".=Error occured while executing the command \"%0\".
 Reformat\ ISSN=Reformat ISSN
 
@@ -2081,6 +2080,12 @@ Use\ selected\ document=Use selected document
 Accept\ changes=Accept changes
 Dismiss\ changes=Dismiss changes
 The\ library\ has\ been\ modified\ by\ another\ program.=The library has been modified by another program.
+
+Browser=Browser
+Execute\ Command=Execute Command
+Open\ File\ Browser=Open File Browser
+Use\ default\ file\ browser=Use default file browser
+
 Set\ rank\ to\ one=Set rank to one
 Set\ rank\ to\ two=Set rank to two
 Set\ rank\ to\ three=Set rank to three

From 6173de37a3c25d5f880f009fd70b229d84b8b3a4 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sat, 13 Apr 2019 18:12:49 +0200
Subject: [PATCH 60/61] fix compile error

(cherry picked from commit cc7b3a945e546c58aa358fc306111a09f96dbb2c)
---
 src/main/java/org/jabref/gui/desktop/JabRefDesktop.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
index befd35ed0af..40993772e54 100644
--- a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
+++ b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -259,7 +259,7 @@ public static void openConsole(File file) throws IOException {
                 String[] subcommands = command.split(" ");
 
                 LOGGER.info("Executing command \"" + command + "\"...");
-                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", commandLoggingText));
+                JabRefGUI.getMainFrame().getDialogService().notify(Localization.lang("Executing command \"%0\"...", command));
 
                 try {
                     new ProcessBuilder(subcommands).start();

From 504c0d30cf87106b514e0a204561d19edde322b3 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sat, 13 Apr 2019 18:22:09 +0200
Subject: [PATCH 61/61] fix missing l10n from previous merge

---
 src/main/resources/l10n/JabRef_en.properties | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 1d75fc2d918..41bfe678055 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -2091,3 +2091,5 @@ Set\ rank\ to\ two=Set rank to two
 Set\ rank\ to\ three=Set rank to three
 Set\ rank\ to\ four=Set rank to four
 Set\ rank\ to\ five=Set rank to five
+
+Executing\ command\ "%0"...=Executing command "%0"...
\ No newline at end of file