Merging from head master

build.gradle

@@ -121,7 +121,7 @@ dependencies {
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:27.1-jre'
+    compile 'com.google.guava:guava:28.0-jre'
 
     // JavaFX stuff
     compile 'de.jensd:fontawesomefx-commons:8.15'
@@ -142,7 +142,7 @@ dependencies {
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     // >1.8.0-beta is required for java 9 compatibility
-    compile 'org.slf4j:slf4j-api:1.8.0-beta4'
+    compile 'org.slf4j:slf4j-api:2.0.0-alpha0'
     compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.2'
     compile 'org.apache.logging.log4j:log4j-jcl:2.11.2'
     compile 'org.apache.logging.log4j:log4j-api:2.11.2'

src/main/java/org/jabref/Globals.java

@@ -1,6 +1,7 @@
 package org.jabref;
 
 import java.awt.GraphicsEnvironment;
+import java.io.IOException;
 import java.util.Optional;
 import java.util.UUID;
 
@@ -24,6 +25,7 @@
 import org.jabref.preferences.JabRefPreferences;
 
 import com.google.common.base.StandardSystemProperty;
+import com.mashape.unirest.http.Unirest;
 import com.microsoft.applicationinsights.TelemetryClient;
 import com.microsoft.applicationinsights.TelemetryConfiguration;
 import com.microsoft.applicationinsights.internal.shutdown.SDKShutdownActivity;
@@ -125,6 +127,9 @@ public static void shutdownThreadPools() {
 
     public static void stopBackgroundTasks() {
         stopTelemetryClient();
+        try {
+            Unirest.shutdown();
+        } catch (IOException ignore) { }
     }
 
     public static Optional<TelemetryClient> getTelemetryClient() {

src/main/java/org/jabref/gui/Base.css

@@ -1028,11 +1028,20 @@ We want to have a look that matches our icons in the tool-bar */
     -fx-background-color: -jr-error;
 }
 
+.titleHeader {
+    -fx-font-size: 150%;
+    -fx-padding: 0em 0em 0.5em 0em;
+}
+
 .sectionHeader {
-    -fx-font-size: 1.5em;
-    -fx-padding: 1em 0em 1em 0em;
+    -fx-font-size: 130%;
+    -fx-padding: 1em 0em 0.2em 0em;
 }
 
 .dialog-pane {
     -fx-background-color: -fx-control-inner-background;
 }
+
+.preference-sidepane {
+    -fx-background-color: -jr-sidepane-background;
+}

src/main/java/org/jabref/gui/JabRefFrame.java

@@ -759,7 +759,7 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs, stateManager, undoManager))
+                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs, stateManager, undoManager, Globals.TASK_EXECUTOR))
         );
 
         // PushToApplication

src/main/java/org/jabref/gui/entryeditor/OtherFieldsTab.java

@@ -37,6 +37,7 @@ protected Collection<String> determineFieldsToShow(BibEntry entry, EntryType ent
                 .filter(field -> !allKnownFields.contains(field)).collect(Collectors.toList());
 
         otherFields.removeAll(entryType.getDeprecatedFields());
+        otherFields.removeAll(entryType.getOptionalFields());
         otherFields.remove(BibEntry.KEY_FIELD);
         otherFields.removeAll(customTabFieldNames);
         return otherFields;

src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java

@@ -13,6 +13,7 @@
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.util.BindingsHelper;
+import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -31,12 +32,14 @@ public class AutoLinkFilesAction extends SimpleCommand {
     private final JabRefPreferences preferences;
     private final StateManager stateManager;
     private UndoManager undoManager;
+    private TaskExecutor taskExecutor;
 
-    public AutoLinkFilesAction(JabRefFrame frame, JabRefPreferences preferences, StateManager stateManager, UndoManager undoManager) {
+    public AutoLinkFilesAction(JabRefFrame frame, JabRefPreferences preferences, StateManager stateManager, UndoManager undoManager, TaskExecutor taskExecutor) {
         this.dialogService = frame.getDialogService();
         this.preferences = preferences;
         this.stateManager = stateManager;
         this.undoManager = undoManager;
+        this.taskExecutor = taskExecutor;
 
         this.executable.bind(needsDatabase(this.stateManager).and(needsEntriesSelected(stateManager)));
         this.statusMessage.bind(BindingsHelper.ifThenElse(executable, "", Localization.lang("This operation requires one or more entries to be selected.")));
@@ -51,6 +54,7 @@ public void execute() {
         final NamedCompound nc = new NamedCompound(Localization.lang("Automatically set file links"));
         AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(database, preferences.getFilePreferences(), preferences.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
         Task<List<BibEntry>> linkFilesTask = new Task<List<BibEntry>>() {
+
             @Override
             protected List<BibEntry> call() {
                 return util.linkAssociatedFiles(entries, nc);
@@ -71,9 +75,9 @@ protected void succeeded() {
         };
 
         dialogService.showProgressDialogAndWait(
-                Localization.lang("Automatically setting file links"),
-                Localization.lang("Searching for files"),
-                linkFilesTask
-        );
+                                                Localization.lang("Automatically setting file links"),
+                                                Localization.lang("Searching for files"),
+                                                linkFilesTask);
+        taskExecutor.execute(linkFilesTask);
     }
 }

src/main/java/org/jabref/gui/preferences/ExternalTab.fxml

@@ -0,0 +1,150 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.CheckBox?>
+<?import javafx.scene.control.ComboBox?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.control.RadioButton?>
+<?import javafx.scene.control.TextField?>
+<?import javafx.scene.control.ToggleGroup?>
+<?import javafx.scene.layout.ColumnConstraints?>
+<?import javafx.scene.layout.GridPane?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.RowConstraints?>
+<?import javafx.scene.layout.VBox?>
+
+<?import javafx.scene.control.Tooltip?>
+<fx:root prefWidth="650.0" spacing="10.0" type="VBox"
+         xmlns="http://javafx.com/javafx/8.0.212" xmlns:fx="http://javafx.com/fxml/1"
+         fx:controller="org.jabref.gui.preferences.ExternalTabView">
+    <fx:define>
+        <ToggleGroup fx:id="openConsole"/>
+        <ToggleGroup fx:id="openPDF"/>
+        <ToggleGroup fx:id="openFileBrowser"/>
+    </fx:define>
+    <children>
+        <Label styleClass="titleHeader" text="%External programs"/>
+        <Label styleClass="sectionHeader" text="%Sending of emails"/>
+        <HBox alignment="CENTER_LEFT" spacing="10.0">
+
+            <children>
+                <Label text="%Subject for sending an email with references"/>
+                <TextField fx:id="eMailReferenceSubject"/>
+            </children>
+        </HBox>
+        <CheckBox fx:id="autoOpenAttachedFolders"
+                  text="%Automatically open folders of attached files"/>
+        <Label styleClass="sectionHeader" text="%Push applications"/>
+        <HBox>
+            <GridPane alignment="CENTER_LEFT">
+                <columnConstraints>
+                    <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="200.0"/>
+                    <ColumnConstraints hgrow="SOMETIMES" percentWidth="0.0" prefWidth="10.0"/>
+                    <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="200.0"/>
+                    <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="10.0"/>
+                    <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="140.0"/>
+                </columnConstraints>
+                <rowConstraints>
+                    <RowConstraints prefHeight="30.0" vgrow="SOMETIMES"/>
+                    <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                    <RowConstraints minHeight="-Infinity" prefHeight="10.0" vgrow="SOMETIMES"/>
+                    <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                </rowConstraints>
+                <children>
+                    <Label text="%Application to push entries to"/>
+                    <ComboBox fx:id="pushToApplicationCombo" minWidth="-Infinity" prefWidth="200.0"
+                              GridPane.columnIndex="2"/>
+                    <Button onAction="#pushToApplicationSettings" prefWidth="140.0"
+                            text="%Application settings" GridPane.columnIndex="4"/>
+                    <Label text="%Cite command" GridPane.rowIndex="1"/>
+                    <TextField fx:id="citeCommand" minWidth="-Infinity" prefWidth="200.0" GridPane.columnIndex="2"
+                               GridPane.rowIndex="1"/>
+                    <Button onAction="#manageExternalFileTypes" prefWidth="200.0"
+                            text="%Manage external file types" GridPane.columnIndex="2" GridPane.rowIndex="3"/>
+                </children>
+            </GridPane>
+        </HBox>
+        <Label styleClass="sectionHeader" text="%Open console"/>
+        <VBox spacing="8.0">
+            <children>
+                <RadioButton fx:id="useTerminalDefault" text="%Use default terminal emulator"
+                             toggleGroup="$openConsole"/>
+                <HBox alignment="CENTER_LEFT" spacing="10.0">
+                    <children>
+                        <RadioButton fx:id="useTerminalSpecial" lineSpacing="10.0"
+                                     prefWidth="200.0" text="%Execute command" toggleGroup="$openConsole"/>
+                        <TextField fx:id="useTerminalCommand" prefWidth="350.0" disable="${!useTerminalSpecial.selected}">
+                            <tooltip>
+                                <Tooltip
+                                        text="%Note: Use the placeholder %DIR% for the location of the opened library file."/>
+                            </tooltip>
+                        </TextField>
+                        <Button fx:id="" text="%Browse" onAction="#useTerminalCommandBrowse" disable="${!useTerminalSpecial.selected}"/>
+                    </children>
+                </HBox>
+            </children>
+        </VBox>
+        <Label styleClass="sectionHeader" text="%Open PDF"/>
+        <HBox>
+            <GridPane alignment="CENTER_LEFT">
+                <columnConstraints>
+                    <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="200.0"/>
+                    <ColumnConstraints hgrow="SOMETIMES" percentWidth="0.0" prefWidth="10.0"/>
+                    <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="350.0"/>
+                    <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" percentWidth="0.0" prefWidth="10.0"/>
+                    <ColumnConstraints hgrow="SOMETIMES"/>
+                </columnConstraints>
+                <rowConstraints>
+                    <RowConstraints prefHeight="30.0" vgrow="SOMETIMES"/>
+                    <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                </rowConstraints>
+                <children>
+                    <RadioButton fx:id="usePDFAcrobat" text="%Adobe Acrobat Reader"
+                                 toggleGroup="$openPDF"/>
+                    <TextField fx:id="usePDFAcrobatCommand" prefWidth="350.0" GridPane.columnIndex="2" disable="${!usePDFAcrobat.selected}"/>
+                    <Button onAction="#usePDFAcrobatCommandBrowse" text="%Browse"
+                            GridPane.columnIndex="4" disable="${!usePDFAcrobat.selected}"/>
+                    <RadioButton fx:id="usePDFSumatra" text="%Sumatra Reader" toggleGroup="$openPDF"
+                                 GridPane.rowIndex="1"/>
+                    <TextField fx:id="usePDFSumatraCommand" prefWidth="350.0" GridPane.columnIndex="2"
+                               GridPane.rowIndex="1" disable="${!usePDFSumatra.selected}"/>
+                    <Button onAction="#usePDFSumatraCommandBrowse" text="%Browse"
+                            GridPane.columnIndex="4" GridPane.rowIndex="1" disable="${!usePDFSumatra.selected}"/>
+                </children>
+            </GridPane>
+        </HBox>
+        <Label styleClass="sectionHeader" text="%Open File Browser"/>
+        <HBox>
+            <children>
+                <GridPane alignment="CENTER_LEFT">
+                    <columnConstraints>
+                        <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="200.0"/>
+                        <ColumnConstraints hgrow="SOMETIMES" percentWidth="0.0" prefWidth="10.0"/>
+                        <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" prefWidth="350.0"/>
+                        <ColumnConstraints hgrow="SOMETIMES" minWidth="-Infinity" percentWidth="0.0" prefWidth="10.0"/>
+                        <ColumnConstraints hgrow="SOMETIMES"/>
+                    </columnConstraints>
+                    <rowConstraints>
+                        <RowConstraints prefHeight="30.0" vgrow="SOMETIMES"/>
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                    </rowConstraints>
+                    <children>
+                        <RadioButton fx:id="useFileBrowserDefault" text="%Use default file browser"
+                                     toggleGroup="$openFileBrowser"/>
+                        <RadioButton fx:id="useFileBrowserSpecial" text="%Execute command"
+                                     toggleGroup="$openFileBrowser" GridPane.rowIndex="1"/>
+                        <TextField fx:id="useFileBrowserSpecialCommand" prefWidth="350.0"
+                                   GridPane.columnIndex="2" GridPane.rowIndex="1" disable="${!useFileBrowserSpecial.selected}">
+                            <tooltip>
+                                <Tooltip
+                                        text="%Note: Use the placeholder %DIR% for the location of the opened library file."/>
+                            </tooltip>
+                        </TextField>
+                        <Button onAction="#useFileBrowserSpecialCommandBrowse" text="%Browse"
+                                GridPane.columnIndex="4" GridPane.rowIndex="1" disable="${!useFileBrowserSpecial.selected}"/>
+                    </children>
+                </GridPane>
+            </children>
+        </HBox>
+    </children>
+</fx:root>