From 454c53b061c805e76dd09bb3415d0f9055b2392d Mon Sep 17 00:00:00 2001
From: Robert <robert@Roberts-MacBook-Pro.local>
Date: Sun, 26 Nov 2017 17:02:40 +0100
Subject: [PATCH 01/47] The grid pane on the right side is disabled if there
 are no annotations in the linked file. Confusion because the gridpane is
 initially disabled even if there are annotations. After clicking on the file
 in the Combobox it works fine.

---
 .../entryeditor/fileannotationtab/FileAnnotationTab.fxml  | 2 +-
 .../fileannotationtab/FileAnnotationTabController.java    | 8 +++++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
index d0891792fc4..b3d7a1ede3e 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
@@ -37,7 +37,7 @@
             </BorderPane>
         </masterNode>
         <detailNode>
-            <GridPane>
+            <GridPane fx:id="grid">
                 <padding>
                     <Insets top="5" right="5" bottom="5" left="10"/>
                 </padding>
diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
index 6eb90070e11..01def5213ee 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
@@ -14,6 +14,7 @@
 import javafx.scene.control.ListView;
 import javafx.scene.control.SelectionMode;
 import javafx.scene.control.TextArea;
+import javafx.scene.layout.GridPane;
 import javafx.scene.layout.HBox;
 import javafx.scene.layout.VBox;
 import javafx.scene.text.Text;
@@ -43,6 +44,8 @@ public class FileAnnotationTabController extends AbstractController<FileAnnotati
     public TextArea content;
     @FXML
     public TextArea marking;
+    @FXML
+    public GridPane grid;
 
     @Inject
     private FileAnnotationCache fileAnnotationCache;
@@ -54,7 +57,7 @@ public class FileAnnotationTabController extends AbstractController<FileAnnotati
     @FXML
     public void initialize() {
         viewModel = new FileAnnotationTabViewModel(fileAnnotationCache, entry, fileMonitor);
-
+        
         // Set-up files list
         files.getItems().setAll(viewModel.filesProperty().get());
         files.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> viewModel.notifyNewSelectedFile(newValue));
@@ -63,6 +66,7 @@ public void initialize() {
         // Set-up annotation list
         annotationList.getSelectionModel().setSelectionMode(SelectionMode.SINGLE);
         annotationList.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> viewModel.notifyNewSelectedAnnotation(newValue));
+        annotationList.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> grid.setDisable(newValue == null));
         ViewModelListCellFactory<FileAnnotationViewModel> cellFactory = new ViewModelListCellFactory<FileAnnotationViewModel>()
                 .withTooltip(FileAnnotationViewModel::getDescription)
                 .withGraphic(annotation -> {
@@ -95,6 +99,8 @@ public void initialize() {
         date.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::dateProperty));
         content.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::contentProperty));
         marking.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::markingProperty));
+        grid.setDisable(true);
+        //grid.disableProperty().bind(Bindings.and(viewModel.isAnnotationsEmpty(), false));
     }
 
     public void copy(ActionEvent event) {

From f19e062fa0d48cebed26166b32ae3f5a080f684a Mon Sep 17 00:00:00 2001
From: Tarix <tarix@fu-berlin.de>
Date: Sun, 26 Nov 2017 17:05:18 +0100
Subject: [PATCH 02/47] add boolean props

---
 .../fileannotationtab/FileAnnotationTabViewModel.java        | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
index 5e7f412fa08..236df1fd0fb 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
@@ -35,6 +35,7 @@ public class FileAnnotationTabViewModel extends AbstractViewModel {
     private final ListProperty<FileAnnotationViewModel> annotations = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ListProperty<Path> files = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ObjectProperty<FileAnnotationViewModel> currentAnnotation = new SimpleObjectProperty<>();
+    private final ObjectProperty<Boolean> annotaionEmpty = new SimpleObjectProperty<Boolean>(null);
 
     private final FileAnnotationCache cache;
     private final BibEntry entry;
@@ -59,6 +60,10 @@ public ObjectProperty<FileAnnotationViewModel> currentAnnotationProperty() {
         return currentAnnotation;
     }
 
+    public boolean isAnnotationsEmpty() {
+        return annotations.isEmpty();
+    }
+
     public ListProperty<FileAnnotationViewModel> annotationsProperty() {
         return annotations;
     }

From 686f72b4fccf69c689032f1f6ced4809248d89a4 Mon Sep 17 00:00:00 2001
From: Tarix <tarix@fu-berlin.de>
Date: Sun, 26 Nov 2017 17:12:37 +0100
Subject: [PATCH 03/47] add isEmpty function with object-boolean

---
 .../fileannotationtab/FileAnnotationTabController.java   | 6 +++---
 .../fileannotationtab/FileAnnotationTabViewModel.java    | 9 ++++++---
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
index 01def5213ee..17ef8600e16 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
@@ -57,7 +57,7 @@ public class FileAnnotationTabController extends AbstractController<FileAnnotati
     @FXML
     public void initialize() {
         viewModel = new FileAnnotationTabViewModel(fileAnnotationCache, entry, fileMonitor);
-        
+
         // Set-up files list
         files.getItems().setAll(viewModel.filesProperty().get());
         files.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> viewModel.notifyNewSelectedFile(newValue));
@@ -66,7 +66,7 @@ public void initialize() {
         // Set-up annotation list
         annotationList.getSelectionModel().setSelectionMode(SelectionMode.SINGLE);
         annotationList.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> viewModel.notifyNewSelectedAnnotation(newValue));
-        annotationList.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> grid.setDisable(newValue == null));
+        //annotationList.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> grid.setDisable(newValue == null));
         ViewModelListCellFactory<FileAnnotationViewModel> cellFactory = new ViewModelListCellFactory<FileAnnotationViewModel>()
                 .withTooltip(FileAnnotationViewModel::getDescription)
                 .withGraphic(annotation -> {
@@ -100,7 +100,7 @@ public void initialize() {
         content.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::contentProperty));
         marking.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::markingProperty));
         grid.setDisable(true);
-        //grid.disableProperty().bind(Bindings.and(viewModel.isAnnotationsEmpty(), false));
+        grid.disableProperty().bind(viewModel.isAnnotationsEmpty());
     }
 
     public void copy(ActionEvent event) {
diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
index 236df1fd0fb..91259d467e7 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
@@ -60,8 +60,8 @@ public ObjectProperty<FileAnnotationViewModel> currentAnnotationProperty() {
         return currentAnnotation;
     }
 
-    public boolean isAnnotationsEmpty() {
-        return annotations.isEmpty();
+    public ObjectProperty<Boolean> isAnnotationsEmpty() {
+        return annotaionEmpty;
     }
 
     public ListProperty<FileAnnotationViewModel> annotationsProperty() {
@@ -89,7 +89,10 @@ public void notifyNewSelectedFile(Path newFile) {
                 .map(FileAnnotationViewModel::new)
                 .collect(Collectors.toList());
         annotations.setAll(newAnnotations);
-
+        if (annotations.isEmpty())
+            annotaionEmpty.setValue(true);
+        else
+            annotaionEmpty.setValue(false);
         try {
             fileMonitor.addListenerForFile(currentFile, fileListener);
         } catch (IOException e) {

From 94754425577c827e6ec022f71bdf0dd4180e4cc7 Mon Sep 17 00:00:00 2001
From: Tarix <tarix@fu-berlin.de>
Date: Sun, 26 Nov 2017 17:21:46 +0100
Subject: [PATCH 04/47] remove comments

---
 .../fileannotationtab/FileAnnotationTabController.java          | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
index 17ef8600e16..9df54542897 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
@@ -66,7 +66,6 @@ public void initialize() {
         // Set-up annotation list
         annotationList.getSelectionModel().setSelectionMode(SelectionMode.SINGLE);
         annotationList.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> viewModel.notifyNewSelectedAnnotation(newValue));
-        //annotationList.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> grid.setDisable(newValue == null));
         ViewModelListCellFactory<FileAnnotationViewModel> cellFactory = new ViewModelListCellFactory<FileAnnotationViewModel>()
                 .withTooltip(FileAnnotationViewModel::getDescription)
                 .withGraphic(annotation -> {
@@ -99,7 +98,6 @@ public void initialize() {
         date.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::dateProperty));
         content.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::contentProperty));
         marking.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::markingProperty));
-        grid.setDisable(true);
         grid.disableProperty().bind(viewModel.isAnnotationsEmpty());
     }
 

From 0bcfff8696590c4f2326353a5aebf46b19d75529 Mon Sep 17 00:00:00 2001
From: Robert <robert@Roberts-MacBook-Pro.local>
Date: Mon, 27 Nov 2017 12:53:06 +0100
Subject: [PATCH 05/47] Added curly braces for if else (if
 (annotations.isEmpty()))

---
 .../fileannotationtab/FileAnnotationTabViewModel.java | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
index 91259d467e7..c77ba4286eb 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
@@ -35,14 +35,14 @@ public class FileAnnotationTabViewModel extends AbstractViewModel {
     private final ListProperty<FileAnnotationViewModel> annotations = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ListProperty<Path> files = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ObjectProperty<FileAnnotationViewModel> currentAnnotation = new SimpleObjectProperty<>();
-    private final ObjectProperty<Boolean> annotaionEmpty = new SimpleObjectProperty<Boolean>(null);
+    private final ObjectProperty<Boolean> annotaionEmpty = new SimpleObjectProperty<>(null);
 
     private final FileAnnotationCache cache;
     private final BibEntry entry;
     private Map<Path, List<FileAnnotation>> fileAnnotations;
     private Path currentFile;
-    private FileUpdateMonitor fileMonitor;
-    private FileUpdateListener fileListener = this::reloadAnnotations;
+    private final FileUpdateMonitor fileMonitor;
+    private final FileUpdateListener fileListener = this::reloadAnnotations;
 
     public FileAnnotationTabViewModel(FileAnnotationCache cache, BibEntry entry, FileUpdateMonitor fileMonitor) {
         this.cache = cache;
@@ -89,10 +89,11 @@ public void notifyNewSelectedFile(Path newFile) {
                 .map(FileAnnotationViewModel::new)
                 .collect(Collectors.toList());
         annotations.setAll(newAnnotations);
-        if (annotations.isEmpty())
+        if (annotations.isEmpty()) {
             annotaionEmpty.setValue(true);
-        else
+        } else {
             annotaionEmpty.setValue(false);
+        }
         try {
             fileMonitor.addListenerForFile(currentFile, fileListener);
         } catch (IOException e) {

From 1dec710df0d8fddd8054f3a3ab22042d0da3c9a7 Mon Sep 17 00:00:00 2001
From: Robert <robert@Roberts-MacBook-Pro.local>
Date: Mon, 27 Nov 2017 12:55:46 +0100
Subject: [PATCH 06/47] Fixed spelling mistake at 'annotationEmpty'

---
 .../fileannotationtab/FileAnnotationTabViewModel.java     | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
index c77ba4286eb..ad87e98be47 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
@@ -35,7 +35,7 @@ public class FileAnnotationTabViewModel extends AbstractViewModel {
     private final ListProperty<FileAnnotationViewModel> annotations = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ListProperty<Path> files = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ObjectProperty<FileAnnotationViewModel> currentAnnotation = new SimpleObjectProperty<>();
-    private final ObjectProperty<Boolean> annotaionEmpty = new SimpleObjectProperty<>(null);
+    private final ObjectProperty<Boolean> annotationEmpty = new SimpleObjectProperty<>(null);
 
     private final FileAnnotationCache cache;
     private final BibEntry entry;
@@ -61,7 +61,7 @@ public ObjectProperty<FileAnnotationViewModel> currentAnnotationProperty() {
     }
 
     public ObjectProperty<Boolean> isAnnotationsEmpty() {
-        return annotaionEmpty;
+        return annotationEmpty;
     }
 
     public ListProperty<FileAnnotationViewModel> annotationsProperty() {
@@ -90,9 +90,9 @@ public void notifyNewSelectedFile(Path newFile) {
                 .collect(Collectors.toList());
         annotations.setAll(newAnnotations);
         if (annotations.isEmpty()) {
-            annotaionEmpty.setValue(true);
+            annotationEmpty.setValue(true);
         } else {
-            annotaionEmpty.setValue(false);
+            annotationEmpty.setValue(false);
         }
         try {
             fileMonitor.addListenerForFile(currentFile, fileListener);

From fb02d7ee8e1dcf5707ab184fcde9b62e637fa7a4 Mon Sep 17 00:00:00 2001
From: Robert <robert@Roberts-MacBook-Pro.local>
Date: Sat, 2 Dec 2017 17:10:52 +0100
Subject: [PATCH 07/47] Sample FXML file for an annotation list entry

---
 .../fileannotationtab/ListItem.fxml           | 49 +++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml
new file mode 100644
index 00000000000..d290fe2e8b3
--- /dev/null
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml
@@ -0,0 +1,49 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.layout.ColumnConstraints?>
+<?import javafx.scene.layout.GridPane?>
+<?import javafx.scene.layout.RowConstraints?>
+<?import javafx.scene.text.Font?>
+
+<GridPane xmlns="http://javafx.com/javafx/8.0.141" xmlns:fx="http://javafx.com/fxml/1">
+   <columnConstraints>
+      <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="10.0" />
+      <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" />
+      <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="10.0" />
+   </columnConstraints>
+   <rowConstraints>
+      <RowConstraints minHeight="10.0" prefHeight="10.0" vgrow="SOMETIMES" />
+      <RowConstraints minHeight="10.0" vgrow="SOMETIMES" />
+   </rowConstraints>
+   <children>
+      <GridPane prefHeight="90.0" prefWidth="597.0" GridPane.columnIndex="1" GridPane.rowIndex="1">
+         <columnConstraints>
+            <ColumnConstraints hgrow="SOMETIMES" maxWidth="502.0" minWidth="10.0" prefWidth="308.0" />
+            <ColumnConstraints hgrow="SOMETIMES" maxWidth="398.0" minWidth="10.0" prefWidth="246.0" />
+         </columnConstraints>
+         <rowConstraints>
+            <RowConstraints maxHeight="20.0" minHeight="10.0" prefHeight="19.0" vgrow="SOMETIMES" />
+            <RowConstraints maxHeight="36.0" minHeight="10.0" prefHeight="36.0" vgrow="SOMETIMES" />
+            <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+            <RowConstraints minHeight="10.0" prefHeight="10.0" vgrow="SOMETIMES" />
+         </rowConstraints>
+         <children>
+            <Label alignment="TOP_LEFT" prefHeight="30.0" prefWidth="241.0" text="Brunch this weekend?">
+               <font>
+                  <Font name="System Bold" size="18.0" />
+               </font>
+            </Label>
+            <Label alignment="TOP_RIGHT" prefHeight="30.0" prefWidth="470.0" text="16:05 26.09.2017" textAlignment="RIGHT" GridPane.columnIndex="1" />
+            <Label alignment="TOP_LEFT" prefHeight="30.0" prefWidth="122.0" text="Brendan Lim" GridPane.rowIndex="1">
+               <font>
+                  <Font size="14.0" />
+               </font>
+            </Label>
+            <Label alignment="TOP_LEFT" prefHeight="30.0" prefWidth="516.0" text="This is a comment that discribes the marked passage in the list. It contains useful information to better understand the marked passage." GridPane.rowIndex="2" />
+            <Label alignment="TOP_RIGHT" prefHeight="30.0" prefWidth="470.0" text="Page 13" textAlignment="RIGHT" GridPane.columnIndex="1" GridPane.rowIndex="1" />
+         </children>
+      </GridPane>
+      <Label alignment="TOP_RIGHT" prefHeight="30.0" prefWidth="470.0" text="16:05 26.09.2017" textAlignment="RIGHT" />
+   </children>
+</GridPane>

From b438c8530206ab770ff00f7cd4018f9e03988052 Mon Sep 17 00:00:00 2001
From: Tarix <tarix@fu-berlin.de>
Date: Sat, 2 Dec 2017 20:01:53 +0100
Subject: [PATCH 08/47] addd table view and change vie for right panel

---
 .../fileannotationtab/FileAnnotationTab.fxml  | 63 +++++-----------
 .../FileAnnotationTabController.java          | 71 ++++++++++++++++---
 .../FileAnnotationViewModel.java              |  2 +-
 .../fileannotationtab/ListItem.fxml           |  6 +-
 4 files changed, 86 insertions(+), 56 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
index b3d7a1ede3e..0e00fd7a62e 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
@@ -1,82 +1,57 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
 <?import javafx.geometry.Insets?>
-<?import javafx.scene.control.Button?>
 <?import javafx.scene.control.ComboBox?>
 <?import javafx.scene.control.Label?>
 <?import javafx.scene.control.ListView?>
 <?import javafx.scene.control.ScrollPane?>
 <?import javafx.scene.control.TextArea?>
-<?import javafx.scene.control.Tooltip?>
 <?import javafx.scene.layout.BorderPane?>
 <?import javafx.scene.layout.ColumnConstraints?>
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.HBox?>
-<?import javafx.scene.layout.Pane?>
 <?import javafx.scene.layout.RowConstraints?>
-<?import de.jensd.fx.glyphs.materialdesignicons.MaterialDesignIconView?>
 <?import org.controlsfx.control.MasterDetailPane?>
-<ScrollPane xmlns:fx="http://javafx.com/fxml/1" fitToHeight="true" fitToWidth="true" hbarPolicy="NEVER"
-            styleClass="fileAnnotationTab" xmlns="http://javafx.com/javafx/8.0.112"
-            fx:controller="org.jabref.gui.entryeditor.fileannotationtab.FileAnnotationTabController">
+
+<ScrollPane fitToHeight="true" fitToWidth="true" hbarPolicy="NEVER" styleClass="fileAnnotationTab" xmlns="http://javafx.com/javafx/8.0.112" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.entryeditor.fileannotationtab.FileAnnotationTabController">
     <MasterDetailPane dividerPosition="0.6">
         <masterNode>
             <BorderPane>
                 <padding>
-                    <Insets top="5" right="5" bottom="5" left="5"/>
+                    <Insets bottom="5" left="5" right="5" top="5" />
                 </padding>
                 <top>
                     <HBox alignment="BASELINE_LEFT">
-                        <Label text="%Filename" prefWidth="70.0" alignment="BASELINE_LEFT"/>
-                        <ComboBox fx:id="files" maxWidth="Infinity" HBox.hgrow="ALWAYS"/>
+                        <Label alignment="BASELINE_LEFT" prefWidth="70.0" text="%Filename" />
+                        <ComboBox fx:id="files" maxWidth="Infinity" HBox.hgrow="ALWAYS" />
                     </HBox>
                 </top>
                 <center>
-                    <ListView fx:id="annotationList"/>
+                    <ListView fx:id="annotationList" />
                 </center>
             </BorderPane>
         </masterNode>
         <detailNode>
             <GridPane fx:id="grid">
                 <padding>
-                    <Insets top="5" right="5" bottom="5" left="10"/>
+                    <Insets bottom="5" left="10" right="5" top="5" />
                 </padding>
                 <columnConstraints>
-                    <ColumnConstraints hgrow="SOMETIMES" minWidth="60.0" prefWidth="70.0"/>
-                    <ColumnConstraints hgrow="ALWAYS" minWidth="10.0"/>
-                    <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="20.0"/>
+                    <ColumnConstraints hgrow="SOMETIMES" minWidth="60.0" prefWidth="70.0" />
+                    <ColumnConstraints hgrow="ALWAYS" minWidth="10.0" />
+                    <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="20.0" />
                 </columnConstraints>
                 <rowConstraints>
-                    <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" valignment="TOP"/>
-                    <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
-                    <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
-                    <RowConstraints minHeight="10.0" prefHeight="100.0" vgrow="ALWAYS"/>
-                    <RowConstraints minHeight="10.0" prefHeight="100.0" vgrow="ALWAYS"/>
+                    <RowConstraints minHeight="10.0" prefHeight="30.0" valignment="TOP" vgrow="SOMETIMES" />
+                    <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                    <RowConstraints minHeight="10.0" prefHeight="100.0" vgrow="ALWAYS" />
+                    <RowConstraints minHeight="10.0" prefHeight="10.0" vgrow="ALWAYS" />
+               <RowConstraints />
                 </rowConstraints>
-                <Label text="%Author" minHeight="35.0" prefHeight="30.0" GridPane.columnIndex="0" GridPane.rowIndex="1"
-                       alignment="TOP_LEFT"/>
-                <HBox GridPane.columnIndex="1" GridPane.rowIndex="1">
-                    <Label fx:id="author"/>
-                    <Pane HBox.hgrow="ALWAYS"/>
-                    <Button onAction="#copy" styleClass="flatButton">
-                        <graphic>
-                            <MaterialDesignIconView glyphName="CONTENT_COPY"/>
-                        </graphic>
-                        <tooltip>
-                            <Tooltip text="%Copy to clipboard"/>
-                        </tooltip>
-                    </Button>
-                </HBox>
-                <Label text="%Page" GridPane.columnIndex="0" GridPane.rowIndex="2"/>
-                <Label fx:id="page" GridPane.columnIndex="1" GridPane.rowIndex="2"/>
-                <Label text="%Date" GridPane.columnIndex="0" GridPane.rowIndex="3"/>
-                <Label fx:id="date" GridPane.columnIndex="1" GridPane.rowIndex="3"/>
-                <Label text="%Content" GridPane.columnIndex="0" GridPane.rowIndex="4"/>
-                <TextArea fx:id="content" GridPane.columnIndex="1" GridPane.rowIndex="4" editable="false"
-                          wrapText="true"/>
-                <Label text="%Marking" GridPane.columnIndex="0" GridPane.rowIndex="5"/>
-                <TextArea fx:id="marking" GridPane.columnIndex="1" GridPane.rowIndex="5" editable="false"
-                          wrapText="true"/>
+                <Label text="%Marking" GridPane.columnIndex="1" GridPane.rowIndex="1" />
+                <TextArea fx:id="marking" editable="false" wrapText="true" GridPane.columnIndex="1" GridPane.rowIndex="2" />
+                <Label text="%Content" GridPane.columnIndex="1" GridPane.rowIndex="3" />
+                <TextArea fx:id="content" editable="false" wrapText="true" GridPane.columnIndex="1" GridPane.rowIndex="4" />
             </GridPane>
         </detailNode>
     </MasterDetailPane>
diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
index 9df54542897..2fe9e344e60 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
@@ -8,17 +8,19 @@
 import javafx.collections.ListChangeListener;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
+import javafx.geometry.HPos;
+import javafx.geometry.Pos;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.Control;
 import javafx.scene.control.Label;
 import javafx.scene.control.ListView;
 import javafx.scene.control.SelectionMode;
 import javafx.scene.control.TextArea;
-import javafx.scene.layout.GridPane;
-import javafx.scene.layout.HBox;
-import javafx.scene.layout.VBox;
+import javafx.scene.layout.*;
+import javafx.scene.text.Font;
 import javafx.scene.text.Text;
 
+import javafx.scene.text.TextAlignment;
 import org.jabref.gui.AbstractController;
 import org.jabref.gui.util.FileUpdateMonitor;
 import org.jabref.gui.util.ViewModelListCellFactory;
@@ -67,8 +69,61 @@ public void initialize() {
         annotationList.getSelectionModel().setSelectionMode(SelectionMode.SINGLE);
         annotationList.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> viewModel.notifyNewSelectedAnnotation(newValue));
         ViewModelListCellFactory<FileAnnotationViewModel> cellFactory = new ViewModelListCellFactory<FileAnnotationViewModel>()
-                .withTooltip(FileAnnotationViewModel::getDescription)
+                .withTooltip(FileAnnotationViewModel::getMarking)
                 .withGraphic(annotation -> {
+
+                    GridPane node = new GridPane();
+
+                    ColumnConstraints firstColumn = new ColumnConstraints();
+                    ColumnConstraints secondColumn = new ColumnConstraints();
+                    firstColumn.setPercentWidth(70);
+                    secondColumn.setPercentWidth(30);
+                    firstColumn.setHalignment(HPos.LEFT);
+                    secondColumn.setHalignment(HPos.RIGHT);
+                    node.getColumnConstraints().addAll(firstColumn, secondColumn);
+
+                    RowConstraints firstRow = new RowConstraints();
+                    RowConstraints secondRow = new RowConstraints();
+                    firstRow.setMinHeight(10);
+                    firstRow.setPrefHeight(15);
+                    secondRow.setMinHeight(10);
+                    secondRow.setPrefHeight(35);
+                    node.getRowConstraints().addAll(firstRow, secondRow);
+
+                    Label marking = new Label(annotation.getMarking());
+                    Label author = new Label(annotation.getAuthor());
+                    Label date = new Label(annotation.getDate());
+                    Label page = new Label(Localization.lang("Page") + ": " + annotation.getPage());
+                    //marking.getStyleClass().setAll("marking");
+
+
+                    marking.setFont(new Font("System Bold", 14));
+                    marking.setPrefWidth(100);
+                    author.setFont(new Font("System", 14));
+
+                    marking.setPrefHeight(10);
+                    author.setPrefHeight(30);
+                    date.setPrefHeight(10);
+                    page.setPrefHeight(30);
+
+                    marking.setTextAlignment(TextAlignment.LEFT);
+                    marking.setAlignment(Pos.TOP_LEFT);
+
+                    author.setTextAlignment(TextAlignment.LEFT);
+                    author.setAlignment(Pos.TOP_LEFT);
+
+                    date.setTextAlignment(TextAlignment.RIGHT);
+                    date.setAlignment(Pos.TOP_RIGHT);
+
+                    page.setTextAlignment(TextAlignment.RIGHT);
+                    page.setAlignment(Pos.TOP_RIGHT);
+
+                    node.add(marking, 0, 0);
+                    node.add(author, 0, 1);
+                    node.add(date, 1, 0);
+                    node.add(page, 1, 1);
+
+                    /*
                     VBox node = new VBox();
 
                     Text text = new Text();
@@ -82,7 +137,7 @@ public void initialize() {
                     details.getChildren().addAll(page);
 
                     node.getChildren().addAll(text, details);
-                    node.setMaxWidth(Control.USE_PREF_SIZE);
+                    node.setMaxWidth(Control.USE_PREF_SIZE);*/
                     return node;
                 });
         annotationList.setCellFactory(cellFactory);
@@ -93,9 +148,9 @@ public void initialize() {
                 (ListChangeListener<? super FileAnnotationViewModel>) c -> annotationList.getSelectionModel().selectFirst());
 
         // Set-up details pane
-        author.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::authorProperty));
-        page.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::pageProperty));
-        date.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::dateProperty));
+        //author.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::authorProperty));
+        //page.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::pageProperty));
+        //date.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::dateProperty));
         content.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::contentProperty));
         marking.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::markingProperty));
         grid.disableProperty().bind(viewModel.isAnnotationsEmpty());
diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationViewModel.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationViewModel.java
index 5796fcc21bd..85ae94d5b42 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationViewModel.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationViewModel.java
@@ -100,7 +100,7 @@ public String toString() {
         return super.toString();
     }
 
-    public String getDescription() {
+    public String getMarking() {
         return marking.get();
     }
 }
diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml
index d290fe2e8b3..87f1f3be75b 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml
@@ -6,7 +6,7 @@
 <?import javafx.scene.layout.RowConstraints?>
 <?import javafx.scene.text.Font?>
 
-<GridPane xmlns="http://javafx.com/javafx/8.0.141" xmlns:fx="http://javafx.com/fxml/1">
+<GridPane xmlns="http://javafx.com/javafx/8.0.112" xmlns:fx="http://javafx.com/fxml/1">
    <columnConstraints>
       <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="10.0" />
       <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" />
@@ -23,13 +23,13 @@
             <ColumnConstraints hgrow="SOMETIMES" maxWidth="398.0" minWidth="10.0" prefWidth="246.0" />
          </columnConstraints>
          <rowConstraints>
-            <RowConstraints maxHeight="20.0" minHeight="10.0" prefHeight="19.0" vgrow="SOMETIMES" />
+            <RowConstraints maxHeight="20.0" minHeight="10.0" prefHeight="20.0" vgrow="SOMETIMES" />
             <RowConstraints maxHeight="36.0" minHeight="10.0" prefHeight="36.0" vgrow="SOMETIMES" />
             <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
             <RowConstraints minHeight="10.0" prefHeight="10.0" vgrow="SOMETIMES" />
          </rowConstraints>
          <children>
-            <Label alignment="TOP_LEFT" prefHeight="30.0" prefWidth="241.0" text="Brunch this weekend?">
+            <Label alignment="TOP_LEFT" prefHeight="21.0" prefWidth="138.0" text="Brunch this weekend?">
                <font>
                   <Font name="System Bold" size="18.0" />
                </font>

From d3324c61704948c268c04c12260d15d2fc62aeee Mon Sep 17 00:00:00 2001
From: Tarix <tarix@fu-berlin.de>
Date: Mon, 4 Dec 2017 11:43:52 +0100
Subject: [PATCH 09/47] - some small fixes - litle ui changes

---
 .../fileannotationtab/FileAnnotationTab.fxml  | 24 ++++++++------
 .../FileAnnotationTabController.java          | 31 +++----------------
 2 files changed, 20 insertions(+), 35 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
index 0e00fd7a62e..ef7678b47b4 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
@@ -37,21 +37,27 @@
                     <Insets bottom="5" left="10" right="5" top="5" />
                 </padding>
                 <columnConstraints>
-                    <ColumnConstraints hgrow="SOMETIMES" minWidth="60.0" prefWidth="70.0" />
+                    <ColumnConstraints hgrow="SOMETIMES" maxWidth="-Infinity" minWidth="10.0" prefWidth="10.0" />
                     <ColumnConstraints hgrow="ALWAYS" minWidth="10.0" />
-                    <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="20.0" />
+                    <ColumnConstraints hgrow="SOMETIMES" maxWidth="-Infinity" minWidth="10.0" prefWidth="10.0" />
                 </columnConstraints>
                 <rowConstraints>
-                    <RowConstraints minHeight="10.0" prefHeight="30.0" valignment="TOP" vgrow="SOMETIMES" />
-                    <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                    <RowConstraints maxHeight="-Infinity" minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
                     <RowConstraints minHeight="10.0" prefHeight="100.0" vgrow="ALWAYS" />
-                    <RowConstraints minHeight="10.0" prefHeight="10.0" vgrow="ALWAYS" />
+                    <RowConstraints maxHeight="-Infinity" minHeight="20.0" prefHeight="40.0" vgrow="ALWAYS" />
                <RowConstraints />
+               <RowConstraints maxHeight="-Infinity" minHeight="10.0" prefHeight="10.0" />
                 </rowConstraints>
-                <Label text="%Marking" GridPane.columnIndex="1" GridPane.rowIndex="1" />
-                <TextArea fx:id="marking" editable="false" wrapText="true" GridPane.columnIndex="1" GridPane.rowIndex="2" />
-                <Label text="%Content" GridPane.columnIndex="1" GridPane.rowIndex="3" />
-                <TextArea fx:id="content" editable="false" wrapText="true" GridPane.columnIndex="1" GridPane.rowIndex="4" />
+                <Label text="%Marking" GridPane.columnIndex="1" GridPane.valignment="BOTTOM">
+               <padding>
+                  <Insets bottom="3.0" />
+               </padding></Label>
+                <TextArea fx:id="marking" editable="false" wrapText="true" GridPane.columnIndex="1" GridPane.rowIndex="1" />
+                <Label text="%Content" GridPane.columnIndex="1" GridPane.rowIndex="2" GridPane.valignment="BOTTOM">
+               <padding>
+                  <Insets bottom="5.0" />
+               </padding></Label>
+                <TextArea fx:id="content" editable="false" wrapText="true" GridPane.columnIndex="1" GridPane.rowIndex="3" />
             </GridPane>
         </detailNode>
     </MasterDetailPane>
diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
index 2fe9e344e60..f1b22bfd680 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
@@ -11,14 +11,15 @@
 import javafx.geometry.HPos;
 import javafx.geometry.Pos;
 import javafx.scene.control.ComboBox;
-import javafx.scene.control.Control;
 import javafx.scene.control.Label;
 import javafx.scene.control.ListView;
 import javafx.scene.control.SelectionMode;
 import javafx.scene.control.TextArea;
-import javafx.scene.layout.*;
+//import javafx.scene.layout.*;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.ColumnConstraints;
+import javafx.scene.layout.RowConstraints;
 import javafx.scene.text.Font;
-import javafx.scene.text.Text;
 
 import javafx.scene.text.TextAlignment;
 import org.jabref.gui.AbstractController;
@@ -94,8 +95,6 @@ public void initialize() {
                     Label author = new Label(annotation.getAuthor());
                     Label date = new Label(annotation.getDate());
                     Label page = new Label(Localization.lang("Page") + ": " + annotation.getPage());
-                    //marking.getStyleClass().setAll("marking");
-
 
                     marking.setFont(new Font("System Bold", 14));
                     marking.setPrefWidth(100);
@@ -106,15 +105,13 @@ public void initialize() {
                     date.setPrefHeight(10);
                     page.setPrefHeight(30);
 
+                    // add alignment for text in the list
                     marking.setTextAlignment(TextAlignment.LEFT);
                     marking.setAlignment(Pos.TOP_LEFT);
-
                     author.setTextAlignment(TextAlignment.LEFT);
                     author.setAlignment(Pos.TOP_LEFT);
-
                     date.setTextAlignment(TextAlignment.RIGHT);
                     date.setAlignment(Pos.TOP_RIGHT);
-
                     page.setTextAlignment(TextAlignment.RIGHT);
                     page.setAlignment(Pos.TOP_RIGHT);
 
@@ -123,21 +120,6 @@ public void initialize() {
                     node.add(date, 1, 0);
                     node.add(page, 1, 1);
 
-                    /*
-                    VBox node = new VBox();
-
-                    Text text = new Text();
-                    text.setText(annotation.getContent());
-                    text.getStyleClass().setAll("text");
-
-                    HBox details = new HBox();
-                    details.getStyleClass().setAll("details");
-                    Text page = new Text();
-                    page.setText(Localization.lang("Page") + ": " + annotation.getPage());
-                    details.getChildren().addAll(page);
-
-                    node.getChildren().addAll(text, details);
-                    node.setMaxWidth(Control.USE_PREF_SIZE);*/
                     return node;
                 });
         annotationList.setCellFactory(cellFactory);
@@ -148,9 +130,6 @@ public void initialize() {
                 (ListChangeListener<? super FileAnnotationViewModel>) c -> annotationList.getSelectionModel().selectFirst());
 
         // Set-up details pane
-        //author.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::authorProperty));
-        //page.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::pageProperty));
-        //date.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::dateProperty));
         content.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::contentProperty));
         marking.textProperty().bind(EasyBind.select(viewModel.currentAnnotationProperty()).selectObject(FileAnnotationViewModel::markingProperty));
         grid.disableProperty().bind(viewModel.isAnnotationsEmpty());

From cace1bee6d3f423ba22c72f7d3bf427bd8707c3c Mon Sep 17 00:00:00 2001
From: Tarix <tarix@fu-berlin.de>
Date: Mon, 4 Dec 2017 11:46:50 +0100
Subject: [PATCH 10/47] - remove sepration

---
 .../fileannotationtab/FileAnnotationTabController.java          | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
index f1b22bfd680..c417bd28ee3 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
@@ -15,12 +15,10 @@
 import javafx.scene.control.ListView;
 import javafx.scene.control.SelectionMode;
 import javafx.scene.control.TextArea;
-//import javafx.scene.layout.*;
 import javafx.scene.layout.GridPane;
 import javafx.scene.layout.ColumnConstraints;
 import javafx.scene.layout.RowConstraints;
 import javafx.scene.text.Font;
-
 import javafx.scene.text.TextAlignment;
 import org.jabref.gui.AbstractController;
 import org.jabref.gui.util.FileUpdateMonitor;

From 1ece5cc4d359af6400b398d5323d4d1f070c0913 Mon Sep 17 00:00:00 2001
From: Tarix <tarix@fu-berlin.de>
Date: Mon, 4 Dec 2017 16:23:10 +0100
Subject: [PATCH 11/47] - add accidently removed copy button

---
 .../fileannotationtab/FileAnnotationTab.fxml  | 22 ++++++++++++++++++-
 .../FileAnnotationTabController.java          |  5 +++--
 2 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
index ef7678b47b4..ce56682551d 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
@@ -1,15 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<?import de.jensd.fx.glyphs.materialdesignicons.MaterialDesignIconView?>
 <?import javafx.geometry.Insets?>
+<?import javafx.scene.Cursor?>
+<?import javafx.scene.control.Button?>
 <?import javafx.scene.control.ComboBox?>
 <?import javafx.scene.control.Label?>
 <?import javafx.scene.control.ListView?>
 <?import javafx.scene.control.ScrollPane?>
 <?import javafx.scene.control.TextArea?>
+<?import javafx.scene.control.Tooltip?>
 <?import javafx.scene.layout.BorderPane?>
 <?import javafx.scene.layout.ColumnConstraints?>
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.Pane?>
 <?import javafx.scene.layout.RowConstraints?>
 <?import org.controlsfx.control.MasterDetailPane?>
 
@@ -39,7 +44,7 @@
                 <columnConstraints>
                     <ColumnConstraints hgrow="SOMETIMES" maxWidth="-Infinity" minWidth="10.0" prefWidth="10.0" />
                     <ColumnConstraints hgrow="ALWAYS" minWidth="10.0" />
-                    <ColumnConstraints hgrow="SOMETIMES" maxWidth="-Infinity" minWidth="10.0" prefWidth="10.0" />
+                    <ColumnConstraints hgrow="SOMETIMES" maxWidth="-Infinity" minWidth="40.0" prefWidth="40.0" />
                 </columnConstraints>
                 <rowConstraints>
                     <RowConstraints maxHeight="-Infinity" minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
@@ -58,6 +63,21 @@
                   <Insets bottom="5.0" />
                </padding></Label>
                 <TextArea fx:id="content" editable="false" wrapText="true" GridPane.columnIndex="1" GridPane.rowIndex="3" />
+                <HBox GridPane.columnIndex="2" GridPane.rowIndex="1">
+                    <Label fx:id="author" />
+                    <Pane HBox.hgrow="ALWAYS" />
+                    <Button onAction="#copy" styleClass="flatButton">
+                        <graphic>
+                            <MaterialDesignIconView glyphName="CONTENT_COPY">
+                        <cursor>
+                           <Cursor fx:constant="HAND" />
+                        </cursor></MaterialDesignIconView>
+                        </graphic>
+                        <tooltip>
+                            <Tooltip text="Copy to clipboard" />
+                        </tooltip>
+                    </Button>
+                </HBox>
             </GridPane>
         </detailNode>
     </MasterDetailPane>
diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
index c417bd28ee3..5db7052f9b9 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
@@ -19,6 +19,7 @@
 import javafx.scene.layout.ColumnConstraints;
 import javafx.scene.layout.RowConstraints;
 import javafx.scene.text.Font;
+
 import javafx.scene.text.TextAlignment;
 import org.jabref.gui.AbstractController;
 import org.jabref.gui.util.FileUpdateMonitor;
@@ -94,8 +95,8 @@ public void initialize() {
                     Label date = new Label(annotation.getDate());
                     Label page = new Label(Localization.lang("Page") + ": " + annotation.getPage());
 
-                    marking.setFont(new Font("System Bold", 14));
-                    marking.setPrefWidth(100);
+                    marking.setFont(new Font("System Bold", 15));
+                    marking.setPrefWidth(250);
                     author.setFont(new Font("System", 14));
 
                     marking.setPrefHeight(10);

From 3ba97a524ee0e83802c61b41fc92d362471be884 Mon Sep 17 00:00:00 2001
From: Robert <robert@Roberts-MacBook-Pro.local>
Date: Mon, 4 Dec 2017 16:40:11 +0100
Subject: [PATCH 12/47] Added CHANGELOG entry for the issue

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 25e77cd291f..fa791c86ff2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,9 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- Reorganised annotation information on the right side of the "File annotations" tab. [#3109](https://github.com/JabRef/jabref/issues/3109)
+- Changed list item format in list of annotations for the "File annotations" tab. [#3109](https://github.com/JabRef/jabref/issues/3109)
+- Added gui solution for "no annotations in linked file" for the "File annotations" tab. [#3109](https://github.com/JabRef/jabref/issues/3109)
 - We added bracketed expresion support for file search patterns, import file name patterns and file directory patters, in addition to bibtexkey patterns.
 - We added support for '[entrytype]' bracketed expression.
 - Updated French translation

From 76502bc09053164c41beec731abf3c2d9d991686 Mon Sep 17 00:00:00 2001
From: Tarix <tarix@fu-berlin.de>
Date: Mon, 4 Dec 2017 16:40:53 +0100
Subject: [PATCH 13/47] - reorder import

---
 .../fileannotationtab/FileAnnotationTabController.java        | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
index 5db7052f9b9..7ed4dda4b4b 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
@@ -16,11 +16,11 @@
 import javafx.scene.control.SelectionMode;
 import javafx.scene.control.TextArea;
 import javafx.scene.layout.GridPane;
-import javafx.scene.layout.ColumnConstraints;
 import javafx.scene.layout.RowConstraints;
+import javafx.scene.layout.ColumnConstraints;
 import javafx.scene.text.Font;
-
 import javafx.scene.text.TextAlignment;
+
 import org.jabref.gui.AbstractController;
 import org.jabref.gui.util.FileUpdateMonitor;
 import org.jabref.gui.util.ViewModelListCellFactory;

From 2f59a7e844737c48c89de059b4de779d0d8c3207 Mon Sep 17 00:00:00 2001
From: Tarix <tarix@fu-berlin.de>
Date: Mon, 11 Dec 2017 15:51:08 +0100
Subject: [PATCH 14/47] - fix localization bug int fileannotaiontab

---
 .../gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
index ce56682551d..6a61e60f190 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
@@ -74,7 +74,7 @@
                         </cursor></MaterialDesignIconView>
                         </graphic>
                         <tooltip>
-                            <Tooltip text="Copy to clipboard" />
+                            <Tooltip text="%Copy to clipboard" />
                         </tooltip>
                     </Button>
                 </HBox>

From 26f874a01abb71d08d60c64ab84d89a6bcb4e4dd Mon Sep 17 00:00:00 2001
From: Robert <robert@Roberts-MacBook-Pro.local>
Date: Sat, 16 Dec 2017 00:09:07 +0100
Subject: [PATCH 15/47] Reorganized imports in FileAnnotationTab.fxml

---
 .../gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
index 6a61e60f190..a9b8bbfb029 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml
@@ -1,8 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<?import de.jensd.fx.glyphs.materialdesignicons.MaterialDesignIconView?>
 <?import javafx.geometry.Insets?>
-<?import javafx.scene.Cursor?>
 <?import javafx.scene.control.Button?>
 <?import javafx.scene.control.ComboBox?>
 <?import javafx.scene.control.Label?>
@@ -10,12 +8,14 @@
 <?import javafx.scene.control.ScrollPane?>
 <?import javafx.scene.control.TextArea?>
 <?import javafx.scene.control.Tooltip?>
+<?import javafx.scene.Cursor?>
 <?import javafx.scene.layout.BorderPane?>
 <?import javafx.scene.layout.ColumnConstraints?>
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.Pane?>
 <?import javafx.scene.layout.RowConstraints?>
+<?import de.jensd.fx.glyphs.materialdesignicons.MaterialDesignIconView?>
 <?import org.controlsfx.control.MasterDetailPane?>
 
 <ScrollPane fitToHeight="true" fitToWidth="true" hbarPolicy="NEVER" styleClass="fileAnnotationTab" xmlns="http://javafx.com/javafx/8.0.112" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.entryeditor.fileannotationtab.FileAnnotationTabController">

From 9f82f5150346de5d3c23ec39f8237f8b3bc2bf68 Mon Sep 17 00:00:00 2001
From: Robert <robert@Roberts-MacBook-Pro.local>
Date: Mon, 18 Dec 2017 12:54:41 +0100
Subject: [PATCH 16/47] Reorganized import order in
 FileAnnotationTabController.java

---
 .../fileannotationtab/FileAnnotationTabController.java          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
index 7ed4dda4b4b..27e56c9175e 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
@@ -15,9 +15,9 @@
 import javafx.scene.control.ListView;
 import javafx.scene.control.SelectionMode;
 import javafx.scene.control.TextArea;
+import javafx.scene.layout.ColumnConstraints;
 import javafx.scene.layout.GridPane;
 import javafx.scene.layout.RowConstraints;
-import javafx.scene.layout.ColumnConstraints;
 import javafx.scene.text.Font;
 import javafx.scene.text.TextAlignment;
 

From a66a525f12611f2888233c7f4635e50c7bb4b180 Mon Sep 17 00:00:00 2001
From: Robert <robert@Roberts-MacBook-Pro.local>
Date: Mon, 18 Dec 2017 16:56:00 +0100
Subject: [PATCH 17/47] Applied simpler way of checking if annotation is empty

---
 .../fileannotationtab/FileAnnotationTabViewModel.java | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
index ad87e98be47..525738dd015 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
@@ -11,6 +11,7 @@
 
 import javafx.beans.property.ListProperty;
 import javafx.beans.property.ObjectProperty;
+import javafx.beans.property.ReadOnlyBooleanProperty;
 import javafx.beans.property.SimpleListProperty;
 import javafx.beans.property.SimpleObjectProperty;
 import javafx.collections.FXCollections;
@@ -35,7 +36,7 @@ public class FileAnnotationTabViewModel extends AbstractViewModel {
     private final ListProperty<FileAnnotationViewModel> annotations = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ListProperty<Path> files = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ObjectProperty<FileAnnotationViewModel> currentAnnotation = new SimpleObjectProperty<>();
-    private final ObjectProperty<Boolean> annotationEmpty = new SimpleObjectProperty<>(null);
+    private ReadOnlyBooleanProperty annotationEmpty;
 
     private final FileAnnotationCache cache;
     private final BibEntry entry;
@@ -60,7 +61,7 @@ public ObjectProperty<FileAnnotationViewModel> currentAnnotationProperty() {
         return currentAnnotation;
     }
 
-    public ObjectProperty<Boolean> isAnnotationsEmpty() {
+    public ReadOnlyBooleanProperty isAnnotationsEmpty() {
         return annotationEmpty;
     }
 
@@ -89,11 +90,7 @@ public void notifyNewSelectedFile(Path newFile) {
                 .map(FileAnnotationViewModel::new)
                 .collect(Collectors.toList());
         annotations.setAll(newAnnotations);
-        if (annotations.isEmpty()) {
-            annotationEmpty.setValue(true);
-        } else {
-            annotationEmpty.setValue(false);
-        }
+        annotationEmpty = annotations.emptyProperty();
         try {
             fileMonitor.addListenerForFile(currentFile, fileListener);
         } catch (IOException e) {

From d721a19fe3b82c17c6efcd1f8fa27e98fc5dc3ee Mon Sep 17 00:00:00 2001
From: Linus Dietz <linus.dietz@tum.de>
Date: Mon, 22 Jan 2018 18:47:27 +0100
Subject: [PATCH 18/47] set jacoco version globally

---
 build.gradle | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 567982ebb7c..e246b69bafa 100644
--- a/build.gradle
+++ b/build.gradle
@@ -364,6 +364,10 @@ task copyTestResources(type: Copy) {
 }
 processTestResources.dependsOn copyTestResources
 
+jacoco {
+    toolVersion = '0.8.0'
+}
+
 tasks.withType(Test) {
     reports.html.destination = file("${reporting.baseDir}/${name}")
 
@@ -391,7 +395,6 @@ afterEvaluate {
     def junitPlatformTest = tasks.junitPlatformTest
 
     jacoco {
-        toolVersion = '0.8.0'
         applyTo(junitPlatformTest)
     }
 

From f3a5cfb50807a71a59baa2cfe67c1026bd119231 Mon Sep 17 00:00:00 2001
From: Linus Dietz <linus.dietz@tum.de>
Date: Tue, 23 Jan 2018 13:51:20 +0100
Subject: [PATCH 19/47] Set jacoco toolVersion earlier

---
 build.gradle | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/build.gradle b/build.gradle
index e246b69bafa..66208865138 100644
--- a/build.gradle
+++ b/build.gradle
@@ -175,6 +175,9 @@ dependencies {
     checkstyle 'com.puppycrawl.tools:checkstyle:8.7'
 }
 
+jacoco {
+    toolVersion = '0.8.0'
+}
 dependencyUpdates {
     outputFormatter = "json"
 }
@@ -364,9 +367,6 @@ task copyTestResources(type: Copy) {
 }
 processTestResources.dependsOn copyTestResources
 
-jacoco {
-    toolVersion = '0.8.0'
-}
 
 tasks.withType(Test) {
     reports.html.destination = file("${reporting.baseDir}/${name}")

From 5c12106ff1c2833034305011b3a96094017b7d25 Mon Sep 17 00:00:00 2001
From: Linus Dietz <linus.dietz@tum.de>
Date: Wed, 31 Jan 2018 11:51:01 +0100
Subject: [PATCH 20/47] Add exception for Jacoco

---
 build.gradle | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/build.gradle b/build.gradle
index 66208865138..000cb51e39f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -138,7 +138,7 @@ dependencies {
     compile 'org.jsoup:jsoup:1.11.2'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
-	// >1.8.0-beta is required for java 9 compatibility
+    // >1.8.0-beta is required for java 9 compatibility
     compile 'org.slf4j:slf4j-api:1.8.0-beta0'
     compile 'org.apache.logging.log4j:log4j-slf4j-impl:2.10.0'
     compile 'org.apache.logging.log4j:log4j-jcl:2.10.0'
@@ -230,7 +230,16 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject("http://dev.mysql.com/downloads/connector/j/ lists the version 5.* as last stable version.")
             }
         }
-
+        withModule("org.jacoco.agent") { ComponentSelection selection ->
+            if (selection.candidate.version.equals("0.8.0")) {
+                selection.reject("As a native plugin we cannot control the actual version of jacoco. This depenency should be hidden.")
+            }
+        }
+        withModule("org.jacoco.ant") { ComponentSelection selection ->
+            if (selection.candidate.version.equals("0.8.0")) {
+                selection.reject("As a native plugin we cannot control the actual version of jacoco. This depenency should be hidden.")
+            }
+        }
     }
 }
 

From 24ed12a69fb5d03464af1c995e679f23366ece34 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Tue, 6 Feb 2018 11:01:28 +0100
Subject: [PATCH 21/47] Add some BibtexNameFomatter comments

---
 .../org/jabref/logic/bst/BibtexNameFormatter.java | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bst/BibtexNameFormatter.java b/src/main/java/org/jabref/logic/bst/BibtexNameFormatter.java
index 6afe53acbe0..a8b0e1b61c4 100644
--- a/src/main/java/org/jabref/logic/bst/BibtexNameFormatter.java
+++ b/src/main/java/org/jabref/logic/bst/BibtexNameFormatter.java
@@ -29,6 +29,15 @@ public class BibtexNameFormatter {
     private BibtexNameFormatter() {
     }
 
+    /**
+     * Formats the nth author of the author name list by a given format string
+     *
+     * @param authorsNameList The string from an author field
+     * @param whichName index of the list, starting with 1
+     * @param formatString TODO
+     * @param warn collects the warnings, may-be-null
+     * @return
+     */
     public static String formatName(String authorsNameList, int whichName, String formatString, Warn warn) {
         AuthorList al = AuthorList.parse(authorsNameList);
 
@@ -40,11 +49,7 @@ public static String formatName(String authorsNameList, int whichName, String fo
     }
 
     /**
-     *
-     * @param author
-     * @param format
-     * @param warn may-be-null
-     * @return
+     * @param warn collects the warnings, may-be-null
      */
     public static String formatName(Author author, String format, Warn warn) {
 

From bd3ef32dc749a6799b4242f6d4a94d2d3f5968b2 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 6 Feb 2018 11:05:14 +0100
Subject: [PATCH 22/47] Use stream in matcher (#3696)

---
 .../model/search/matchers/AndMatcher.java     | 19 ++++---------------
 .../model/search/matchers/OrMatcher.java      | 19 ++++---------------
 2 files changed, 8 insertions(+), 30 deletions(-)

diff --git a/src/main/java/org/jabref/model/search/matchers/AndMatcher.java b/src/main/java/org/jabref/model/search/matchers/AndMatcher.java
index c39b3c36ffc..81839607ad0 100644
--- a/src/main/java/org/jabref/model/search/matchers/AndMatcher.java
+++ b/src/main/java/org/jabref/model/search/matchers/AndMatcher.java
@@ -1,26 +1,15 @@
 package org.jabref.model.search.matchers;
 
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.search.SearchMatcher;
 
 /**
- * Subclass of MatcherSet that ANDs or ORs between its rules, returning 0 or
- * 1.
+ * A set of matchers that returns true if all matcher match the given entry.
  */
 public class AndMatcher extends MatcherSet {
 
     @Override
-    public boolean isMatch(BibEntry bibEntry) {
-        int score = 0;
-
-        // We let each rule add a maximum of 1 to the score.
-        for (SearchMatcher rule : matchers) {
-            if (rule.isMatch(bibEntry)) {
-                score++;
-            }
-        }
-
-        // Then an AND rule demands that score == number of rules
-        return score == matchers.size();
+    public boolean isMatch(BibEntry entry) {
+        return matchers.stream()
+                       .allMatch(rule -> rule.isMatch(entry));
     }
 }
diff --git a/src/main/java/org/jabref/model/search/matchers/OrMatcher.java b/src/main/java/org/jabref/model/search/matchers/OrMatcher.java
index ffd2ebf1e28..c0a0eddf1d9 100644
--- a/src/main/java/org/jabref/model/search/matchers/OrMatcher.java
+++ b/src/main/java/org/jabref/model/search/matchers/OrMatcher.java
@@ -1,26 +1,15 @@
 package org.jabref.model.search.matchers;
 
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.search.SearchMatcher;
 
 /**
- * Subclass of MatcherSet that ANDs or ORs between its rules, returning 0 or
- * 1.
+ * A set of matchers that returns true if any matcher matches the given entry.
  */
 public class OrMatcher extends MatcherSet {
 
     @Override
-    public boolean isMatch(BibEntry bibEntry) {
-        int score = 0;
-
-        // We let each rule add a maximum of 1 to the score.
-        for (SearchMatcher rule : matchers) {
-            if (rule.isMatch(bibEntry)) {
-                score++;
-            }
-        }
-
-        // OR rule demands score > 0.
-        return score > 0;
+    public boolean isMatch(BibEntry entry) {
+        return matchers.stream()
+                       .anyMatch(rule -> rule.isMatch(entry));
     }
 }

From b760319972e2ac8f1e4291ca37232c67acf93b0a Mon Sep 17 00:00:00 2001
From: Joerg Lenhard <joerg.lenhard@kau.se>
Date: Tue, 6 Feb 2018 11:31:21 +0100
Subject: [PATCH 23/47] Remove deprecated static BibtexParser.parse method

---
 .../importer/fileformat/BibtexParser.java     | 13 -----
 .../importer/fileformat/BibtexParserTest.java | 58 ++++++++-----------
 .../org/jabref/logic/xmp/XMPUtilTest.java     | 30 +++++-----
 3 files changed, 37 insertions(+), 64 deletions(-)

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java b/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
index 37c71543d3e..c21c37ddc8c 100644
--- a/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
+++ b/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
@@ -78,19 +78,6 @@ public BibtexParser(ImportFormatPreferences importFormatPreferences, FileUpdateM
         metaDataParser = new MetaDataParser(fileMonitor);
     }
 
-    /**
-     * Shortcut usage to create a Parser and read the input.
-     *
-     * @param in the Reader to read from
-     * @param fileMonitor
-     * @throws IOException
-     * @deprecated inline this method
-     */
-    @Deprecated
-    public static ParserResult parse(Reader in, ImportFormatPreferences importFormatPreferences, FileUpdateMonitor fileMonitor) throws IOException {
-        return new BibtexParser(importFormatPreferences, fileMonitor).parse(in);
-    }
-
     /**
      * Parses BibtexEntries from the given string and returns one entry found (or null if none found)
      * <p>
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 b346f548901..b963f63c4de 100644
--- a/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
+++ b/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
@@ -280,7 +280,7 @@ public void parseRecognizesEntryInParenthesis() throws IOException {
     @Test
     public void parseRecognizesEntryWithBigNumbers() throws IOException {
         ParserResult result = parser.parse(new StringReader("@article{canh05," + "isbn = 1234567890123456789,\n"
-                + "isbn2 = {1234567890123456789},\n" + "small = 1234,\n" + "}"), importFormatPreferences, fileMonitor);
+                + "isbn2 = {1234567890123456789},\n" + "small = 1234,\n" + "}"));
 
         Collection<BibEntry> parsed = result.getDatabase().getEntries();
         BibEntry entry = parsed.iterator().next();
@@ -367,10 +367,9 @@ public void parseRecognizesMultipleEntries() throws IOException {
         secondEntry.setField("author", "Norton Bar");
         expected.add(secondEntry);
 
-        ParserResult result = BibtexParser.parse(
+        ParserResult result = parser.parse(
                 new StringReader("@article{canh05," + "  author = {Crowston, K. and Annabi, H.},\n"
-                        + "  title = {Title A}}\n" + "@inProceedings{foo," + "  author={Norton Bar}}"),
-                importFormatPreferences, fileMonitor);
+                        + "  title = {Title A}}\n" + "@inProceedings{foo," + "  author={Norton Bar}}"));
         List<BibEntry> parsed = result.getDatabase().getEntries();
 
         assertEquals(expected, parsed);
@@ -467,8 +466,7 @@ public void parseRecognizesHeaderButIgnoresEncoding() throws IOException {
                 + "  title = {Effective work practices for floss development: A model and propositions}," + "\n"
                 + "  booktitle = {Hawaii International Conference On System Sciences (HICSS)}," + "\n"
                 + "  year = {2005}," + "\n" + "  owner = {oezbek}," + "\n" + "  timestamp = {2006.05.29}," + "\n"
-                + "  url = {http://james.howison.name/publications.html}" + "\n" + "}))"),
-                importFormatPreferences, fileMonitor);
+                + "  url = {http://james.howison.name/publications.html}" + "\n" + "}))"));
 
         Collection<BibEntry> parsed = result.getDatabase().getEntries();
         BibEntry entry = parsed.iterator().next();
@@ -497,8 +495,7 @@ public void parseRecognizesFormatedEntry() throws IOException {
                         + "  title = {Effective work practices for floss development: A model and propositions}," + "\n"
                         + "  booktitle = {Hawaii International Conference On System Sciences (HICSS)}," + "\n"
                         + "  year = {2005}," + "\n" + "  owner = {oezbek}," + "\n" + "  timestamp = {2006.05.29},"
-                        + "\n" + "  url = {http://james.howison.name/publications.html}" + "\n" + "}))"),
-                importFormatPreferences, fileMonitor);
+                        + "\n" + "  url = {http://james.howison.name/publications.html}" + "\n" + "}))"));
 
         Collection<BibEntry> parsed = result.getDatabase().getEntries();
         BibEntry entry = parsed.iterator().next();
@@ -600,8 +597,7 @@ public void parseReturnsEmptyListIfNoEntryRecognized() throws IOException {
                         + "  title = {Effective work practices for floss development: A model and propositions}," + "\n"
                         + "  booktitle = {Hawaii International Conference On System Sciences (HICSS)}," + "\n"
                         + "  year = {2005}," + "\n" + "  owner = {oezbek}," + "\n" + "  timestamp = {2006.05.29},"
-                        + "\n" + "  url = {http://james.howison.name/publications.html}" + "\n" + "}))"),
-                importFormatPreferences, fileMonitor);
+                        + "\n" + "  url = {http://james.howison.name/publications.html}" + "\n" + "}))"));
 
         Collection<BibEntry> parsed = result.getDatabase().getEntries();
 
@@ -622,8 +618,7 @@ public void parseReturnsEmptyListIfNoEntryExistent() throws IOException {
     public void parseRecognizesDuplicateBibtexKeys() throws IOException {
         ParserResult result = parser
                 .parse(new StringReader("@article{canh05," + "  author = {Crowston, K. and Annabi, H.},\n"
-                        + "  title = {Title A}}\n" + "@inProceedings{canh05," + "  author={Norton Bar}}"),
-                        importFormatPreferences, fileMonitor);
+                        + "  title = {Title A}}\n" + "@inProceedings{canh05," + "  author={Norton Bar}}"));
 
         List<String> duplicateKeys = result.getDuplicateKeys();
 
@@ -710,8 +705,7 @@ public void parseIgnoresArbitraryContentAfterEntry() throws IOException {
 
     @Test
     public void parseWarnsAboutUnmatchedContentInEntryWithoutComma() throws IOException {
-        ParserResult result = parser.parse(new StringReader("@article{test,author={author bracket } too much}"),
-                importFormatPreferences, fileMonitor);
+        ParserResult result = parser.parse(new StringReader("@article{test,author={author bracket } too much}"));
 
         List<BibEntry> entries = result.getDatabase().getEntries();
 
@@ -720,8 +714,7 @@ public void parseWarnsAboutUnmatchedContentInEntryWithoutComma() throws IOExcept
 
     @Test
     public void parseWarnsAboutUnmatchedContentInEntry() throws IOException {
-        ParserResult result = parser.parse(new StringReader("@article{test,author={author bracket }, too much}"),
-                importFormatPreferences, fileMonitor);
+        ParserResult result = parser.parse(new StringReader("@article{test,author={author bracket }, too much}"));
 
         List<BibEntry> entries = result.getDatabase().getEntries();
 
@@ -801,8 +794,7 @@ public void parseIgnoresAndWarnsAboutEntryWithFieldsThatAreNotSeperatedByComma()
     public void parseIgnoresAndWarnsAboutCorruptedEntryButRecognizeOthers() throws IOException {
         ParserResult result = parser.parse(
                 new StringReader(
-                        "@article{test,author={author missing bracket}" + "@article{test,author={Ed von Test}}"),
-                importFormatPreferences, fileMonitor);
+                        "@article{test,author={author missing bracket}" + "@article{test,author={Ed von Test}}"));
 
         Collection<BibEntry> parsed = result.getDatabase().getEntries();
         BibEntry entry = parsed.iterator().next();
@@ -943,12 +935,11 @@ public void parseRecognizesMultipleStrings() throws IOException {
 
     @Test
     public void parseRecognizesStringAndEntry() throws IOException {
-        ParserResult result = BibtexParser.parse(
+        ParserResult result = parser.parse(
                 new StringReader("" + "@string{bourdieu = {Bourdieu, Pierre}}"
                         + "@book{bourdieu-2002-questions-sociologie, " + "	Address = {Paris}," + "	Author = bourdieu,"
                         + "	Isbn = 2707318256," + "	Publisher = {Minuit}," + "	Title = {Questions de sociologie},"
-                        + "	Year = 2002" + "}"),
-                importFormatPreferences, fileMonitor);
+                        + "	Year = 2002" + "}"));
 
 
         BibtexString parsedString = result.getDatabase().getStringValues().iterator().next();
@@ -1120,8 +1111,9 @@ public void parseConvertsMultipleTabsToSpace() throws IOException {
     public void parsePreservesMultipleSpacesInNonWrappableField() throws IOException {
         when(importFormatPreferences.getFieldContentParserPreferences().getNonWrappableFields())
                 .thenReturn(Collections.singletonList("file"));
-        ParserResult result = BibtexParser
-                .parse(new StringReader("@article{canh05,file = {ups  sala}}"), importFormatPreferences, fileMonitor);
+        BibtexParser parser = new BibtexParser(importFormatPreferences, fileMonitor);
+        ParserResult result = parser
+                .parse(new StringReader("@article{canh05,file = {ups  sala}}"));
 
         Collection<BibEntry> parsedEntries = result.getDatabase().getEntries();
         BibEntry parsedEntry = parsedEntries.iterator().next();
@@ -1131,8 +1123,7 @@ public void parsePreservesMultipleSpacesInNonWrappableField() throws IOException
 
     @Test
     public void parsePreservesTabsInAbstractField() throws IOException {
-        ParserResult result = parser.parse(new StringReader("@article{canh05,abstract = {ups  \tsala}}"),
-                importFormatPreferences, fileMonitor);
+        ParserResult result = parser.parse(new StringReader("@article{canh05,abstract = {ups  \tsala}}"));
 
         Collection<BibEntry> parsedEntries = result.getDatabase().getEntries();
         BibEntry parsedEntry = parsedEntries.iterator().next();
@@ -1142,8 +1133,7 @@ public void parsePreservesTabsInAbstractField() throws IOException {
 
     @Test
     public void parsePreservesNewlineInAbstractField() throws IOException {
-        ParserResult result = parser.parse(new StringReader("@article{canh05,abstract = {ups \nsala}}"),
-                importFormatPreferences, fileMonitor);
+        ParserResult result = parser.parse(new StringReader("@article{canh05,abstract = {ups \nsala}}"));
 
         Collection<BibEntry> parsedEntries = result.getDatabase().getEntries();
         BibEntry parsedEntry = parsedEntries.iterator().next();
@@ -1351,10 +1341,9 @@ public void integrationTestCustomEntryType() throws IOException {
 
     @Test
     public void integrationTestSaveOrderConfig() throws IOException {
-        ParserResult result = BibtexParser.parse(
+        ParserResult result = parser.parse(
                 new StringReader(
-                        "@Comment{jabref-meta: saveOrderConfig:specified;author;false;year;true;abstract;false;}"),
-                importFormatPreferences, fileMonitor);
+                        "@Comment{jabref-meta: saveOrderConfig:specified;author;false;year;true;abstract;false;}"));
 
         Optional<SaveOrderConfig> saveOrderConfig = result.getMetaData().getSaveOrderConfig();
 
@@ -1367,7 +1356,7 @@ public void integrationTestSaveOrderConfig() throws IOException {
     public void integrationTestCustomKeyPattern() throws IOException {
         ParserResult result = parser
                 .parse(new StringReader("@comment{jabref-meta: keypattern_article:articleTest;}" + OS.NEWLINE
-                        + "@comment{jabref-meta: keypatterndefault:test;}"), importFormatPreferences, fileMonitor);
+                        + "@comment{jabref-meta: keypatterndefault:test;}"));
 
         GlobalBibtexKeyPattern pattern = mock(GlobalBibtexKeyPattern.class);
         AbstractBibtexKeyPattern bibtexKeyPattern = result.getMetaData().getCiteKeyPattern(pattern);
@@ -1394,7 +1383,7 @@ public void integrationTestGroupTree() throws IOException, ParseException {
                 + "@comment{jabref-meta: groupstree:" + OS.NEWLINE + "0 AllEntriesGroup:;" + OS.NEWLINE
                 + "1 KeywordGroup:Fréchet\\;0\\;keywords\\;FrechetSpace\\;0\\;1\\;;" + OS.NEWLINE
                 + "1 KeywordGroup:Invariant theory\\;0\\;keywords\\;GIT\\;0\\;0\\;;" + OS.NEWLINE
-                + "1 ExplicitGroup:TestGroup\\;0\\;Key1\\;Key2\\;;" + "}"), importFormatPreferences, fileMonitor);
+                + "1 ExplicitGroup:TestGroup\\;0\\;Key1\\;Key2\\;;" + "}"));
 
         GroupTreeNode root = result.getMetaData().getGroups().get();
 
@@ -1421,7 +1410,7 @@ public void integrationTestProtectedFlag() throws IOException {
     @Test
     public void integrationTestContentSelectors() throws IOException {
         ParserResult result = parser.parse(
-                new StringReader("@Comment{jabref-meta: selector_status:approved;captured;received;status;}"), importFormatPreferences, fileMonitor);
+                new StringReader("@Comment{jabref-meta: selector_status:approved;captured;received;status;}"));
 
         List<String> values = new ArrayList(4);
         values.add("approved");
@@ -1495,8 +1484,7 @@ public void parseDoesNotRecognizeDatabaseIDasUserComment() throws Exception {
     public void integrationTestFileDirectories() throws IOException {
         ParserResult result = parser.parse(
                 new StringReader("@comment{jabref-meta: fileDirectory:\\\\Literature\\\\;}"
-                        + "@comment{jabref-meta: fileDirectory-defaultOwner-user:D:\\\\Documents;}"),
-                importFormatPreferences, fileMonitor);
+                        + "@comment{jabref-meta: fileDirectory-defaultOwner-user:D:\\\\Documents;}"));
 
         assertEquals("\\Literature\\", result.getMetaData().getDefaultFileDirectory().get());
         assertEquals("D:\\Documents", result.getMetaData().getUserFileDirectory("defaultOwner-user").get());
diff --git a/src/test/java/org/jabref/logic/xmp/XMPUtilTest.java b/src/test/java/org/jabref/logic/xmp/XMPUtilTest.java
index d8d60c5e671..3d934e5741f 100644
--- a/src/test/java/org/jabref/logic/xmp/XMPUtilTest.java
+++ b/src/test/java/org/jabref/logic/xmp/XMPUtilTest.java
@@ -79,9 +79,10 @@ public class XMPUtilTest {
 
     private XMPPreferences xmpPreferences;
 
-
     private ImportFormatPreferences importFormatPreferences;
 
+    private BibtexParser parser;
+
     /**
      * Wrap bibtex-data (<bibtex:author>...) into an rdf:Description.
      *
@@ -248,6 +249,8 @@ public void setUp() throws IOException, COSVisitorException {
         when(xmpPreferences.isUseXMPPrivacyFilter()).thenReturn(false);
 
         when(xmpPreferences.getKeywordSeparator()).thenReturn(',');
+
+        parser = new BibtexParser(importFormatPreferences, fileMonitor);
     }
 
     /**
@@ -446,13 +449,12 @@ public void testWriteReadManually() throws COSVisitorException, IOException {
      */
     @Test
     public void testReadWriteXMP() throws IOException, TransformerException {
-        ParserResult result = BibtexParser.parse(new StringReader(
+        ParserResult result = parser.parse(new StringReader(
                 "@article{canh05," + "  author = {Crowston, K. and Annabi, H. and Howison, J. and Masango, C.}," + "\n"
                         + "  title = {Effective work practices for floss development: A model and propositions}," + "\n"
                         + "  booktitle = {Hawaii International Conference On System Sciences (HICSS)}," + "\n"
                         + "  year = {2005}," + "\n" + "  owner = {oezbek}," + "\n" + "  timestamp = {2006.05.29},"
-                        + "\n" + "  url = {http://james.howison.name/publications.html}" + "\n" + "}"),
-                importFormatPreferences, fileMonitor);
+                        + "\n" + "  url = {http://james.howison.name/publications.html}" + "\n" + "}"));
 
         Collection<BibEntry> c = result.getDatabase().getEntries();
         Assert.assertEquals(1, c.size());
@@ -724,13 +726,12 @@ public void testSimpleUpdate() throws Exception {
      */
     @Test
     public void testXMLEscape() throws Exception {
-        ParserResult result = BibtexParser.parse(new StringReader(
+        ParserResult result = parser.parse(new StringReader(
                 "@article{canh05," + "  author = {Crowston, K. and Annabi, H. and Howison, J. and Masango, C.}," + "\n"
                         + "  title = {</bibtex:title> \" bla \" '' '' && &  for floss development: A model and propositions},"
                         + "\n" + "  booktitle = {<randomXML>}," + "\n" + "  year = {2005}," + "\n"
                         + "  owner = {oezbek}," + "\n" + "  timestamp = {2006.05.29}," + "\n"
-                        + "  url = {http://james.howison.name/publications.html}" + "\n" + "}"),
-                importFormatPreferences, fileMonitor);
+                        + "  url = {http://james.howison.name/publications.html}" + "\n" + "}"));
 
         Collection<BibEntry> c = result.getDatabase().getEntries();
         Assert.assertEquals(1, c.size());
@@ -774,10 +775,9 @@ public void assertEqualsBibtexEntry(BibEntry expected, BibEntry actual) {
     @Test
     public void testXMPreadString() throws Exception {
 
-        ParserResult result = BibtexParser
+        ParserResult result = parser
                 .parse(new StringReader("@article{canh05," + "  author = {Crowston, K. and Annabi, H.},\n"
-                        + "  title = {Title A}}\n" + "@inProceedings{foo," + "  author={Norton Bar}}"),
-                        importFormatPreferences, fileMonitor);
+                        + "  title = {Title A}}\n" + "@inProceedings{foo," + "  author={Norton Bar}}"));
 
         Collection<BibEntry> c = result.getDatabase().getEntries();
         Assert.assertEquals(2, c.size());
@@ -1045,13 +1045,12 @@ public void testWriteSingleUpdatesDCAndInfo() throws IOException, TransformerExc
     @Test
     public void testReadRawXMP() throws IOException, TransformerException {
 
-        ParserResult result = BibtexParser.parse(new StringReader(
+        ParserResult result = parser.parse(new StringReader(
                 "@article{canh05," + "  author = {Crowston, K. and Annabi, H. and Howison, J. and Masango, C.},\n"
                         + "  title = {Effective work practices for floss development: A model and propositions},\n"
                         + "  booktitle = {Hawaii International Conference On System Sciences (HICSS)},\n"
                         + "  year = {2005},\n" + "  owner = {oezbek},\n" + "  timestamp = {2006.05.29},\n"
-                        + "  url = {http://james.howison.name/publications.html}}"),
-                importFormatPreferences, fileMonitor);
+                        + "  url = {http://james.howison.name/publications.html}}"));
 
         Collection<BibEntry> c = result.getDatabase().getEntries();
         Assert.assertEquals(1, c.size());
@@ -1285,15 +1284,14 @@ public void testCommandLineSeveral() throws IOException, TransformerException {
      */
     @Test
     public void testResolveStrings() throws IOException, TransformerException {
-        ParserResult original = BibtexParser
+        ParserResult original = parser
                 .parse(new StringReader("@string{ crow = \"Crowston, K.\"}\n" + "@string{ anna = \"Annabi, H.\"}\n"
                         + "@string{ howi = \"Howison, J.\"}\n" + "@string{ masa = \"Masango, C.\"}\n"
                         + "@article{canh05," + "  author = {#crow# and #anna# and #howi# and #masa#}," + "\n"
                         + "  title = {Effective work practices for floss development: A model and propositions}," + "\n"
                         + "  booktitle = {Hawaii International Conference On System Sciences (HICSS)}," + "\n"
                         + "  year = {2005}," + "\n" + "  owner = {oezbek}," + "\n" + "  timestamp = {2006.05.29},"
-                        + "\n" + "  url = {http://james.howison.name/publications.html}" + "\n" + "}"),
-                        importFormatPreferences, fileMonitor);
+                        + "\n" + "  url = {http://james.howison.name/publications.html}" + "\n" + "}"));
 
         Collection<BibEntry> c = original.getDatabase().getEntries();
         Assert.assertEquals(1, c.size());

From 250d8e65bb4f9c88196657c6c65200be210171a0 Mon Sep 17 00:00:00 2001
From: Naitoreivun <dominik646@gmail.com>
Date: Mon, 5 Feb 2018 00:53:22 +0100
Subject: [PATCH 24/47] differentiate inbooks with the same author and title,
 but different chapter

---
 .../jabref/logic/bibtex/DuplicateCheck.java   | 11 ++++++++
 .../logic/bibtex/DuplicateCheckTest.java      | 27 +++++++++++++++++++
 2 files changed, 38 insertions(+)

diff --git a/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java b/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java
index 617ab01cf2e..3b673cf9a7a 100644
--- a/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java
+++ b/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java
@@ -78,6 +78,10 @@ public static boolean isDuplicate(BibEntry one, BibEntry two, BibDatabaseMode bi
             return false;
         }
 
+        if (haveDifferentChaptersOfTheSameBook(one, two)) {
+            return false;
+        }
+
         EntryType type = EntryTypes.getTypeOrDefault(one.getType(), bibDatabaseMode);
         // The check if they have the same required fields:
         Collection<String> var = type.getRequiredFieldsFlat();
@@ -120,6 +124,13 @@ private static boolean haveSameIdentifier(BibEntry one, BibEntry two) {
         return false;
     }
 
+    private static boolean haveDifferentChaptersOfTheSameBook(final BibEntry one, final BibEntry two) {
+        return compareSingleField(FieldName.AUTHOR, one, two) == EQUAL &&
+                compareSingleField(FieldName.TITLE, one, two) == EQUAL &&
+                compareSingleField(FieldName.CHAPTER, one, two) == NOT_EQUAL;
+
+    }
+
     private static double[] compareFieldSet(Collection<String> fields, BibEntry one, BibEntry two) {
         double res = 0;
         double totWeights = 0.;
diff --git a/src/test/java/org/jabref/logic/bibtex/DuplicateCheckTest.java b/src/test/java/org/jabref/logic/bibtex/DuplicateCheckTest.java
index ab802782ddf..aed2c1f63c8 100644
--- a/src/test/java/org/jabref/logic/bibtex/DuplicateCheckTest.java
+++ b/src/test/java/org/jabref/logic/bibtex/DuplicateCheckTest.java
@@ -142,6 +142,33 @@ public void twoEntriesWithSameDoiButDifferentTypesAreDuplicates() {
         assertTrue(DuplicateCheck.isDuplicate(simpleArticle, duplicateWithDifferentType, BibDatabaseMode.BIBTEX));
     }
 
+    @Test
+    public void twoInbooksWithDifferentChaptersAreNotDuplicates() {
+        final String title = "Alice in Wonderland";
+        final String author = "Charles Lutwidge Dodgson";
+        final String language = "English";
+        final String publisher = "Macmillan";
+        final String year = "1865";
+
+        final BibEntry editionOne = new BibEntry(BibtexEntryTypes.INBOOK.getName());
+        editionOne.setField(FieldName.TITLE, title);
+        editionOne.setField(FieldName.AUTHOR, author);
+        editionOne.setField(FieldName.CHAPTER, "Chapter One – Down the Rabbit Hole");
+        editionOne.setField(FieldName.LANGUAGE, language);
+        editionOne.setField(FieldName.PUBLISHER, publisher);
+        editionOne.setField(FieldName.YEAR, year);
+
+        BibEntry editionTwo = new BibEntry(BibtexEntryTypes.INBOOK.getName());
+        editionTwo.setField(FieldName.TITLE, title);
+        editionTwo.setField(FieldName.AUTHOR, author);
+        editionTwo.setField(FieldName.CHAPTER, "Chapter Two – The Pool of Tears");
+        editionTwo.setField(FieldName.LANGUAGE, language);
+        editionTwo.setField(FieldName.PUBLISHER, publisher);
+        editionTwo.setField(FieldName.YEAR, year);
+
+        assertFalse(DuplicateCheck.isDuplicate(editionOne, editionTwo, BibDatabaseMode.BIBTEX));
+    }
+
     @Test
     public void twoBooksWithDifferentEditionsAreNotDuplicates() {
         BibEntry editionOne = new BibEntry(BibtexEntryTypes.BOOK.getName());

From a1626ed5e45095b4b89cd4a238391c32de853c40 Mon Sep 17 00:00:00 2001
From: Naitoreivun <dominik646@gmail.com>
Date: Tue, 6 Feb 2018 00:06:12 +0100
Subject: [PATCH 25/47] code review fixes - consider pages of the same book
 separately in duplications detection process; add more tests

---
 .../jabref/logic/bibtex/DuplicateCheck.java   | 11 ++-
 .../logic/bibtex/DuplicateCheckTest.java      | 77 +++++++++++++------
 2 files changed, 63 insertions(+), 25 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java b/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java
index 3b673cf9a7a..78c7699a2b9 100644
--- a/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java
+++ b/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java
@@ -78,7 +78,7 @@ public static boolean isDuplicate(BibEntry one, BibEntry two, BibDatabaseMode bi
             return false;
         }
 
-        if (haveDifferentChaptersOfTheSameBook(one, two)) {
+        if (haveDifferentChaptersOrPagesOfTheSameBook(one, two)) {
             return false;
         }
 
@@ -124,10 +124,11 @@ private static boolean haveSameIdentifier(BibEntry one, BibEntry two) {
         return false;
     }
 
-    private static boolean haveDifferentChaptersOfTheSameBook(final BibEntry one, final BibEntry two) {
+    private static boolean haveDifferentChaptersOrPagesOfTheSameBook(final BibEntry one, final BibEntry two) {
         return compareSingleField(FieldName.AUTHOR, one, two) == EQUAL &&
                 compareSingleField(FieldName.TITLE, one, two) == EQUAL &&
-                compareSingleField(FieldName.CHAPTER, one, two) == NOT_EQUAL;
+                (compareSingleField(FieldName.CHAPTER, one, two) == NOT_EQUAL ||
+                        compareSingleField(FieldName.PAGES, one, two) == NOT_EQUAL);
 
     }
 
@@ -201,6 +202,10 @@ private static int compareSingleField(String field, BibEntry one, BibEntry two)
         } else {
             stringOne = stringOne.toLowerCase(Locale.ROOT);
             stringTwo = stringTwo.toLowerCase(Locale.ROOT);
+            if (FieldName.CHAPTER.equals(field)) {
+                stringOne = stringOne.replaceAll("chapter", "").trim();
+                stringTwo = stringTwo.replaceAll("chapter", "").trim();
+            }
             double similarity = DuplicateCheck.correlateByWords(stringOne, stringTwo);
             if (similarity > 0.8) {
                 return EQUAL;
diff --git a/src/test/java/org/jabref/logic/bibtex/DuplicateCheckTest.java b/src/test/java/org/jabref/logic/bibtex/DuplicateCheckTest.java
index aed2c1f63c8..c0a54568f82 100644
--- a/src/test/java/org/jabref/logic/bibtex/DuplicateCheckTest.java
+++ b/src/test/java/org/jabref/logic/bibtex/DuplicateCheckTest.java
@@ -16,6 +16,8 @@ public class DuplicateCheckTest {
 
     private BibEntry simpleArticle;
     private BibEntry unrelatedArticle;
+    private BibEntry simpleInbook;
+    private BibEntry simpleIncollection;
 
     @Before
     public void setUp() {
@@ -27,6 +29,19 @@ public void setUp() {
                 .withField(FieldName.AUTHOR, "Completely Different")
                 .withField(FieldName.TITLE, "Holy Moly Uffdada und Trallalla")
                 .withField(FieldName.YEAR, "1992");
+        simpleInbook = new BibEntry(BibtexEntryTypes.INBOOK.getName())
+                .withField(FieldName.TITLE, "Alice in Wonderland")
+                .withField(FieldName.AUTHOR, "Charles Lutwidge Dodgson")
+                .withField(FieldName.CHAPTER, "Chapter One – Down the Rabbit Hole")
+                .withField(FieldName.LANGUAGE, "English")
+                .withField(FieldName.PUBLISHER, "Macmillan")
+                .withField(FieldName.YEAR, "1865");
+        simpleIncollection = new BibEntry(BibtexEntryTypes.INCOLLECTION.getName())
+                .withField(FieldName.TITLE, "Innovation and Intellectual Property Rights")
+                .withField(FieldName.AUTHOR, "Ove Grandstrand")
+                .withField(FieldName.BOOKTITLE, "The Oxford Handbook of Innovation")
+                .withField(FieldName.PUBLISHER, "Oxford University Press")
+                .withField(FieldName.YEAR, "2004");
     }
 
     @Test
@@ -144,29 +159,47 @@ public void twoEntriesWithSameDoiButDifferentTypesAreDuplicates() {
 
     @Test
     public void twoInbooksWithDifferentChaptersAreNotDuplicates() {
-        final String title = "Alice in Wonderland";
-        final String author = "Charles Lutwidge Dodgson";
-        final String language = "English";
-        final String publisher = "Macmillan";
-        final String year = "1865";
-
-        final BibEntry editionOne = new BibEntry(BibtexEntryTypes.INBOOK.getName());
-        editionOne.setField(FieldName.TITLE, title);
-        editionOne.setField(FieldName.AUTHOR, author);
-        editionOne.setField(FieldName.CHAPTER, "Chapter One – Down the Rabbit Hole");
-        editionOne.setField(FieldName.LANGUAGE, language);
-        editionOne.setField(FieldName.PUBLISHER, publisher);
-        editionOne.setField(FieldName.YEAR, year);
-
-        BibEntry editionTwo = new BibEntry(BibtexEntryTypes.INBOOK.getName());
-        editionTwo.setField(FieldName.TITLE, title);
-        editionTwo.setField(FieldName.AUTHOR, author);
-        editionTwo.setField(FieldName.CHAPTER, "Chapter Two – The Pool of Tears");
-        editionTwo.setField(FieldName.LANGUAGE, language);
-        editionTwo.setField(FieldName.PUBLISHER, publisher);
-        editionTwo.setField(FieldName.YEAR, year);
+        twoEntriesWithDifferentSpecificFieldsAreNotDuplicates(simpleInbook, FieldName.CHAPTER,
+                "Chapter One – Down the Rabbit Hole",
+                "Chapter Two – The Pool of Tears");
+    }
 
-        assertFalse(DuplicateCheck.isDuplicate(editionOne, editionTwo, BibDatabaseMode.BIBTEX));
+    @Test
+    public void twoInbooksWithDifferentPagesAreNotDuplicates() {
+        twoEntriesWithDifferentSpecificFieldsAreNotDuplicates(simpleInbook, FieldName.PAGES, "1-20", "21-40");
+    }
+
+    @Test
+    public void twoIncollectionsWithDifferentChaptersAreNotDuplicates() {
+        twoEntriesWithDifferentSpecificFieldsAreNotDuplicates(simpleIncollection, FieldName.CHAPTER, "10", "9");
+    }
+
+    @Test
+    public void twoIncollectionsWithDifferentPagesAreNotDuplicates() {
+        twoEntriesWithDifferentSpecificFieldsAreNotDuplicates(simpleIncollection, FieldName.PAGES, "1-20", "21-40");
+    }
+
+    private void twoEntriesWithDifferentSpecificFieldsAreNotDuplicates(final BibEntry cloneable,
+                                                                       final String fieldType,
+                                                                       final String firstValue,
+                                                                       final String secondValue) {
+        final BibEntry entry1 = (BibEntry) cloneable.clone();
+        entry1.setField(fieldType, firstValue);
+
+        final BibEntry entry2 = (BibEntry) cloneable.clone();
+        entry2.setField(fieldType, secondValue);
+
+        assertFalse(DuplicateCheck.isDuplicate(entry1, entry2, BibDatabaseMode.BIBTEX));
+    }
+
+    @Test
+    public void inbookWithoutChapterCouldBeDuplicateOfInbookWithChapter() {
+        final BibEntry inbook1 = (BibEntry) simpleInbook.clone();
+        final BibEntry inbook2 = (BibEntry) simpleInbook.clone();
+        inbook2.setField(FieldName.CHAPTER, "");
+
+        assertTrue(DuplicateCheck.isDuplicate(inbook1, inbook2, BibDatabaseMode.BIBTEX));
+        assertTrue(DuplicateCheck.isDuplicate(inbook2, inbook1, BibDatabaseMode.BIBTEX));
     }
 
     @Test

From 5eda399f5d6be86ef7ee28e3e9e616e2c1cae550 Mon Sep 17 00:00:00 2001
From: Naitoreivun <dominik646@gmail.com>
Date: Tue, 6 Feb 2018 01:14:30 +0100
Subject: [PATCH 26/47] cleanup and refactoring in DuplicateCheck class

---
 .../jabref/logic/bibtex/DuplicateCheck.java   | 285 ++++++++++--------
 1 file changed, 166 insertions(+), 119 deletions(-)

diff --git a/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java b/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java
index 78c7699a2b9..01b54ce0103 100644
--- a/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java
+++ b/src/main/java/org/jabref/logic/bibtex/DuplicateCheck.java
@@ -22,6 +22,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import static org.jabref.model.entry.FieldName.AUTHOR;
+import static org.jabref.model.entry.FieldName.CHAPTER;
+import static org.jabref.model.entry.FieldName.EDITION;
+import static org.jabref.model.entry.FieldName.EDITOR;
+import static org.jabref.model.entry.FieldName.JOURNAL;
+import static org.jabref.model.entry.FieldName.PAGES;
+import static org.jabref.model.entry.FieldName.TITLE;
+
 /**
  * This class contains utility method for duplicate checking of entries.
  */
@@ -48,10 +56,10 @@ public class DuplicateCheck {
     private static final Map<String, Double> FIELD_WEIGHTS = new HashMap<>();
 
     static {
-        DuplicateCheck.FIELD_WEIGHTS.put(FieldName.AUTHOR, 2.5);
-        DuplicateCheck.FIELD_WEIGHTS.put(FieldName.EDITOR, 2.5);
-        DuplicateCheck.FIELD_WEIGHTS.put(FieldName.TITLE, 3.);
-        DuplicateCheck.FIELD_WEIGHTS.put(FieldName.JOURNAL, 2.);
+        DuplicateCheck.FIELD_WEIGHTS.put(AUTHOR, 2.5);
+        DuplicateCheck.FIELD_WEIGHTS.put(EDITOR, 2.5);
+        DuplicateCheck.FIELD_WEIGHTS.put(TITLE, 3.);
+        DuplicateCheck.FIELD_WEIGHTS.put(JOURNAL, 2.);
     }
 
     private DuplicateCheck() {
@@ -64,80 +72,89 @@ private DuplicateCheck() {
      * @param two BibEntry
      * @return boolean
      */
-    public static boolean isDuplicate(BibEntry one, BibEntry two, BibDatabaseMode bibDatabaseMode) {
+    public static boolean isDuplicate(final BibEntry one, final BibEntry two, final BibDatabaseMode bibDatabaseMode) {
         if (haveSameIdentifier(one, two)) {
             return true;
         }
 
-        // same entry type
-        if (!one.getType().equals(two.getType())) {
+        if (haveDifferentEntryType(one, two) ||
+                haveDifferentEditions(one, two) ||
+                haveDifferentChaptersOrPagesOfTheSameBook(one, two)) {
             return false;
         }
 
-        if (haveDifferentEditions(one, two)) {
-            return false;
-        }
+        final EntryType type = EntryTypes.getTypeOrDefault(one.getType(), bibDatabaseMode);
+        final double[] reqCmpResult = compareRequiredFields(type, one, two);
 
-        if (haveDifferentChaptersOrPagesOfTheSameBook(one, two)) {
-            return false;
-        }
-
-        EntryType type = EntryTypes.getTypeOrDefault(one.getType(), bibDatabaseMode);
-        // The check if they have the same required fields:
-        Collection<String> var = type.getRequiredFieldsFlat();
-        double[] req;
-        if (var == null) {
-            req = new double[]{0., 0.};
-        } else {
-            req = DuplicateCheck.compareFieldSet(var, one, two);
+        if (isFarFromThreshold(reqCmpResult[0])) {
+            // Far from the threshold value, so we base our decision on the required fields only
+            return reqCmpResult[0] >= DuplicateCheck.DUPLICATE_THRESHOLD;
         }
 
-        if (Math.abs(req[0] - DuplicateCheck.DUPLICATE_THRESHOLD) > DuplicateCheck.DOUBT_RANGE) {
-            // Far from the threshold value, so we base our decision on the req. fields only
-            return req[0] >= DuplicateCheck.DUPLICATE_THRESHOLD;
-        }
         // Close to the threshold value, so we take a look at the optional fields, if any:
-        Collection<String> optionalFields = type.getOptionalFields();
-        if (optionalFields != null) {
-            double[] opt = DuplicateCheck.compareFieldSet(optionalFields, one, two);
-            double totValue = ((DuplicateCheck.REQUIRED_WEIGHT * req[0] * req[1]) + (opt[0] * opt[1])) / ((req[1] * DuplicateCheck.REQUIRED_WEIGHT) + opt[1]);
-            return totValue >= DuplicateCheck.DUPLICATE_THRESHOLD;
-        }
-        return req[0] >= DuplicateCheck.DUPLICATE_THRESHOLD;
+        return compareOptionalFields(type, one, two, reqCmpResult);
     }
 
-    private static boolean haveDifferentEditions(BibEntry one, BibEntry two) {
-        if (one.getField(FieldName.EDITION).isPresent() && two.getField(FieldName.EDITION).isPresent()) {
-            if (!one.getField(FieldName.EDITION).get().equals(two.getField(FieldName.EDITION).get())) {
+    private static boolean haveSameIdentifier(final BibEntry one, final BibEntry two) {
+        for (final String name : FieldName.getIdentifierFieldNames()) {
+            if (one.getField(name).isPresent() && one.getField(name).equals(two.getField(name))) {
                 return true;
             }
         }
         return false;
     }
 
-    private static boolean haveSameIdentifier(BibEntry one, BibEntry two) {
-        for (String name : FieldName.getIdentifierFieldNames()) {
-            if (one.getField(name).isPresent() && one.getField(name).equals(two.getField(name))) {
-                return true;
-            }
-        }
-        return false;
+    private static boolean haveDifferentEntryType(final BibEntry one, final BibEntry two) {
+        return !one.getType().equals(two.getType());
+    }
+
+    private static boolean haveDifferentEditions(final BibEntry one, final BibEntry two) {
+        final Optional<String> editionOne = one.getField(EDITION);
+        final Optional<String> editionTwo = two.getField(EDITION);
+        return editionOne.isPresent() &&
+                editionTwo.isPresent() &&
+                !editionOne.get().equals(editionTwo.get());
     }
 
     private static boolean haveDifferentChaptersOrPagesOfTheSameBook(final BibEntry one, final BibEntry two) {
-        return compareSingleField(FieldName.AUTHOR, one, two) == EQUAL &&
-                compareSingleField(FieldName.TITLE, one, two) == EQUAL &&
-                (compareSingleField(FieldName.CHAPTER, one, two) == NOT_EQUAL ||
-                        compareSingleField(FieldName.PAGES, one, two) == NOT_EQUAL);
+        return compareSingleField(AUTHOR, one, two) == EQUAL &&
+                compareSingleField(TITLE, one, two) == EQUAL &&
+                (compareSingleField(CHAPTER, one, two) == NOT_EQUAL ||
+                        compareSingleField(PAGES, one, two) == NOT_EQUAL);
+
+    }
+
+    private static double[] compareRequiredFields(final EntryType type, final BibEntry one, final BibEntry two) {
+        final Collection<String> requiredFields = type.getRequiredFieldsFlat();
+        return requiredFields == null
+                ? new double[]{0., 0.}
+                : DuplicateCheck.compareFieldSet(requiredFields, one, two);
+    }
 
+    private static boolean isFarFromThreshold(double value) {
+        return Math.abs(value - DuplicateCheck.DUPLICATE_THRESHOLD) > DuplicateCheck.DOUBT_RANGE;
     }
 
-    private static double[] compareFieldSet(Collection<String> fields, BibEntry one, BibEntry two) {
+    private static boolean compareOptionalFields(final EntryType type,
+                                                 final BibEntry one,
+                                                 final BibEntry two,
+                                                 final double[] req) {
+        final Collection<String> optionalFields = type.getOptionalFields();
+        if (optionalFields == null) {
+            return req[0] >= DuplicateCheck.DUPLICATE_THRESHOLD;
+        }
+        final double[] opt = DuplicateCheck.compareFieldSet(optionalFields, one, two);
+        final double numerator = (DuplicateCheck.REQUIRED_WEIGHT * req[0] * req[1]) + (opt[0] * opt[1]);
+        final double denominator = (req[1] * DuplicateCheck.REQUIRED_WEIGHT) + opt[1];
+        final double totValue = numerator / denominator;
+        return totValue >= DuplicateCheck.DUPLICATE_THRESHOLD;
+    }
+
+    private static double[] compareFieldSet(final Collection<String> fields, final BibEntry one, final BibEntry two) {
         double res = 0;
         double totWeights = 0.;
-        for (String field : fields) {
-            double weight;
-            weight = DuplicateCheck.FIELD_WEIGHTS.getOrDefault(field, 1.0);
+        for (final String field : fields) {
+            final double weight = DuplicateCheck.FIELD_WEIGHTS.getOrDefault(field, 1.0);
             totWeights += weight;
             int result = DuplicateCheck.compareSingleField(field, one, two);
             if (result == EQUAL) {
@@ -152,9 +169,9 @@ private static double[] compareFieldSet(Collection<String> fields, BibEntry one,
         return new double[]{0.5, 0.0};
     }
 
-    private static int compareSingleField(String field, BibEntry one, BibEntry two) {
-        Optional<String> optionalStringOne = one.getField(field);
-        Optional<String> optionalStringTwo = two.getField(field);
+    private static int compareSingleField(final String field, final BibEntry one, final BibEntry two) {
+        final Optional<String> optionalStringOne = one.getField(field);
+        final Optional<String> optionalStringTwo = two.getField(field);
         if (!optionalStringOne.isPresent()) {
             if (!optionalStringTwo.isPresent()) {
                 return EMPTY_IN_BOTH;
@@ -165,72 +182,96 @@ private static int compareSingleField(String field, BibEntry one, BibEntry two)
         }
 
         // Both strings present
-        String stringOne = optionalStringOne.get();
-        String stringTwo = optionalStringTwo.get();
+        final String stringOne = optionalStringOne.get();
+        final String stringTwo = optionalStringTwo.get();
 
         if (InternalBibtexFields.getFieldProperties(field).contains(FieldProperty.PERSON_NAMES)) {
-            // Specific for name fields.
-            // Harmonise case:
-            String authorOne = AuthorList.fixAuthorLastNameOnlyCommas(stringOne, false).replace(" and ", " ").toLowerCase(Locale.ROOT);
-            String authorTwo = AuthorList.fixAuthorLastNameOnlyCommas(stringTwo, false).replace(" and ", " ").toLowerCase(Locale.ROOT);
-            double similarity = DuplicateCheck.correlateByWords(authorOne, authorTwo);
-            if (similarity > 0.8) {
-                return EQUAL;
-            }
-            return NOT_EQUAL;
-        } else if (FieldName.PAGES.equals(field)) {
-            // Pages can be given with a variety of delimiters, "-", "--", " - ", " -- ".
-            // We do a replace to harmonize these to a simple "-":
-            // After this, a simple test for equality should be enough:
-            stringOne = stringOne.replaceAll("[- ]+", "-");
-            stringTwo = stringTwo.replaceAll("[- ]+", "-");
-            if (stringOne.equals(stringTwo)) {
-                return EQUAL;
-            }
-            return NOT_EQUAL;
-        } else if (FieldName.JOURNAL.equals(field)) {
-            // We do not attempt to harmonize abbreviation state of the journal names,
-            // but we remove periods from the names in case they are abbreviated with
-            // and without dots:
-            stringOne = stringOne.replace(".", "").toLowerCase(Locale.ROOT);
-            stringTwo = stringTwo.replace(".", "").toLowerCase(Locale.ROOT);
-            double similarity = DuplicateCheck.correlateByWords(stringOne, stringTwo);
-            if (similarity > 0.8) {
-                return EQUAL;
-            }
-            return NOT_EQUAL;
-        } else {
-            stringOne = stringOne.toLowerCase(Locale.ROOT);
-            stringTwo = stringTwo.toLowerCase(Locale.ROOT);
-            if (FieldName.CHAPTER.equals(field)) {
-                stringOne = stringOne.replaceAll("chapter", "").trim();
-                stringTwo = stringTwo.replaceAll("chapter", "").trim();
-            }
-            double similarity = DuplicateCheck.correlateByWords(stringOne, stringTwo);
-            if (similarity > 0.8) {
-                return EQUAL;
-            }
-            return NOT_EQUAL;
+            return compareAuthorField(stringOne, stringTwo);
+
+        } else if (PAGES.equals(field)) {
+            return comparePagesField(stringOne, stringTwo);
+
+        } else if (JOURNAL.equals(field)) {
+            return compareJournalField(stringOne, stringTwo);
+
+        } else if (CHAPTER.equals(field)) {
+            return compareChapterField(stringOne, stringTwo);
+        }
+
+        return compareField(stringOne, stringTwo);
+    }
+
+    private static int compareAuthorField(final String stringOne, final String stringTwo) {
+        // Specific for name fields.
+        // Harmonise case:
+        final String authorOne = AuthorList.fixAuthorLastNameOnlyCommas(stringOne, false).replace(" and ", " ").toLowerCase(Locale.ROOT);
+        final String authorTwo = AuthorList.fixAuthorLastNameOnlyCommas(stringTwo, false).replace(" and ", " ").toLowerCase(Locale.ROOT);
+        final double similarity = DuplicateCheck.correlateByWords(authorOne, authorTwo);
+        if (similarity > 0.8) {
+            return EQUAL;
+        }
+        return NOT_EQUAL;
+    }
+
+    /**
+     * Pages can be given with a variety of delimiters, "-", "--", " - ", " -- ".
+     * We do a replace to harmonize these to a simple "-"
+     * After this, a simple test for equality should be enough
+     */
+    private static int comparePagesField(final String stringOne, final String stringTwo) {
+        final String processedStringOne = stringOne.replaceAll("[- ]+", "-");
+        final String processedStringTwo = stringTwo.replaceAll("[- ]+", "-");
+        if (processedStringOne.equals(processedStringTwo)) {
+            return EQUAL;
+        }
+        return NOT_EQUAL;
+    }
+
+    /**
+     * We do not attempt to harmonize abbreviation state of the journal names,
+     * but we remove periods from the names in case they are abbreviated with and without dots:
+     */
+    private static int compareJournalField(final String stringOne, final String stringTwo) {
+        final String processedStringOne = stringOne.replace(".", "").toLowerCase(Locale.ROOT);
+        final String processedStringTwo = stringTwo.replace(".", "").toLowerCase(Locale.ROOT);
+        final double similarity = DuplicateCheck.correlateByWords(processedStringOne, processedStringTwo);
+        if (similarity > 0.8) {
+            return EQUAL;
         }
+        return NOT_EQUAL;
+    }
+
+    private static int compareChapterField(final String stringOne, final String stringTwo) {
+        final String processedStringOne = stringOne.replaceAll("(?i)chapter", "").trim();
+        final String processedStringTwo = stringTwo.replaceAll("(?i)chapter", "").trim();
+        return compareField(processedStringOne, processedStringTwo);
+    }
+
+    private static int compareField(final String stringOne, final String stringTwo) {
+        final String processedStringOne = stringOne.toLowerCase(Locale.ROOT).trim();
+        final String processedStringTwo = stringTwo.toLowerCase(Locale.ROOT).trim();
+        final double similarity = DuplicateCheck.correlateByWords(processedStringOne, processedStringTwo);
+        if (similarity > 0.8) {
+            return EQUAL;
+        }
+        return NOT_EQUAL;
     }
 
     public static double compareEntriesStrictly(BibEntry one, BibEntry two) {
-        Set<String> allFields = new HashSet<>();
+        final Set<String> allFields = new HashSet<>();
         allFields.addAll(one.getFieldNames());
         allFields.addAll(two.getFieldNames());
 
         int score = 0;
-        for (String field : allFields) {
-            Optional<String> stringOne = one.getField(field);
-            Optional<String> stringTwo = two.getField(field);
+        for (final String field : allFields) {
+            final Optional<String> stringOne = one.getField(field);
+            final Optional<String> stringTwo = two.getField(field);
             if (stringOne.equals(stringTwo)) {
                 score++;
             }
         }
         if (score == allFields.size()) {
-            return 1.01; // Just to make sure we can
-            // use score>1 without
-            // trouble.
+            return 1.01; // Just to make sure we can use score > 1 without trouble.
         }
         return (double) score / allFields.size();
     }
@@ -245,8 +286,10 @@ public static double compareEntriesStrictly(BibEntry one, BibEntry two) {
      * @param entry    The entry of which we are looking for duplicates.
      * @return The first duplicate entry found. Empty Optional if no duplicates are found.
      */
-    public static Optional<BibEntry> containsDuplicate(BibDatabase database, BibEntry entry, BibDatabaseMode bibDatabaseMode) {
-        for (BibEntry other : database.getEntries()) {
+    public static Optional<BibEntry> containsDuplicate(final BibDatabase database,
+                                                       final BibEntry entry,
+                                                       final BibDatabaseMode bibDatabaseMode) {
+        for (final BibEntry other : database.getEntries()) {
             if (DuplicateCheck.isDuplicate(entry, other, bibDatabaseMode)) {
                 return Optional.of(other); // Duplicate found.
             }
@@ -261,10 +304,10 @@ public static Optional<BibEntry> containsDuplicate(BibDatabase database, BibEntr
      * @param s2 The second string
      * @return a value in the interval [0, 1] indicating the degree of match.
      */
-    public static double correlateByWords(String s1, String s2) {
-        String[] w1 = s1.split("\\s");
-        String[] w2 = s2.split("\\s");
-        int n = Math.min(w1.length, w2.length);
+    public static double correlateByWords(final String s1, final String s2) {
+        final String[] w1 = s1.split("\\s");
+        final String[] w2 = s2.split("\\s");
+        final int n = Math.min(w1.length, w2.length);
         int misses = 0;
         for (int i = 0; i < n; i++) {
             double corr = similarity(w1[i], w2[i]);
@@ -272,7 +315,7 @@ public static double correlateByWords(String s1, String s2) {
                 misses++;
             }
         }
-        double missRate = (double) misses / (double) n;
+        final double missRate = (double) misses / (double) n;
         return 1 - missRate;
     }
 
@@ -281,22 +324,26 @@ public static double correlateByWords(String s1, String s2) {
      * Calculates the similarity (a number within 0 and 1) between two strings.
      * http://stackoverflow.com/questions/955110/similarity-string-comparison-in-java
      */
-    private static double similarity(String first, String second) {
-        String longer = first;
-        String shorter = second;
+    private static double similarity(final String first, final String second) {
+        final String longer;
+        final String shorter;
 
         if (first.length() < second.length()) {
             longer = second;
             shorter = first;
+        } else {
+            longer = first;
+            shorter = second;
         }
 
-        int longerLength = longer.length();
+        final int longerLength = longer.length();
         // both strings are zero length
         if (longerLength == 0) {
             return 1.0;
         }
-        double sim = (longerLength - new StringSimilarity().editDistanceIgnoreCase(longer, shorter)) / (double) longerLength;
-        LOGGER.debug("Longer string: " + longer + " Shorter string: " + shorter + " Similarity: " + sim);
-        return sim;
+        final double distanceIgnoredCase = new StringSimilarity().editDistanceIgnoreCase(longer, shorter);
+        final double similarity = (longerLength - distanceIgnoredCase) / (double) longerLength;
+        LOGGER.debug("Longer string: " + longer + " Shorter string: " + shorter + " Similarity: " + similarity);
+        return similarity;
     }
 }

From 0de617911a05d7b3af124078b38d65070c29fa8e Mon Sep 17 00:00:00 2001
From: Stefan Kolb <stefan-kolb@users.noreply.github.com>
Date: Tue, 6 Feb 2018 11:40:39 +0100
Subject: [PATCH 27/47] Update build.gradle

---
 build.gradle | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/build.gradle b/build.gradle
index 788c8e1ccc7..2f55c303e34 100644
--- a/build.gradle
+++ b/build.gradle
@@ -178,6 +178,7 @@ dependencies {
 jacoco {
     toolVersion = '0.8.0'
 }
+
 dependencyUpdates {
     outputFormatter = "json"
 }
@@ -232,12 +233,12 @@ dependencyUpdates.resolutionStrategy = {
         }
         withModule("org.jacoco.agent") { ComponentSelection selection ->
             if (selection.candidate.version.equals("0.8.0")) {
-                selection.reject("As a native plugin we cannot control the actual version of jacoco. This depenency should be hidden.")
+                selection.reject("As a native plugin we cannot control the actual version of jacoco. This dependency should be hidden.")
             }
         }
         withModule("org.jacoco.ant") { ComponentSelection selection ->
             if (selection.candidate.version.equals("0.8.0")) {
-                selection.reject("As a native plugin we cannot control the actual version of jacoco. This depenency should be hidden.")
+                selection.reject("As a native plugin we cannot control the actual version of jacoco. This dependency should be hidden.")
             }
         }
     }

From ca503a3c4dcd9707f652d36a8b82ded98efa8a17 Mon Sep 17 00:00:00 2001
From: Stefan Kolb <stefan-kolb@users.noreply.github.com>
Date: Tue, 6 Feb 2018 11:41:12 +0100
Subject: [PATCH 28/47] Update build.gradle

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

diff --git a/build.gradle b/build.gradle
index 2f55c303e34..14dfff9886d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -377,7 +377,6 @@ task copyTestResources(type: Copy) {
 }
 processTestResources.dependsOn copyTestResources
 
-
 tasks.withType(Test) {
     reports.html.destination = file("${reporting.baseDir}/${name}")
 

From 834e6fa614ef6ed96da242851734cfb4febc319f Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Sun, 21 Jan 2018 21:22:46 +0100
Subject: [PATCH 29/47] Better code style for chained methods

---
 config/IntelliJ Code Style.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/config/IntelliJ Code Style.xml b/config/IntelliJ Code Style.xml
index 6be214756e6..489f44c1a5c 100644
--- a/config/IntelliJ Code Style.xml	
+++ b/config/IntelliJ Code Style.xml	
@@ -31,6 +31,7 @@
     <option name="KEEP_BLANK_LINES_IN_DECLARATIONS" value="1" />
     <option name="KEEP_BLANK_LINES_IN_CODE" value="1" />
     <option name="KEEP_BLANK_LINES_BEFORE_RBRACE" value="0" />
+    <option name="ALIGN_MULTILINE_CHAINED_METHODS" value="true" />
     <arrangement>
       <rules>
         <section>

From 2f9328da184c1d14020c3ae62bd1c39911752f54 Mon Sep 17 00:00:00 2001
From: Stefan Kolb <stefan-kolb@web.de>
Date: Tue, 6 Feb 2018 12:29:57 +0100
Subject: [PATCH 30/47] Eclipse Django style #3655

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

diff --git a/eclipse.gradle b/eclipse.gradle
index 771789957fb..e4ab6fbc1ae 100644
--- a/eclipse.gradle
+++ b/eclipse.gradle
@@ -154,7 +154,7 @@ tasks.eclipse.doFirst {
         org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16
         org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16
         org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=88
-        org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=16
+        org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=80
         org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=16
         org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=0
         org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16

From 7a52d3ee4ef89f3c6aa262f84ad7d093067299b9 Mon Sep 17 00:00:00 2001
From: Stefan Kolb <stefan-kolb@web.de>
Date: Tue, 6 Feb 2018 12:54:41 +0100
Subject: [PATCH 31/47] Adapt log4j configuration for cleaner junit tests #3511

---
 .../org/jabref/logic/remote/client/RemoteListenerClient.java  | 4 ++--
 src/test/resources/log4j2.xml                                 | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/java/org/jabref/logic/remote/client/RemoteListenerClient.java b/src/main/java/org/jabref/logic/remote/client/RemoteListenerClient.java
index ab319ffcaf0..ce2b24998f3 100644
--- a/src/main/java/org/jabref/logic/remote/client/RemoteListenerClient.java
+++ b/src/main/java/org/jabref/logic/remote/client/RemoteListenerClient.java
@@ -35,8 +35,8 @@ public static boolean sendToActiveJabRefInstance(String[] args, int remoteServer
 
                 if (!Protocol.IDENTIFIER.equals(identifier)) {
                     String port = String.valueOf(remoteServerPort);
-                    String error = Localization.lang("Cannot use port %0 for remote operation; another application may be using it. Try specifying another port.", port);
-                    System.out.println(error);
+                    String errorMessage = Localization.lang("Cannot use port %0 for remote operation; another application may be using it. Try specifying another port.", port);
+                    LOGGER.error(errorMessage);
                     return false;
                 }
                 protocol.sendMessage(String.join("\n", args));
diff --git a/src/test/resources/log4j2.xml b/src/test/resources/log4j2.xml
index c447f41c6cc..8c6a336420a 100644
--- a/src/test/resources/log4j2.xml
+++ b/src/test/resources/log4j2.xml
@@ -2,7 +2,7 @@
 <Configuration status="INFO" packages="org.jabref">
     <Appenders>
         <Console name="CONSOLE" target="SYSTEM_OUT">
-            <PatternLayout pattern="%d{HH:mm:ss.SSS} [%t] %-5level %logger{36} - %msg%n"/>
+            <PatternLayout pattern="%d{HH:mm:ss.SSS} [%t] %-5level %logger{36} - %msg - %ex{5} %n"/>
         </Console>
     </Appenders>
     <Loggers>

From a9fab73e843c65831cf1239e07ecabc0f4a1c8eb Mon Sep 17 00:00:00 2001
From: Joerg Lenhard <joerg.lenhard@kau.se>
Date: Tue, 6 Feb 2018 13:01:25 +0100
Subject: [PATCH 32/47] Remove irrelevant log messages during XMP reading

---
 src/main/java/org/jabref/logic/xmp/XMPUtil.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/logic/xmp/XMPUtil.java b/src/main/java/org/jabref/logic/xmp/XMPUtil.java
index 73d63a4b1b1..97be1498ec9 100644
--- a/src/main/java/org/jabref/logic/xmp/XMPUtil.java
+++ b/src/main/java/org/jabref/logic/xmp/XMPUtil.java
@@ -1033,7 +1033,7 @@ public static boolean hasMetadata(Path path, XMPPreferences xmpPreferences) {
         try (InputStream inputStream = Files.newInputStream(path, StandardOpenOption.READ)) {
             return hasMetadata(inputStream, xmpPreferences);
         } catch (IOException e) {
-            LOGGER.error("XMP reading failed", e);
+            // happens if no metadata is found, no reason to log the exception
             return false;
         }
     }
@@ -1056,7 +1056,7 @@ public static boolean hasMetadata(InputStream inputStream, XMPPreferences xmpPre
             LOGGER.info("Encryption not supported by XMPUtil");
             return false;
         } catch (IOException e) {
-            LOGGER.error("XMP reading failed", e);
+            // happens if no metadata is found, no reason to log the exception
             return false;
         }
     }

From 1ee1c6a805d377d980329b3c093a3170edbd745d Mon Sep 17 00:00:00 2001
From: johannes-manner <johannes.manner@web.de>
Date: Tue, 6 Feb 2018 12:54:59 +0100
Subject: [PATCH 33/47] Allow spaces in DOIs

---
 src/main/java/org/jabref/gui/EntryTypeDialog.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/java/org/jabref/gui/EntryTypeDialog.java b/src/main/java/org/jabref/gui/EntryTypeDialog.java
index 4a8961c937d..30669a5306e 100644
--- a/src/main/java/org/jabref/gui/EntryTypeDialog.java
+++ b/src/main/java/org/jabref/gui/EntryTypeDialog.java
@@ -288,6 +288,7 @@ protected Optional<BibEntry> doInBackground() throws Exception {
                 generateButton.setText(Localization.lang("Searching..."));
             });
             searchID = idTextField.getText().trim();
+            searchID = searchID.replaceAll(" ", "");
             fetcher = WebFetchers.getIdBasedFetchers(Globals.prefs.getImportFormatPreferences()).get(comboBox.getSelectedIndex());
             if (!searchID.isEmpty()) {
                 try {

From 7920b92623466a9850e337b1625d07a6ff774413 Mon Sep 17 00:00:00 2001
From: johannes-manner <johannes.manner@web.de>
Date: Tue, 6 Feb 2018 16:29:58 +0100
Subject: [PATCH 34/47] Fix koppor issues #3

Fixed the issue "DOI: encoded URLs should be supported". New divider within the DOI % is supported.
---
 src/main/java/org/jabref/model/entry/identifier/DOI.java     | 2 +-
 src/test/java/org/jabref/model/entry/identifier/DOITest.java | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/model/entry/identifier/DOI.java b/src/main/java/org/jabref/model/entry/identifier/DOI.java
index 754eaed239c..38c66733758 100644
--- a/src/main/java/org/jabref/model/entry/identifier/DOI.java
+++ b/src/main/java/org/jabref/model/entry/identifier/DOI.java
@@ -30,7 +30,7 @@ public class DOI implements Identifier {
             + "("                               // begin group \1
             + "10"                              // directory indicator
             + "(?:\\.[0-9]+)+"                  // registrant codes
-            + "[/:]"                            // divider
+            + "[/:%]" // divider
             + "(?:.+)"                          // suffix alphanumeric string
             + ")";                              // end group \1
     private static final String FIND_DOI_EXP = ""
diff --git a/src/test/java/org/jabref/model/entry/identifier/DOITest.java b/src/test/java/org/jabref/model/entry/identifier/DOITest.java
index 86d79a82e96..d6db25c4278 100644
--- a/src/test/java/org/jabref/model/entry/identifier/DOITest.java
+++ b/src/test/java/org/jabref/model/entry/identifier/DOITest.java
@@ -64,6 +64,8 @@ public void acceptURLDoi() {
         Assert.assertEquals("10.1006/jmbi.1998.2354", new DOI("http://doi.org/10.1006/jmbi.1998.2354").getDOI());
         // https
         Assert.assertEquals("10.1006/jmbi.1998.2354", new DOI("https://doi.org/10.1006/jmbi.1998.2354").getDOI());
+        // https with % divider
+        Assert.assertEquals("10.2307/1990888", new DOI("https://dx.doi.org/10.2307%2F1990888").getDOI());
         // other domains
         Assert.assertEquals("10.1145/1294928.1294933", new DOI("http://doi.acm.org/10.1145/1294928.1294933").getDOI());
         Assert.assertEquals("10.1145/1294928.1294933", new DOI("http://doi.acm.net/10.1145/1294928.1294933").getDOI());

From c914834b805d9cf3e0a2022d9f4493d7ebea1aa8 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Tue, 6 Feb 2018 16:30:05 +0100
Subject: [PATCH 35/47] Fixes #2964

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

diff --git a/src/main/java/org/jabref/gui/groups/GroupTree.fxml b/src/main/java/org/jabref/gui/groups/GroupTree.fxml
index ffb5b401c47..e328b2b15ef 100644
--- a/src/main/java/org/jabref/gui/groups/GroupTree.fxml
+++ b/src/main/java/org/jabref/gui/groups/GroupTree.fxml
@@ -16,7 +16,7 @@
         <TreeTableView fx:id="groupTree" layoutY="-7.0" prefHeight="600.0" prefWidth="250.0" styleClass="groupsPane">
             <columns>
                 <TreeTableColumn fx:id="mainColumn"/>
-                <TreeTableColumn fx:id="numberColumn" minWidth="43.0" maxWidth="55.0"
+                <TreeTableColumn fx:id="numberColumn" minWidth="50.0" maxWidth="70.0" prefWidth="60.0"
                                  styleClass="numberColumn"/>
                 <TreeTableColumn fx:id="disclosureNodeColumn" maxWidth="14.0" minWidth="14.0"
                                  styleClass="disclosureNodeColumn" text="Column X"/>

From 97d00f832464efec5c8426044eb91b12ca30e293 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 6 Feb 2018 18:07:37 +0100
Subject: [PATCH 36/47] Fix color highlight of odd linked files

---
 CHANGELOG.md                                  |  3 +-
 .../jabref/gui/entryeditor/EntryEditor.css    | 36 +++++++++++++++----
 2 files changed, 32 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cb2b075e783..a91b832e51a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,7 +18,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added a new type of group that shows all items referenced in a given LaTeX file (actually the generated AUX file). [#1664](https://github.com/JabRef/jabref/issues/1664)
 - We added the export of the `translator` field to the according MS-Office XML field. [#1750, comment](https://github.com/JabRef/jabref/issues/1750#issuecomment-357350986)
 - We changed the import of the MS-Office XML fields `bookauthor` and `translator`. Both are now imported to their corresponding bibtex/biblatex fields.
-- We improved the export of the `address` and `location` field to the MS-Office XML fields. If the address field does not contain a comma, it is treated as single value and exported to the field `city`. [#1750, comment](https://github.com/JabRef/jabref/issues/1750#issuecomment-357539167) 
+- We improved the export of the `address` and `location` field to the MS-Office XML fields. If the address field does not contain a comma, it is treated as single value and exported to the field `city`. [#1750, comment](https://github.com/JabRef/jabref/issues/1750#issuecomment-357539167)
 For more details refer to the [field mapping help page](http://help.jabref.org/en/MsOfficeBibFieldMapping)
 - We added Facebook and Twitter icons in the toolbar to link to our [Facebook](https://www.facebook.com/JabRef/) and [Twitter](https://twitter.com/jabref_org) pages.
 - We no longer print empty lines when exporting an entry in RIS format [#3634](https://github.com/JabRef/jabref/issues/3634)
@@ -29,6 +29,7 @@ The new default removes the linked file from the entry instead of deleting the f
 ### Fixed
 - We fixed the missing dot in the name of an exported file. [#3576](https://github.com/JabRef/jabref/issues/3576)
 - Autocompletion in the search bar can now be disabled via the preferences. [#3598](https://github.com/JabRef/jabref/issues/3598)
+- We fixed an issue where odd linked files could not be selected in the entry editor. [#3639](https://github.com/JabRef/jabref/issues/3639)
 - We fixed and extended the RIS import functionality to cover more fields. [#3634](https://github.com/JabRef/jabref/issues/3634) [#2607](https://github.com/JabRef/jabref/issues/2607)
 - Chaining modifiers in BibTeX key pattern now works as described in the documentation. [#3648](https://github.com/JabRef/jabref/issues/3648)
 - We fixed an issue where not all bibtex/biblatex fields would be exported as latex-free to MS-Office XML [koppor#284](https://github.com/koppor/jabref/issues/284)
diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.css b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.css
index 0f6952433f0..e99ceaa589d 100644
--- a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.css
+++ b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.css
@@ -11,7 +11,7 @@
     -fx-hgap: 10;
     -fx-vgap: 6;
     -fx-background-color: -fx-light-background;
-    -fx-padding: 5 5 0 15;
+    -fx-padding: 5 5 5 15;
 }
 
 .date-picker > .date-picker-display-node {
@@ -23,17 +23,41 @@
     -fx-text-origin: bottom;
 }
 
-.label > *.text {
-    -fx-translate-y: 0;
-}
-
 .combo-box > *.text {
     -fx-text-fill: text-area-foreground;
     -fx-text-origin: baseline;
 }
 
 .list-cell:odd {
-    -fx-background-color: text-area-background;
+    -fx-background: text-area-background;
+}
+
+/* Selected rows */
+.list-view:focused > .virtual-flow > .clipped-container > .sheet > .list-cell:filled:selected,
+.tree-view:focused > .virtual-flow > .clipped-container > .sheet > .tree-cell:filled:selected,
+.table-view:focused > .virtual-flow > .clipped-container > .sheet > .table-row-cell:filled:selected,
+.tree-table-view:focused > .virtual-flow > .clipped-container > .sheet > .tree-table-row-cell:filled:selected,
+.table-view:focused > .virtual-flow > .clipped-container > .sheet > .table-row-cell .table-cell:selected,
+.tree-table-view:focused > .virtual-flow > .clipped-container > .sheet > .tree-table-row-cell .tree-table-cell:selected {
+    -fx-background: -fx-selection-bar;
+}
+/* Selected when control is not focused */
+.list-cell:filled:selected,
+.tree-cell:filled:selected,
+.table-row-cell:filled:selected,
+.tree-table-row-cell:filled:selected,
+.table-row-cell:filled > .table-cell:selected,
+.tree-table-row-cell:filled > .tree-table-cell:selected {
+    -fx-background: -fx-selection-bar-non-focused;
+}
+/* focused cell (keyboard navigation) */
+.list-view:focused > .virtual-flow > .clipped-container > .sheet > .list-cell:focused,
+.tree-view:focused > .virtual-flow > .clipped-container > .sheet > .tree-cell:focused,
+.table-view:focused:row-selection > .virtual-flow > .clipped-container > .sheet > .table-row-cell:focused,
+.tree-table-view:focused:row-selection > .virtual-flow > .clipped-container > .sheet > .tree-table-row-cell:focused,
+.table-view:focused:cell-selection > .virtual-flow > .clipped-container > .sheet > .table-row-cell > .table-cell:focused,
+.tree-table-view:focused:cell-selection > .virtual-flow > .clipped-container > .sheet > .tree-table-row-cell > .tree-table-cell:focused {
+    -fx-background: -fx-selection-bar;
 }
 
 #typeLabel {

From 0458b32bdd6af9961209ac1879fb56cfc542b1c3 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Tue, 6 Feb 2018 18:20:43 +0100
Subject: [PATCH 37/47] use processbuilder for calling external apps

---
 .../java/org/jabref/gui/push/AbstractPushToApplication.java | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/gui/push/AbstractPushToApplication.java b/src/main/java/org/jabref/gui/push/AbstractPushToApplication.java
index 5942a95959b..b901293c849 100644
--- a/src/main/java/org/jabref/gui/push/AbstractPushToApplication.java
+++ b/src/main/java/org/jabref/gui/push/AbstractPushToApplication.java
@@ -71,9 +71,11 @@ public void pushEntries(BibDatabase database, List<BibEntry> entries, String key
         try {
             if (OS.OS_X) {
                 String[] commands = getCommandLine(keyString);
-                Runtime.getRuntime().exec("open -a " + commands[0] + " -n --args " + commands[1] + " " + commands[2]);
+                ProcessBuilder processBuilder = new ProcessBuilder("open -a " + commands[0] + " -n --args " + commands[1] + " " + commands[2]);
+                processBuilder.start();
             } else {
-                Runtime.getRuntime().exec(getCommandLine(keyString));
+                ProcessBuilder processBuilder = new ProcessBuilder(getCommandLine(keyString));
+                processBuilder.start();
             }
         }
 

From 9cd1ef574d15d4676ddb608a26cd05b421fc0ed3 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 6 Feb 2018 13:06:49 +0100
Subject: [PATCH 38/47] Remove unnecessary file

---
 .../fileannotationtab/ListItem.fxml           | 49 -------------------
 1 file changed, 49 deletions(-)
 delete mode 100644 src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml
deleted file mode 100644
index 87f1f3be75b..00000000000
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/ListItem.fxml
+++ /dev/null
@@ -1,49 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<?import javafx.scene.control.Label?>
-<?import javafx.scene.layout.ColumnConstraints?>
-<?import javafx.scene.layout.GridPane?>
-<?import javafx.scene.layout.RowConstraints?>
-<?import javafx.scene.text.Font?>
-
-<GridPane xmlns="http://javafx.com/javafx/8.0.112" xmlns:fx="http://javafx.com/fxml/1">
-   <columnConstraints>
-      <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="10.0" />
-      <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" />
-      <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="10.0" />
-   </columnConstraints>
-   <rowConstraints>
-      <RowConstraints minHeight="10.0" prefHeight="10.0" vgrow="SOMETIMES" />
-      <RowConstraints minHeight="10.0" vgrow="SOMETIMES" />
-   </rowConstraints>
-   <children>
-      <GridPane prefHeight="90.0" prefWidth="597.0" GridPane.columnIndex="1" GridPane.rowIndex="1">
-         <columnConstraints>
-            <ColumnConstraints hgrow="SOMETIMES" maxWidth="502.0" minWidth="10.0" prefWidth="308.0" />
-            <ColumnConstraints hgrow="SOMETIMES" maxWidth="398.0" minWidth="10.0" prefWidth="246.0" />
-         </columnConstraints>
-         <rowConstraints>
-            <RowConstraints maxHeight="20.0" minHeight="10.0" prefHeight="20.0" vgrow="SOMETIMES" />
-            <RowConstraints maxHeight="36.0" minHeight="10.0" prefHeight="36.0" vgrow="SOMETIMES" />
-            <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
-            <RowConstraints minHeight="10.0" prefHeight="10.0" vgrow="SOMETIMES" />
-         </rowConstraints>
-         <children>
-            <Label alignment="TOP_LEFT" prefHeight="21.0" prefWidth="138.0" text="Brunch this weekend?">
-               <font>
-                  <Font name="System Bold" size="18.0" />
-               </font>
-            </Label>
-            <Label alignment="TOP_RIGHT" prefHeight="30.0" prefWidth="470.0" text="16:05 26.09.2017" textAlignment="RIGHT" GridPane.columnIndex="1" />
-            <Label alignment="TOP_LEFT" prefHeight="30.0" prefWidth="122.0" text="Brendan Lim" GridPane.rowIndex="1">
-               <font>
-                  <Font size="14.0" />
-               </font>
-            </Label>
-            <Label alignment="TOP_LEFT" prefHeight="30.0" prefWidth="516.0" text="This is a comment that discribes the marked passage in the list. It contains useful information to better understand the marked passage." GridPane.rowIndex="2" />
-            <Label alignment="TOP_RIGHT" prefHeight="30.0" prefWidth="470.0" text="Page 13" textAlignment="RIGHT" GridPane.columnIndex="1" GridPane.rowIndex="1" />
-         </children>
-      </GridPane>
-      <Label alignment="TOP_RIGHT" prefHeight="30.0" prefWidth="470.0" text="16:05 26.09.2017" textAlignment="RIGHT" />
-   </children>
-</GridPane>

From 8941c95b450fb0efdc782b69ec4c6c78412ee38a Mon Sep 17 00:00:00 2001
From: Joerg Lenhard <joerg.lenhard@kau.se>
Date: Tue, 6 Feb 2018 18:25:53 +0100
Subject: [PATCH 39/47] Fix NPE

# Conflicts:
#	src/main/java/org/jabref/gui/DefaultInjector.java
---
 .../FileAnnotationTabViewModel.java                 | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
index 525738dd015..bb5755379ff 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java
@@ -36,7 +36,7 @@ public class FileAnnotationTabViewModel extends AbstractViewModel {
     private final ListProperty<FileAnnotationViewModel> annotations = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ListProperty<Path> files = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ObjectProperty<FileAnnotationViewModel> currentAnnotation = new SimpleObjectProperty<>();
-    private ReadOnlyBooleanProperty annotationEmpty;
+    private final ReadOnlyBooleanProperty annotationEmpty = annotations.emptyProperty();
 
     private final FileAnnotationCache cache;
     private final BibEntry entry;
@@ -49,11 +49,7 @@ public FileAnnotationTabViewModel(FileAnnotationCache cache, BibEntry entry, Fil
         this.cache = cache;
         this.entry = entry;
         this.fileMonitor = fileMonitor;
-        initialize();
-    }
-
-    private void initialize() {
-        fileAnnotations = cache.getFromCache(entry);
+        fileAnnotations = this.cache.getFromCache(this.entry);
         files.setAll(fileAnnotations.keySet());
     }
 
@@ -90,7 +86,7 @@ public void notifyNewSelectedFile(Path newFile) {
                 .map(FileAnnotationViewModel::new)
                 .collect(Collectors.toList());
         annotations.setAll(newAnnotations);
-        annotationEmpty = annotations.emptyProperty();
+
         try {
             fileMonitor.addListenerForFile(currentFile, fileListener);
         } catch (IOException e) {
@@ -103,7 +99,8 @@ private void reloadAnnotations() {
         DefaultTaskExecutor.runInJavaFXThread(() -> {
             // Remove annotations for the current entry and reinitialize annotation/cache
             cache.remove(entry);
-            initialize();
+            fileAnnotations = cache.getFromCache(entry);
+            files.setAll(fileAnnotations.keySet());
 
             // Pretend that we just switched to the current file in order to refresh the display
             notifyNewSelectedFile(currentFile);

From b47c5cfb38c3692fffd204b2264bae9e2cb78b9f Mon Sep 17 00:00:00 2001
From: Joerg Lenhard <joerg.lenhard@kau.se>
Date: Tue, 6 Feb 2018 18:35:06 +0100
Subject: [PATCH 40/47] Fix changelog

---
 CHANGELOG.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8a71a7fb77b..6d713d7dff9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,8 +13,6 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Changed
 - Reorganised annotation information on the right side of the "File annotations" tab. [#3109](https://github.com/JabRef/jabref/issues/3109)
-- Changed list item format in list of annotations for the "File annotations" tab. [#3109](https://github.com/JabRef/jabref/issues/3109)
-- Added gui solution for "no annotations in linked file" for the "File annotations" tab. [#3109](https://github.com/JabRef/jabref/issues/3109)
 - We now show a small notification icon in the entry editor when we detect data inconsistency or other problems. [#3145](https://github.com/JabRef/jabref/issues/3145)
 - We added [oaDOI](https://oadoi.org/) as a fulltext provider, so that JabRef is now able to provide fulltexts for more than 90 million open-access articles.
 - We changed one default of [Cleanup entries dialog](http://help.jabref.org/en/CleanupEntries): Per default, the PDF are not moved to the default file directory anymore. [#3619](https://github.com/JabRef/jabref/issues/3619)

From 9090b6bce8b10eb3acec72dd7ef76a317cadf8b2 Mon Sep 17 00:00:00 2001
From: Joerg Lenhard <joerg.lenhard@kau.se>
Date: Tue, 6 Feb 2018 18:39:03 +0100
Subject: [PATCH 41/47] Extract creation of the contents of
 FileAnnotationTabController

---
 .../FileAnnotationTabController.java          | 102 +++++++++---------
 1 file changed, 53 insertions(+), 49 deletions(-)

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
index ff08e251df6..40f8dc874b7 100644
--- a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
+++ b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java
@@ -10,6 +10,7 @@
 import javafx.fxml.FXML;
 import javafx.geometry.HPos;
 import javafx.geometry.Pos;
+import javafx.scene.Node;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.Label;
 import javafx.scene.control.ListView;
@@ -71,55 +72,7 @@ public void initialize() {
         ViewModelListCellFactory<FileAnnotationViewModel> cellFactory = new ViewModelListCellFactory<FileAnnotationViewModel>()
                 .withTooltip(FileAnnotationViewModel::getMarking)
                 .withGraphic(annotation -> {
-
-                    GridPane node = new GridPane();
-
-                    ColumnConstraints firstColumn = new ColumnConstraints();
-                    ColumnConstraints secondColumn = new ColumnConstraints();
-                    firstColumn.setPercentWidth(70);
-                    secondColumn.setPercentWidth(30);
-                    firstColumn.setHalignment(HPos.LEFT);
-                    secondColumn.setHalignment(HPos.RIGHT);
-                    node.getColumnConstraints().addAll(firstColumn, secondColumn);
-
-                    RowConstraints firstRow = new RowConstraints();
-                    RowConstraints secondRow = new RowConstraints();
-                    firstRow.setMinHeight(10);
-                    firstRow.setPrefHeight(15);
-                    secondRow.setMinHeight(10);
-                    secondRow.setPrefHeight(35);
-                    node.getRowConstraints().addAll(firstRow, secondRow);
-
-                    Label marking = new Label(annotation.getMarking());
-                    Label author = new Label(annotation.getAuthor());
-                    Label date = new Label(annotation.getDate());
-                    Label page = new Label(Localization.lang("Page") + ": " + annotation.getPage());
-
-                    marking.setFont(new Font("System Bold", 15));
-                    marking.setPrefWidth(250);
-                    author.setFont(new Font("System", 14));
-
-                    marking.setPrefHeight(10);
-                    author.setPrefHeight(30);
-                    date.setPrefHeight(10);
-                    page.setPrefHeight(30);
-
-                    // add alignment for text in the list
-                    marking.setTextAlignment(TextAlignment.LEFT);
-                    marking.setAlignment(Pos.TOP_LEFT);
-                    author.setTextAlignment(TextAlignment.LEFT);
-                    author.setAlignment(Pos.TOP_LEFT);
-                    date.setTextAlignment(TextAlignment.RIGHT);
-                    date.setAlignment(Pos.TOP_RIGHT);
-                    page.setTextAlignment(TextAlignment.RIGHT);
-                    page.setAlignment(Pos.TOP_RIGHT);
-
-                    node.add(marking, 0, 0);
-                    node.add(author, 0, 1);
-                    node.add(date, 1, 0);
-                    node.add(page, 1, 1);
-
-                    return node;
+                    return createFileAnnotationNode(annotation);
                 });
         annotationList.setCellFactory(cellFactory);
         annotationList.setPlaceholder(new Label(Localization.lang("File has no attached annotations")));
@@ -134,6 +87,57 @@ public void initialize() {
         grid.disableProperty().bind(viewModel.isAnnotationsEmpty());
     }
 
+    private Node createFileAnnotationNode(FileAnnotationViewModel annotation) {
+        GridPane node = new GridPane();
+
+        ColumnConstraints firstColumn = new ColumnConstraints();
+        ColumnConstraints secondColumn = new ColumnConstraints();
+        firstColumn.setPercentWidth(70);
+        secondColumn.setPercentWidth(30);
+        firstColumn.setHalignment(HPos.LEFT);
+        secondColumn.setHalignment(HPos.RIGHT);
+        node.getColumnConstraints().addAll(firstColumn, secondColumn);
+
+        RowConstraints firstRow = new RowConstraints();
+        RowConstraints secondRow = new RowConstraints();
+        firstRow.setMinHeight(10);
+        firstRow.setPrefHeight(15);
+        secondRow.setMinHeight(10);
+        secondRow.setPrefHeight(35);
+        node.getRowConstraints().addAll(firstRow, secondRow);
+
+        Label marking = new Label(annotation.getMarking());
+        Label author = new Label(annotation.getAuthor());
+        Label date = new Label(annotation.getDate());
+        Label page = new Label(Localization.lang("Page") + ": " + annotation.getPage());
+
+        marking.setFont(new Font("System Bold", 15));
+        marking.setPrefWidth(250);
+        author.setFont(new Font("System", 14));
+
+        marking.setPrefHeight(10);
+        author.setPrefHeight(30);
+        date.setPrefHeight(10);
+        page.setPrefHeight(30);
+
+        // add alignment for text in the list
+        marking.setTextAlignment(TextAlignment.LEFT);
+        marking.setAlignment(Pos.TOP_LEFT);
+        author.setTextAlignment(TextAlignment.LEFT);
+        author.setAlignment(Pos.TOP_LEFT);
+        date.setTextAlignment(TextAlignment.RIGHT);
+        date.setAlignment(Pos.TOP_RIGHT);
+        page.setTextAlignment(TextAlignment.RIGHT);
+        page.setAlignment(Pos.TOP_RIGHT);
+
+        node.add(marking, 0, 0);
+        node.add(author, 0, 1);
+        node.add(date, 1, 0);
+        node.add(page, 1, 1);
+
+        return node;
+    }
+
     public void copy(ActionEvent event) {
         viewModel.copyCurrentAnnotation();
     }

From 0bcd11932420e87db748f1cddce9ec5b48efa544 Mon Sep 17 00:00:00 2001
From: Stefan Kolb <stefan-kolb@web.de>
Date: Tue, 6 Feb 2018 18:43:27 +0100
Subject: [PATCH 42/47] Fix #3669

---
 .../jabref/logic/importer/fileformat/IsiImporter.java    | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/IsiImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/IsiImporter.java
index e25196a4476..2fae91e67fa 100644
--- a/src/main/java/org/jabref/logic/importer/fileformat/IsiImporter.java
+++ b/src/main/java/org/jabref/logic/importer/fileformat/IsiImporter.java
@@ -26,14 +26,10 @@
  * Documentation about ISI WOS format:
  * <p>
  * <ul>
- * <li>http://wos.isitrial.com/help/helpprn.html</li>
+ * <li>https://web.archive.org/web/20131031052339/http://wos.isitrial.com/help/helpprn.html</li>
  * </ul>
  * <p>
  * <ul>
- * <li>Check compatibility with other ISI2Bib tools like:
- * http://www-lab.imr.tohoku.ac.jp/~t-nissie/computer/software/isi/ or
- * http://www.tug.org/tex-archive/biblio/bibtex/utils/isi2bibtex/isi2bibtex or
- * http://web.mit.edu/emilio/www/utils.html</li>
  * <li>Deal with capitalization correctly</li>
  * </ul>
  */
@@ -330,8 +326,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
     }
 
     private static String parsePages(String value) {
-        int lastDash = value.lastIndexOf('-');
-        return value.substring(0, lastDash) + "--" + value.substring(lastDash + 1);
+        return value.replace("-", "--");
     }
 
     public static String parseMonth(String value) {

From cec899959ed966a66586074fb168ce6f960a1930 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Tue, 6 Feb 2018 18:44:20 +0100
Subject: [PATCH 43/47] Fix space leads to jump in entry editor (#3699)

---
 CHANGELOG.md                                  |  1 +
 .../org/jabref/gui/entryeditor/SourceTab.java |  2 +-
 .../jabref/gui/util/DefaultTaskExecutor.java  | 34 +++++++++++++++++++
 3 files changed, 36 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a91b832e51a..740e0fe1744 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ For more details refer to the [field mapping help page](http://help.jabref.org/e
 The new default removes the linked file from the entry instead of deleting the file from disk. [#3679](https://github.com/JabRef/jabref/issues/3679)
 
 ### Fixed
+- We fixed an issue where pressing space caused the cursor to jump to the start of the text field. [#3471](https://github.com/JabRef/jabref/issues/3471)
 - We fixed the missing dot in the name of an exported file. [#3576](https://github.com/JabRef/jabref/issues/3576)
 - Autocompletion in the search bar can now be disabled via the preferences. [#3598](https://github.com/JabRef/jabref/issues/3598)
 - We fixed an issue where odd linked files could not be selected in the entry editor. [#3639](https://github.com/JabRef/jabref/issues/3639)
diff --git a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
index 517180b9ad6..b48def74d21 100644
--- a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
@@ -103,7 +103,7 @@ protected void bindToEntry(BibEntry entry) {
         // Store source for every change in the source code
         // and update source code for every change of entry field values
         BindingsHelper.bindContentBidirectional(entry.getFieldsObservable(), codeArea.textProperty(), this::storeSource, fields -> {
-            DefaultTaskExecutor.runInJavaFXThread(() -> {
+            DefaultTaskExecutor.runAndWaitInJavaFXThread(() -> {
                 codeArea.clear();
                 try {
                     codeArea.appendText(getSourceString(entry, mode, fieldFormatterPreferences));
diff --git a/src/main/java/org/jabref/gui/util/DefaultTaskExecutor.java b/src/main/java/org/jabref/gui/util/DefaultTaskExecutor.java
index 7697e7e34bf..acb06b8e7bd 100644
--- a/src/main/java/org/jabref/gui/util/DefaultTaskExecutor.java
+++ b/src/main/java/org/jabref/gui/util/DefaultTaskExecutor.java
@@ -1,6 +1,7 @@
 package org.jabref.gui.util;
 
 import java.util.concurrent.Callable;
+import java.util.concurrent.CountDownLatch;
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
@@ -38,6 +39,39 @@ public static <V> V runInJavaFXThread(Callable<V> callable) {
         }
     }
 
+    /**
+     * Runs the specified {@link Runnable} on the JavaFX application thread and waits for completion.
+     *
+     * @param action the {@link Runnable} to run
+     * @throws NullPointerException if {@code action} is {@code null}
+     */
+    public static void runAndWaitInJavaFXThread(Runnable action) {
+        if (action == null)
+            throw new NullPointerException("action");
+
+        // Run synchronously on JavaFX thread
+        if (Platform.isFxApplicationThread()) {
+            action.run();
+            return;
+        }
+
+        // Queue on JavaFX thread and wait for completion
+        final CountDownLatch doneLatch = new CountDownLatch(1);
+        Platform.runLater(() -> {
+            try {
+                action.run();
+            } finally {
+                doneLatch.countDown();
+            }
+        });
+
+        try {
+            doneLatch.await();
+        } catch (InterruptedException e) {
+            LOGGER.error("Problem running action on JavaFX thread", e);
+        }
+    }
+
     public static void runInJavaFXThread(Runnable runnable) {
         Platform.runLater(runnable);
     }

From dfd62b0fbff053da8c76e2e9d5ca38a46ea9daca Mon Sep 17 00:00:00 2001
From: johannes-manner <johannes.manner@web.de>
Date: Tue, 6 Feb 2018 19:09:33 +0100
Subject: [PATCH 44/47] fix https://github.com/JabRef/jabref/issues/3693
 (#3702)

Duplicated functionality, if file already exists. Asks twice, if a file should be overriden.
---
 src/main/java/org/jabref/gui/exporter/ExportAction.java | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/src/main/java/org/jabref/gui/exporter/ExportAction.java b/src/main/java/org/jabref/gui/exporter/ExportAction.java
index 3856520a45a..5dfa5cb5fcf 100644
--- a/src/main/java/org/jabref/gui/exporter/ExportAction.java
+++ b/src/main/java/org/jabref/gui/exporter/ExportAction.java
@@ -1,7 +1,6 @@
 package org.jabref.gui.exporter;
 
 import java.awt.event.ActionEvent;
-import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -81,14 +80,6 @@ private void export(Path file, FileChooser.ExtensionFilter selectedExtensionFilt
                     FileUtil.addExtension(file, selectedExtension);
                     }
 
-                if (Files.exists(file)) {
-                        // Warn that the file exists:
-                        if (JOptionPane.showConfirmDialog(frame,
-                                Localization.lang("'%0' exists. Overwrite file?", file.getFileName().toString()),
-                                Localization.lang("Export"), JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) {
-                            return;
-                        }
-                    }
                 final Exporter format = FileFilterConverter.getExporter(selectedExtensionFilter, exporters).orElseThrow(() -> new IllegalStateException("User didn't selected a file type for the extension"));
                     List<BibEntry> entries;
                     if (selectedOnly) {

From 8d1f9c109bbcc0b844a9cf30936735bb9b122bbb Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Tue, 6 Feb 2018 19:11:27 +0100
Subject: [PATCH 45/47] remove import preferences test mock import and convert
 to junit5

---
 .../org/jabref/JabRefPreferencesTest.java     | 40 +++++--------------
 .../LastFocusedTabPreferencesTest.java        | 12 +++---
 2 files changed, 15 insertions(+), 37 deletions(-)

diff --git a/src/test/java/org/jabref/JabRefPreferencesTest.java b/src/test/java/org/jabref/JabRefPreferencesTest.java
index 0deaf3e6b24..4a07bb58840 100644
--- a/src/test/java/org/jabref/JabRefPreferencesTest.java
+++ b/src/test/java/org/jabref/JabRefPreferencesTest.java
@@ -1,52 +1,30 @@
 package org.jabref;
 
-import java.io.File;
 import java.nio.charset.StandardCharsets;
 
 import org.jabref.preferences.JabRefPreferences;
 
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
 
 import static org.junit.Assert.assertEquals;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 public class JabRefPreferencesTest {
 
     private JabRefPreferences prefs;
 
-    private JabRefPreferences backup;
-
-
-    @Before
+    @BeforeEach
     public void setUp() {
-        prefs = JabRefPreferences.getInstance();
-        backup = prefs;
-    }
-
-    @Test
-    public void testPreferencesImport() throws JabRefException {
-        // the primary sort field has been changed to "editor" in this case
-        File importFile = new File("src/test/resources/org/jabref/customPreferences.xml");
-
-        prefs.importPreferences(importFile.getAbsolutePath());
-
-        String expected = "dummyvalue";
-        String actual = prefs.get("dummykey");
-
-        assertEquals(expected, actual);
+        prefs = mock(JabRefPreferences.class);
+        when(prefs.getDefaultEncoding()).thenReturn(StandardCharsets.UTF_8);
     }
 
     @Test
     public void getDefaultEncodingReturnsPreviouslyStoredEncoding() {
-        prefs.setDefaultEncoding(StandardCharsets.UTF_16BE);
-        assertEquals(StandardCharsets.UTF_16BE, prefs.getDefaultEncoding());
-    }
-
-    @After
-    public void tearDown() {
-        //clean up preferences to default state
-        prefs.overwritePreferences(backup);
+        prefs.setDefaultEncoding(StandardCharsets.UTF_8);
+        assertEquals(StandardCharsets.UTF_8, prefs.getDefaultEncoding());
     }
 
 }
diff --git a/src/test/java/org/jabref/preferences/LastFocusedTabPreferencesTest.java b/src/test/java/org/jabref/preferences/LastFocusedTabPreferencesTest.java
index d1cf9847d44..3e39b69fa63 100644
--- a/src/test/java/org/jabref/preferences/LastFocusedTabPreferencesTest.java
+++ b/src/test/java/org/jabref/preferences/LastFocusedTabPreferencesTest.java
@@ -2,22 +2,22 @@
 
 import java.io.File;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
 
-import static org.junit.Assert.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class LastFocusedTabPreferencesTest {
 
     private static String previousValue;
 
-    @BeforeClass
+    @BeforeAll
     public static void savePreferenceLastFocus() {
         previousValue = JabRefPreferences.getInstance().get(JabRefPreferences.LAST_FOCUSED);
     }
 
-    @AfterClass
+    @AfterAll
     public static void restorePreferenceLastFocus() {
         if (previousValue != null) {
             JabRefPreferences.getInstance().put(JabRefPreferences.LAST_FOCUSED, previousValue);

From bb0f5d5d8cc872cd676eeb907ed1808e5b77fc07 Mon Sep 17 00:00:00 2001
From: Stefan Kolb <stefan-kolb@web.de>
Date: Tue, 6 Feb 2018 21:58:54 +0100
Subject: [PATCH 46/47] Use english for all LCID mappings #1851

---
 src/main/java/org/jabref/logic/msbib/MSBibMapping.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/logic/msbib/MSBibMapping.java b/src/main/java/org/jabref/logic/msbib/MSBibMapping.java
index d7d9e9506b6..de9a8998b47 100644
--- a/src/main/java/org/jabref/logic/msbib/MSBibMapping.java
+++ b/src/main/java/org/jabref/logic/msbib/MSBibMapping.java
@@ -131,8 +131,8 @@ public static MSBibEntryType getMSBibEntryType(String bibtexType) {
      */
     public static int getLCID(String language) {
         // TODO: add language to LCID mapping
-        // 0 is English
-        return 0;
+        // 0x0409 is American English
+        return 0x0409;
     }
 
     /**

From 5e96d46bd24a851ad958af982f80ac383df44a3d Mon Sep 17 00:00:00 2001
From: Stefan Kolb <stefan-kolb@web.de>
Date: Tue, 6 Feb 2018 22:55:10 +0100
Subject: [PATCH 47/47] Fix Google Scholar fetcher

---
 .../java/org/jabref/logic/importer/fetcher/GoogleScholar.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/logic/importer/fetcher/GoogleScholar.java b/src/main/java/org/jabref/logic/importer/fetcher/GoogleScholar.java
index 38698ddf612..2d98c03f89d 100644
--- a/src/main/java/org/jabref/logic/importer/fetcher/GoogleScholar.java
+++ b/src/main/java/org/jabref/logic/importer/fetcher/GoogleScholar.java
@@ -73,7 +73,7 @@ public Optional<URL> findFullText(BibEntry entry) throws IOException, FetcherExc
             // Check results for PDF link
             // TODO: link always on first result or none?
             for (int i = 0; i < NUM_RESULTS; i++) {
-                Elements link = doc.select(String.format("#gs_ggsW%s a", i));
+                Elements link = doc.select(String.format("div[data-rp=%S] div.gs_or_ggsm a", i));
 
                 if (link.first() != null) {
                     String s = link.first().attr("href");