Merge remote-tracking branch 'upstream/master' into sharelatex

* upstream/master: (47 commits)
  Fix Google Scholar fetcher
  Use english for all LCID mappings #1851
  remove import preferences test mock import and convert to junit5
  fix #3693 (#3702)
  Fix space leads to jump in entry editor (#3699)
  Fix #3669
  Extract creation of the contents of FileAnnotationTabController
  Fix changelog
  Fix NPE
  Remove unnecessary file
  use processbuilder for calling external apps
  Fix color highlight of odd linked files
  Fixes #2964
  Fix koppor issues #3
  Allow spaces in DOIs
  Remove irrelevant log messages during XMP reading
  Adapt log4j configuration for cleaner junit tests #3511
  Eclipse Django style #3655
  Better code style for chained methods
  Update build.gradle
  ...

Author: Siedlerchr

CHANGELOG.md

@@ -12,13 +12,14 @@ 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)
 - 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)
 - 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)
@@ -27,8 +28,10 @@ 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)
 - 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)

build.gradle

@@ -182,6 +182,10 @@ dependencies {
     checkstyle 'com.puppycrawl.tools:checkstyle:8.8'
 }
 
+jacoco {
+    toolVersion = '0.8.0'
+}
+
 dependencyUpdates {
     outputFormatter = "json"
 }
@@ -234,7 +238,16 @@ 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 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 dependency should be hidden.")
+            }
+        }
     }
 }
 
@@ -398,7 +411,6 @@ afterEvaluate {
     def junitPlatformTest = tasks.junitPlatformTest
 
     jacoco {
-        toolVersion = '0.8.0'
         applyTo(junitPlatformTest)
     }
 

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>

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

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 {

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 {

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));

src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTab.fxml

@@ -8,6 +8,7 @@
 <?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?>
@@ -16,67 +17,67 @@
 <?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>
+            <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" maxWidth="-Infinity" minWidth="10.0" prefWidth="10.0" />
+                    <ColumnConstraints hgrow="ALWAYS" minWidth="10.0" />
+                    <ColumnConstraints hgrow="SOMETIMES" maxWidth="-Infinity" minWidth="40.0" prefWidth="40.0" />
                 </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 maxHeight="-Infinity" minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                    <RowConstraints minHeight="10.0" prefHeight="100.0" 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="%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"/>
+                <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" />
+                <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"/>
+                            <MaterialDesignIconView glyphName="CONTENT_COPY">
+                        <cursor>
+                           <Cursor fx:constant="HAND" />
+                        </cursor></MaterialDesignIconView>
                         </graphic>
                         <tooltip>
-                            <Tooltip text="%Copy to clipboard"/>
+                            <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"/>
             </GridPane>
         </detailNode>
     </MasterDetailPane>