Merge branch 'master' of https://github.com/JabRef/jabref into improvePersonNamesChecker

Author: tobiasdiez

CHANGELOG.md

@@ -27,12 +27,13 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The integrity check for person names now also tests that the names are specified in one of the standard BibTeX formats.
 
 ### Fixed
+- We fixed the adding of a new entry from DOI which led to a connection error. The DOI resolution now uses HTTPS to protect the user's privacy.[#2879](https://github.com/JabRef/jabref/issues/2897)
 - We fixed the IEEE Xplore web search functionality [#2789](https://github.com/JabRef/jabref/issues/2789)
 - We fixed an error in the CrossRef fetcher that occurred if one of the fetched entries had no title
 - We fixed an issue that prevented new entries to be automatically assigned to the currently selected group [#2783](https://github.com/JabRef/jabref/issues/2783).
-- We fixed a bug that only allowed parsing positive timezones from a FileAnnotation [#2839](https://github.com/JabRef/jabref/issues/22839)
+- We fixed a bug that only allowed parsing positive timezones from a FileAnnotation [#2839](https://github.com/JabRef/jabref/issues/2839)
 - We fixed a bug that did not allow the correct re-export of the MS-Office XML field `msbib-accessed` with a different date format [#2859](https://github.com/JabRef/jabref/issues/2859).
-
+- We fixed some bugs that prevented the display of FileAnnotations that were created using the Foxit Reader. [#2839, comment](https://github.com/JabRef/jabref/issues/2839#issuecomment-302058227).
 ### Removed
 
 

CONTRIBUTING.md

@@ -1,7 +1,7 @@
 ## Understanding the basics
 We welcome contributions to JabRef and encourage to create a fork, clone, **create a new branch** (such as `fix-for-issue-121`), **work on the new branch — not master**, and create a pull request.
 Be sure to create a **separate branch** for each improvement you implement.
-Take a look at GitHub's excellent [help documentation] for a detailed explanation.
+Take a look at GitHub's excellent [help documentation] for a detailed explanation and the explanation of [Feature Branch Workflow](https://de.atlassian.com/git/tutorials/comparing-workflows#feature-branch-workflow) for the idea behind this kind of development.
 
 We also have [code howtos](https://github.com/JabRef/jabref/wiki/Code-Howtos) and [guidelines for setting up a local workspace](https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).
 

build.gradle

@@ -100,7 +100,7 @@ dependencies {
     compile 'org.antlr:antlr4-runtime:4.7'
 
     // VersionEye states that 6.0.5 is the most recent version, but http://dev.mysql.com/downloads/connector/j/ shows that as "Development Release"
-    compile 'mysql:mysql-connector-java:5.1.40'
+    compile 'mysql:mysql-connector-java:5.1.42'
 
     compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.7.1'
 
@@ -125,7 +125,7 @@ dependencies {
 
     compile 'org.jsoup:jsoup:1.10.2'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
-    compile 'info.debatty:java-string-similarity:0.23'
+    compile 'info.debatty:java-string-similarity:0.24'
 
     compile 'org.apache.logging.log4j:log4j-jcl:2.8.2'
     compile 'org.apache.logging.log4j:log4j-api:2.8.2'
@@ -290,7 +290,7 @@ tasks.withType(Test) {
 }
 
 task jacocoMerge(type: JacocoMerge) {
-    executionData test, fetcherTest, databaseTest
+    executionData test, databaseTest
 }
 
 jacocoTestReport {

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

@@ -6,7 +6,7 @@
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
-import org.jabref.preferences.JabRefPreferences;
+import org.jabref.preferences.PreferencesService;
 
 import com.airhacks.afterburner.injection.Injector;
 import com.airhacks.afterburner.injection.PresenterFactory;
@@ -27,7 +27,7 @@ private static Object createDependency(Class<?> clazz) {
             return new FXDialogService();
         } else if (clazz == TaskExecutor.class) {
             return Globals.taskExecutor;
-        } else if (clazz == JabRefPreferences.class) {
+        } else if (clazz == PreferencesService.class) {
             return Globals.prefs;
         } else if (clazz == KeyBindingRepository.class) {
             return Globals.getKeyPrefs();

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

@@ -80,7 +80,6 @@
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.gui.undo.UndoableKeyChange;
 import org.jabref.gui.undo.UndoableRemoveEntry;
-import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.component.CheckBoxMessage;
 import org.jabref.gui.util.component.VerticalLabelUI;
 import org.jabref.logic.TypedBibEntry;
@@ -239,8 +238,6 @@ public EntryEditor(JabRefFrame frame, BasePanel panel, BibEntry entry) {
         if (Globals.prefs.getBoolean(JabRefPreferences.DEFAULT_SHOW_SOURCE)) {
             tabbed.setSelectedIndex(sourceIndex);
         }
-
-        DefaultTaskExecutor.runInJavaFXThread(() -> setEntry(entry));
     }
 
     private static String getSourceString(BibEntry entry, BibDatabaseMode type) throws IOException {
@@ -457,17 +454,6 @@ public BibEntry getEntry() {
         return entry;
     }
 
-    /**
-     * Sets all the text areas according to the shown entry.
-     */
-    private void setEntry(BibEntry entry) {
-        for (Object tab : tabs) {
-            if (tab instanceof EntryEditorTab) {
-                ((EntryEditorTab) tab).setEntry(entry);
-            }
-        }
-    }
-
     public BibDatabase getDatabase() {
         return panel.getDatabase();
     }

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

@@ -15,6 +15,7 @@
 import javax.swing.JComponent;
 
 import javafx.embed.swing.JFXPanel;
+import javafx.geometry.VPos;
 import javafx.scene.Node;
 import javafx.scene.Parent;
 import javafx.scene.Scene;
@@ -55,7 +56,6 @@ class EntryEditorTab {
     private final BasePanel basePanel;
     private FieldEditorFX activeField;
     private BibEntry entry;
-    private boolean updating;
 
     public EntryEditorTab(JabRefFrame frame, BasePanel basePanel, List<String> fields, EntryEditor parent,
             boolean addKeyField, boolean compressed, String tabTitle, BibEntry entry) {
@@ -152,9 +152,9 @@ private Region setupPanel(JabRefFrame frame, BasePanel bPanel, boolean addKeyFie
             fieldEditor.setAutoCompleteListener(autoCompleteListener);
             */
 
-            FieldEditorFX fieldEditor = FieldEditors.getForField(fieldName, Globals.taskExecutor, new FXDialogService(),
-                    Globals.journalAbbreviationLoader, Globals.prefs.getJournalAbbreviationPreferences(), Globals.prefs,
-                    bPanel.getBibDatabaseContext(), entry.getType());
+            FieldEditorFX fieldEditor = FieldEditors.getForField(fieldName, Globals.taskExecutor, new FXDialogService(), Globals.journalAbbreviationLoader, Globals.prefs.getJournalAbbreviationPreferences(), Globals.prefs, bPanel.getBibDatabaseContext(), entry.getType());
+            fieldEditor.bindToEntry(entry);
+          
             editors.put(fieldName, fieldEditor);
             /*
             // TODO: Reenable this
@@ -217,6 +217,7 @@ private Region setupPanel(JabRefFrame frame, BasePanel bPanel, boolean addKeyFie
 
         RowConstraints rowExpand = new RowConstraints();
         rowExpand.setVgrow(Priority.ALWAYS);
+        rowExpand.setValignment(VPos.TOP);
         if (rows == 0) {
             rowExpand.setPercentHeight(100);
         } else {
@@ -252,18 +253,6 @@ private String getPrompt(String field) {
         return "";
     }
 
-    public void setEntry(BibEntry entry) {
-        try {
-            updating = true;
-            for (FieldEditorFX editor : editors.values()) {
-                editor.bindToEntry(entry);
-            }
-            this.entry = entry;
-        } finally {
-            updating = false;
-        }
-    }
-
     /**
      * Only sets the activeField variable but does not focus it.
      * <p>

src/main/java/org/jabref/gui/fieldeditors/DateEditor.fxml

@@ -3,5 +3,6 @@
 <?import javafx.scene.layout.HBox?>
 <?import org.jabref.gui.util.component.TemporalAccessorPicker?>
 <fx:root xmlns:fx="http://javafx.com/fxml/1" type="HBox" xmlns="http://javafx.com/javafx/8.0.112">
-    <TemporalAccessorPicker fx:id="datePicker" prefHeight="0" HBox.hgrow="ALWAYS"/>
+    <TemporalAccessorPicker fx:id="datePicker" prefHeight="0" HBox.hgrow="ALWAYS" maxHeight="Infinity"
+                            maxWidth="Infinity"/>
 </fx:root>

src/main/java/org/jabref/gui/fieldeditors/FieldNameLabel.java

@@ -1,5 +1,6 @@
 package org.jabref.gui.fieldeditors;
 
+import javafx.geometry.Insets;
 import javafx.scene.control.Label;
 
 import org.jabref.model.entry.FieldName;
@@ -9,6 +10,7 @@ public class FieldNameLabel extends Label {
     public FieldNameLabel(String fieldName) {
         super(FieldName.getDisplayName(fieldName));
 
+        setPadding(new Insets(4, 0, 0, 0));
         // TODO: style!
         //setVerticalAlignment(SwingConstants.TOP);
         //setForeground(GUIGlobals.ENTRY_EDITOR_LABEL_COLOR);

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.fxml

@@ -8,7 +8,7 @@
 <?import javafx.scene.layout.StackPane?>
 <?import de.jensd.fx.glyphs.materialdesignicons.MaterialDesignIconView?>
 <fx:root xmlns:fx="http://javafx.com/fxml/1" type="HBox" xmlns="http://javafx.com/javafx/8.0.112">
-    <ListView fx:id="listView" prefHeight="0" HBox.hgrow="ALWAYS"/>
+    <ListView fx:id="listView" prefHeight="0" HBox.hgrow="ALWAYS" maxHeight="100"/>
     <Button onAction="#addNewFile"
             styleClass="flatButton">
         <graphic>

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java

@@ -1,5 +1,6 @@
 package org.jabref.gui.fieldeditors;
 
+import javafx.beans.binding.Bindings;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
 import javafx.scene.Node;
@@ -38,7 +39,7 @@ public LinkedFilesEditor(String fieldName, DialogService dialogService, BibDatab
                 .withTooltip(LinkedFileViewModel::getDescription)
                 .withGraphic(LinkedFilesEditor::createFileDisplay);
         listView.setCellFactory(cellFactory);
-        listView.itemsProperty().bind(viewModel.filesProperty());
+        Bindings.bindContent(listView.itemsProperty().get(), viewModel.filesProperty());
     }
 
     private static Node createFileDisplay(LinkedFileViewModel linkedFile) {