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

* upstream/master: (21 commits) Bump applicationinsights-core from 2.3.0 to 2.3.1 (#4656) Bump applicationinsights-logging-log4j2 from 2.3.0 to 2.3.1 (#4657) Bump bcprov-jdk15on from 1.60 to 1.61 (#4653) Bump log4j-jcl from 2.11.1 to 2.11.2 (#4646) Bump log4j-api from 2.11.1 to 2.11.2 (#4650) Bump assertj-swing-junit from 3.8.0 to 3.9.2 (#4647) Bump log4j-jul from 2.11.1 to 2.11.2 (#4648) Bump log4j-slf4j18-impl from 2.11.1 to 2.11.2 (#4649) Bump log4j-core from 2.11.1 to 2.11.2 (#4651) Remove old code for PDF import (#4634) Reorder conditional checks Automatically created groups with Field to group by as entrytype (#4539) (#4555) Fix for issue 4641: Remove usage of TempDirectory extension from junit-pioneer (#4644) Edit localization file Add Integrity check for books with edition reported as 1 Use 'junit-jupiter' aggregator module (#4640) Bump junit-jupiter-params from 5.3.2 to 5.4.0 (#4638) Bump junit-vintage-engine from 5.3.2 to 5.4.0 (#4637) Bump junit-platform-launcher from 1.3.2 to 1.4.0 (#4636) Bump junit-jupiter-api from 5.3.2 to 5.4.0 (#4639) ... # Conflicts: # src/main/resources/l10n/JabRef_en.properties
JabRef · Feb 15, 2019 · 634bed4 · 634bed4
2 parents 30d5bf1 + d95c06b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -48,6 +48,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
 - We added an option in the preference dialog box that allows user to choose behavior after dragging and dropping files in Entry Editor. [#4356](https://github.com/JabRef/jabref/issues/4356)
 - We added the ability to have an export preference where previously "File"-->"Export"/"Export selected entries" would not save the user's preference[#4495](https://github.com/JabRef/jabref/issues/4495)
+- For automatically created groups, added ability to filter groups by entry type. [#4539](https://github.com/JabRef/jabref/issues/4539)
 - We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added the ability change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)

diff --git a/build.gradle b/build.gradle
@@ -102,7 +102,7 @@ dependencies {
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.20'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    compile 'org.bouncycastle:bcprov-jdk15on:1.60'
+    compile 'org.bouncycastle:bcprov-jdk15on:1.61'
 
     compile 'commons-cli:commons-cli:1.4'
 
@@ -147,32 +147,29 @@ dependencies {
 
     // >1.8.0-beta is required for java 9 compatibility
     compile 'org.slf4j:slf4j-api:1.8.0-beta2'
-    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.1'
-    compile 'org.apache.logging.log4j:log4j-jcl:2.11.1'
-    compile 'org.apache.logging.log4j:log4j-api:2.11.1'
-    compile 'org.apache.logging.log4j:log4j-core:2.11.1'
+    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.11.2'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.11.2'
+    compile 'org.apache.logging.log4j:log4j-api:2.11.2'
+    compile 'org.apache.logging.log4j:log4j-core:2.11.2'
 
     compile 'de.undercouch:citeproc-java:1.0.1'
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
     errorproneJavac 'com.google.errorprone:javac:1.8.0-u20'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.0'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.3.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.3.1'
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.3.2'
-    testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.2'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.3.2'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.3.2'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.3.2'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.4.0'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.0'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.4.0'
 
-    testCompile 'org.junit-pioneer:junit-pioneer:0.3.0'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
-    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.1'
+    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.2'
     testCompile 'org.mockito:mockito-core:2.24.0'
     testCompile 'com.github.tomakehurst:wiremock:2.21.0'
-    testCompile 'org.assertj:assertj-swing-junit:3.8.0'
+    testCompile 'org.assertj:assertj-swing-junit:3.9.2'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
@@ -192,9 +189,6 @@ dependencyUpdates {
     outputFormatter = "json"
 }
 
-//We have to use this as long as junit-pioneer has no official release
-dependencyUpdates.revision = 'integration'
-
 // We have some dependencies which cannot be updated due to various reasons.
 dependencyUpdates.resolutionStrategy = {
     componentSelection { rules ->

diff --git a/src/main/java/org/jabref/gui/DuplicateResolverDialog.java b/src/main/java/org/jabref/gui/DuplicateResolverDialog.java
@@ -68,7 +68,7 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
                 second = new ButtonType(Localization.lang("Remove entry from import"), ButtonData.APPLY);
                 both = new ButtonType(Localization.lang("Keep both"), ButtonData.APPLY);
                 me = new MergeEntries(one, two, Localization.lang("Old entry"),
-                                      Localization.lang("From import"), frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
+                        Localization.lang("From import"), frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
                 break;
             case DUPLICATE_SEARCH_WITH_EXACT:
                 first = new ButtonType(Localization.lang("Keep left"), ButtonData.APPLY);
@@ -84,7 +84,7 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
                 second = new ButtonType(Localization.lang("Do not import entry"), ButtonData.APPLY);
                 both = new ButtonType(Localization.lang("Import and keep old entry"), ButtonData.APPLY);
                 me = new MergeEntries(one, two, Localization.lang("Old entry"),
-                                      Localization.lang("From import"), frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
+                        Localization.lang("From import"), frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
                 break;
         }
         if (removeExactVisible) {

diff --git a/src/main/java/org/jabref/gui/DuplicateSearch.java b/src/main/java/org/jabref/gui/DuplicateSearch.java
@@ -127,7 +127,7 @@ private void askResolveStrategy(DuplicateSearchResult result, BibEntry first, Bi
         DuplicateResolverResult resolverResult = dialog.showAndWait().orElse(DuplicateResolverResult.BREAK);
 
         if ((resolverResult == DuplicateResolverResult.KEEP_LEFT)
-            || (resolverResult == DuplicateResolverResult.AUTOREMOVE_EXACT)) {
+                || (resolverResult == DuplicateResolverResult.AUTOREMOVE_EXACT)) {
             result.remove(second);
             if (resolverResult == DuplicateResolverResult.AUTOREMOVE_EXACT) {
                 autoRemoveExactDuplicates.set(true); // Remember choice
@@ -167,7 +167,7 @@ private void handleDuplicates(DuplicateSearchResult result) {
         }
 
         dialogService.notify(Localization.lang("Duplicates found") + ": " + duplicateCount.get() + ' '
-                             + Localization.lang("pairs processed") + ": " + result.getDuplicateCount());
+                + Localization.lang("pairs processed") + ": " + result.getDuplicateCount());
         compoundEdit.end();
         panel.getUndoManager().addEdit(compoundEdit);
 

diff --git a/src/main/java/org/jabref/gui/EntryType.fxml b/src/main/java/org/jabref/gui/EntryType.fxml
@@ -12,41 +12,43 @@
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.RowConstraints?>
 <?import javafx.scene.layout.VBox?>
-
-<DialogPane prefWidth="476.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.EntryTypeView">
-      <buttonTypes>
-        <ButtonType fx:constant="CANCEL" />
-        <ButtonType fx:id="generateButton" buttonData="OK_DONE" text="%Generate" />
-      </buttonTypes>
+<DialogPane xmlns:fx="http://javafx.com/fxml/1" prefWidth="476.0" xmlns="http://javafx.com/javafx/8.0.171"
+            fx:controller="org.jabref.gui.EntryTypeView">
+    <buttonTypes>
+        <ButtonType fx:constant="CANCEL"/>
+        <ButtonType fx:id="generateButton" buttonData="OK_DONE" text="%Generate"/>
+    </buttonTypes>
    <content>
-      <VBox prefHeight="200.0" prefWidth="400.0">
-         <children>
-            <TitledPane fx:id="biblatexTitlePane" animated="false" collapsible="false" text="Biblatex">
-               <content>
-                  <FlowPane fx:id="biblatexPane" prefHeight="200.0" prefWidth="200.0" />
-               </content>
-            </TitledPane>
-            <TitledPane fx:id="bibTexTitlePane" animated="false" collapsible="false" text="BibTeX">
-               <content>
-                  <FlowPane fx:id="bibTexPane" prefHeight="200.0" prefWidth="200.0" />
-               </content>
-            </TitledPane>
-            <TitledPane fx:id="ieeeTranTitlePane" animated="false" collapsible="false" text="IEEETran">
-               <content>
-                  <FlowPane fx:id="ieeetranPane" prefHeight="200.0" prefWidth="200.0" />
-               </content>
-            </TitledPane>
-            <TitledPane fx:id="customTitlePane" animated="false" collapsible="false" text="%Custom">
-               <content>
-                  <FlowPane fx:id="customPane" prefHeight="200.0" prefWidth="200.0" />
-               </content>
-            </TitledPane>
-            <GridPane alignment="CENTER">
+       <VBox prefHeight="200.0" prefWidth="400.0">
+           <children>
+               <TitledPane fx:id="biblatexTitlePane" animated="false" collapsible="false" text="Biblatex">
+                   <content>
+                       <FlowPane fx:id="biblatexPane" prefHeight="200.0" prefWidth="200.0"/>
+                   </content>
+               </TitledPane>
+               <TitledPane fx:id="bibTexTitlePane" animated="false" collapsible="false" text="BibTeX">
+                   <content>
+                       <FlowPane fx:id="bibTexPane" prefHeight="200.0" prefWidth="200.0"/>
+                   </content>
+               </TitledPane>
+               <TitledPane fx:id="ieeeTranTitlePane" animated="false" collapsible="false" text="IEEETran">
+                   <content>
+                       <FlowPane fx:id="ieeetranPane" prefHeight="200.0" prefWidth="200.0"/>
+                   </content>
+               </TitledPane>
+               <TitledPane fx:id="customTitlePane" animated="false" collapsible="false" text="%Custom">
+                   <content>
+                       <FlowPane fx:id="customPane" prefHeight="200.0" prefWidth="200.0"/>
+                   </content>
+               </TitledPane>
+               <GridPane alignment="CENTER">
                <children>
-                  <Label text="%ID type"/>
-                  <ComboBox fx:id="idBasedFetchers" onAction="#focusTextField" prefHeight="30.0" prefWidth="300.0" GridPane.columnIndex="1" />            
-                  <Label text="%ID" GridPane.rowIndex="1" />
-                  <TextField fx:id="idTextField" onAction="#runFetcherWorker" prefHeight="30.0" prefWidth="300.0" GridPane.columnIndex="1" GridPane.rowIndex="1" />
+                   <Label text="%ID type"/>
+                   <ComboBox fx:id="idBasedFetchers" onAction="#focusTextField" prefHeight="30.0" prefWidth="300.0"
+                             GridPane.columnIndex="1"/>
+                   <Label text="%ID" GridPane.rowIndex="1" />
+                   <TextField fx:id="idTextField" onAction="#runFetcherWorker" prefHeight="30.0" prefWidth="300.0"
+                              GridPane.columnIndex="1" GridPane.rowIndex="1"/>
                </children>
                <columnConstraints>
                   <ColumnConstraints hgrow="SOMETIMES" maxWidth="122.0" minWidth="10.0" prefWidth="100.0" />
@@ -56,11 +58,11 @@
                   <Insets bottom="4.0" left="4.0" right="4.0" top="4.0" />
                </opaqueInsets>
                <rowConstraints>
-                  <RowConstraints minHeight="30.0" prefHeight="30.0" vgrow="SOMETIMES" />
-                  <RowConstraints minHeight="30.0" prefHeight="30.0" vgrow="SOMETIMES" />
+                   <RowConstraints minHeight="30.0" prefHeight="30.0" vgrow="SOMETIMES"/>
+                   <RowConstraints minHeight="30.0" prefHeight="30.0" vgrow="SOMETIMES"/>
                </rowConstraints>
             </GridPane>
-         </children>
-      </VBox>
+           </children>
+       </VBox>
    </content>
 </DialogPane>
diff --git a/src/main/java/org/jabref/gui/PreviewPanel.java b/src/main/java/org/jabref/gui/PreviewPanel.java
@@ -24,7 +24,7 @@
 import javafx.scene.web.WebView;
 
 import org.jabref.Globals;
-import org.jabref.gui.externalfiles.NewDroppedFileHandler;
+import org.jabref.gui.externalfiles.ExternalFilesEntryLinker;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.keyboard.KeyBinding;
@@ -61,9 +61,9 @@ public class PreviewPanel extends ScrollPane implements SearchQueryHighlightList
     private final DialogService dialogService;
     private final KeyBindingRepository keyBindingRepository;
 
+    private final String defaultPreviewStyle = "Preview";
     private String previewStyle;
     private CitationStyle citationStyle;
-    private final String defaultPreviewStyle = "Preview";
     private Optional<BasePanel> basePanel = Optional.empty();
 
     private boolean fixedLayout;
@@ -80,7 +80,7 @@ public class PreviewPanel extends ScrollPane implements SearchQueryHighlightList
     private final WebView previewView;
     private Optional<Future<?>> citationStyleFuture = Optional.empty();
 
-    private final NewDroppedFileHandler fileHandler;
+    private final ExternalFilesEntryLinker fileLinker;
 
     /**
      * @param panel           (may be null) Only set this if the preview is associated to the main window.
@@ -93,11 +93,7 @@ public PreviewPanel(BasePanel panel, BibDatabaseContext databaseContext, KeyBind
         this.clipBoardManager = Globals.clipboardManager;
         this.keyBindingRepository = keyBindingRepository;
 
-        fileHandler = new NewDroppedFileHandler(dialogService, databaseContext, externalFileTypes,
-                                                Globals.prefs.getFilePreferences(),
-                                                Globals.prefs.getImportFormatPreferences(),
-                                                Globals.prefs.getUpdateFieldPreferences(),
-                                                Globals.getFileUpdateMonitor());
+        fileLinker = new ExternalFilesEntryLinker(externalFileTypes, Globals.prefs.getFilePreferences(), databaseContext);
 
         // Set up scroll pane for preview pane
         setFitToHeight(true);
@@ -135,19 +131,18 @@ public PreviewPanel(BasePanel panel, BibDatabaseContext databaseContext, KeyBind
                 List<Path> files = event.getDragboard().getFiles().stream().map(File::toPath).collect(Collectors.toList());
 
                 if (event.getTransferMode() == TransferMode.MOVE) {
-
                     LOGGER.debug("Mode MOVE"); //shift on win or no modifier
-                    fileHandler.addToEntryRenameAndMoveToFileDir(entry, files);
+                    fileLinker.moveFilesToFileDirAndAddToEntry(entry, files);
                 }
                 if (event.getTransferMode() == TransferMode.LINK) {
                     LOGGER.debug("Node LINK"); //alt on win
-                    fileHandler.addToEntry(entry, files);
-
+                    fileLinker.addFilesToEntry(entry, files);
                 }
                 if (event.getTransferMode() == TransferMode.COPY) {
                     LOGGER.debug("Mode Copy"); //ctrl on win, no modifier on Xubuntu
-                    fileHandler.copyFilesToFileDirAndAddToEntry(entry, files);
+                    fileLinker.copyFilesToFileDirAndAddToEntry(entry, files);
                 }
+                success = true;
             }
 
             event.setDropCompleted(success);

diff --git a/src/main/java/org/jabref/gui/SidePaneManager.java b/src/main/java/org/jabref/gui/SidePaneManager.java
@@ -31,10 +31,10 @@ public SidePaneManager(JabRefPreferences preferences, JabRefFrame frame) {
 
         OpenOfficePreferences openOfficePreferences = preferences.getOpenOfficePreferences();
         Stream.of(
-                  new FileUpdatePanel(this),
-                  new GroupSidePane(this, preferences, frame.getDialogService()),
-                  new WebSearchPane(this, preferences, frame),
-                  new OpenOfficeSidePanel(this, preferences, frame))
+                new FileUpdatePanel(this),
+                new GroupSidePane(this, preferences, frame.getDialogService()),
+                new WebSearchPane(this, preferences, frame),
+                new OpenOfficeSidePanel(this, preferences, frame))
               .forEach(pane -> components.put(pane.getType(), pane));
 
         if (preferences.getBoolean(JabRefPreferences.GROUP_SIDEPANE_VISIBLE)) {

diff --git a/src/main/java/org/jabref/gui/bibtexkeypattern/ResolveDuplicateLabelDialog.java b/src/main/java/org/jabref/gui/bibtexkeypattern/ResolveDuplicateLabelDialog.java
@@ -48,7 +48,7 @@ public ResolveDuplicateLabelDialog(BasePanel panel, String key, List<BibEntry> e
         diag = new JDialog((JFrame) null, Localization.lang("Duplicate BibTeX key"), true);
 
         FormBuilder b = FormBuilder.create().layout(new FormLayout(
-                                                                   "left:pref, 4dlu, fill:pref", "p"));
+                "left:pref, 4dlu, fill:pref", "p"));
         b.add(new JLabel(Localization.lang("Duplicate BibTeX key") + ": " + key)).xyw(1, 1, 3);
         b.getPanel().setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
 

diff --git a/src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java b/src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java
@@ -112,7 +112,6 @@ protected List<CopyFilesResultItemViewModel> call() throws InterruptedException,
                             writeLogMessage(newFile, bw, localizedErrorMessage);
                             addResultToList(newFile, success, localizedErrorMessage);
                         }
-
                     }
 
                 }
-Original file line number
+Diff line change
@@ Expand Up @@
                                 writeLogMessage(newFile, bw, localizedErrorMessage);
                                 addResultToList(newFile, success, localizedErrorMessage);
                             }
                         }
                     }
@@ Expand Down @@