Merge remote-tracking branch 'upstream/master' into release-5-0-beta

* upstream/master: Fix upload to GitHub artifacts (#5712) Try to fix csl update (#5718) Fix import into currently open library (#5717) Add throttle to AutosaveUIManager (#5680) Do not couple search position to sidebar width (#5716) fix springer fetcher tests Bump controlsfx from 11.0.0 to 11.0.1 (#5714)
JabRef · Dec 8, 2019 · ef69299 · ef69299
2 parents 7c79ea9 + a86b0bf
commit ef69299
Show file tree

Hide file tree

Showing 11 changed files with 104 additions and 88 deletions.
diff --git a/.github/failure-csl-update b/.github/failure-csl-update
@@ -0,0 +1,5 @@
+---
+title: Error while updating citation styles
+labels: code-quality, dependencies
+---
+[Update of citation styles failed!](https://github.com/JabRef/jabref/actions?query=workflow%3A%22Refresh+Citation+Style+Language+Files%22) 
diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -94,11 +94,6 @@ jobs:
         export BADASS_JLINK_JPACKAGE_HOME="${GITHUB_WORKSPACE}${{ matrix.jdk14Path }}"
         ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
       shell: bash
-    - name: Add installer as artifact
-      uses: actions/upload-artifact@master
-      with:
-        name: JabRef-${{ matrix.displayName }}
-        path: build/distribution
     - name: Package application image
       run: ${{ matrix.archivePortable }}
       shell: bash
@@ -115,6 +110,11 @@ jobs:
         get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
         get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
       shell: pwsh
+    - name: Upload to GitHub workflow artifacts store
+      uses: actions/upload-artifact@master
+      with:
+        name: JabRef-${{ matrix.displayName }}
+        path: build/distribution
     - name: Upload to builds.jabref.org
       uses: garygrossgarten/github-action-scp@release
       with:

diff --git a/.github/workflows/refresh-csl-subtrees.yml b/.github/workflows/refresh-csl-subtrees.yml
@@ -11,7 +11,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v1
+        uses: actions/checkout@v2-beta
+        with:
+          ref: master
       - name: Add csl-styles remote
         run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
       - name: Update csl-styles
@@ -23,3 +25,10 @@ jobs:
       - uses: ad-m/github-push-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Report issues
+        if: failure()
+        uses: JasonEtco/create-an-issue@master
+        env: 
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          filename: .github/failure-csl-update.md
diff --git a/.idea/runConfigurations/JabRef_Main.xml b/.idea/runConfigurations/JabRef_Main.xml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,6 +24,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added support to switch between biblatex and bibtex library types. [#5550](https://github.com/JabRef/jabref/issues/5550)
 - We changed the save action buttons to be easier to understand. [#5565](https://github.com/JabRef/jabref/issues/5565)
 - We made the columns for groups, files and uri in the main table reorderable and merged the clickable icon columns for uri, url, doi and eprint. [#5544](https://github.com/JabRef/jabref/pull/5544)
+- We reduced the number of write actions performed when autosave is enabled [#5679](https://github.com/JabRef/jabref/issues/5679)
 
 ### Fixed
 
@@ -61,13 +62,15 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The "Automatically set file links" feature now follows symbolic links. [#5664](https://github.com/JabRef/jabref/issues/5664)
 - After successful import of one or multiple bib entries the main table scrolls to the first imported entry [#5383](https://github.com/JabRef/jabref/issues/5383)
 - We fixed an exception which occurred when an invalid jstyle was loaded. [#5452](https://github.com/JabRef/jabref/issues/5452)
+- We fixed an issue where the command line arguments `importBibtex` and `importToOpen` did not import into the currently open library, but opened a new one. [#5537](https://github.com/JabRef/jabref/issues/5537)
 - We fixed an error where the preview theme did not adapt to the "Dark" mode [#5463](https://github.com/JabRef/jabref/issues/5463)
 - We fixed an issue where the merge dialog showed the wrong text colour in "Dark" mode [#5516](https://github.com/JabRef/jabref/issues/5516)
 - We fixed visibility issues with the scrollbar and group selection highlight in "Dark" mode, and enabled "Dark" mode for the OpenOffice preview in the style selection window. [#5522](https://github.com/JabRef/jabref/issues/5522)
 - We fixed an issue where the author field was not correctly parsed during bibtex key-generation. [#5551](https://github.com/JabRef/jabref/issues/5551)
 - We fixed an issue where notifications where shown during autosave. [#5555](https://github.com/JabRef/jabref/issues/5555)
 - We fixed an issue where the side pane was not remembering its position. [#5615](https://github.com/JabRef/jabref/issues/5615)
 - We fixed an issue where JabRef could not interact with [Oracle XE](https://www.oracle.com/de/database/technologies/appdev/xe.html) in the [shared SQL database setup](https://docs.jabref.org/collaborative-work/sqldatabase).
+- We fixed an issue where the toolbar icons were hidden on smaller screens.
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -166,7 +166,7 @@ dependencies {
     compile 'org.fxmisc.richtext:richtextfx:0.10.3'
     compile group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     compile 'com.jfoenix:jfoenix:9.0.9'
-    compile 'org.controlsfx:controlsfx:11.0.0'
+    compile 'org.controlsfx:controlsfx:11.0.1'
 
     compile 'org.jsoup:jsoup:1.12.1'
     compile 'com.konghq:unirest-java:3.2.00'

diff --git a/src/main/java/org/jabref/JabRefGUI.java b/src/main/java/org/jabref/JabRefGUI.java
@@ -3,8 +3,8 @@
 import java.io.File;
 import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
+import java.util.stream.Collectors;
 
 import javafx.application.Platform;
 import javafx.scene.Scene;
@@ -97,6 +97,13 @@ private void openDatabases() {
             openLastEditedDatabases();
         }
 
+        // Remove invalid databases
+        List<ParserResult> invalidDatabases = bibDatabases.stream()
+                                                          .filter(ParserResult::isInvalid)
+                                                          .collect(Collectors.toList());
+        failed.addAll(invalidDatabases);
+        bibDatabases.removeAll(invalidDatabases);
+
         // passed file (we take the first one) should be focused
         String focusedFile = bibDatabases.stream()
                                          .findFirst()
@@ -106,40 +113,34 @@ private void openDatabases() {
 
         // Add all bibDatabases databases to the frame:
         boolean first = false;
-        if (!bibDatabases.isEmpty()) {
-            for (Iterator<ParserResult> parserResultIterator = bibDatabases.iterator(); parserResultIterator.hasNext();) {
-                ParserResult pr = parserResultIterator.next();
-                // Define focused tab
-                if (pr.getFile().filter(path -> path.getAbsolutePath().equals(focusedFile)).isPresent()) {
-                    first = true;
-                }
+        for (ParserResult pr : bibDatabases) {
+            // Define focused tab
+            if (pr.getFile().filter(path -> path.getAbsolutePath().equals(focusedFile)).isPresent()) {
+                first = true;
+            }
 
-                if (pr.isInvalid()) {
-                    failed.add(pr);
-                    parserResultIterator.remove();
-                } else if (pr.getDatabase().isShared()) {
-                    try {
-                        new SharedDatabaseUIManager(mainFrame).openSharedDatabaseFromParserResult(pr);
-                    } catch (SQLException | DatabaseNotSupportedException | InvalidDBMSConnectionPropertiesException |
-                            NotASharedDatabaseException e) {
-                        pr.getDatabaseContext().clearDatabaseFile(); // do not open the original file
-                        pr.getDatabase().clearSharedDatabaseID();
-
-                        LOGGER.error("Connection error", e);
-                        mainFrame.getDialogService().showErrorDialogAndWait(
-                                Localization.lang("Connection error"),
-                                Localization.lang("A local copy will be opened."),
-                                e);
-                    }
-                    toOpenTab.add(pr);
-                } else if (pr.toOpenTab()) {
-                    // things to be appended to an opened tab should be done after opening all tabs
-                    // add them to the list
-                    toOpenTab.add(pr);
-                } else {
-                    mainFrame.addParserResult(pr, first);
-                    first = false;
+            if (pr.getDatabase().isShared()) {
+                try {
+                    new SharedDatabaseUIManager(mainFrame).openSharedDatabaseFromParserResult(pr);
+                } catch (SQLException | DatabaseNotSupportedException | InvalidDBMSConnectionPropertiesException |
+                        NotASharedDatabaseException e) {
+                    pr.getDatabaseContext().clearDatabaseFile(); // do not open the original file
+                    pr.getDatabase().clearSharedDatabaseID();
+
+                    LOGGER.error("Connection error", e);
+                    mainFrame.getDialogService().showErrorDialogAndWait(
+                            Localization.lang("Connection error"),
+                            Localization.lang("A local copy will be opened."),
+                            e);
                 }
+                toOpenTab.add(pr);
+            } else if (pr.toOpenTab()) {
+                // things to be appended to an opened tab should be done after opening all tabs
+                // add them to the list
+                toOpenTab.add(pr);
+            } else {
+                mainFrame.addParserResult(pr, first);
+                first = false;
             }
         }
 

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -422,8 +422,6 @@ public void changed(ObservableValue<? extends Boolean> observable, Boolean oldVa
 
                     EasyBind.subscribe(sidePane.visibleProperty(), visible -> {
                         if (visible) {
-                            // Run SplitPane.setResizableWithParent later to avoid miscalculation during initial layouting
-                            Platform.runLater(() -> SplitPane.setResizableWithParent(sidePane, Boolean.FALSE));
                             if (!splitPane.getItems().contains(sidePane)) {
                                 splitPane.getItems().add(0, sidePane);
                                 setDividerPosition();
@@ -452,6 +450,7 @@ private void setDividerPosition() {
 
     private Node createToolbar() {
         Pane leftSpacer = new Pane();
+        leftSpacer.setMinWidth(50);
         HBox.setHgrow(leftSpacer, Priority.SOMETIMES);
         Pane rightSpacer = new Pane();
         HBox.setHgrow(rightSpacer, Priority.SOMETIMES);
@@ -471,9 +470,6 @@ private Node createToolbar() {
                 factory.createIconButton(StandardActions.SAVE_LIBRARY, new OldDatabaseCommandWrapper(Actions.SAVE, this, stateManager)),
                 leftSpacer
         );
-        leftSide.setMinWidth(100);
-        leftSide.prefWidthProperty().bind(sidePane.widthProperty());
-        leftSide.maxWidthProperty().bind(sidePane.widthProperty());
 
         final PushToApplicationAction pushToApplicationAction = getPushToApplicationsManager().getPushToApplicationAction();
         final Button pushToApplicationButton = factory.createIconButton(pushToApplicationAction.getActionInformation(), pushToApplicationAction);
@@ -976,37 +972,35 @@ public void updateAllTabTitles() {
     }
 
     public void addTab(BasePanel basePanel, boolean raisePanel) {
-        DefaultTaskExecutor.runInJavaFXThread(() -> {
-            // add tab
-            Tab newTab = new Tab(basePanel.getTabTitle(), basePanel);
-            tabbedPane.getTabs().add(newTab);
-            newTab.setOnCloseRequest(event -> {
-                closeTab((BasePanel) newTab.getContent());
-                event.consume();
-            });
+        // add tab
+        Tab newTab = new Tab(basePanel.getTabTitle(), basePanel);
+        tabbedPane.getTabs().add(newTab);
+        newTab.setOnCloseRequest(event -> {
+            closeTab((BasePanel) newTab.getContent());
+            event.consume();
+        });
 
-            // update all tab titles
-            updateAllTabTitles();
+        // update all tab titles
+        updateAllTabTitles();
 
-            if (raisePanel) {
-                tabbedPane.getSelectionModel().select(newTab);
-            }
+        if (raisePanel) {
+            tabbedPane.getSelectionModel().select(newTab);
+        }
 
-            // Register undo/redo listener
-            basePanel.getUndoManager().registerListener(new UndoRedoEventManager());
+        // Register undo/redo listener
+        basePanel.getUndoManager().registerListener(new UndoRedoEventManager());
 
-            BibDatabaseContext context = basePanel.getBibDatabaseContext();
+        BibDatabaseContext context = basePanel.getBibDatabaseContext();
 
-            if (readyForAutosave(context)) {
-                AutosaveManager autosaver = AutosaveManager.start(context);
-                autosaver.registerListener(new AutosaveUIManager(basePanel));
-            }
+        if (readyForAutosave(context)) {
+            AutosaveManager autosaver = AutosaveManager.start(context);
+            autosaver.registerListener(new AutosaveUIManager(basePanel));
+        }
 
-            BackupManager.start(context, Globals.entryTypesManager, prefs);
+        BackupManager.start(context, Globals.entryTypesManager, prefs);
 
-            // Track opening
-            trackOpenNewDatabase(basePanel);
-        });
+        // Track opening
+        trackOpenNewDatabase(basePanel);
     }
 
     private void trackOpenNewDatabase(BasePanel basePanel) {