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

* upstream/master: (21 commits) New Crowdin translations (#5729) Update license of Oracle JDBC Changes string representation when detecting custom entry types. (#5741) Try to fix GitVersion Also run workflow on tag creation Add README.md with an initial help to work on command line para… (#5720) Bugfix for Multiscreen (#5738) Fix #2868 - keep source groups selected after drag and drop retrigger build Squashed 'src/main/resources/csl-styles/' changes from f71cd32..49a1841 try to fix pull of csl styles try to fix csl update Fixed untranslated Strings issue #5701 Fix #5603 - account for file extension in file name length (#5726) New translations JabRef_en.properties (French) Bump unirest-java from 3.2.00 to 3.3.00 Bump postgresql from 42.2.8 to 42.2.9 Bump tika-core from 1.22 to 1.23 Fix upload to GitHub artifacts (#5712) Try to fix csl update (#5718) ...
JabRef · Dec 14, 2019 · 21b4de3 · 21b4de3
2 parents 743554a + 2e056e6
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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
@@ -1,6 +1,6 @@
 name: Deployment
 
-on: [push]
+on: [create, push]
 
 jobs:
   deploy:
@@ -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
@@ -11,15 +11,28 @@ 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
-        run: git subtree pull --prefix src/main/resources/csl-styles csl-styles master --squash
+        run: | 
+          git checkout master
+          git subtree pull --prefix src/main/resources/csl-styles csl-styles master --squash
       - name: Add csl-locales remote
         run: git remote add -f csl-locales https://github.com/citation-style-language/locales.git
       - name: Update csl-locales
-        run: git subtree pull --prefix src/main/resources/csl-locales csl-locales master --squash
+        run: |
+          git checkout master
+          git subtree pull --prefix src/main/resources/csl-locales csl-locales master --squash
       - 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/CHANGELOG.md b/CHANGELOG.md
@@ -62,6 +62,7 @@ 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)
@@ -70,6 +71,10 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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.
+- We fixed an issue where renaming referenced files for bib entries with long titles was not possible. [#5603](https://github.com/JabRef/jabref/issues/5603)
+- We fixed an issue where a window which is on an external screen gets unreachable when external screen is removed. [#5037](https://github.com/JabRef/jabref/issues/5037)
+- We fixed a bug where the selection of groups was lost after drag and drop. [#2868](https://github.com/JabRef/jabref/issues/2868)
+- We fixed an issue where the custom entry types didn't show the correct display name [#5651](https://github.com/JabRef/jabref/issues/5651)
 
 ### Removed
 

diff --git a/GitVersion.yml b/GitVersion.yml
@@ -1,2 +1,10 @@
-assembly-versioning-format: '{major}.{minor}.{buildmetadata}'
+assembly-versioning-format: '{major}.{minor}.{WeightedPreReleaseNumber}'
 assembly-informational-format: '{major}.{minor}{PreReleaseTagWithDash}--{CommitDate}--{ShortSha}'
+
+branches:
+  master:
+    regex: ^master
+    mode: ContinuousDelivery
+    tag: beta
+    increment: Minor
+    pre-release-weight: 30000 # 0 after stable release, 15000 before alpha release, 30000 before beta release, 50000 before stable release
diff --git a/README.md b/README.md
@@ -36,14 +36,14 @@ JabRef supports you in every step of your research work.
 - Attach related documents: 20 different kinds of documents supported out of the box, completely customizable and extendable
 - Automatically rename and move associated documents according to customizable rules
 - Keep track of what you read: ranking, priority, printed, quality-assured 
-	
+
 #### Cite
 
 - Native [BibTeX] and [Biblatex] support
 - Cite-as-you-write functionality for external applications such as Emacs, Kile, LyX, Texmaker, TeXstudio, Vim and WinEdt.
 - Format references in one of the many thousand built-in citation styles or create your style
 - Support for Word and LibreOffice/OpenOffice for inserting and formatting citations
-	
+
 #### Share
 
 - Many built-in export options or create your export format

diff --git a/build.gradle b/build.gradle
@@ -116,7 +116,7 @@ dependencies {
 
     compile group: 'org.apache.commons', name: 'commons-csv', version: '1.7'
 
-    compile group: 'org.apache.tika', name: 'tika-core', version: '1.22'
+    compile group: 'org.apache.tika', name: 'tika-core', version: '1.23'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     compile 'org.bouncycastle:bcprov-jdk15on:1.64'
@@ -142,7 +142,7 @@ dependencies {
 
     compile group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.5.2'
 
-    compile 'org.postgresql:postgresql:42.2.8'
+    compile 'org.postgresql:postgresql:42.2.9'
 
     compile ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -169,7 +169,7 @@ dependencies {
     compile 'org.controlsfx:controlsfx:11.0.1'
 
     compile 'org.jsoup:jsoup:1.12.1'
-    compile 'com.konghq:unirest-java:3.2.00'
+    compile 'com.konghq:unirest-java:3.3.00'
 
     compile 'org.slf4j:slf4j-api:2.0.0-alpha1'
     compile group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'

diff --git a/docs/README.md b/docs/README.md
@@ -0,0 +1,41 @@
+# Develop JabRef
+
+This page presents all development informatation around JabRef. For users documentation see <https://docs.jabref.org>.
+
+## Command Line
+
+The package `org.jabref.cli` is responsible for handling the command line options.
+
+During development, one can configure IntelliJ to pass command line paramters:
+
+![IntelliJ-run-configuration](images/intellij-run-configuration-command-line.png)
+
+Passing command line arguments using gradle is currently not possible as all arguments (such as `-Dfile.encoding=windows-1252`) are passed to the application.
+
+Without jlink, it is not possible to generate a fat jar any more. During development, the capabilities of the IDE has to be used.
+
+## Groups
+
+UML diagram showing aspects of groups: [Groups.uml](Gropus.uml).
+
+## Decision Records
+
+This log lists the decisions for JabRef.
+
+<!-- adrlog -->
+
+- [ADR-0000](0000-use-markdown-architectural-decision-records.md) - Use Markdown Architectural Decision Records
+- [ADR-0001](0001-use-crowdin-for-translations.md) - Use Crowdin for translations
+- [ADR-0002](0002-use-slf4j-for-logging.md) - Use slf4j together with log4j2 for logging
+- [ADR-0003](0003-use-gradle-as-build-tool.md) - Use Gradle as build tool
+- [ADR-0003](0003-use-openjson-as-replacement-for-org-json.md) - Use openjson as replacement for org.json
+- [ADR-0004](0004-use-mariadb-connector.md) - Use MariaDB Connector
+- [ADR-0005](0005-fully-support-utf8-only-for-latex-files.md) - Fully Support UTF-8 Only For LaTeX Files
+- [ADR-0006](0006-only-translated-strings-in-language-file.md) - Only translated strings in language file
+- [ADR-0007](0007-human-readable-changelog.md) - Provide a human-readable changelog
+
+<!-- adrlogstop -->
+
+For new ADRs, please use [docs/template.md](docs/template.md) as basis.
+More information on MADR is available at <https://adr.github.io/madr/>.
+General information about architectural decision records is available at <https://adr.github.io/>.
diff --git a/docs/adr/README.md b/docs/adr/README.md
diff --git a/docs/images/intellij-run-configuration-command-line.png b/docs/images/intellij-run-configuration-command-line.png
diff --git a/external-libraries.txt b/external-libraries.txt
@@ -67,8 +67,8 @@ License: MIT
 
 Id:      com.oracle.ojdbc:ojdbc10
 Project: Oracle's JDBC drivers
-URL:     https://medium.com/oracledevs/oracle-jdbc-drivers-on-maven-central-64fcf724d8b
-License: Proprietary
+URL:     https://repo1.maven.org/maven2/com/oracle/ojdbc/ojdbc10/19.3.0.0/ojdbc10-19.3.0.0.pom
+License: Oracle Free Use Terms and Conditions (FUTC)
 
 Id:      com.sibvisions.external.jvxfx:DnDTabPane
 Project: Drag'n'Drop TabPane

diff --git a/src/main/java/org/jabref/JabRefGUI.java b/src/main/java/org/jabref/JabRefGUI.java
@@ -3,11 +3,12 @@
 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;
+import javafx.stage.Screen;
 import javafx.stage.Stage;
 
 import org.jabref.gui.BasePanel;
@@ -40,12 +41,14 @@ public class JabRefGUI {
 
     private final List<ParserResult> bibDatabases;
     private final boolean isBlank;
+    private boolean correctedWindowPos;
     private final List<ParserResult> failed = new ArrayList<>();
     private final List<ParserResult> toOpenTab = new ArrayList<>();
 
     public JabRefGUI(Stage mainStage, List<ParserResult> databases, boolean isBlank) {
         this.bibDatabases = databases;
         this.isBlank = isBlank;
+        this.correctedWindowPos = false;
         mainFrame = new JabRefFrame(mainStage);
 
         openWindow(mainStage);
@@ -62,12 +65,21 @@ private void openWindow(Stage mainStage) {
         // Restore window location and/or maximised state
         if (Globals.prefs.getBoolean(JabRefPreferences.WINDOW_MAXIMISED)) {
             mainStage.setMaximized(true);
+        } else if (Screen.getScreens().size() == 1 && isWindowPositionOutOfBounds()) {
+            //corrects the Window, if its outside of the mainscreen
+            LOGGER.debug("The Jabref Window is outside the Main Monitor\n");
+            mainStage.setX(0);
+            mainStage.setY(0);
+            mainStage.setWidth(1024);
+            mainStage.setHeight(768);
+            correctedWindowPos = true;
         } else {
             mainStage.setX(Globals.prefs.getDouble(JabRefPreferences.POS_X));
             mainStage.setY(Globals.prefs.getDouble(JabRefPreferences.POS_Y));
             mainStage.setWidth(Globals.prefs.getDouble(JabRefPreferences.SIZE_X));
             mainStage.setHeight(Globals.prefs.getDouble(JabRefPreferences.SIZE_Y));
         }
+        printWindowState(mainStage);
 
         // We create a decoration pane ourselves for performance reasons
         // (otherwise it has to be injected later, leading to a complete redraw/relayout of the complete scene)
@@ -82,7 +94,11 @@ private void openWindow(Stage mainStage) {
         mainStage.show();
 
         mainStage.setOnCloseRequest(event -> {
-            saveWindowState(mainStage);
+            if (!correctedWindowPos) {
+                //saves the window position only if its not  corrected -> the window will rest at the old Position,
+                //if the external Screen is connected again.
+                saveWindowState(mainStage);
+            }
             boolean reallyQuit = mainFrame.quit();
             if (!reallyQuit) {
                 event.consume();
@@ -97,6 +113,13 @@ 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 +129,34 @@ 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;
             }
         }
 
@@ -187,6 +204,33 @@ private void saveWindowState(Stage mainStage) {
         Globals.prefs.putDouble(JabRefPreferences.POS_Y, mainStage.getY());
         Globals.prefs.putDouble(JabRefPreferences.SIZE_X, mainStage.getWidth());
         Globals.prefs.putDouble(JabRefPreferences.SIZE_Y, mainStage.getHeight());
+        printWindowState(mainStage);
+    }
+
+    /**
+     * outprints the Data from the Screen
+     * (only in debug mode)
+     * @param mainStage
+     */
+    private void printWindowState(Stage mainStage) {
+        StringBuilder bob = new StringBuilder();
+        bob.append("SCREEN DATA:");
+        bob.append("mainStage.WINDOW_MAXIMISED: " + mainStage.isMaximized() + "\n");
+        bob.append("mainStage.POS_X: " + mainStage.getX() + "\n");
+        bob.append("mainStage.POS_Y: " + mainStage.getY() + "\n");
+        bob.append("mainStage.SIZE_X: " + mainStage.getWidth() + "\n");
+        bob.append("mainStages.SIZE_Y: " + mainStage.getHeight() + "\n");
+        LOGGER.debug(bob.toString());
+    }
+
+    /**
+     * Tests if the window coordinates are out of the mainscreen
+     * @return outbounds
+     */
+    private boolean isWindowPositionOutOfBounds() {
+
+       return  !Screen.getPrimary().getBounds().contains(Globals.prefs.getDouble(JabRefPreferences.POS_X) , Globals.prefs.getDouble(JabRefPreferences.POS_Y));
+
     }
 
     private void openLastEditedDatabases() {