Merge remote-tracking branch 'upstream/main' into addSourceToChangesD…

…ialog

* upstream/main:
  Fixed ADS tests
  Bump junit-jupiter from 5.9.1 to 5.9.2 (#9579)
  Bump actions/configure-pages from 2 to 3
  open office csv format correction for abstract column (#9570)
  Update CHANGELOG.md
  add change log entry for the given change
  typo removed (#9577)
  remove filter that consumes mouse rightclick

.github/workflows/pages.yml

@@ -37,7 +37,7 @@ jobs:
           working-directory: docs/
       - name: Setup Pages
         id: pages
-        uses: actions/configure-pages@v2
+        uses: actions/configure-pages@v3
       - name: Build with Jekyll
         run: |
           cd docs

CHANGELOG.md

@@ -67,6 +67,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - For portable versions, the `.deb` file now works on plain debian again. [#9472](https://github.com/JabRef/jabref/issues/9472)
 - We fixed an issue where the download of linked online files failed after an import of entries for certain urls. [#9518](https://github.com/JabRef/jabref/issues/9518)
 - We fixed an issue where an exception occured when manually downloading a file from an URL in the entry editor. [#9521](https://github.com/JabRef/jabref/issues/9521)
+- We fixed an issue with open office csv file formatting where commas in the abstract field where not escaped. [#9087][https://github.com/JabRef/jabref/issues/9087]
+- We fixed an issue with deleting groups where subgroups different from the selected group were deleted. [#9281][https://github.com/JabRef/jabref/issues/9281]
 
 ## [5.8] - 2022-12-18
 

CONTRIBUTING.md

@@ -10,7 +10,7 @@ General overview about contributing for programmers and non-programmers is avail
 ## Pull Request Process
 
 1. Understand the basics listed at <https://devdocs.jabref.org/contributing>.
-2. Follow the "formal requirements". They are not too hard, they merely support the maintainers to focus on supportive feedback than just stating the obvious. The also have helpful hints how to work with localization.
+2. Follow the "formal requirements". They are not too hard, they merely support the maintainers to focus on supportive feedback than just stating the obvious. They also have helpful hints how to work with localization.
 3. Create a pull request. You can create a draft pull request to enable automatic checks.
 4. Wait for feedback of the developers
 5. Address the feedback of the developers

build.gradle

@@ -204,7 +204,7 @@ dependencies {
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
     testImplementation 'io.github.classgraph:classgraph:4.8.154'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.9.1'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.9.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.9.2'
 
     testImplementation 'org.mockito:mockito-core:5.0.0'

src/main/java/org/jabref/gui/groups/GroupTreeView.java

@@ -28,7 +28,6 @@
 import javafx.scene.control.TreeTableView;
 import javafx.scene.input.ClipboardContent;
 import javafx.scene.input.Dragboard;
-import javafx.scene.input.MouseButton;
 import javafx.scene.input.MouseEvent;
 import javafx.scene.input.TransferMode;
 import javafx.scene.layout.BorderPane;
@@ -266,10 +265,7 @@ private void initialize() {
                             .mapOpt(this::createContextMenuForGroup)
                             .orElseOpt((ContextMenu) null));
             row.addEventFilter(MouseEvent.MOUSE_PRESSED, event -> {
-                if (event.getButton() == MouseButton.SECONDARY) {
-                    // Prevent right-click to select group
-                    event.consume();
-                } else if (event.getTarget() instanceof StackPane pane) {
+                if (event.getTarget() instanceof StackPane pane) {
                     if (pane.getStyleClass().contains("arrow") || pane.getStyleClass().contains("tree-disclosure-node")) {
                         event.consume();
                     }

src/main/java/org/jabref/logic/layout/LayoutEntry.java

@@ -72,6 +72,7 @@
 import org.jabref.logic.layout.format.RemoveTilde;
 import org.jabref.logic.layout.format.RemoveWhitespace;
 import org.jabref.logic.layout.format.Replace;
+import org.jabref.logic.layout.format.ReplaceWithEscapedDoubleQuotes;
 import org.jabref.logic.layout.format.RisAuthors;
 import org.jabref.logic.layout.format.RisKeywords;
 import org.jabref.logic.layout.format.RisMonth;
@@ -475,6 +476,7 @@ private LayoutFormatter getLayoutFormatterByName(String name) {
             case "Markdown" -> new MarkdownFormatter();
             case "CSLType" -> new CSLType();
             case "ShortMonth" -> new ShortMonthFormatter();
+            case "ReplaceWithEscapedDoubleQuotes" -> new ReplaceWithEscapedDoubleQuotes();
             default -> null;
         };
     }

src/main/java/org/jabref/logic/layout/format/ReplaceWithEscapedDoubleQuotes.java

@@ -0,0 +1,19 @@
+package org.jabref.logic.layout.format;
+
+import org.jabref.logic.layout.LayoutFormatter;
+
+public class ReplaceWithEscapedDoubleQuotes implements LayoutFormatter {
+    @Override
+    public String format(String fieldText) {
+        StringBuilder builder = new StringBuilder(fieldText.length());
+
+        for (char c : fieldText.toCharArray()) {
+            if (c == '\"') {
+                builder.append("\"\"");
+            } else {
+                builder.append(c);
+            }
+        }
+        return builder.toString();
+    }
+}

src/main/resources/resource/layout/openoffice/openoffice-csv.layout

@@ -1 +1 @@
-\format[GetOpenOfficeType]{\entrytype},"\begin{isbn}\isbn\end{isbn}","\citationkey","\format[Authors(LastFirst,FullName,Semicolon,Semicolon)]{\author}","\format[RemoveBrackets,RemoveWhitespace]{\title}","\journal",\volume,\number,"\month","\pages",\year,"\address","\note","\url","\booktitle","\chapter","\edition","\series","\format[Authors(LastFirst,FullName,Semicolon,Semicolon)]{\editor}","\publisher","\begin{reporttype}\reporttype\end{reporttype}","\howpublished","\institution","\organization","\school","\annote","\format[Replace(\n, )]{\abstract}","\comment","\keywords","\format[FileLink(pdf)]{\file}","\key"
+\format[GetOpenOfficeType]{\entrytype},"\begin{isbn}\isbn\end{isbn}","\citationkey","\format[Authors(LastFirst,FullName,Semicolon,Semicolon)]{\author}","\format[RemoveBrackets,RemoveWhitespace]{\title}","\journal",\volume,\number,"\month","\pages",\year,"\address","\note","\url","\booktitle","\chapter","\edition","\series","\format[Authors(LastFirst,FullName,Semicolon,Semicolon)]{\editor}","\publisher","\begin{reporttype}\reporttype\end{reporttype}","\howpublished","\institution","\organization","\school","\annote","\format[Replace(\n, ),ReplaceWithEscapedDoubleQuotes]{\abstract}","\comment","\keywords","\format[FileLink(pdf)]{\file}","\key"

src/test/java/org/jabref/logic/formatter/bibtexfields/ReplaceWithEscapedDoubleQuotesTest.java

@@ -0,0 +1,38 @@
+package org.jabref.logic.formatter.bibtexfields;
+
+import org.jabref.logic.layout.format.ReplaceWithEscapedDoubleQuotes;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class ReplaceWithEscapedDoubleQuotesTest {
+
+    private ReplaceWithEscapedDoubleQuotes formatter;
+
+    @BeforeEach
+    public void setUp() {
+        formatter = new ReplaceWithEscapedDoubleQuotes();
+    }
+
+    @Test
+    public void replacingSingleDoubleQuote() {
+        assertEquals("single \"\"double quote", formatter.format("single \"double quote"));
+    }
+
+    @Test
+    public void replacingMultipleDoubleQuote() {
+        assertEquals("multiple \"\"double\"\" quote", formatter.format("multiple \"double\" quote"));
+    }
+
+    @Test
+    public void replacingSingleDoubleQuoteHavingCommas() {
+        assertEquals("this \"\"is\"\", a test", formatter.format("this \"is\", a test"));
+    }
+
+    @Test
+    public void doNothing() {
+        assertEquals("this is a test", formatter.format("this is a test"));
+    }
+}

src/test/java/org/jabref/logic/importer/fetcher/AstrophysicsDataSystemTest.java

@@ -49,6 +49,7 @@ public void setUp() throws Exception {
                 .withField(StandardField.TITLE, "Slice theorem and orbit type stratification in infinite dimensions")
                 .withField(StandardField.YEAR, "2018")
                 .withField(StandardField.ARCHIVEPREFIX, "arXiv")
+                .withField(StandardField.DOI, "10.48550/arXiv.1812.04698")
                 .withField(StandardField.EPRINT, "1812.04698")
                 .withField(StandardField.JOURNAL, "arXiv e-prints")
                 .withField(StandardField.KEYWORDS, "Mathematics - Differential Geometry, Mathematical Physics, 58B25, (58D19, 58B20, 22E99, 58A35)")
@@ -70,7 +71,7 @@ public void setUp() throws Exception {
                 .withField(StandardField.MONTH, "#sep#")
                 .withField(StandardField.NUMBER, "1")
                 .withField(StandardField.ARCHIVEPREFIX, "arXiv")
-                .withField(StandardField.DOI, "10.12942/lrr-2012-10")
+                .withField(StandardField.DOI, "10.12942/lrr-2012-1010.48550/arXiv.1112.3960")
                 .withField(StandardField.PRIMARYCLASS, "astro-ph.CO")
                 .withField(StandardField.EID, "10")
                 .withField(StandardField.EPRINT, "1112.3960")