Merge remote-tracking branch 'upstream/main' into pushToExternalConfig

* upstream/main:
  Use OpenRewrite UseStringReplace (#10299)
  Add ReplaceStringBuilderWithString (#10302)
  Apply ShortenFullyQualifiedTypeReferences (#10301)
  Apply StaticMethodNotFinal (#10300)
  Apply exit early pattern (#10297)
  Avoid GH_TOKEN_UPDATE_GRADLE_WRAPPER at refresh-csl-subtrees
  Update snapcraft.yaml
  Fix exception when opening preferences (#10294)
  gnome-42-2204
  use gnome 4.2
  Use gnome
  Update base 22

.github/workflows/refresh-csl-subtrees.yml

@@ -13,19 +13,22 @@ jobs:
   publish:
     name: Refresh Citation Style Language Files
     runs-on: ubuntu-latest
-    if: github.repository == 'JabRef/jabref'
+    permissions:
+      contents: write  # for peter-evans/create-pull-request to create branch
+      pull-requests: write  # for peter-evans/create-pull-request to create a PR
+    if: (github.repository == 'JabRef/jabref' || github.repository == 'koppor/jabref')
     steps:
-      - name: Checkout source
-        uses: actions/checkout@v3
+      - uses: actions/checkout@v3
         with:
+          persist-credentials: true
           ref: main
           fetch-depth: 0
       - name: Initialize git
         run: |
           git checkout main
           git config --local core.editor /usr/bin/cat
-          git config user.name "github actions"
-          git config user.email "jabrefmail+webfeedback@gmail.com"
+          git config user.name 'github-actions[bot]'
+          git config user.email 'github-actions[bot]@users.noreply.github.com'
       - name: Add csl-styles remote
         run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
       - name: Update csl-styles
@@ -48,8 +51,8 @@ jobs:
           git commit -m"Refresh example styles" || true
       - uses: peter-evans/create-pull-request@v5
         with:
-          token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}
+          token: ${{ secrets.GITHUB_TOKEN }}
           branch: refresh-csl
-          commit-message: Update CSL styles
           title: "[Bot] Update CSL styles"
+          commit-message: Update CSL styles
           labels: dependencies

build.gradle

@@ -292,10 +292,10 @@ tasks.register("generateBstGrammarSource", JavaExec) {
 }
 
 tasks.register("generateSearchGrammarSource", JavaExec) {
-    main = "org.antlr.v4.Tool"
-    classpath = configurations.antlr4
     group = 'JabRef'
     description = "Generates java files for Search.g antlr4."
+    classpath = configurations.antlr4
+    main = "org.antlr.v4.Tool"
 
     inputs.dir("src/main/antlr4/org/jabref/search/")
     outputs.dir("src-gen/main/java/org/jabref/search/")

rewrite.yml

@@ -99,6 +99,8 @@ recipeList:
   # We voted against it
   #  - org.openrewrite.staticanalysis.ExplicitInitialization
 
+  - org.openrewrite.java.ShortenFullyQualifiedTypeReferences
+
   - org.openrewrite.staticanalysis.AtomicPrimitiveEqualsUsesGet
   - org.openrewrite.staticanalysis.BigDecimalRoundingConstantsToEnums
   - org.openrewrite.staticanalysis.BooleanChecksNotInverted
@@ -156,13 +158,14 @@ recipeList:
 #  - org.openrewrite.staticanalysis.RenameLocalVariablesToCamelCase
   - org.openrewrite.staticanalysis.RenameMethodsNamedHashcodeEqualOrTostring
   - org.openrewrite.staticanalysis.ReplaceRedundantFormatWithPrintf
+  - org.openrewrite.staticanalysis.ReplaceStringBuilderWithString
 #  - org.openrewrite.staticanalysis.ShortenFullyQualifiedTypeReferences
 #  - org.openrewrite.staticanalysis.SimplifyConsecutiveAssignments
 #  - org.openrewrite.staticanalysis.SimplifyCompoundStatement
   - org.openrewrite.staticanalysis.SimplifyBooleanExpression
   - org.openrewrite.staticanalysis.SimplifyBooleanReturn
   - org.openrewrite.staticanalysis.SimplifyDurationCreationUnits
-#  - org.openrewrite.staticanalysis.StaticMethodNotFinal
+  - org.openrewrite.staticanalysis.StaticMethodNotFinal
   - org.openrewrite.staticanalysis.StringLiteralEquality
   - org.openrewrite.staticanalysis.TypecastParenPad
   - org.openrewrite.staticanalysis.UnwrapRepeatableAnnotations
@@ -172,7 +175,7 @@ recipeList:
 #  - org.openrewrite.staticanalysis.UseListSort
   - org.openrewrite.staticanalysis.UseObjectNotifyAll
   - org.openrewrite.staticanalysis.UseStandardCharset
-#  - org.openrewrite.staticanalysis.UseStringReplace
+  - org.openrewrite.staticanalysis.UseStringReplace
   - org.openrewrite.staticanalysis.UseSystemLineSeparator
   - org.openrewrite.staticanalysis.WhileInsteadOfFor
 #  - org.openrewrite.staticanalysis.WriteOctalValuesAsDecimal

snap/snapcraft.yaml

@@ -10,10 +10,11 @@ description: |
   `snap connect jabref:removable-media`
 grade: stable
 confinement: strict
-base: core20
+base: core22
 compression: lzo
 architectures:
-  - build-on: amd64
+ - build-on: [amd64, arm64]
+   build-for: [amd64]
 
 plugs:
   home:
@@ -45,10 +46,10 @@ layout:
 apps:
   jabref:
     command: bin/JabRef
-    extensions: [gnome-3-38]
+    extensions: [gnome]
   browser-proxy:
     command: lib/jabrefHost.py
-    extensions: [gnome-3-38]
+    extensions: [gnome]
 
 environment:
   _JAVA_OPTIONS: "-Duser.home=$SNAP_USER_DATA"
@@ -80,10 +81,10 @@ parts:
       - jabref-launcher
     plugin: nil
     build-snaps:
-      - gnome-3-38-2004
+      - gnome-42-2204
     override-prime: |
       set -eux
-      for snap in "gnome-3-38-2004"; do  # List all content-snaps you're using here
+      for snap in "gnome-42-2204"; do  # List all content-snaps you're using here
           cd "/snap/$snap/current" && find . -type f,l -exec rm -f "$SNAPCRAFT_PRIME/{}" "$SNAPCRAFT_PRIME/usr/{}" \;
       done
       for CRUFT in bug lintian man; do

src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FulltextSearchResultsTab.java

@@ -99,7 +99,7 @@ protected void bindToEntry(BibEntry entry) {
             // Iterate through pages (within file) with search hits
             for (SearchResult searchResult : resultsForPath.getValue()) {
                 for (String resultTextHtml : searchResult.getContentResultStringsHtml()) {
-                    content.getChildren().addAll(TooltipTextUtil.createTextsFromHtml(resultTextHtml.replaceAll("</b> <b>", " ")));
+                    content.getChildren().addAll(TooltipTextUtil.createTextsFromHtml(resultTextHtml.replace("</b> <b>", " ")));
                     content.getChildren().addAll(new Text(System.lineSeparator()), lineSeparator(0.8), createPageLink(searchResult.getPageNumber()));
                 }
                 if (!searchResult.getAnnotationsResultStringsHtml().isEmpty()) {
@@ -108,7 +108,7 @@ protected void bindToEntry(BibEntry entry) {
                     content.getChildren().add(annotationsText);
                 }
                 for (String resultTextHtml : searchResult.getAnnotationsResultStringsHtml()) {
-                    content.getChildren().addAll(TooltipTextUtil.createTextsFromHtml(resultTextHtml.replaceAll("</b> <b>", " ")));
+                    content.getChildren().addAll(TooltipTextUtil.createTextsFromHtml(resultTextHtml.replace("</b> <b>", " ")));
                     content.getChildren().addAll(new Text(System.lineSeparator()), lineSeparator(0.8), createPageLink(searchResult.getPageNumber()));
                 }
             }

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

@@ -13,6 +13,7 @@
 
 import javax.net.ssl.HostnameVerifier;
 import javax.net.ssl.HttpsURLConnection;
+import javax.net.ssl.SSLHandshakeException;
 import javax.net.ssl.SSLSocketFactory;
 
 import javafx.beans.Observable;
@@ -500,7 +501,7 @@ public boolean checkSSLHandshake(URLDownload urlDownload) {
             try {
             urlDownload.canBeReached();
         } catch (kong.unirest.UnirestException ex) {
-            if (ex.getCause() instanceof javax.net.ssl.SSLHandshakeException) {
+            if (ex.getCause() instanceof SSLHandshakeException) {
                 if (dialogService.showConfirmationDialogAndWait(Localization.lang("Download file"),
                         Localization.lang("Unable to find valid certification path to requested target(%0), download anyway?",
                                           urlDownload.getSource().toString()))) {

src/main/java/org/jabref/gui/journals/AbbreviateAction.java

@@ -110,13 +110,14 @@ private String abbreviate(BibDatabaseContext databaseContext, List<BibEntry> ent
             }
         }).count();
 
-        if (count > 0) {
-            ce.end();
-            frame.getUndoManager().addEdit(ce);
-            frame.getCurrentLibraryTab().markBaseChanged();
-            return Localization.lang("Abbreviated %0 journal names.", String.valueOf(count));
+        if (count == 0) {
+            return Localization.lang("No journal names could be abbreviated.");
         }
-        return Localization.lang("No journal names could be abbreviated.");
+
+        ce.end();
+        frame.getUndoManager().addEdit(ce);
+        frame.getCurrentLibraryTab().markBaseChanged();
+        return Localization.lang("Abbreviated %0 journal names.", String.valueOf(count));
     }
 
     private String unabbreviate(BibDatabaseContext databaseContext, List<BibEntry> entries) {
@@ -126,12 +127,13 @@ private String unabbreviate(BibDatabaseContext databaseContext, List<BibEntry> e
         int count = entries.stream().mapToInt(entry ->
                 (int) FieldFactory.getJournalNameFields().stream().filter(journalField ->
                         undoableAbbreviator.unabbreviate(databaseContext.getDatabase(), entry, journalField, ce)).count()).sum();
-        if (count > 0) {
-            ce.end();
-            frame.getUndoManager().addEdit(ce);
-            frame.getCurrentLibraryTab().markBaseChanged();
-            return Localization.lang("Unabbreviated %0 journal names.", String.valueOf(count));
+        if (count == 0) {
+            return Localization.lang("No journal names could be unabbreviated.");
         }
-        return Localization.lang("No journal names could be unabbreviated.");
+
+        ce.end();
+        frame.getUndoManager().addEdit(ce);
+        frame.getCurrentLibraryTab().markBaseChanged();
+        return Localization.lang("Unabbreviated %0 journal names.", String.valueOf(count));
     }
 }

src/main/java/org/jabref/gui/openoffice/Bootstrap.java

@@ -21,6 +21,7 @@
 package org.jabref.gui.openoffice;
 
 import java.io.BufferedReader;
+import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.PrintStream;
@@ -107,7 +108,7 @@ private static void insertBasicFactories(XSet xSet, XImplementationLoader xImpLo
      * @see #bootstrap(String[])
      * @since LibreOffice 5.1
      */
-    public static final String[] getDefaultOptions() {
+    public static String[] getDefaultOptions() {
         return new String[] {"--nologo", "--nodefault", "--norestore", "--nolockcheck"};
     }
 
@@ -176,7 +177,7 @@ public static XMultiServiceFactory createSimpleServiceManager() throws Exception
      * <code>cppuhelper/defaultBootstrap_InitialComponentContext()</code>.
      * @throws Exception if things go awry.
      */
-    public static final XComponentContext defaultBootstrap_InitialComponentContext() throws Exception {
+    public static XComponentContext defaultBootstrap_InitialComponentContext() throws Exception {
         return defaultBootstrap_InitialComponentContext((String) null, (Map<String, String>) null);
     }
 
@@ -188,7 +189,7 @@ public static final XComponentContext defaultBootstrap_InitialComponentContext()
      * @return a freshly bootstrapped component context.
      * @throws Exception if things go awry.
      */
-    public static final XComponentContext defaultBootstrap_InitialComponentContext(String ini_file, Hashtable<String, String> bootstrap_parameters) throws Exception {
+    public static XComponentContext defaultBootstrap_InitialComponentContext(String ini_file, Hashtable<String, String> bootstrap_parameters) throws Exception {
         return defaultBootstrap_InitialComponentContext(ini_file, (Map<String, String>) bootstrap_parameters);
     }
 
@@ -203,7 +204,7 @@ public static final XComponentContext defaultBootstrap_InitialComponentContext(S
      * @return a freshly bootstrapped component context.
      * @throws Exception if things go awry.
      */
-    public static final XComponentContext defaultBootstrap_InitialComponentContext(String ini_file, Map<String, String> bootstrap_parameters) throws Exception {
+    public static XComponentContext defaultBootstrap_InitialComponentContext(String ini_file, Map<String, String> bootstrap_parameters) throws Exception {
         // jni convenience: easier to iterate over array than calling Hashtable
         String pairs[] = null;
         if (null != bootstrap_parameters) {
@@ -253,7 +254,7 @@ public static final XComponentContext defaultBootstrap_InitialComponentContext(S
      * @throws BootstrapException if things go awry.
      * @since UDK 3.1.0
      */
-    public static final XComponentContext bootstrap(Path ooPath) throws BootstrapException {
+    public static XComponentContext bootstrap(Path ooPath) throws BootstrapException {
         String[] defaultArgArray = getDefaultOptions();
         return bootstrap(defaultArgArray, ooPath);
     }
@@ -267,7 +268,7 @@ public static final XComponentContext bootstrap(Path ooPath) throws BootstrapExc
      * @see #getDefaultOptions()
      * @since LibreOffice 5.1
      */
-    public static final XComponentContext bootstrap(String[] argArray, Path path) throws BootstrapException {
+    public static XComponentContext bootstrap(String[] argArray, Path path) throws BootstrapException {
 
         XComponentContext xContext = null;
 
@@ -326,7 +327,7 @@ public static final XComponentContext bootstrap(String[] argArray, Path path) th
             throw e;
         } catch (java.lang.RuntimeException e) {
             throw e;
-        } catch (java.lang.Exception e) {
+        } catch (Exception e) {
             throw new BootstrapException(e);
         }
 
@@ -349,7 +350,7 @@ public void run() {
                     }
                 } catch (UnsupportedEncodingException e) {
                     e.printStackTrace(System.err);
-                } catch (java.io.IOException e) {
+                } catch (IOException e) {
                     e.printStackTrace(System.err);
                 }
             }

src/main/java/org/jabref/gui/openoffice/OOBibBaseConnect.java

@@ -64,7 +64,7 @@ private XDesktop simpleBootstrap(Path loPath)
             BootstrapException {
 
         // Get the office component context:
-        XComponentContext context = org.jabref.gui.openoffice.Bootstrap.bootstrap(loPath);
+        XComponentContext context = Bootstrap.bootstrap(loPath);
         XMultiComponentFactory sem = context.getServiceManager();
 
         // Create the desktop, which is the root frame of the
@@ -85,7 +85,7 @@ public static void closeOfficeConnection() {
         try {
             // get the bridge factory from the local service manager
             XBridgeFactory bridgeFactory = queryInterface(XBridgeFactory.class,
-                                                          org.jabref.gui.openoffice.Bootstrap.createSimpleServiceManager()
+                                                          Bootstrap.createSimpleServiceManager()
                     .createInstance("com.sun.star.bridge.BridgeFactory"));
 
             if (bridgeFactory != null) {

src/main/java/org/jabref/gui/search/GlobalSearchBar.java

@@ -1,6 +1,7 @@
 package org.jabref.gui.search;
 
 import java.lang.reflect.Field;
+import java.time.Duration;
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
@@ -200,7 +201,7 @@ public GlobalSearchBar(JabRefFrame frame, StateManager stateManager, Preferences
         this.setSpacing(4.0);
         this.setAlignment(Pos.CENTER_LEFT);
 
-        Timer searchTask = FxTimer.create(java.time.Duration.ofMillis(SEARCH_DELAY), this::performSearch);
+        Timer searchTask = FxTimer.create(Duration.ofMillis(SEARCH_DELAY), this::performSearch);
         BindingsHelper.bindBidirectional(
                 stateManager.activeSearchQueryProperty(),
                 searchField.textProperty(),

src/main/java/org/jabref/logic/citationkeypattern/BracketedPattern.java

@@ -756,7 +756,7 @@ private static String firstAuthorForenameInitials(AuthorList authorList) {
      */
     private static String firstAuthorVonAndLast(AuthorList authorList) {
         return authorList.isEmpty() ? "" :
-                authorList.getAuthor(0).getLastOnly().replaceAll(" ", "");
+                authorList.getAuthor(0).getLastOnly().replace(" ", "");
     }
 
     /**

src/main/java/org/jabref/logic/importer/AuthorListParser.java

@@ -129,7 +129,7 @@ public AuthorList parse(String listOfNames) {
             // Usually the getAsLastFirstNamesWithAnd method would separate them if pre- and lastname are separated with "and"
             // If not, we check if spaces separate pre- and lastname
             if (spaceInAllParts) {
-                listOfNames = listOfNames.replaceAll(",", " and");
+                listOfNames = listOfNames.replace(",", " and");
             } else {
                 // Looking for name affixes to avoid
                 // arrayNameList needs to reduce by the count off avoiding terms

src/main/java/org/jabref/logic/importer/fetcher/ArXivFetcher.java

@@ -392,7 +392,7 @@ public String getIdentifierName() {
      */
     protected class ArXiv implements FulltextFetcher, PagedSearchBasedFetcher, IdBasedFetcher, IdFetcher<ArXivIdentifier> {
 
-        private static final Logger LOGGER = LoggerFactory.getLogger(org.jabref.logic.importer.fetcher.ArXivFetcher.ArXiv.class);
+        private static final Logger LOGGER = LoggerFactory.getLogger(ArXivFetcher.ArXiv.class);
 
         private static final String API_URL = "https://export.arxiv.org/api/query";
 

src/main/java/org/jabref/logic/importer/fetcher/MrDLibFetcher.java

@@ -101,8 +101,8 @@ private String makeServerRequest(String queryByTitle) throws FetcherException {
             String response = urlDownload.asString();
 
             // Conversion of < and >
-            response = response.replaceAll("&gt;", ">");
-            response = response.replaceAll("&lt;", "<");
+            response = response.replace("&gt;", ">");
+            response = response.replace("&lt;", "<");
             return response;
         } catch (IOException e) {
             throw new FetcherException("Problem downloading", e);
@@ -117,7 +117,7 @@ private String makeServerRequest(String queryByTitle) throws FetcherException {
      */
     private String constructQuery(String queryWithTitle) {
         // The encoding does not work for / so we convert them by our own
-        queryWithTitle = queryWithTitle.replaceAll("/", " ");
+        queryWithTitle = queryWithTitle.replace("/", " ");
         URIBuilder builder = new URIBuilder();
         builder.setScheme("http");
         builder.setHost(MDL_URL);

src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java

@@ -340,7 +340,7 @@ private void addAbstract(Map<Field, String> hm, String lab, String value) {
             if (value.contains("Copyright")) {
                 int copyrightIndex = value.lastIndexOf("Copyright");
                 // remove the copyright from the field since the name of the field is copyright
-                String copyrightInfo = value.substring(copyrightIndex).replaceAll("Copyright ", "");
+                String copyrightInfo = value.substring(copyrightIndex).replace("Copyright ", "");
                 hm.put(new UnknownField("copyright"), copyrightInfo);
                 abstractValue = value.substring(0, copyrightIndex);
             } else {

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

@@ -1,9 +1,11 @@
 package org.jabref.logic.layout;
 
+import java.io.Serializable;
+
 /**
  * String and integer value.
  */
-public class StringInt implements java.io.Serializable {
+public class StringInt implements Serializable {
 
     /**
      * Description of the Field

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

@@ -6,6 +6,6 @@ public class AuthorAndToSemicolonReplacer implements LayoutFormatter {
 
     @Override
     public String format(String fieldText) {
-        return fieldText.replaceAll(" and ", "; ");
+        return fieldText.replace(" and ", "; ");
     }
 }