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

.github/workflows/tests.yml

@@ -208,3 +208,11 @@ jobs:
           CI: "false" # we pretend to run locally - even if tests fail on the CI, they count towards test coverage
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           DBMS: "postgresql"
+  # This is https://github.com/marketplace/actions/gradle-wrapper-validation
+  # It ensures that the jar file is from gradle and not by a strange third party.
+  gradlevalidation:
+    name: "Validate Gradle Wrapper"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: gradle/wrapper-validation-action@v1

CHANGELOG.md

@@ -45,6 +45,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the most bottom group in the list got lost, if it was dragged on itself. [#5983](https://github.com/JabRef/jabref/issues/5983)
 - We fixed an issue where changing entry type doesn't always work when biblatex source is shown. [#5905](https://github.com/JabRef/jabref/issues/5905)
 - We fixed an issue where the group and the link column were not updated after changing the entry in the main table. [#5985](https://github.com/JabRef/jabref/issues/5985)
+- We fixed an issue where reordering the groups was not possible after inserting an article. [#6008](https://github.com/JabRef/jabref/issues/6008)
 
 ### Removed
 

docs/README.md

@@ -2,9 +2,15 @@
 
 This page presents all development informatation around JabRef. For users documentation see <https://docs.jabref.org>.
 
+## Excersises
+
+Uni Basel offers a German (🇩🇪) Software Engineering course which uses JabRef as one example.
+Look at [Exercise 5](https://github.com/unibas-marcelluethi/software-engineering/blob/master/docs/week5/exercises/practical-exercises.md) for an exercise where some important points of JabRef are touched.
+
 ## How tos
 
-- [Sync your fork with the JabRef repository](https://help.github.com/articles/syncing-a-fork/)
+- External: [Sync your fork with the JabRef repository](https://help.github.com/articles/syncing-a-fork/)
+- External (🇩🇪): Branches and pull requests: <https://github.com/unibas-marcelluethi/software-engineering/blob/master/docs/week2/exercises/practical-exercises.md>
 
 ## Command Line
 

docs/code-quality.md

@@ -2,9 +2,9 @@
 
 We monitor the general source code quality at three places:
 
-* [Teamscale](https://www.cqse.eu/de/produkte/teamscale/landing/) is a popular German product analyzing code quality. The analysis results are available at <https://demo.teamscale.com/dashboard.html#show//?id=kinnen%2FJabref%20Overview>.
-* [codacy](https://www.codacy.com/) is a hosted service to monitor code quality. The code quality analysis for JabRef is available at <https://www.codacy.com/app/simonharrer/jabref/dashboard>.
+* [codacy](https://www.codacy.com/) is a hosted service to monitor code quality. It thereby combines the results of available open source code quality checkers such as [Checkstyle](https://checkstyle.sourceforge.io/) or [PMD](https://pmd.github.io/). The code quality analysis for JabRef is available at <https://app.codacy.com/gh/JabRef/jabref/dashboard>, especially the [list of open issues](https://app.codacy.com/gh/JabRef/jabref/issues/index). In case a rule feels wrong, it is most likely a PMD rule. The JabRef team can change the configuration at <https://app.codacy.com/p/306789/patterns/list?engine=9ed24812-b6ee-4a58-9004-0ed183c45b8f>.
 * [codecov](https://codecov.io/) is a solution to check code coverage of test cases. The code coverage metrics for JabRef are available at <https://codecov.io/github/JabRef/jabref>.
+* [Teamscale](https://www.cqse.eu/de/produkte/teamscale/landing/) is a popular German product analyzing code quality. The analysis results are available at <https://demo.teamscale.com/findings.html#/jabref/?>.
 
 We strongly recommend to read following two books on code quality:
 

src/main/java/module-info.java

@@ -6,6 +6,7 @@
     requires java.sql;
 
     // JavaFX
+    requires javafx.base;
     requires javafx.graphics;
     requires javafx.swing;
     requires javafx.controls;
@@ -17,6 +18,7 @@
     requires de.jensd.fx.fontawesomefx.commons;
     requires de.jensd.fx.fontawesomefx.materialdesignicons;
     requires org.controlsfx.controls;
+    requires org.fxmisc.richtext;
 
     provides com.airhacks.afterburner.views.ResourceLocator
             with org.jabref.gui.util.JabRefResourceLocator;
@@ -62,7 +64,6 @@
     requires org.graalvm.js;
     requires org.apache.xmpbox;
     requires de.saxsys.mvvmfx.validation;
-    requires richtextfx;
     requires com.google.gson;
     requires unirest.java;
     requires org.apache.httpcomponents.httpclient;
@@ -72,9 +73,10 @@
     requires java.string.similarity;
     requires ojdbc10;
     requires org.postgresql.jdbc;
+    requires org.mariadb.jdbc;
+    uses org.mariadb.jdbc.credential.CredentialPlugin;
     requires org.apache.commons.lang3;
     requires org.antlr.antlr4.runtime;
     requires flowless;
     requires org.apache.tika.core;
-    requires javafx.base;
 }

src/main/java/org/jabref/gui/JabRefFrame.java

@@ -660,6 +660,7 @@ private MenuBar createMenu() {
         Menu edit = new Menu(Localization.lang("Edit"));
         Menu library = new Menu(Localization.lang("Library"));
         Menu quality = new Menu(Localization.lang("Quality"));
+        Menu lookup = new Menu(Localization.lang("Lookup"));
         Menu view = new Menu(Localization.lang("View"));
         Menu tools = new Menu(Localization.lang("Tools"));
         Menu options = new Menu(Localization.lang("Options"));
@@ -773,6 +774,10 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs, stateManager, undoManager, Globals.TASK_EXECUTOR))
         );
 
+        lookup.getItems().addAll(
+                factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(this, dialogService, stateManager))
+        );
+
         // PushToApplication
         final PushToApplicationAction pushToApplicationAction = pushToApplicationsManager.getPushToApplicationAction();
         final MenuItem pushToApplicationMenuItem = factory.createMenuItem(pushToApplicationAction.getActionInformation(), pushToApplicationAction);

src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java

@@ -65,7 +65,7 @@ public LatexCitationsTabViewModel(BibDatabaseContext databaseContext, Preference
         this.preferencesService = preferencesService;
         this.taskExecutor = taskExecutor;
         this.dialogService = dialogService;
-        this.directory = new SimpleObjectProperty<>(databaseContext.getMetaData().getLaTexFileDirectory(preferencesService.getUser())
+        this.directory = new SimpleObjectProperty<>(databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getUser())
                                                                    .orElseGet(preferencesService::getWorkingDir));
         this.citationList = FXCollections.observableArrayList();
         this.status = new SimpleObjectProperty<>(Status.IN_PROGRESS);
@@ -126,7 +126,7 @@ private void cancelSearch() {
     }
 
     private Collection<Citation> searchAndParse(String citeKey) throws IOException {
-        Path newDirectory = databaseContext.getMetaData().getLaTexFileDirectory(preferencesService.getUser())
+        Path newDirectory = databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getUser())
                                            .orElseGet(preferencesService::getWorkingDir);
 
         if (texParserResult == null || !newDirectory.equals(directory.get())) {
@@ -168,7 +168,7 @@ public void setLatexDirectory() {
                 .withInitialDirectory(directory.get()).build();
 
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(selectedDirectory ->
-                databaseContext.getMetaData().setLaTexFileDirectory(preferencesService.getUser(), selectedDirectory.toAbsolutePath()));
+                databaseContext.getMetaData().setLatexFileDirectory(preferencesService.getUser(), selectedDirectory.toAbsolutePath()));
 
         init(currentEntry);
     }

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

@@ -1,6 +1,5 @@
 package org.jabref.gui.fieldeditors;
 
-import java.io.UnsupportedEncodingException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLDecoder;
@@ -53,15 +52,15 @@ public static String cleanGoogleSearchURL(String url) {
                 if (pair.startsWith("url=")) {
                     String value = pair.substring(pair.indexOf('=') + 1);
 
-                    String decode = URLDecoder.decode(value, StandardCharsets.UTF_8.name());
+                    String decode = URLDecoder.decode(value, StandardCharsets.UTF_8);
                     // url?
                     if (decode.matches(URL_EXP)) {
                         return decode;
                     }
                 }
             }
             return url;
-        } catch (UnsupportedEncodingException | MalformedURLException e) {
+        } catch (MalformedURLException e) {
             return url;
         }
     }

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

@@ -392,7 +392,7 @@ public void openHelpPage() {
     private List<Path> getFileDirectoriesAsPaths() {
         List<Path> fileDirs = new ArrayList<>();
         MetaData metaData = currentDatabase.getMetaData();
-        metaData.getLaTexFileDirectory(preferencesService.getFilePreferences().getUser()).ifPresent(fileDirs::add);
+        metaData.getLatexFileDirectory(preferencesService.getFilePreferences().getUser()).ifPresent(fileDirs::add);
 
         return fileDirs;
     }

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

@@ -201,6 +201,10 @@ public void initialize() {
                     }
                 }
 
+                if (groupsToMove.size() > 0) {
+                    localDragboard.clearAll();
+                }
+
                 // Put the group nodes as content
                 Dragboard dragboard = treeTable.startDragAndDrop(TransferMode.MOVE);
                 // Display the group when dragging

src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml

@@ -65,9 +65,9 @@
                     <Button text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="5"
                             onAction="#browseUserSpecificFileDirectory"/>
 
-                    <Label text="%LaTex file directory" GridPane.columnIndex="0" GridPane.rowIndex="6"/>
+                    <Label text="%LaTeX file directory" GridPane.columnIndex="0" GridPane.rowIndex="6"/>
                     <TextField fx:id="laTexFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="6"/>
-                    <Button text="%Browse" onAction="#browseLaTexFileDirectory" GridPane.columnIndex="2"
+                    <Button text="%Browse" onAction="#browseLatexFileDirectory" GridPane.columnIndex="2"
                             GridPane.rowIndex="6"/>
                 </GridPane>
 

src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java

@@ -112,8 +112,8 @@ public void browseUserSpecificFileDirectory(ActionEvent event) {
     }
 
     @FXML
-    void browseLaTexFileDirectory(ActionEvent event) {
-        viewModel.browseLaTexDir();
+    void browseLatexFileDirectory(ActionEvent event) {
+        viewModel.browseLatexDir();
     }
 
     private void storeSettings() {
@@ -143,9 +143,9 @@ private void storeSettings() {
 
         text = viewModel.laTexFileDirectoryProperty().getValue();
         if (text.isEmpty()) {
-            metaData.clearLaTexFileDirectory(preferencesService.getUser());
+            metaData.clearLatexFileDirectory(preferencesService.getUser());
         } else {
-            metaData.setLaTexFileDirectory(preferencesService.getUser(), Paths.get(text));
+            metaData.setLatexFileDirectory(preferencesService.getUser(), Paths.get(text));
         }
 
         if (viewModel.libraryProtectedProperty().getValue()) {

src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java

@@ -42,7 +42,7 @@ public class LibraryPropertiesDialogViewModel {
 
     private final String oldUserSpecificFileDir;
     private final String oldGeneralFileDir;
-    private final String oldLaTexFileDir;
+    private final String oldLatexFileDir;
     private final boolean oldLibraryProtected;
 
     public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogService, PreferencesService preferencesService) {
@@ -67,11 +67,11 @@ public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogSer
         Optional<String> fileDI = metaData.getUserFileDirectory(preferencesService.getUser());
         fileDI.ifPresent(userSpecificFileDirectoryProperty::setValue);
 
-        metaData.getLaTexFileDirectory(preferencesService.getUser()).map(Path::toString).ifPresent(laTexFileDirectoryProperty::setValue);
+        metaData.getLatexFileDirectory(preferencesService.getUser()).map(Path::toString).ifPresent(laTexFileDirectoryProperty::setValue);
 
         oldUserSpecificFileDir = generalFileDirectoryProperty.getValue();
         oldGeneralFileDir = userSpecificFileDirectoryProperty.getValue();
-        oldLaTexFileDir = laTexFileDirectoryProperty.getValue();
+        oldLatexFileDir = laTexFileDirectoryProperty.getValue();
 
         libraryProtectedProperty.setValue(metaData.isProtected());
         oldLibraryProtected = libraryProtectedProperty.getValue();
@@ -117,7 +117,7 @@ public void browseUserDir() {
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> userSpecificFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
     }
 
-    public void browseLaTexDir() {
+    public void browseLatexDir() {
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> laTexFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
     }
 
@@ -134,7 +134,7 @@ public boolean userFileDirChanged() {
     }
 
     public boolean laTexFileDirChanged() {
-        return !oldLaTexFileDir.equals(laTexFileDirectoryProperty.getValue());
+        return !oldLatexFileDir.equals(laTexFileDirectoryProperty.getValue());
     }
 
     public boolean protectedValueChanged() {

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

@@ -27,6 +27,7 @@
 import java.io.PrintStream;
 import java.io.UnsupportedEncodingException;
 import java.net.URLClassLoader;
+import java.nio.charset.StandardCharsets;
 import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.Map;
@@ -360,7 +361,7 @@ private static void pipe(final InputStream in, final PrintStream out, final Stri
             @Override
             public void run() {
                 try {
-                    BufferedReader r = new BufferedReader(new InputStreamReader(in, "UTF-8"));
+                    BufferedReader r = new BufferedReader(new InputStreamReader(in, StandardCharsets.UTF_8));
 
                     for (;;) {
                         String s = r.readLine();

src/main/java/org/jabref/gui/texparser/ParseTexDialogViewModel.java

@@ -66,7 +66,7 @@ public ParseTexDialogViewModel(BibDatabaseContext databaseContext, DialogService
         this.taskExecutor = taskExecutor;
         this.preferencesService = preferencesService;
         this.fileMonitor = fileMonitor;
-        this.texDirectory = new SimpleStringProperty(databaseContext.getMetaData().getLaTexFileDirectory(preferencesService.getUser())
+        this.texDirectory = new SimpleStringProperty(databaseContext.getMetaData().getLatexFileDirectory(preferencesService.getUser())
                                                                     .orElseGet(preferencesService::getWorkingDir)
                                                                     .toAbsolutePath().toString());
         this.root = new SimpleObjectProperty<>();

src/main/java/org/jabref/logic/bibtex/comparator/MetaDataDiff.java

@@ -53,8 +53,8 @@ public List<String> getDifferences(JabRefPreferences preferences) {
         if (!Objects.equals(originalMetaData.getUserFileDirectories(), newMetaData.getUserFileDirectories())) {
             changes.add(Localization.lang("User-specific file directory"));
         }
-        if (!Objects.equals(originalMetaData.getLaTexFileDirectories(), newMetaData.getLaTexFileDirectories())) {
-            changes.add(Localization.lang("LaTex file directory"));
+        if (!Objects.equals(originalMetaData.getLatexFileDirectories(), newMetaData.getLatexFileDirectories())) {
+            changes.add(Localization.lang("LaTeX file directory"));
         }
         if (!Objects.equals(originalMetaData.getDefaultCiteKeyPattern(), newMetaData.getDefaultCiteKeyPattern())) {
             changes.add(Localization.lang("Default pattern"));

src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java

@@ -44,7 +44,7 @@ public static Map<String, String> getSerializedStringMap(MetaData metaData,
                 path -> stringyMetaData.put(MetaData.FILE_DIRECTORY, Collections.singletonList(path.trim())));
         metaData.getUserFileDirectories().forEach((user, path) -> stringyMetaData
                 .put(MetaData.FILE_DIRECTORY + '-' + user, Collections.singletonList(path.trim())));
-        metaData.getLaTexFileDirectories().forEach((user, path) -> stringyMetaData
+        metaData.getLatexFileDirectories().forEach((user, path) -> stringyMetaData
                 .put(MetaData.FILE_DIRECTORY + "Latex-" + user, Collections.singletonList(path.toString().trim())));
 
         for (ContentSelector selector: metaData.getContentSelectorList()) {

src/main/java/org/jabref/logic/formatter/bibtexfields/CleanupUrlFormatter.java

@@ -1,6 +1,5 @@
 package org.jabref.logic.formatter.bibtexfields;
 
-import java.io.UnsupportedEncodingException;
 import java.net.URLDecoder;
 import java.nio.charset.StandardCharsets;
 import java.util.regex.Matcher;
@@ -40,13 +39,7 @@ public String format(String value) {
         if (matcher.find()) {
             toDecode = matcher.group(1);
         }
-        try {
-            decodedLink = URLDecoder.decode(toDecode, StandardCharsets.UTF_8.name());
-        } catch (UnsupportedEncodingException e) {
-            LOGGER.warn("Used unsupported character encoding", e);
-        }
-
-        return decodedLink;
+        return URLDecoder.decode(toDecode, StandardCharsets.UTF_8);
     }
 
     @Override

src/main/java/org/jabref/logic/formatter/bibtexfields/OrdinalsToSuperscriptFormatter.java

@@ -8,7 +8,7 @@
 import org.jabref.model.cleanup.Formatter;
 
 /**
- * This class transforms ordinal numbers into LaTex superscripts.
+ * This class transforms ordinal numbers into LaTeX superscripts.
  */
 public class OrdinalsToSuperscriptFormatter extends Formatter {
 

src/main/java/org/jabref/logic/importer/util/MetaDataParser.java

@@ -69,7 +69,7 @@ public MetaData parse(MetaData metaData, Map<String, String> data, Character key
                 // The user name comes directly after "FILE_DIRECTORYLatex-"
                 String user = entry.getKey().substring(MetaData.FILE_DIRECTORY.length() + 6);
                 Path path = Paths.get(getSingleItem(value)).normalize();
-                metaData.setLaTexFileDirectory(user, path);
+                metaData.setLatexFileDirectory(user, path);
                 continue;
             }
 

src/main/java/org/jabref/logic/xmp/XmpUtilWriter.java

@@ -192,12 +192,12 @@ private static String generateXmpStringWithXmpDeclaration(List<BibEntry> entries
         try (ByteArrayOutputStream os = new ByteArrayOutputStream()) {
             XmpSerializer serializer = new XmpSerializer();
             serializer.serialize(meta, os, true);
-            return os.toString(StandardCharsets.UTF_8.name());
+            return os.toString(StandardCharsets.UTF_8);
         } catch (TransformerException e) {
-            LOGGER.warn("Tranformation into xmp not possible: " + e.getMessage(), e);
+            LOGGER.warn("Transformation into XMP not possible: " + e.getMessage(), e);
             return "";
         } catch (UnsupportedEncodingException e) {
-            LOGGER.warn("Unsupported encoding to UTF-8 of bib entries in xmp metadata.", e);
+            LOGGER.warn("Unsupported encoding to UTF-8 of bib entries in XMP metadata.", e);
             return "";
         } catch (IOException e) {
             LOGGER.warn("IO Exception thrown by closing the output stream.", e);

src/main/java/org/jabref/model/entry/field/StandardField.java

@@ -7,7 +7,7 @@
 import java.util.Set;
 
 /**
- * Standard BibTeX and BibLaTex fields
+ * Standard BibTeX and BibLaTeX fields
  */
 public enum StandardField implements Field {