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

* upstream/master:
  Bump archunit-junit5-api from 0.15.0 to 0.16.0 (#7407)
  Bump classgraph from 4.8.98 to 4.8.102 (#7401)
  Bump archunit-junit5-engine from 0.15.0 to 0.16.0 (#7402)
  Bump mariadb-java-client from 2.7.1 to 2.7.2 (#7406)
  Bump org.beryx.jlink from 2.23.2 to 2.23.3 (#7400)
  Bump checkstyle from 8.39 to 8.40 (#7404)
  Ignore codecov status for automerge
  Fixes issue of Changing font size makes font size field too small (#7398)
  fix "Alt + keyboard shortcuts do not work" (#7379)
  Fixed invisible file path in the dark theme (#7396)
  Fix File Filter and some layout issues (#7385)
  Feature/implement complex queries (#7350)
  Change format for study definition to yaml (#7126)
  Fix handling of URL in file field (#7347)
  Fix expansion of bracketed expressions in RegExpBasedFileFinder (#7338)

.github/workflows/automerge.yml

@@ -11,7 +11,7 @@ jobs:
         id: waitforstatuschecks
         uses: "WyriHaximus/github-action-wait-for-status@v1.3"
         with:
-          ignoreActions: Automerge Dependabot
+          ignoreActions: Automerge Dependabot,codecov/project
           checkInterval: 13
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

CHANGELOG.md

@@ -34,11 +34,16 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the "Find unlinked files" dialog would freeze JabRef on importing. [#7205](https://github.com/JabRef/jabref/issues/7205)
 - We fixed an issue where the "Find unlinked files" would stop importing when importing a single file failed. [#7206](https://github.com/JabRef/jabref/issues/7206)
 - We fixed an issue where an exception would be displayed for previewing and preferences when a custom theme has been configured but is missing [#7177](https://github.com/JabRef/jabref/issues/7177)
+- We fixed an issue where URLs in `file` fields could not be handled on Windows. [#7359](https://github.com/JabRef/jabref/issues/7359)
+- We fixed an issue where the regex based file search miss-interpreted specific symbols. [#4342](https://github.com/JabRef/jabref/issues/4342)
 - We fixed an issue where the Harvard RTF exporter used the wrong default file extension. [4508](https://github.com/JabRef/jabref/issues/4508)
 - We fixed an issue where the Harvard RTF exporter did not use the new authors formatter and therefore did not export "organization" authors correctly. [4508](https://github.com/JabRef/jabref/issues/4508)
 - We fixed an issue where the field `urldate` was not exported to the corresponding fields `YearAccessed`, `MonthAccessed`, `DayAccessed` in MS Office XML [#7354](https://github.com/JabRef/jabref/issues/7354)
 - We fixed an issue where the password for a shared SQL database was only remembered if it was the same as the username [#6869](https://github.com/JabRef/jabref/issues/6869)
 - We fixed an issue where some custom exports did not use the new authors formatter and therefore did not export authors correctly [#7356]((https://github.com/JabRef/jabref/issues/7356))
+- We fixed an issue where alt+keyboard shortcuts do not work [#6994](https://github.com/JabRef/jabref/issues/6994)
+- We fixed an issue where the file path is invisible in dark theme. [#7382](https://github.com/JabRef/jabref/issues/7382)
+- We fixed an issue where changing the font size makes the font size field too small. [#7085](https://github.com/JabRef/jabref/issues/7085)
 
 ### Removed
 

build.gradle

@@ -14,7 +14,7 @@ plugins {
     id 'com.github.ben-manes.versions' version '0.36.0'
     id 'org.javamodularity.moduleplugin' version '1.7.0'
     id 'org.openjfx.javafxplugin' version '0.0.9'
-    id 'org.beryx.jlink' version '2.23.2'
+    id 'org.beryx.jlink' version '2.23.3'
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
     id 'com.adarshr.test-logger' version '2.1.1'
@@ -42,6 +42,7 @@ java {
 
 application {
     mainClassName = "org.jabref.gui.JabRefLauncher"
+    mainModule = 'org.jabref'
 }
 
 // TODO: Ugly workaround to temporarily ignore build errors to dependencies of latex2unicode
@@ -132,7 +133,10 @@ dependencies {
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.10.0.202012080955-r'
 
-    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.1'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.12.0-rc2'
+    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.12.0-rc2'
+
+    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.2'
 
     implementation 'org.postgresql:postgresql:42.2.18'
 
@@ -190,7 +194,7 @@ dependencies {
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.62.2'
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.62.2'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.98'
+    testImplementation 'io.github.classgraph:classgraph:4.8.102'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.7.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.7.0'
@@ -201,13 +205,13 @@ dependencies {
     testImplementation 'org.mockito:mockito-core:3.7.7'
     testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.15.0'
-    testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.15.0'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.16.0'
+    testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.16.0'
     testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.39'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.40'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
 }
 

docs/adr/0018-use-Jackson-to-parse-study-yml.md

@@ -0,0 +1,56 @@
+# Use Jackson to parse study.yml
+
+## Context and Problem Statement
+
+The study definition file is formulated as a YAML document.
+To accessed the definition within JabRef this document has to be parsed.
+What parser should be used to parse YAML files?
+
+## Considered Options
+
+* [Jackson](https://github.com/FasterXML/jackson-dataformat-yaml)
+* [SnakeYAML Engine](https://bitbucket.org/asomov/snakeyaml)
+* [yamlbeans](https://github.com/EsotericSoftware/yamlbeans)
+* [eo-yaml](https://github.com/decorators-squad/eo-yaml)
+* Self-written parser
+
+## Decision Outcome
+
+Chosen option: Jackson, because as it is a dedicated library for parsing YAML. yamlbeans also seem to be viable. They all offer similar functionality
+
+## Pros and Cons of the Options
+
+### Jackson
+
+* Good, because established YAML parser library
+* Good, because supports YAML 1.2
+* Good, because it can parse LocalDate
+
+### SnakeYAML Engine
+
+* Good, because established YAML parser library
+* Good, because supports YAML 1.2
+* Bad, because cannot parse YAML into Java DTOs, only into [basic Java structures](https://bitbucket.org/asomov/snakeyaml-engine/src/master/), this then has to be assembled into DTOs
+
+### yamlbeans
+
+* Good, because established YAML parser library
+* Good, because [nice getting started page](https://github.com/EsotericSoftware/yamlbeans)
+* Bad, because objects need to be annotated in the yaml file to be parsed into Java objects
+
+### eo-yaml
+
+* Good, because established YAML parser library
+* Good, because supports YAML 1.2
+* Bad, because cannot parse YAML into Java DTOs
+
+### Own parser
+
+* Good, because easily customizable
+* Bad, because high effort
+* Bad, because has to be tested extensively
+
+## Links
+
+* [Winery's ADR-0009](https://github.com/eclipse/winery/blob/master/docs/adr/0009-manual-tosca-yaml-serialisation.md)
+* [Winery's ADR-0010](https://github.com/eclipse/winery/blob/master/docs/adr/0010-tosca-yaml-deserialisation-using-snakeyaml.md)

docs/adr/0019-keep-study-as-a-dto.md

@@ -0,0 +1,30 @@
+# Keep study as a DTO
+
+## Context and Problem Statement
+
+The study holds query and library entries that could be replaced respectively with complex query and fetcher instances.
+This poses the question: should the study remain a pure DTO object or should it contain direct object instances?
+
+## Considered Options
+
+* Keep study as DTO and use transformers
+* Replace entries with instances
+
+## Decision Outcome
+
+Chosen option: "Keep study as DTO and use transformators", because comes out best (see below).
+
+## Pros and Cons of the Options
+
+### Keep study as DTO and use transformators
+
+* Good, because no need for custom serialization
+* Good, because deactivated fetchers can be documented (important for traceable Searching (SLRs))
+* Bad, because Entries for databases and queries needed
+
+### Replace entries with instances
+
+* Good, because no need for database and query entries
+* Bad, because custom de-/serializers for fetchers and complex queries needed
+* Bad, because harder to maintain than using "vanilla" jackson de-/serialization
+* … <!-- numbers of pros and cons can vary -->

src/main/java/module-info.java

@@ -88,4 +88,7 @@
     requires lucene.queryparser;
     requires lucene.core;
     requires org.eclipse.jgit;
+    requires com.fasterxml.jackson.databind;
+    requires com.fasterxml.jackson.dataformat.yaml;
+    requires com.fasterxml.jackson.datatype.jsr310;
 }

src/main/java/org/jabref/gui/Base.css

@@ -642,6 +642,10 @@
     -fx-background-color: -jr-warn;
 }
 
+.file-row-text{
+    -fx-fill: -jr-search-text;
+}
+
 .combo-box-base {
     -fx-background-color: -fx-outer-border, -fx-control-inner-background;
     -fx-background-insets: 0, 1;
@@ -1217,6 +1221,10 @@ TextFlow * {
 
 }
 
-.mainTable-header{
+.mainTable-header {
     -fx-fill: -fx-mid-text-color;
 }
+
+.fontsizeSpinner{
+    -fx-pref-width: 5em;
+}

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

@@ -829,26 +829,22 @@ private MenuBar createMenu() {
         SidePaneComponent groups = sidePaneManager.getComponent(SidePaneType.GROUPS);
         SidePaneComponent openOffice = sidePaneManager.getComponent(SidePaneType.OPEN_OFFICE);
 
-        view.getItems().add(new SeparatorMenuItem());
-        view.setOnShowing(event -> {
-            view.getItems().clear();
-            view.getItems().addAll(
-                    factory.createCheckMenuItem(webSearch.getToggleAction(), webSearch.getToggleCommand(), sidePaneManager.isComponentVisible(SidePaneType.WEB_SEARCH)),
-                    factory.createCheckMenuItem(groups.getToggleAction(), groups.getToggleCommand(), sidePaneManager.isComponentVisible(SidePaneType.GROUPS)),
-                    factory.createCheckMenuItem(openOffice.getToggleAction(), openOffice.getToggleCommand(), sidePaneManager.isComponentVisible(SidePaneType.OPEN_OFFICE)),
+        view.getItems().addAll(
+                factory.createCheckMenuItem(webSearch.getToggleAction(), webSearch.getToggleCommand(), sidePaneManager.isComponentVisible(SidePaneType.WEB_SEARCH)),
+                factory.createCheckMenuItem(groups.getToggleAction(), groups.getToggleCommand(), sidePaneManager.isComponentVisible(SidePaneType.GROUPS)),
+                factory.createCheckMenuItem(openOffice.getToggleAction(), openOffice.getToggleCommand(), sidePaneManager.isComponentVisible(SidePaneType.OPEN_OFFICE)),
 
-                    new SeparatorMenuItem(),
+                new SeparatorMenuItem(),
 
-                    factory.createMenuItem(StandardActions.NEXT_PREVIEW_STYLE, new PreviewSwitchAction(PreviewSwitchAction.Direction.NEXT, this, stateManager)),
-                    factory.createMenuItem(StandardActions.PREVIOUS_PREVIEW_STYLE, new PreviewSwitchAction(PreviewSwitchAction.Direction.PREVIOUS, this, stateManager)),
+                factory.createMenuItem(StandardActions.NEXT_PREVIEW_STYLE, new PreviewSwitchAction(PreviewSwitchAction.Direction.NEXT, this, stateManager)),
+                factory.createMenuItem(StandardActions.PREVIOUS_PREVIEW_STYLE, new PreviewSwitchAction(PreviewSwitchAction.Direction.PREVIOUS, this, stateManager)),
 
-                    new SeparatorMenuItem(),
+                new SeparatorMenuItem(),
 
-                    factory.createMenuItem(StandardActions.SHOW_PDF_VIEWER, new ShowDocumentViewerAction(stateManager, prefs)),
-                    factory.createMenuItem(StandardActions.EDIT_ENTRY, new OpenEntryEditorAction(this, stateManager)),
-                    factory.createMenuItem(StandardActions.OPEN_CONSOLE, new OpenConsoleAction(stateManager))
-            );
-        });
+                factory.createMenuItem(StandardActions.SHOW_PDF_VIEWER, new ShowDocumentViewerAction(stateManager, prefs)),
+                factory.createMenuItem(StandardActions.EDIT_ENTRY, new OpenEntryEditorAction(this, stateManager)),
+                factory.createMenuItem(StandardActions.OPEN_CONSOLE, new OpenConsoleAction(stateManager))
+        );
 
         options.getItems().addAll(
                 factory.createMenuItem(StandardActions.SHOW_PREFS, new ShowPreferencesAction(this, Globals.TASK_EXECUTOR)),

src/main/java/org/jabref/gui/externalfiles/FileExtensionViewModel.java

@@ -19,7 +19,7 @@ public class FileExtensionViewModel {
     private final ExternalFileTypes externalFileTypes;
 
     FileExtensionViewModel(FileType fileType, ExternalFileTypes externalFileTypes) {
-        this.description = Localization.lang("%0 file", fileType.toString());
+        this.description = Localization.lang("%0 file", fileType.getName());
         this.extensions = fileType.getExtensionsWithDot();
         this.externalFileTypes = externalFileTypes;
     }

src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java

@@ -74,7 +74,7 @@ private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter
         Map<Boolean, List<Path>> fileListPartition;
 
         try (Stream<Path> filesStream = StreamSupport.stream(Files.newDirectoryStream(directory, fileFilter).spliterator(), false)) {
-            fileListPartition = filesStream.collect(Collectors.partitioningBy(path -> path.toFile().isDirectory()));
+            fileListPartition = filesStream.collect(Collectors.partitioningBy(Files::isDirectory));
         } catch (IOException e) {
             LOGGER.error(String.format("%s while searching files: %s", e.getClass().getName(), e.getMessage()));
             return parent;

src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml

@@ -34,14 +34,14 @@
                 <ColumnConstraints hgrow="SOMETIMES"/>
             </columnConstraints>
             <rowConstraints>
-                <RowConstraints minHeight="10.0" vgrow="SOMETIMES"/>
-                <RowConstraints minHeight="10.0" vgrow="SOMETIMES"/>
+                <RowConstraints minHeight="20.0" vgrow="SOMETIMES"/>
+                <RowConstraints minHeight="20.0" vgrow="SOMETIMES"/>
             </rowConstraints>
                 <Label text="%Start directory:" GridPane.columnIndex="0" GridPane.rowIndex="0"/>
                 <TextField fx:id="directoryPathField" GridPane.columnIndex="1" GridPane.rowIndex="0"/>
                 <Button onAction="#browseFileDirectory" styleClass="icon-button,narrow"
                         GridPane.columnIndex="2" GridPane.rowIndex="0"
-                        prefHeight="20.0" prefWidth="20.0">
+                        minWidth="20.0" minHeight="20.0" prefHeight="20.0" prefWidth="20.0">
                     <graphic>
                         <JabRefIconView glyph="OPEN"/>
                     </graphic>
@@ -50,9 +50,9 @@
                     </tooltip>
                 </Button>
 
-                <Label text="%File extension:" GridPane.columnIndex="0" GridPane.rowIndex="1"/>
+                <Label text="%File type:" GridPane.columnIndex="0" GridPane.rowIndex="1"/>
                 <ComboBox fx:id="fileTypeCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="1"/>
-                <Button fx:id="scanButton" onAction="#scanFiles" text="%Scan directory"
+                <Button fx:id="scanButton" onAction="#scanFiles" text="%Search"
                         GridPane.columnIndex="2" GridPane.rowIndex="1">
                     <tooltip>
                         <Tooltip text="%Searches the selected directory for unlinked files."/>
@@ -71,11 +71,11 @@
                             <TableView fx:id="importResultTable">
                                 <columns>
                                     <TableColumn fx:id="colStatus" prefWidth="100.0" text="%Status"/>
-                                    <TableColumn fx:id="colMessage" prefWidth="300.0" text="%Message"/>
                                     <TableColumn fx:id="colFile" prefWidth="500.0" text="%File"/>
+                                    <TableColumn fx:id="colMessage" prefWidth="300.0" text="%Message"/>
                                 </columns>
                                 <columnResizePolicy>
-                                    <TableView fx:constant="CONSTRAINED_RESIZE_POLICY"/>
+                                    <TableView fx:constant="UNCONSTRAINED_RESIZE_POLICY"/>
                                 </columnResizePolicy>
                             </TableView>
                         </TitledPane>

src/main/java/org/jabref/gui/externalfiles/UnlinkedPDFFileFilter.java

@@ -4,6 +4,7 @@
 import java.io.IOException;
 import java.nio.file.DirectoryStream;
 import java.nio.file.DirectoryStream.Filter;
+import java.nio.file.Files;
 import java.nio.file.Path;
 
 import org.jabref.logic.util.io.DatabaseFileLookup;
@@ -31,6 +32,11 @@ public UnlinkedPDFFileFilter(DirectoryStream.Filter<Path> fileFilter, BibDatabas
 
     @Override
     public boolean accept(Path pathname) throws IOException {
-        return fileFilter.accept(pathname) && !lookup.lookupDatabase(pathname.toFile());
+
+        if (Files.isDirectory(pathname)) {
+            return true;
+        } else {
+            return fileFilter.accept(pathname) && !lookup.lookupDatabase(pathname);
+        }
     }
 }

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

@@ -141,8 +141,10 @@ private static Node createFileDisplay(LinkedFileViewModel linkedFile) {
         icon.setOnMouseClicked(event -> linkedFile.open());
         Text link = new Text();
         link.textProperty().bind(linkedFile.linkProperty());
+        link.getStyleClass().setAll("file-row-text");
         Text desc = new Text();
         desc.textProperty().bind(linkedFile.descriptionProperty());
+        desc.getStyleClass().setAll("file-row-text");
 
         ProgressBar progressIndicator = new ProgressBar();
         progressIndicator.progressProperty().bind(linkedFile.downloadProgressProperty());

src/main/java/org/jabref/gui/preferences/AppearanceTab.fxml

@@ -25,7 +25,7 @@
     <CheckBox fx:id="fontOverride" text="%Override default font settings"/>
     <HBox alignment="CENTER_LEFT" spacing="4.0">
         <Label text="%Size" disable="${!fontOverride.selected}"/>
-        <Spinner fx:id="fontSize" prefWidth="60.0" editable="true"/>
+        <Spinner fx:id="fontSize" styleClass="fontsizeSpinner" editable="true"/>
         <padding>
             <Insets left="20.0"/>
         </padding>

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

@@ -187,7 +187,7 @@ public static String expandBrackets(String pattern, Character keywordDelimiter,
      * @param database         The {@link BibDatabase} for field resolving. May be null.
      * @return a function accepting a bracketed expression and returning the result of expanding it
      */
-    private static Function<String, String> expandBracketContent(Character keywordDelimiter, BibEntry entry, BibDatabase database) {
+    public static Function<String, String> expandBracketContent(Character keywordDelimiter, BibEntry entry, BibDatabase database) {
         return (String bracket) -> {
             String expandedPattern;
             List<String> fieldParts = parseFieldAndModifiers(bracket);

src/main/java/org/jabref/logic/crawler/Crawler.java

@@ -11,7 +11,6 @@
 import org.jabref.logic.preferences.TimestampPreferences;
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.study.QueryResult;
-import org.jabref.model.study.Study;
 import org.jabref.model.util.FileUpdateMonitor;
 
 import org.eclipse.jgit.api.errors.GitAPIException;
@@ -36,9 +35,8 @@ public class Crawler {
     public Crawler(Path studyDefinitionFile, GitHandler gitHandler, FileUpdateMonitor fileUpdateMonitor, ImportFormatPreferences importFormatPreferences, SavePreferences savePreferences, TimestampPreferences timestampPreferences, BibEntryTypesManager bibEntryTypesManager) throws IllegalArgumentException, IOException, ParseException, GitAPIException {
         Path studyRepositoryRoot = studyDefinitionFile.getParent();
         studyRepository = new StudyRepository(studyRepositoryRoot, gitHandler, importFormatPreferences, fileUpdateMonitor, savePreferences, timestampPreferences, bibEntryTypesManager);
-        Study study = studyRepository.getStudy();
-        LibraryEntryToFetcherConverter libraryEntryToFetcherConverter = new LibraryEntryToFetcherConverter(study.getActiveLibraryEntries(), importFormatPreferences);
-        this.studyFetcher = new StudyFetcher(libraryEntryToFetcherConverter.getActiveFetchers(), study.getSearchQueryStrings());
+        StudyDatabaseToFetcherConverter studyDatabaseToFetcherConverter = new StudyDatabaseToFetcherConverter(studyRepository.getActiveLibraryEntries(), importFormatPreferences);
+        this.studyFetcher = new StudyFetcher(studyDatabaseToFetcherConverter.getActiveFetchers(), studyRepository.getSearchQueryStrings());
     }
 
     /**