Merge remote-tracking branch 'upstream/controlsfx-tags' into controls…

…fx-tags

# Conflicts:
#	build.gradle

.github/workflows/tests.yml

@@ -37,9 +37,10 @@ jobs:
       - name: Run check style reporter
         uses: nikitasavinov/checkstyle-action@master
         with:
-          reporter: github-pr-check
+          reporter: github-pr-review
+          github_token: ${{ secrets.GITHUB_TOKEN }}
           checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
-          checkstyle_version: '10.1'
+          checkstyle_version: '10.3'
       - name: Run checkstyle gradle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
       - name: Run markdown-lint

.gitpod.Dockerfile

@@ -0,0 +1,8 @@
+# See https://www.gitpod.io/docs/java-in-gitpod/ for a full documentation of Java in GitPod
+
+FROM gitpod/workspace-full
+
+# All available versions can be listed using sdk ls java
+# More information about SDKMAN available at https://github.com/sdkman/sdkman-cli#sdkman-cli
+RUN bash -c ". /home/gitpod/.sdkman/bin/sdkman-init.sh \
+             && sdk install java 18.0.1.1-open"

.gitpod.yml

@@ -0,0 +1,16 @@
+image:
+  file: .gitpod.Dockerfile
+tasks:
+  - init: ./gradlew assemble
+jetbrains:
+  intellij:
+    plugins:
+      - CheckStyle-IDEA
+      - zielu.gittoolbox
+vscode:
+  extensions:
+    - redhat.java
+    - richardwillis.vscode-gradle
+    - vscjava.vscode-java-debug
+    - kiteco.kite
+    - DavidAnson.vscode-markdownlint

CHANGELOG.md

@@ -11,32 +11,49 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
-- We added a fetcher for [Biodiversity Heritage Library)](https://www.biodiversitylibrary.org/) [8539](https://github.com/JabRef/jabref/issues/8539)
+- We added a fetcher for [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/). [8539](https://github.com/JabRef/jabref/issues/8539)
 - We added support for multiple messages in the snackbar. [#7340](https://github.com/JabRef/jabref/issues/7340)
+- We added an extra option in the 'Find Unlinked Files' dialog view to ignore unnecessary files like Thumbs.db, DS_Store, etc. [koppor#373](https://github.com/koppor/jabref/issues/373)
 - JabRef now writes log files. Linux: `$home/.cache/jabref/logs/version`, Windows: `%APPDATA%\..\Local\harawata\jabref\version\logs`, Mac: `Users/.../Library/Logs/jabref/version`
+- We added an importer for Citavi backup files, support ".ctv5bak" and ".ctv6bak" file formats. [#8322](https://github.com/JabRef/jabref/issues/8322)
 
 ### Changed
 
+- The file column in the main table now shows the corresponding defined icon for the linked file [8930](https://github.com/JabRef/jabref/issues/8930).
+- We improved the color of the selected entries and the color of the summary in the Import Entries Dialog in the dark theme. [#7927](https://github.com/JabRef/jabref/issues/7927)
+- We upgraded to Lucene 9.2 for the fulltext search.
+  Thus, the now created search index cannot be read from older versions of JabRef anylonger.
+  ⚠️ JabRef will recreate the index in a new folder for new files and this will take a long time for a huge library.
+  Moreover, switching back and forth JabRef versions and meanwhile adding PDFs also requires rebuilding the index now and then.
+  [#8868](https://github.com/JabRef/jabref/pull/8868)
 - We improved the Latex2Unicode conversion [#8639](https://github.com/JabRef/jabref/pull/8639)
 - Writing BibTeX data into a PDF (XMP) removes braces. [#8452](https://github.com/JabRef/jabref/issues/8452)
 - Writing BibTeX data into a PDF (XMP) does not write the `file` field.
 - Writing BibTeX data into a PDF (XMP) considers the configured keyword separator (and does not use "," as default any more)
 - The Medline/Pubmed search now also supports the [default fields and operators for searching](https://docs.jabref.org/collect/import-using-online-bibliographic-database#search-syntax). [forum#3554](https://discourse.jabref.org/t/native-pubmed-search/3354)
 - We improved group expansion arrow that prevent it from activating group when expanding or collapsing. [#7982](https://github.com/JabRef/jabref/issues/7982), [#3176](https://github.com/JabRef/jabref/issues/3176)
+- When configured SSL certificates changed, JabRef warns the user to restart to apply the configuration.
+- We improved the appearances and logic of the "Manage field names & content" dialog, and renamed it to "Automatic field editor". [#6536](https://github.com/JabRef/jabref/issues/6536)
+- We fixed an issue that caused JabRef to sometimes open multiple instances when "Remote Operation" is enabled. [#8653](https://github.com/JabRef/jabref/issues/8653)
 
 ### Fixed
 
+- We fixed an issue where linked files with the filetype "application/pdf" in an entry were not shown with the correct PDF-Icon in the main table [8930](https://github.com/JabRef/jabref/issues/8930)
+- We fixed an issue where "open folder" for linked files did not open the folder and did not select the file unter certain Linux desktop environments [#8679](https://github.com/JabRef/jabref/issues/8679), [#8849](https://github.com/JabRef/jabref/issues/8849)
 - We fixed an issue where the content of a big shared database library is not shown [#8788](https://github.com/JabRef/jabref/issues/8788)
 - We fixed the unnecessary horizontal scroll bar in group panel [#8467](https://github.com/JabRef/jabref/issues/8467)
 - We fixed an issue where the notification bar message, icon and actions appeared to be invisible. [#8761](https://github.com/JabRef/jabref/issues/8761)
 - We fixed an issue where deprecated fields tab is shown when the fields don't contain any values. [#8396](https://github.com/JabRef/jabref/issues/8396)
+- We fixed an issue where an exception for DOI search occurred when the DOI contained urlencoded characters. [#8787](https://github.com/JabRef/jabref/issues/8787)
 - We fixed an issue which allow us to select and open identifiers from a popup list in the maintable [#8758](https://github.com/JabRef/jabref/issues/8758), [8802](https://github.com/JabRef/jabref/issues/8802)
 - We fixed an issue where the escape button had no functionality within the "Filter groups" textfield. [koppor#562](https://github.com/koppor/jabref/issues/562)
-- We fixed an issue where right clicking a group and choose "remove selected entries from this group" leads to error when Bibtex source tab is selected. [#8012](https://github.com/JabRef/jabref/issues/8012)
+- We fixed an issue where the exception that there are invalid characters in filename. [#8786](https://github.com/JabRef/jabref/issues/8786)
+- When the proxy configuration removed the proxy user/password, this change is applied immediately.
+- We fixed an issue where removing several groups deletes only one of them. [#8390](https://github.com/JabRef/jabref/issues/8390)
 
 ### Removed
 
-
+- We removed the social media buttons for our Twitter and Facebook pages. [#8774](https://github.com/JabRef/jabref/issues/8774)
 
 
 
@@ -64,7 +81,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ### Changed
 
 - We upgraded to Lucene 9.1 for the fulltext search.
-  Thus, the now created search index cannot be read from older versions of JabRef anylonger.
+  Thus, the now created search index cannot be read from older versions of JabRef any longer.
   ⚠️ JabRef will recreate the index in a new folder for new files and this will take a long time for a huge library.
   Moreover, switching back and forth JabRef versions and meanwhile adding PDFs also requires rebuilding the index now and then.
   [#8362](https://github.com/JabRef/jabref/pull/8362)
@@ -91,7 +108,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where "Copy DOI url" in the right-click menu of the Entry List would just copy the DOI and not the DOI url. [#8389](https://github.com/JabRef/jabref/issues/8389)
 - We fixed an issue where opening the console from the drop-down menu would cause an exception. [#8466](https://github.com/JabRef/jabref/issues/8466)
 - We fixed an issue when reading non-UTF-8 encoded. When no encoding header is present, the encoding is now detected from the file content (and the preference option is disregarded). [#8417](https://github.com/JabRef/jabref/issues/8417)
-- We fixed an issue where pasting a URL was replacing + signs by spaces making the URL unreachable. [#8448](https://github.com/JabRef/jabref/issues/8448)
+- We fixed an issue where pasting a URL was replacing `+` signs by spaces making the URL unreachable. [#8448](https://github.com/JabRef/jabref/issues/8448)
 - We fixed an issue where creating subsidiary files from aux files created with some versions of biblatex would produce incorrect results. [#8513](https://github.com/JabRef/jabref/issues/8513)
 - We fixed an issue where opening the changelog from withing JabRef led to a 404 error. [#8563](https://github.com/JabRef/jabref/issues/8563)
 - We fixed an issue where not all found unlinked local files were imported correctly due to some race condition. [#8444](https://github.com/JabRef/jabref/issues/8444)
@@ -100,6 +117,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where no citationkey was generated on import, pasting a doi or an entry on the main table. [8406](https://github.com/JabRef/jabref/issues/8406), [koppor#553](https://github.com/koppor/jabref/issues/553)
 - We fixed an issue where accent search does not perform consistently. [#6815](https://github.com/JabRef/jabref/issues/6815)
 - We fixed an issue where the incorrect entry was selected when "New Article" is pressed while search filters are active. [#8674](https://github.com/JabRef/jabref/issues/8674)
+- We fixed an issue where "Write BibTeXEntry metadata to PDF" button remains enabled while writing to PDF is in-progress. [#8691](https://github.com/JabRef/jabref/issues/8691)
 
 ### Removed
 

README.md

@@ -71,7 +71,7 @@ An explanation of donation possibilities and usage of donations is available at
 [![OpenHub](https://www.openhub.net/p/jabref/widgets/project_thin_badge.gif)](https://www.openhub.net/p/jabref)
 [![Deployment Status](https://github.com/JabRef/jabref/workflows/Deployment/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ADeployment)
 [![Test Status](https://github.com/JabRef/jabref/workflows/Tests/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ATests)
-[![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)
+[![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=main)
 
 Want to be part of a free and open-source project that tens of thousands of scientists use every day?
 Check out the ways you can contribute, below:
@@ -84,7 +84,7 @@ Check out the ways you can contribute, below:
 
 We view pull requests as a collaborative process.
 Submit a pull request early to get feedback from the team on work in progress.
-We will discuss improvements with you and agree to merge them once the [developers](https://github.com/JabRef/jabref/blob/main/MAINTAINERS) approve.
+We will discuss improvements with you and agree to merge them once the [developers](https://github.com/JabRef/jabref/blob/main/MAINTAINERS) approve. Please also remember to discuss bigger changes early with the core developers to avoid a waste of time and work. Some fundamental design decisions can be found within our list of [Architectural Decision Records](https://devdocs.jabref.org/adr.html).
 
 If you want a step-by-step walk-through on how to set-up your workspace, please check [this guideline](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace).
 

build.gradle

@@ -10,7 +10,7 @@ plugins {
 
     id 'me.champeau.gradle.jmh' version '0.5.3'
 
-    id 'org.javamodularity.moduleplugin' version '1.8.10'
+    id 'org.javamodularity.moduleplugin' version '1.8.11'
 
     id 'org.openjfx.javafxplugin' version '0.0.13'
 
@@ -81,7 +81,7 @@ repositories {
     mavenLocal()
     mavenCentral()
     maven { url 'https://oss.sonatype.org/content/groups/public' }
-    maven { url 'https://repository.apache.org/snapshots' }
+    maven { url 'https://jitpack.io' }
 }
 
 configurations {
@@ -95,6 +95,10 @@ configurations {
     }
 }
 
+dependencyLocking {
+    lockAllConfigurations()
+}
+
 javafx {
     version = "18"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
@@ -112,44 +116,44 @@ dependencies {
     implementation 'org.apache.pdfbox:fontbox:3.0.0-RC1'
     implementation 'org.apache.pdfbox:xmpbox:3.0.0-RC1'
 
-    implementation 'org.apache.lucene:lucene-core:9.1.0'
-    implementation 'org.apache.lucene:lucene-queryparser:9.1.0'
-    implementation 'org.apache.lucene:lucene-queries:9.1.0'
-    implementation 'org.apache.lucene:lucene-analysis-common:9.1.0'
-    implementation 'org.apache.lucene:lucene-highlighter:9.1.0'
+    implementation 'org.apache.lucene:lucene-core:9.2.0'
+    implementation 'org.apache.lucene:lucene-queryparser:9.2.0'
+    implementation 'org.apache.lucene:lucene-queries:9.2.0'
+    implementation 'org.apache.lucene:lucene-analysis-common:9.2.0'
+    implementation 'org.apache.lucene:lucene-highlighter:9.2.0'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0'
-    implementation 'com.h2database:h2-mvstore:2.1.212'
+    implementation 'com.h2database:h2-mvstore:2.1.214'
 
-    implementation group: 'org.apache.tika', name: 'tika-core', version: '2.4.0'
+    implementation group: 'org.apache.tika', name: 'tika-core', version: '2.4.1'
     implementation 'com.ibm.icu:icu4j-charset:71.1'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk18on:1.71'
 
     implementation 'commons-cli:commons-cli:1.5.0'
 
-    implementation 'org.libreoffice:libreoffice:7.3.3'
-    implementation 'org.libreoffice:unoloader:7.3.3'
+    implementation 'org.libreoffice:libreoffice:7.3.4'
+    implementation 'org.libreoffice:unoloader:7.3.4'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.11'
     implementation 'info.debatty:java-string-similarity:2.0.0'
 
     antlr3 'org.antlr:antlr:3.5.3'
-    implementation 'org.antlr:antlr-runtime:3.5.2'
+    implementation 'org.antlr:antlr-runtime:3.5.3'
 
     antlr4 'org.antlr:antlr4:4.9.3'
     implementation 'org.antlr:antlr4-runtime:4.9.3'
 
-    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.1.0.202203080745-r'
+    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.2.0.202206071550-r'
 
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.13.3'
-    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.13.2'
+    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.13.3'
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.5'
 
-    implementation 'org.postgresql:postgresql:42.3.5'
+    implementation 'org.postgresql:postgresql:42.4.0'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -166,21 +170,21 @@ dependencies {
     // JavaFX stuff
     implementation 'org.kordamp.ikonli:ikonli-javafx:12.3.1'
     implementation 'org.kordamp.ikonli:ikonli-materialdesign2-pack:12.3.1'
-    implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
+    implementation 'com.github.sialcasa.mvvmFX:mvvmfx-validation:f195849ca9' //jitpack
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.2'
-    implementation 'org.fxmisc.flowless:flowless:0.6.9'
+    implementation 'org.fxmisc.flowless:flowless:0.6.10'
     implementation 'org.fxmisc.richtext:richtextfx:0.10.9'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
-    implementation ('com.dlsc.gemsfx:gemsfx:1.47.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '1.47.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude group: 'com.dlsc.unitfx'
     }
 
     implementation 'org.controlsfx:controlsfx:11.1.1'
 
-    implementation 'org.jsoup:jsoup:1.14.3'
-    implementation 'com.konghq:unirest-java:3.13.8'
+    implementation 'org.jsoup:jsoup:1.15.1'
+    implementation 'com.konghq:unirest-java:3.13.10'
 
     implementation 'org.slf4j:slf4j-api:2.0.0-alpha7'
     implementation "org.tinylog:tinylog-api:2.4.1"
@@ -208,17 +212,17 @@ dependencies {
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.146'
+    testImplementation 'io.github.classgraph:classgraph:4.8.147'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
 
-    testImplementation 'org.mockito:mockito-core:4.5.1'
+    testImplementation 'org.mockito:mockito-core:4.6.1'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.23.1'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.23.1'
-    testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
-    testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
+    testImplementation "org.testfx:testfx-core:4.0.16-alpha"
+    testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
     checkstyle 'com.puppycrawl.tools:checkstyle:10.1'
@@ -267,7 +271,8 @@ task generateSource(dependsOn: ["generateBstGrammarSource",
                                 "generateMedlineSource",
                                 "generateBibtexmlSource",
                                 "generateEndnoteSource",
-                                "generateModsSource"]) {
+                                "generateModsSource",
+                                "generateCitaviSource"]) {
     group = 'JabRef'
     description 'Generates all necessary (Java) source files.'
 }
@@ -321,6 +326,15 @@ task generateEndnoteSource(type: XjcTask) {
     javaPackage = "org.jabref.logic.importer.fileformat.endnote"
 }
 
+task generateCitaviSource(type: XjcTask) {
+    group = 'JabRef'
+    description = "Generates java files for the citavi importer."
+
+    schemaFile = "src/main/resources/xjc/citavi/citavi.xsd"
+    outputDirectory = "src-gen/main/java/"
+    javaPackage = "org.jabref.logic.importer.fileformat.citavi"
+}
+
 task generateModsSource(type: XjcTask) {
     group = 'JabRef'
     description = "Generates java files for the mods importer."

buildSrc/build.gradle

@@ -6,7 +6,7 @@ repositories {
 }
 
 dependencies {
-    implementation 'com.h2database:h2-mvstore:2.1.212'
+    implementation 'com.h2database:h2-mvstore:2.1.214'
     implementation 'org.apache.commons:commons-csv:1.9.0'
     implementation 'org.slf4j:slf4j-api:2.0.0-alpha7'
 }

buildres/csl/csl-locales/.github/workflows/merge.yaml

@@ -19,9 +19,9 @@ jobs:
       GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       DISTRIBUTION_UPDATER_TOKEN: "${{ secrets.DISTRIBUTION_UPDATER_TOKEN }}"
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       if: github.event_name == 'push'
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       if: github.event_name == 'workflow_dispatch'
       with:
         fetch-depth: 0
@@ -30,7 +30,7 @@ jobs:
       id: release
       run: echo ::set-output name=branch::v1.0.2
     - name: Checkout release branch
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: ${{ steps.release.outputs.branch }}
         path: './release'
@@ -63,7 +63,7 @@ jobs:
         ruby-version: 3.0.2
     - name: but use cache to speed that up
       if: github.event_name == 'workflow_dispatch' || (github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true'))
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}