Merge remote-tracking branch 'upstream/main' into controlsfx-tags

* upstream/main: (27 commits)
  Add gitpod config (#8921)
  Fix javafx version not displayed in About Dialog (#8918)
  Redesign "Manage field names & content" dialog (#8892)
  Rework IACR fetcher (#8904)
  Bump h2-mvstore from 2.1.212 to 2.1.214 in /buildSrc (#8915)
  Bump unoloader from 7.3.3 to 7.3.4 (#8912)
  Bump libreoffice from 7.3.3 to 7.3.4 (#8913)
  Bump tika-core from 2.4.0 to 2.4.1 (#8914)
  Bump org.eclipse.jgit from 6.1.0.202203080745-r to 6.2.0.202206071550-r (#8916)
  Squashed 'buildres/csl/csl-styles/' changes from e740261..845dee0 (#8903)
  Bump flowless from 0.6.9 to 0.6.10 (#8898)
  Bump postgresql from 42.3.5 to 42.4.0 (#8900)
  Bump mockito-core from 4.6.0 to 4.6.1 (#8899)
  Bump antlr-runtime from 3.5.2 to 3.5.3 (#8897)
  Update to MADR 3.0.0-beta.2 (#8896)
  Increase the network connection timeout and improve error message (#8894)
  Fix linux terminal opening process error (#8891)
  Fix exception if linked file has masked umlauts / invalid characters in path (#8851)
  Remove obsolte CHANGELOG.md entry
  Revert "Fix right clicking a group and choosing "remove selected entries from this group" leads to error when Bibtex source tab is selected (#8821)"
  ...

# 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 +1,8 @@
+image:
+  file: .gitpod.Dockerfile
+tasks:
+  - init: ./gradlew assemble
+vscode:
+  extensions:
+    - redhat.java
+    - vscjava

CHANGELOG.md

@@ -14,6 +14,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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)
 - 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
 
@@ -29,17 +30,20 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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 "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)
 

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:

build.gradle

@@ -120,36 +120,36 @@ dependencies {
 
     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: '2.13.3'
 
     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
@@ -169,7 +169,7 @@ dependencies {
     implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
     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 (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '1.45.2') {
@@ -211,7 +211,9 @@ dependencies {
     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'
+    testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
+    testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
+    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'
@@ -266,7 +268,8 @@ task generateSource(dependsOn: ["generateBstGrammarSource",
                                 "generateMedlineSource",
                                 "generateBibtexmlSource",
                                 "generateEndnoteSource",
-                                "generateModsSource"]) {
+                                "generateModsSource",
+                                "generateCitaviSource"]) {
     group = 'JabRef'
     description 'Generates all necessary (Java) source files.'
 }
@@ -320,6 +323,15 @@ 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-styles/Gemfile.lock

@@ -65,10 +65,10 @@ GEM
     mini_portile2 (2.8.0)
     multipart-post (2.1.1)
     namae (1.1.1)
-    nokogiri (1.13.4)
+    nokogiri (1.13.6)
       mini_portile2 (~> 2.8.0)
       racc (~> 1.4)
-    nokogiri (1.13.4-x64-mingw32)
+    nokogiri (1.13.6-x64-mingw32)
       racc (~> 1.4)
     octokit (4.21.0)
       faraday (>= 0.9)

buildres/csl/csl-styles/dependent/avian-research.csl

@@ -1,16 +1,15 @@
 <?xml version="1.0" encoding="utf-8"?>
 <style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-US">
-  <!-- Generated with https://github.com/citation-style-language/utilities/tree/master/generate_dependent_styles/data/springer -->
   <info>
     <title>Avian Research</title>
     <id>http://www.zotero.org/styles/avian-research</id>
     <link href="http://www.zotero.org/styles/avian-research" rel="self"/>
-    <link href="http://www.zotero.org/styles/springer-vancouver-author-date" rel="independent-parent"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/Key_Style_Points_1.0.pdf" rel="documentation"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/manuscript-guidelines-1.0.pdf" rel="documentation"/>
+    <link href="http://www.zotero.org/styles/elsevier-harvard2" rel="independent-parent"/>
+    <link href="https://www.keaipublishing.com/en/journals/avian-research/guide-for-authors/" rel="documentation"/>
     <category citation-format="author-date"/>
+    <issn>2055-6187</issn>
     <eissn>2053-7166</eissn>
-    <updated>2014-05-15T12:00:00+00:00</updated>
+    <updated>2022-05-27T12:00:00+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
 </style>