Merge branch 'main' into min-http-api

.devcontainer/devcontainer.json

@@ -16,7 +16,8 @@
             "extensions": [
                 "vscjava.vscode-java-pack",
                 "vscjava.vscode-gradle",
-                "shengchen.vscode-checkstyle"
+                "shengchen.vscode-checkstyle",
+                "DavidAnson.vscode-markdownlint"
             ]
         }
     },
@@ -35,8 +36,8 @@
 
         // Install java
         "java": {
-            "version": "18",
-            "installGradle": true,
+            "version": "20",
+            "installGradle": false,
             "jdkDistro": "sem"
         }
     }

.github/workflows/GreetingFirstTimeCodeContribution.yml

@@ -13,7 +13,7 @@ jobs:
       issues: write
     steps:
     - name: GreetingFirstTimeCodeContribution
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v3
       with:
         issue-number: ${{ github.event.issue.number }}
         body: |

.github/workflows/cleanup_pr.yml

@@ -27,7 +27,7 @@ jobs:
           echo "branch=${{ github.event.pull_request.head.ref }}" >> $GITHUB_OUTPUT
       - name: Delete folder on builds.jabref.org
         if: steps.checksecrets.outputs.secretspresent == 'YES'
-        uses: appleboy/[email protected].8
+        uses: appleboy/[email protected].10
         with:
           script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
           host: build-upload.jabref.org

.github/workflows/deployment-arm64.yml

@@ -6,7 +6,6 @@ on:
    branches:
     - arm64mac-release
 
-
 env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
@@ -59,8 +58,8 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 19
-          distribution: 'liberica'
+          java-version: 20
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Clean up keychain
         if: (matrix.os == 'self-hosted') && (steps.checksecrets.outputs.secretspresent == 'YES')

.github/workflows/deployment.yml

@@ -75,7 +75,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 19
+          java-version: 20
           distribution: 'temurin'
           cache: 'gradle'
       - name: Setup OSX key chain on OSX
@@ -112,11 +112,11 @@ jobs:
           jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type pkg --vendor JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
           productsign --sign "Developer ID Installer: JabRef e.V. (6792V39SK3)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Package application image
-        if: (matrix.os != 'macos-latest')
+        # if: (matrix.os != 'macos-latest')
         shell: bash
         run: ${{ matrix.archivePortable }}
       - name: Rename files
-        if: (matrix.os != 'macos-latest')
+        # if: (matrix.os != 'macos-latest')
         shell: pwsh
         run: |
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
@@ -203,7 +203,7 @@ jobs:
       - name: Package application image
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
-        run: brew install pigz && tar -c -C build/distribution JabRef.app | pigz --rsyncable > build/distribution/JabRef-portable_macos.tar.gz && rm -R build/distribution/JabRef.app
+        run: ${{ matrix.archivePortable }}
       - name: Rename files
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: pwsh

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

@@ -46,7 +46,7 @@ jobs:
           cp buildres/csl/csl-locales/locales-en-US.xml src/main/resources/csl-locales/
           git add .
           git commit -m"Refresh example styles" || true
-      - uses: peter-evans/create-pull-request@v4
+      - uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}
           branch: refresh-csl

.github/workflows/refresh-journal-lists.yml

@@ -21,7 +21,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 19
+          java-version: 20
           distribution: 'temurin'
           cache: 'gradle'
       - name: Update journal lists
@@ -53,7 +53,7 @@ jobs:
           # create .mv file
           cd $GITHUB_WORKSPACE
           ./gradlew generateJournalAbbreviationList
-      - uses: peter-evans/create-pull-request@v4
+      - uses: peter-evans/create-pull-request@v5
         if: github.ref == 'refs/heads/main'
         with:
           token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tests-fetchers.yml

@@ -43,7 +43,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 19
+          java-version: 20
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run fetcher tests

.github/workflows/tests.yml

@@ -31,7 +31,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 19
+          java-version: 20
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run check style reporter
@@ -57,7 +57,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 19
+          java-version: 20
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run tests
@@ -89,7 +89,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 19
+          java-version: 20
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run tests on PostgreSQL
@@ -123,7 +123,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 19
+          java-version: 20
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run GUI tests
@@ -161,7 +161,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 19
+          java-version: 20
           distribution: 'temurin'
           cache: 'gradle'
       - name: Update test coverage metrics

.vscode/extensions.json

@@ -0,0 +1,6 @@
+{
+    "recommendations": [
+        "davidanson.vscode-markdownlint",
+        "valentjn.vscode-ltex"
+    ]
+}

.vscode/ltex.dictionary.en-US.txt

@@ -0,0 +1,3 @@
+JabDrive
+JabRef
+CouchDB

CHANGELOG.md

@@ -17,13 +17,15 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added "Attach file from URL" to right-click context menu to download and store a file with the reference library. [#9646](https://github.com/JabRef/jabref/issues/9646)
 - We enabled updating an existing entry with data from InspireHEP. [#9351](https://github.com/JabRef/jabref/issues/9351)
 - We added a fetcher for the Bibliotheksverbund Bayern (experimental). [#9641](https://github.com/JabRef/jabref/pull/9641)
+- We added support for multiple languages for exporting to and importing references from MS Office. [#9699](https://github.com/JabRef/jabref/issues/9699)
 - We enabled scrolling in the groups list when dragging a group on another group. [#2869](https://github.com/JabRef/jabref/pull/2869)
-
-
+- We added the option to automatically download online files when a new entry is created from an existing ID (e.g. DOI). The option can be disabled in the preferences under "Import and Export" [#9756](https://github.com/JabRef/jabref/issues/9756)
+- We added a new Integrity check for unscaped ampersands. [koppor#585](https://github.com/koppor/jabref/issues/585)
 
 
 ### Changed
 
+- We upgraded to Lucene 9.5 for the fulltext search. The search index will be rebuild. [#9584](https://github.com/JabRef/jabref/pull/9584)
 - 'Get full text' now also checks the file url. [#568](https://github.com/koppor/jabref/issues/568)
 - JabRef writes a new backup file only if there is a change. Before, JabRef created a backup upon start. [#9679](https://github.com/JabRef/jabref/pull/9679)
 - We modified the `Add Group` dialog to use the most recently selected group hierarchical context. [#9141](https://github.com/JabRef/jabref/issues/9141)
@@ -37,6 +39,10 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We improved the Medline importer to correctly import ISO dates for `revised`. [#9536](https://github.com/JabRef/jabref/issues/9536)
 - To avoid cluttering of the directory, We always delete the `.sav` file upon successful write. [#9675](https://github.com/JabRef/jabref/pull/9675)
 - We improved the unlinking/deletion of multiple linked files of an entry using the <kbd>Delete</kbd> key. [#9473](https://github.com/JabRef/jabref/issues/9473)
+- We moved the custom entry types dialog into the preferences dialog. [#9760](https://github.com/JabRef/jabref/pull/9760)
+- We moved the manage content selectors dialog to the library properties. [#9768](https://github.com/JabRef/jabref/pull/9768)
+- We moved the preferences menu command from the options menu to the file menu. [#9768](https://github.com/JabRef/jabref/pull/9768)
+
 
 
 ### Fixed
@@ -55,14 +61,16 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed the issue where the size of the global search window was not retained after closing. [#9362](https://github.com/JabRef/jabref/issues/9362)
 - We fixed an issue where the Global Search UI preview is still white in dark theme. [#9362](https://github.com/JabRef/jabref/issues/9362)
 - We fixed the double paste issue when <kbd>Cmd</kbd> + <kbd>v</kbd> is pressed on 'New entry from plaintext' dialog. [#9367](https://github.com/JabRef/jabref/issues/9367)
+- We fixed an issue where the pin button on the Global Search dialog was located at the bottom and not at the top. [#9362](https://github.com/JabRef/jabref/issues/9362)
 - We fixed the log text color in the event log console when using dark mode. [#9732](https://github.com/JabRef/jabref/issues/9732)
-
+- We fixed an issue where searching for unlinked files would include the current library's .bib file [#9735](https://github.com/JabRef/jabref/issues/9735)
+- We fixed an issue where it was no longer possible to connect to a shared mysql database due to an exception [#9761](https://github.com/JabRef/jabref/issues/9761)
 
 ### Removed
 
 - We removed the support of BibTeXML. [#9540](https://github.com/JabRef/jabref/issues/9540)
 - We removed support for Markdown syntax for strikethrough and task lists in comment fields. [#9726](https://github.com/JabRef/jabref/pull/9726)
-
+- We removed the options menu, because the two contents were moved to the File menu or the properties of the library. [#9768](https://github.com/JabRef/jabref/pull/9768)
 
 
 

README.md

@@ -88,7 +88,7 @@ We will discuss improvements with you and agree to merge them once the [develope
 
 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).
 
-To compile JabRef from source, you need a Java Development Kit 19 and `JAVA_HOME` pointing to this JDK.
+To compile JabRef from source, you need a Java Development Kit 20 and `JAVA_HOME` pointing to this JDK.
 To run it, just execute `gradlew run`.
 When you want to develop, it is necessary to generate additional sources using `gradlew generateSource`
 and then generate the Eclipse `gradlew eclipse`.

build.gradle

@@ -6,7 +6,7 @@ import org.jabref.build.xjc.XjcTask
 plugins {
     id 'application'
 
-    id 'com.github.andygoossens.modernizer' version '1.7.0'
+    id 'com.github.andygoossens.modernizer' version '1.8.0'
 
     id 'me.champeau.gradle.jmh' version '0.5.3'
 
@@ -40,8 +40,8 @@ group = "org.jabref"
 version = project.findProperty('projVersion') ?: '100.0.0'
 
 java {
-    sourceCompatibility = JavaVersion.VERSION_19
-    targetCompatibility = JavaVersion.VERSION_19
+    sourceCompatibility = JavaVersion.VERSION_20
+    targetCompatibility = JavaVersion.VERSION_20
     // Workaround needed for Eclipse, probably because of https://github.com/gradle/gradle/issues/16922
     // Should be removed as soon as Gradle 7.0.1 is released ( https://github.com/gradle/gradle/issues/16922#issuecomment-828217060 )
     modularity.inferModulePath.set(false)
@@ -80,6 +80,7 @@ repositories {
     mavenLocal()
     mavenCentral()
     maven { url 'https://oss.sonatype.org/content/groups/public' }
+    maven { url 'https://s01.oss.sonatype.org/content/repositories/snapshots/' }
     maven { url 'https://jitpack.io' }
 }
 
@@ -114,18 +115,18 @@ 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:9.4.2'
-    implementation 'org.apache.lucene:lucene-queryparser:9.4.2'
-    implementation 'org.apache.lucene:lucene-queries:9.4.2'
-    implementation 'org.apache.lucene:lucene-analysis-common:9.4.2'
-    implementation 'org.apache.lucene:lucene-highlighter:9.4.2'
+    implementation 'org.apache.lucene:lucene-core:9.5.0'
+    implementation 'org.apache.lucene:lucene-queryparser:9.5.0'
+    implementation 'org.apache.lucene:lucene-queries:9.5.0'
+    implementation 'org.apache.lucene:lucene-analysis-common:9.5.0'
+    implementation 'org.apache.lucene:lucene-highlighter:9.5.0'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.10.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0'
     implementation 'com.h2database:h2-mvstore:2.1.214'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk18on:1.71.1'
+    implementation 'org.bouncycastle:bcprov-jdk18on:1.73'
 
     implementation 'commons-cli:commons-cli:1.5.0'
 
@@ -143,7 +144,7 @@ dependencies {
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.14.2'
     implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.14.2'
 
-    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.7'
+    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.9'
 
     implementation 'org.postgresql:postgresql:42.6.0'
 
@@ -161,7 +162,7 @@ dependencies {
     implementation 'jakarta.inject:jakarta.inject-api:2.0.1'
 
 
-    implementation 'com.github.JabRef:afterburner.fx:testmoduleinfo-SNAPSHOT'
+    implementation 'org.jabref:afterburner.fx:1.1.0-SNAPSHOT'
     implementation 'org.kordamp.ikonli:ikonli-javafx:12.3.1'
     implementation 'org.kordamp.ikonli:ikonli-materialdesign2-pack:12.3.1'
     implementation 'com.github.sialcasa.mvvmFX:mvvmfx-validation:f195849ca9' //jitpack
@@ -223,7 +224,7 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.9.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.9.2'
 
-    testImplementation 'org.mockito:mockito-core:5.2.0'
+    testImplementation 'org.mockito:mockito-core:5.3.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.1'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.1'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.0.1'

buildres/csl/csl-styles/dependent/consumption-and-society.csl

@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-GB">
+  <!-- Bristol University Press, generated from "bup" metadata at https://github.com/citation-style-language/journals -->
+  <info>
+    <title>Consumption and Society</title>
+    <title-short>#TITLESHORT#</title-short>
+    <id>http://www.zotero.org/styles/consumption-and-society</id>
+    <link href="http://www.zotero.org/styles/consumption-and-society" rel="self"/>
+    <link href="http://www.zotero.org/styles/bristol-university-press" rel="independent-parent"/>
+    <category citation-format="author-date"/>
+    <eissn>2752-8499</eissn>
+    <updated>2023-02-27T12:00:00+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>

buildres/csl/csl-styles/dependent/critical-and-radical-social-work.csl

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-GB">
+  <!-- Bristol University Press, generated from "bup" metadata at https://github.com/citation-style-language/journals -->
+  <info>
+    <title>Critical and Radical Social Work</title>
+    <title-short>#TITLESHORT#</title-short>
+    <id>http://www.zotero.org/styles/critical-and-radical-social-work</id>
+    <link href="http://www.zotero.org/styles/critical-and-radical-social-work" rel="self"/>
+    <link href="http://www.zotero.org/styles/bristol-university-press" rel="independent-parent"/>
+    <category citation-format="author-date"/>
+    <issn>2049-8608</issn>
+    <eissn>2049-8675</eissn>
+    <updated>2023-02-27T12:00:00+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>

buildres/csl/csl-styles/dependent/emotions-and-society.csl

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-GB">
+  <!-- Bristol University Press, generated from "bup" metadata at https://github.com/citation-style-language/journals -->
+  <info>
+    <title>Emotions and Society</title>
+    <title-short>#TITLESHORT#</title-short>
+    <id>http://www.zotero.org/styles/emotions-and-society</id>
+    <link href="http://www.zotero.org/styles/emotions-and-society" rel="self"/>
+    <link href="http://www.zotero.org/styles/bristol-university-press" rel="independent-parent"/>
+    <category citation-format="author-date"/>
+    <issn>2631-6897</issn>
+    <eissn>2631-6900</eissn>
+    <updated>2023-02-27T12:00:00+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>

buildres/csl/csl-styles/dependent/european-journal-of-politics-and-gender.csl

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-GB">
+  <!-- Bristol University Press, generated from "bup" metadata at https://github.com/citation-style-language/journals -->
+  <info>
+    <title>European Journal of Politics and Gender</title>
+    <title-short>#TITLESHORT#</title-short>
+    <id>http://www.zotero.org/styles/european-journal-of-politics-and-gender</id>
+    <link href="http://www.zotero.org/styles/european-journal-of-politics-and-gender" rel="self"/>
+    <link href="http://www.zotero.org/styles/bristol-university-press" rel="independent-parent"/>
+    <category citation-format="author-date"/>
+    <issn>2515-1088</issn>
+    <eissn>2515-1096</eissn>
+    <updated>2023-02-27T12:00:00+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>