Merge remote-tracking branch 'upstream/main' into fix-for-issue-8189

* upstream/main: (28 commits) [Bot] Update CSL styles (JabRef#8978) New Crowdin updates (JabRef#8972) New Crowdin updates (JabRef#8969) Fix .bat errorlevel handling with pwsh.exe check (JabRef#8965) revert jsoup version upgrade Fix charset detection with utf16 and others (JabRef#8947) Bump classgraph from 4.8.147 to 4.8.149 (JabRef#8968) Bump jsoup from 1.15.1 to 1.15.2 (JabRef#8967) Keep UTF-8 encoding header if present (JabRef#8964) Cleanup index when opening a library (JabRef#8962) Refactor context menu entry types changing (JabRef#8957) Improvement on check for missing commas when importing or opening a .bib file (JabRef#8840) Disable ResearchGateTest on CI (JabRef#8955) Bump checkstyle from 10.1 to 10.3.1 (JabRef#8950) Bump checkstyle from 10.1 to 10.3.1 (JabRef#8950) Bump mariadb-java-client from 2.7.5 to 2.7.6 (JabRef#8953) Add notification when adding previous entries to new group configuration (JabRef#8919) Remember Sidepane width after restart (JabRef#8936) move "Warn about duplicates on import" preferences option (JabRef#8937) Fix theme switching exception (JabRef#8939) ... # Conflicts: # src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java
LIM0000 · Jul 15, 2022 · 33de3cf · 33de3cf
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,11 +13,14 @@ 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)
+- 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.
@@ -31,10 +34,15 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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)
+- We improved the message explaining the options when modifying an automatic keyword group [#8911](https://github.com/JabRef/jabref/issues/8911)
+- We moved the preferences option "Warn about duplicates on import" option from the tab "File" to the tab "Import and Export". [koppor#570](https://github.com/koppor/jabref/issues/570)
+- When JabRef encounters `% Encoding: UTF-8` header, it is kept during writing (and not removed). [#8964](https://github.com/JabRef/jabref/pull/8964)
+- We replace characters which cannot be decoded using the specified encoding by a (probably another) valid character. This happens if JabRef detects the wrong charset (e.g., UTF-8 instead of Windows 1252). One can use the [Integrity Check](https://docs.jabref.org/finding-sorting-and-cleaning-entries/checkintegrity) to find those characters.
 
 ### Fixed
 
+- 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)
+- 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)
@@ -46,6 +54,10 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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)
+- We fixed an issue where the Sidepane (groups, web search and open office) width is not remembered after restarting JabRef. [#8907](https://github.com/JabRef/jabref/issues/8907)
+- We fixed a bug where switching between themes will cause an error/exception. [#8939](https://github.com/JabRef/jabref/pull/8939)
+- We fixed a bug where files that were deleted in the source bibtex file were kept in the index. [#8962](https://github.com/JabRef/jabref/pull/8962)
+- We fixed "Error while sending to JabRef" when the browser extension interacts with JabRef. [JabRef-Browser-Extension#479](https://github.com/JabRef/JabRef-Browser-Extension/issues/479)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -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 {
@@ -95,8 +95,12 @@ configurations {
     }
 }
 
+dependencyLocking {
+    lockAllConfigurations()
+}
+
 javafx {
-    version = "18"
+    version = "18.0.1"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -123,7 +127,6 @@ dependencies {
     implementation 'com.h2database:h2-mvstore:2.1.214'
 
     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'
@@ -147,7 +150,7 @@ dependencies {
     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 group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.6'
 
     implementation 'org.postgresql:postgresql:42.4.0'
 
@@ -166,7 +169,7 @@ 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:0.6.10'
@@ -204,22 +207,20 @@ dependencies {
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.147'
+    testImplementation 'io.github.classgraph:classgraph:4.8.149'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
 
-    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'
     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'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.1'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'

diff --git a/buildres/csl/csl-locales/.github/workflows/merge.yaml b/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'
@@ -48,6 +48,10 @@ jobs:
             - deleted: [ '*.csl', 'dependent/*.csl', '*.xml' ]
           workflows:
             - added|modified: .github/workflows/*.yaml
+          updated_composer:
+            - added|modified: composer.json
+          deleted_composer:
+            - deleted: composer.json
 
     - name: Changed files
       if: github.event_name == 'push'
@@ -63,7 +67,7 @@ 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') }}
@@ -87,11 +91,24 @@ jobs:
       run: cd release && git rm ${{ steps.update.outputs.deleted_files }}
       if: github.event_name == 'push' && steps.update.outputs.deleted == 'true'
 
+    - name: Update composer.json
+      if: steps.update.outputs.updated_composer == 'true'
+      run: |
+        cp composer.json release/composer.json
+        cd release
+        git add composer.json
+  
+    - name: Delete composer.json
+      if: steps.update.outputs.deleted_composer == 'true'
+      run: |
+        cd release
+        git rm composer.json
+    
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
         repository: 'release'
-        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }}
-      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true' || steps.update.outputs.updated_composer == 'true' || steps.update.outputs.deleted_composer == 'true')
 
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
@@ -116,3 +133,21 @@ jobs:
         git-user: "csl-bot"
         git-user-email: github@citationstyles.org
         git-commit-message: copied ${{ steps.update.outputs.workflows_files }} from styles
+
+    - name: Bump version and push tag
+      id: tag_version
+      uses: mathieudutour/github-tag-action@v5.6
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        default_bump: patch
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+
+    - name: Create a GitHub release
+      uses: softprops/action-gh-release@v0.1.14
+      env:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        tag_name: ${{ steps.tag_version.outputs.new_tag }}
+        name: Release ${{ steps.tag_version.outputs.new_tag }}
+        body: Released ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
diff --git a/buildres/csl/csl-locales/.github/workflows/sheldon.yaml b/buildres/csl/csl-locales/.github/workflows/sheldon.yaml
@@ -15,17 +15,17 @@ jobs:
     # labels to a PR
     # https://securitylab.github.com/research/github-actions-preventing-pwn-requests
     - name: Checkout repo for OWNER TEST
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: contains(github.event.pull_request.labels.*.name, 'safe to test')
       with:
         ref: ${{ github.event.pull_request.head.ref }}
 
     # otherwise, checkout the current master, and the pr to the subdirectory 'pull-request'
     - name: Checkout base repo for pull-request test
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
     - name: Checkout pull-request
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
       with:
         repository: ${{ github.event.pull_request.head.repo.full_name }}
@@ -54,7 +54,7 @@ jobs:
       with:
         ruby-version: 3.0.2
     - name: but use cache to speed that up
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

diff --git a/buildres/csl/csl-locales/Gemfile.lock b/buildres/csl/csl-locales/Gemfile.lock
@@ -33,7 +33,7 @@ GEM
     csl-styles (2.0.0)
       csl (~> 2.0)
     diff-lcs (1.5.0)
-    diffy (3.4.0)
+    diffy (3.4.2)
     dotenv (2.7.6)
     erubis (2.7.0)
     faraday (1.8.0)

diff --git a/buildres/csl/csl-styles/.github/dependabot.yml b/buildres/csl/csl-styles/.github/dependabot.yml
@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/buildres/csl/csl-styles/.github/workflows/merge.yaml b/buildres/csl/csl-styles/.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'
@@ -48,6 +48,10 @@ jobs:
             - deleted: [ '*.csl', 'dependent/*.csl', '*.xml' ]
           workflows:
             - added|modified: .github/workflows/*.yaml
+          updated_composer:
+            - added|modified: composer.json
+          deleted_composer:
+            - deleted: composer.json
 
     - name: Changed files
       if: github.event_name == 'push'
@@ -63,7 +67,7 @@ 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') }}
@@ -87,11 +91,24 @@ jobs:
       run: cd release && git rm ${{ steps.update.outputs.deleted_files }}
       if: github.event_name == 'push' && steps.update.outputs.deleted == 'true'
 
+    - name: Update composer.json
+      if: steps.update.outputs.updated_composer == 'true'
+      run: |
+        cp composer.json release/composer.json
+        cd release
+        git add composer.json
+  
+    - name: Delete composer.json
+      if: steps.update.outputs.deleted_composer == 'true'
+      run: |
+        cd release
+        git rm composer.json
+    
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
         repository: 'release'
-        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }}
-      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true' || steps.update.outputs.updated_composer == 'true' || steps.update.outputs.deleted_composer == 'true')
 
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
@@ -116,3 +133,21 @@ jobs:
         git-user: "csl-bot"
         git-user-email: github@citationstyles.org
         git-commit-message: copied ${{ steps.update.outputs.workflows_files }} from styles
+
+    - name: Bump version and push tag
+      id: tag_version
+      uses: mathieudutour/github-tag-action@v5.6
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        default_bump: patch
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+
+    - name: Create a GitHub release
+      uses: softprops/action-gh-release@v0.1.14
+      env:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        tag_name: ${{ steps.tag_version.outputs.new_tag }}
+        name: Release ${{ steps.tag_version.outputs.new_tag }}
+        body: Released ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
diff --git a/buildres/csl/csl-styles/.github/workflows/sheldon.yaml b/buildres/csl/csl-styles/.github/workflows/sheldon.yaml
@@ -15,17 +15,17 @@ jobs:
     # labels to a PR
     # https://securitylab.github.com/research/github-actions-preventing-pwn-requests
     - name: Checkout repo for OWNER TEST
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: contains(github.event.pull_request.labels.*.name, 'safe to test')
       with:
         ref: ${{ github.event.pull_request.head.ref }}
 
     # otherwise, checkout the current master, and the pr to the subdirectory 'pull-request'
     - name: Checkout base repo for pull-request test
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
     - name: Checkout pull-request
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
       with:
         repository: ${{ github.event.pull_request.head.repo.full_name }}
@@ -54,7 +54,7 @@ jobs:
       with:
         ruby-version: 3.0.2
     - name: but use cache to speed that up
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

diff --git a/buildres/csl/csl-styles/Gemfile.lock b/buildres/csl/csl-styles/Gemfile.lock
@@ -33,7 +33,7 @@ GEM
     csl-styles (2.0.0)
       csl (~> 2.0)
     diff-lcs (1.5.0)
-    diffy (3.4.0)
+    diffy (3.4.2)
     dotenv (2.7.6)
     erubis (2.7.0)
     faraday (1.8.0)