Merge remote-tracking branch 'upstream/main' into restapi

* upstream/main: (42 commits)
  Place subgroups w.r.t. alphabetical ordering (#9228)
  DOAB Fetcher now fetches ISBN and imprint fields where possible (#9229)
  ISSUE-9145: implement isbn fetcher (#9205)
  Remove explicit javafx jmod stuff (#9245)
  New Crowdin updates (#9239)
  Support Arabic language (#9243)
  Process CLI arguments before starting gui (#9217)
  Update README Decision Records link (#9241)
  Opening a file removes duplicate keywords and triggers lib changed (#9216)
  New Crowdin updates (#9237)
  Add Ukrainian as language (#9236)
  Add ADR-0026 on using Swing's FileChooser (#9235)
  Log exception (#9227)
  Fix archunit (#9234)
  Bump tika-core from 2.4.1 to 2.5.0 (#9232)
  Check group type before showing dialog in edit group (#8909)
  Fix unexpected closing of preferences dialog (#9225)
  Fix typo in connection error message (#9226)
  Improve VSCode config (#9218)
  Searching for an entry on the web shouldn't take forever (#9199)
  ...

# Conflicts:
#	build.gradle
#	lib/afterburner.fx.jar
#	src/main/java/org/jabref/cli/Launcher.java
#	src/main/java/org/jabref/gui/EntryTypeView.java
#	src/main/java/org/jabref/gui/auximport/FromAuxDialog.java
#	src/main/java/org/jabref/gui/bibtexextractor/ExtractBibtexDialog.java
#	src/main/java/org/jabref/gui/collab/ExternalChangesResolverDialog.java
#	src/main/java/org/jabref/gui/commonfxcontrols/CitationKeyPatternPanel.java
#	src/main/java/org/jabref/gui/contentselector/ContentSelectorDialogView.java
#	src/main/java/org/jabref/gui/customentrytypes/CustomizeEntryTypeDialogView.java
#	src/main/java/org/jabref/gui/documentviewer/DocumentViewerView.java
#	src/main/java/org/jabref/gui/edit/ManageKeywordsDialog.java
#	src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
#	src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabView.java
#	src/main/java/org/jabref/gui/errorconsole/ErrorConsoleView.java
#	src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogView.java
#	src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java
#	src/main/java/org/jabref/gui/help/AboutDialogView.java
#	src/main/java/org/jabref/gui/importer/ImportCustomEntryTypesDialog.java
#	src/main/java/org/jabref/gui/importer/ImportEntriesDialog.java
#	src/main/java/org/jabref/gui/integrity/IntegrityCheckDialog.java
#	src/main/java/org/jabref/gui/libraryproperties/AbstractPropertiesTabView.java
#	src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesView.java
#	src/main/java/org/jabref/gui/libraryproperties/constants/ConstantsPropertiesView.java
#	src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesView.java
#	src/main/java/org/jabref/gui/libraryproperties/keypattern/KeyPatternPropertiesView.java
#	src/main/java/org/jabref/gui/libraryproperties/saving/SavingPropertiesView.java
#	src/main/java/org/jabref/gui/linkedfile/LinkedFileEditDialogView.java
#	src/main/java/org/jabref/gui/openoffice/ManageCitationsDialogView.java
#	src/main/java/org/jabref/gui/openoffice/StyleSelectDialogView.java
#	src/main/java/org/jabref/gui/preferences/AbstractPreferenceTabView.java
#	src/main/java/org/jabref/gui/preferences/PreferencesDialogView.java
#	src/main/java/org/jabref/gui/preferences/customexporter/CustomExporterTab.java
#	src/main/java/org/jabref/gui/preferences/externalfiletypes/EditExternalFileTypeEntryDialog.java
#	src/main/java/org/jabref/gui/preferences/journals/JournalAbbreviationsTab.java
#	src/main/java/org/jabref/gui/preferences/keybindings/KeyBindingsTab.java
#	src/main/java/org/jabref/gui/preferences/preview/PreviewTab.java
#	src/main/java/org/jabref/gui/preferences/protectedterms/ProtectedTermsTab.java
#	src/main/java/org/jabref/gui/search/GlobalSearchResultDialog.java
#	src/main/java/org/jabref/gui/shared/SharedDatabaseLoginDialogView.java
#	src/main/java/org/jabref/gui/slr/ManageStudyDefinitionView.java
#	src/main/java/org/jabref/gui/texparser/ParseLatexDialogView.java
#	src/main/java/org/jabref/gui/texparser/ParseLatexResultView.java

.devcontainer/devcontainer.json

@@ -14,12 +14,17 @@
 
             // Add the IDs of extensions you want installed when the container is created.
             "extensions": [
-                "vscjava.vscode-java-pack"
+                "vscjava.vscode-java-pack",
+                "vscjava.vscode-gradle",
+                "shengchen.vscode-checkstyle"
             ]
         }
     },
 
-    "onCreateCommand": "yes | sdk install java 18.0.2-tem && gradle assemble",
+    "onCreateCommand": "gradle assemble",
+
+    // Forward the noVNC port (desktop-lite: https://github.com/devcontainers/features/tree/main/src/desktop-lite)  
+    "forwardPorts": [6080],
 
     // Need to connect as root otherwise we run into issues with gradle.
     // default option is "vscode". More info: https://aka.ms/vscode-remote/containers/non-root.
@@ -28,10 +33,11 @@
         // Adds a lightweight desktop that can be accessed using a VNC viewer or the web
         "desktop-lite": "latest",
 
-        // Install java 17 (java 18 is not yet available from ms)
+        // Install java
         "java": {
-            "version": "17",
-            "installGradle": true
+            "version": "18",
+            "installGradle": true,
+            "jdkDistro": "sem"
         }
     }
 }

.github/workflows/automerge.yml

@@ -9,7 +9,7 @@ jobs:
     steps:
       - name: 'Wait for status checks'
         id: waitforstatuschecks
-        uses: "WyriHaximus/github-action-wait-for-status@v1.6"
+        uses: "WyriHaximus/github-action-wait-for-status@v1.7.1"
         with:
           ignoreActions: Automerge Dependabot,Code coverage,Create snapcraft image,Deploy binaries on builds.jabref.org,codecov/project,markdown-link-check
           checkInterval: 13

.vscode/settings.json

@@ -0,0 +1,6 @@
+{
+    "java.configuration.updateBuildConfiguration": "interactive",
+    "java.format.settings.url": "/config/VSCode Code Style.xml",
+    "java.checkstyle.configuration": "${workspaceFolder}/config/checkstyle/checkstyle_reviewdog.xml",
+    "java.checkstyle.version": "10.3.4",
+}

CHANGELOG.md

@@ -18,25 +18,36 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added a warning message next to the authors field in the merge dialog to warn users when the authors are the same but formatted differently. [#8745](https://github.com/JabRef/jabref/issues/8745)
 - The properties of an existing systematic literature review can be edited. [koppor#604](https://github.com/koppor/jabref/issues/604)
 - An SLR can now be started from the SLR itself. [#9131](https://github.com/JabRef/jabref/pull/9131), [koppor#601](https://github.com/koppor/jabref/issues/601)
+- Implement a new ISBN Fetcher ([doi-to-bibtex-converter.herokuapp.com](http://doi-to-bibtex-converter.herokuapp.com) as source). [#9145](https://github.com/JabRef/jabref/pull/9145)
+- We added support for the Ukrainian and Arabic languages. [#9236](https://github.com/JabRef/jabref/pull/9236), [#9243](https://github.com/JabRef/jabref/pull/9243)
 
 ### Changed
 
+- We disabled the conversion menu for empty fields [#9200](https://github.com/JabRef/jabref/issues/9200)
+- We upgraded to Lucene 9.4 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.
+  [#9213](https://github.com/JabRef/jabref/pull/9213)
+- Genres are now mapped correctly to entry types when importing MODS files. [#9185](https://github.com/JabRef/jabref/issues/9185)
 - We improved the Citavi Importer to also import so called Knowledge-items into the field `comment` of the corresponding entry [#9025](https://github.com/JabRef/jabref/issues/9025)
 - We removed wrapping of string constants when writing to a `.bib` file.
 - We call backup files `.bak` and temporary writing files now `.sav`.
 - JabRef keeps 10 older versions of a `.bib` file in the [user data dir](https://github.com/harawata/appdirs#supported-directories) (instead of a single `.sav` (now: `.bak`) file in the directory of the `.bib` file)
 - We changed the button label from "Return to JabRef" to "Return to library" to better indicate the purpose of the action.
-- We removed "last-search-date" from the SLR feature, because the last-search-date can be deducted from the git logs. [#9116](https://github.com/JabRef/jabref/pull/9116)
 - A user can now add arbitrary data into `study.yml`. JabRef just ignores this data. [#9124](https://github.com/JabRef/jabref/pull/9124)
 - We reworked the External Changes Resolver dialog. [#9021](https://github.com/JabRef/jabref/pull/9021)
 - The fallback directory of the file folder now is the general file directory. In case there was a directory configured for a library and this directory was not found, JabRef placed the PDF next to the .bib file and not into the general file directory.
 - The global default directory for storing PDFs is now the subdirectory "JabRef" in the user's home.
 - We reworked the Define study parameters dialog. [#9123](https://github.com/JabRef/jabref/pull/9123)
 - We simplified the actions to fast-resolve duplicates to 'Keep Left', 'Keep Right', 'Keep Both' and 'Keep Merged'. [#9056](https://github.com/JabRef/jabref/issues/9056)
 - We fixed an issue where a message about changed metadata would occur on saving although nothing changed. [#9159](https://github.com/JabRef/jabref/issues/9159)
+- When adding or editing a subgroup it is placed w.r.t. to alphabetical ordering rather than at the end. [koppor#577](https://github.com/koppor/jabref/issues/577)
+- We modified the Directory of Open Access Books (DOAB) fetcher so that it will now also fetch the ISBN when possible. [#8708](https://github.com/JabRef/jabref/issues/8708)
 
 ### Fixed
 
+- We fixed the display of the "Customize Entry Types" dialogue title [#9198](https://github.com/JabRef/jabref/issues/9198)
 - We fixed an issue where author names with tilde accents (for example ñ) were marked as "Names are not in the standard BibTex format" [#8071](https://github.com/JabRef/jabref/issues/8071)
 - We fixed an issue where the possibility to generate a subdatabase from an aux file was writing empty files when called from the commandline [#9115](https://github.com/JabRef/jabref/issues/9115), [forum#3516](https://discourse.jabref.org/t/export-subdatabase-from-aux-file-on-macos-command-line/3516)
 - We fixed the display of issue, number, eid and pages fields in the entry preview. [#8607](https://github.com/JabRef/jabref/pull/8607), [#8372](https://github.com/JabRef/jabref/issues/8372), [Koppor#514](https://github.com/koppor/jabref/issues/514), [forum#2390](https://discourse.jabref.org/t/unable-to-edit-my-bibtex-file-that-i-used-before-vers-5-1/2390), [forum#3462](https://discourse.jabref.org/t/jabref-5-6-need-help-with-export-from-jabref-to-microsoft-word-entry-preview-of-apa-7-not-rendering-correctly/3462)
@@ -52,9 +63,16 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where JabRef would not exit when a connection to a LibreOffice document was established previously and the document is still open. [#9075](https://github.com/JabRef/jabref/issues/9075)
 - We fixed an issue about selecting the save order in the preferences. [#9175](https://github.com/JabRef/jabref/issues/9147)
 - We fixed an issue where the CSS styles are missing in some dialogs. [#9150](https://github.com/JabRef/jabref/pull/9150)
+- We fixed an issue where pdfs were re-indexed on each startup. [#9166](https://github.com/JabRef/jabref/pull/9166)
+- We fixed an issue where Capitalize didn't capitalize words after hyphen characters. [#9157](https://github.com/JabRef/jabref/issues/9157)
+- We fixed an issue with the message that is displayed when fetcher returns an empty list of entries for given query. [#9195](https://github.com/JabRef/jabref/issues/9195)
+- We fixed an issue where an exception was not logged correctly. [koppor#627](https://github.com/JabRef/koppor/issues/627)
+- We fixed an issue where hitting enter on the search field within the preferences dialog closed the dialog. [koppor#630](https://github.com/koppor/jabref/issues/630)
+- We fixed a typo within a connection error message. [koppor#625](https://github.com/koppor/jabref/issues/625)
 
 ### Removed
 
+- We removed "last-search-date" from the SLR feature, because the last-search-date can be deducted from the git logs. [#9116](https://github.com/JabRef/jabref/pull/9116)
 
 
 

README.md

@@ -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. 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).
+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/decisions/).
 
 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

@@ -49,7 +49,7 @@ java {
 }
 
 application {
-    mainClass.set('org.jabref.gui.JabRefLauncher')
+    mainClass.set('org.jabref.cli.Launcher')
     mainModule.set('org.jabref')
 }
 
@@ -115,17 +115,17 @@ 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:9.3.0'
-    implementation 'org.apache.lucene:lucene-queryparser:9.3.0'
-    implementation 'org.apache.lucene:lucene-queries:9.3.0'
-    implementation 'org.apache.lucene:lucene-analysis-common:9.3.0'
-    implementation 'org.apache.lucene:lucene-highlighter:9.3.0'
+    implementation 'org.apache.lucene:lucene-core:9.4.0'
+    implementation 'org.apache.lucene:lucene-queryparser:9.4.0'
+    implementation 'org.apache.lucene:lucene-queries:9.4.0'
+    implementation 'org.apache.lucene:lucene-analysis-common:9.4.0'
+    implementation 'org.apache.lucene:lucene-highlighter:9.4.0'
 
     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:2.1.214'
 
-    implementation group: 'org.apache.tika', name: 'tika-core', version: '2.4.1'
+    implementation group: 'org.apache.tika', name: 'tika-core', version: '2.5.0'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk18on:1.71.1'
@@ -160,10 +160,11 @@ dependencies {
         exclude module: "jsr305"
     }
 
-    implementation group: 'jakarta.annotation', name: 'jakarta.annotation-api', version: '1.3.5'
+    implementation 'jakarta.annotation:jakarta.annotation-api:2.1.1'
     implementation 'jakarta.inject:jakarta.inject-api:2.0.1'
 
-    // JavaFX stuff
+
+    implementation 'com.github.JabRef:afterburner.fx:testmoduleinfo-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
@@ -177,7 +178,7 @@ dependencies {
     implementation 'org.jsoup:jsoup:1.15.3'
     implementation 'com.konghq:unirest-java:3.13.11'
 
-    implementation 'org.slf4j:slf4j-api:2.0.1'
+    implementation 'org.slf4j:slf4j-api:2.0.3'
     implementation "org.tinylog:tinylog-api:2.5.0"
     implementation "org.tinylog:slf4j-tinylog:2.5.0"
     implementation "org.tinylog:tinylog-impl:2.5.0"
@@ -208,19 +209,19 @@ dependencies {
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
     testImplementation 'io.github.classgraph:classgraph:4.8.149'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.9.0'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.9.0'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.9.1'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.9.1'
 
     testImplementation 'org.mockito:mockito-core:4.8.0'
     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'
+    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.0.0'
+    testImplementation 'com.tngtech.archunit:archunit-junit5-api:1.0.0'
     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:10.3.3'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.4'
     // 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'
@@ -564,7 +565,6 @@ jlink {
         requires 'java.transaction.xa'
         requires 'java.rmi'
         requires 'java.xml'
-        requires 'jdk.jfr'
         requires 'jdk.jsobject'
         requires 'jdk.unsupported'
         requires 'jdk.unsupported.desktop'
@@ -573,8 +573,6 @@ jlink {
         requires 'com.google.gson'
         requires 'org.slf4j'
         requires 'jakarta.xml.bind'
-        uses 'com.airhacks.afterburner.views.ResourceLocator'
-        uses 'com.airhacks.afterburner.injection.PresenterFactory'
         uses 'org.mariadb.jdbc.credential.CredentialPlugin'
         uses 'org.mariadb.jdbc.authentication.AuthenticationPlugin'
         uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'

buildSrc/build.gradle

@@ -8,7 +8,7 @@ repositories {
 dependencies {
     implementation 'com.h2database:h2-mvstore:2.1.214'
     implementation 'org.apache.commons:commons-csv:1.9.0'
-    implementation 'org.slf4j:slf4j-api:2.0.1'
+    implementation 'org.slf4j:slf4j-api:2.0.3'
 }
 
 sourceSets{

buildres/csl/csl-locales/.github/workflows/label-gun.yml

@@ -6,8 +6,13 @@ on:
   issue_comment:
     types: [created, edited, closed]
 
+permissions: {}
 jobs:
   label:
+    permissions:
+      issues: write # to add label to an issues (retorquere/label-gun)
+      pull-requests: write # to add label, comment on pull request (retorquere/label-gun)
+
     runs-on: ubuntu-latest
     steps:
       - uses: retorquere/label-gun@main

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

@@ -12,8 +12,13 @@ on:
         description: Commit message
         required: true
 
+permissions: {}
 jobs:
   release:
+    permissions:
+      contents: write # to create a release
+      pull-requests: read # to read pull requests (dorny/paths-filter)
+
     runs-on: ubuntu-latest
     env:
       GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

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

@@ -4,8 +4,13 @@ on:
   pull_request_target:
     types: [ opened, synchronize, workflow_dispatch]
 
+permissions: {}
 jobs:
   test:
+    permissions:
+      contents: write # to push code in repo (stefanzweifel/git-auto-commit-action)
+      pull-requests: write # to comment on pull requests
+
     runs-on: ubuntu-latest
     env:
       GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"