Merge remote-tracking branch 'upstream/main' into extract-entry-editor

.github/ghprcomment.yml

@@ -4,6 +4,9 @@
     We use [Checkstyle](https://checkstyle.sourceforge.io/) to identify issues.
     Please carefully follow [the setup guide for the codestyle](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
     Afterwards, please [run checkstyle locally](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html#run-checkstyle) and fix the issues.
+
+    In case of issues with the import order, double check that you [activated Auto Import](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html#enable-proper-import-cleanup).
+    You can trigger fixing imports by pressing <kbd>Ctrl</kbd>+<kbd>Alt</kbd>+<kbd>O</kbd> to trigger [Optimize Imports](https://www.jetbrains.com/guide/tips/optimize-imports/).
 - jobName: OpenRewrite
   message: |
     Your code currently does not meet JabRef's code guidelines.

.moderne/moderne.yml

@@ -0,0 +1,3 @@
+specs: specs.moderne.ai/v1/cli
+java:
+  selectedJdk: '23'

CHANGELOG.md

@@ -38,6 +38,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a different background color to the search bar to indicate when the search syntax is wrong. [#11658](https://github.com/JabRef/jabref/pull/11658)
 - We added a setting which always adds the literal "Cited on pages" text before each JStyle citation. [#11691](https://github.com/JabRef/jabref/pull/11732)
 - We added a new plain citation parser that uses LLMs. [#11825](https://github.com/JabRef/jabref/issues/11825)
+- We added support for `langid` field for biblatex libraries. [#10868](https://github.com/JabRef/jabref/issues/10868)
 - We added support for modifier keys when dropping a file on an entry in the main table. [#12001](https://github.com/JabRef/jabref/pull/12001)
 - We added an importer for SSRN URLs. [#12021](https://github.com/JabRef/jabref/pull/12021)
 - We added a compare button to the duplicates in the citation relations tab to open the "Possible duplicate entries" window. [#11192](https://github.com/JabRef/jabref/issues/11192)
@@ -123,6 +124,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where trying to open a library from a failed mounted directory on Mac would cause an error. [#10548](https://github.com/JabRef/jabref/issues/10548)
 - We fixed an issue when the preview was out of sync. [#9172](https://github.com/JabRef/jabref/issues/9172)
 - We fixed an issue where identifier paste couldn't work with Unicode REPLACEMENT CHARACTER. [#11986](https://github.com/JabRef/jabref/issues/11986)
+- We fixed an issue when click on entry at "Check Integrity" wasn't properly focusing the entry and field. [#11997](https://github.com/JabRef/jabref/issues/11997)
+- We fixed an issue with the ui not scaling when changing the font size [#11219](https://github.com/JabRef/jabref/issues/11219)
 
 ### Removed
 

README.md

@@ -95,6 +95,33 @@ We will discuss improvements with you and agree to merge them once the [develope
 Please also remember to discuss bigger changes early with the core developers to ensure properly spend time and work.
 Some fundamental design decisions can be found within our list of [Architectural Decision Records](https://devdocs.jabref.org/decisions/).
 
+## Research and Education
+
+JabRef welcomes research applied to it.
+The current list of papers where JabRef helped to enhance science is maintained at <https://github.com/JabRef/jabref/wiki/JabRef-in-the-Media>.
+
+The JabRef team also fosters to use JabRef in Software Engineering training.
+We offer guidelines for this at <https://devdocs.jabref.org/teaching.html>.
+
+When citing JabRef, please use following citation:
+
+```bibtex
+@Article{jabref,
+  author  = {Oliver Kopp and Carl Christian Snethlage and Christoph Schwentker},
+  title   = {JabRef: BibTeX-based literature management software},
+  journal = {TUGboat},
+  volume  = {44},
+  number  = {3},
+  pages   = {441--447},
+  doi     = {10.47397/tb/44-3/tb138kopp-jabref},
+  issn    = {0896-3207},
+  issue   = {138},
+  year    = {2023},
+}
+```
+
+DOI (also includes [full text](https://tug.org/TUGboat/tb44-3/tb138kopp-jabref.pdf)): [10.47397/tb/44-3/tb138kopp-jabref](https://doi.org/10.47397/tb/44-3/tb138kopp-jabref).
+
 ## Sponsoring
 
 JabRef development is powered by YourKit Java Profiler  

build.gradle

@@ -54,13 +54,14 @@ java {
 
     toolchain {
         // If this is updated, also update
-        // - .gitpod.Dockerfile
+        // - build.gradle -> jacoco -> toolVersion (because JaCoCo does not support newest JDK out of the box. Check versions at https://www.jacoco.org/jacoco/trunk/doc/changes.html)
         // - .devcontainer/devcontainer.json#L34 and
+        // - .gitpod.Dockerfile
+        // - .moderne/moderne.yml
         // - .github/workflows/deployment*.yml
         // - .github/workflows/tests*.yml
         // - .github/workflows/update-gradle-wrapper.yml
         // - docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md
-        // - build.gradle -> jacoco -> toolVersion (because JaCoCo does not support newest JDK out of the box. Check versions at https://www.jacoco.org/jacoco/trunk/doc/changes.html)
         languageVersion = JavaLanguageVersion.of(23)
         // See https://docs.gradle.org/current/javadoc/org/gradle/jvm/toolchain/JvmVendorSpec.html for a full list
         // vendor = JvmVendorSpec.AMAZON
@@ -196,7 +197,7 @@ dependencies {
     implementation 'io.github.thibaultmeyer:cuid:2.0.3'
     // endregion
 
-    implementation 'io.github.java-diff-utils:java-diff-utils:4.12'
+    implementation 'io.github.java-diff-utils:java-diff-utils:4.15'
     implementation 'info.debatty:java-string-similarity:2.0.0'
     implementation 'com.github.javakeyring:java-keyring:1.0.4'
 
@@ -255,7 +256,7 @@ dependencies {
         exclude group: 'tech.units'
     }
     // Required by gemsfx
-    implementation 'tech.units:indriya:2.2'
+    implementation 'tech.units:indriya:2.2.1'
     // Required by gemsfx and langchain4j
     implementation ('com.squareup.retrofit2:retrofit:2.11.0') {
         exclude group: 'com.squareup.okhttp3'
@@ -267,7 +268,7 @@ dependencies {
     implementation 'org.jsoup:jsoup:1.18.1'
     implementation 'com.konghq:unirest-java-core:4.4.5'
     implementation 'com.konghq:unirest-modules-gson:4.4.5'
-    implementation 'org.apache.httpcomponents.client5:httpclient5:5.4'
+    implementation 'org.apache.httpcomponents.client5:httpclient5:5.4.1'
     // endregion
 
     implementation 'org.slf4j:slf4j-api:2.0.16'
@@ -336,7 +337,7 @@ dependencies {
     // region AI
     implementation 'dev.langchain4j:langchain4j:0.36.0'
     // Even though we use jvm-openai for LLM connection, we still need this package for tokenization.
-    implementation('dev.langchain4j:langchain4j-open-ai:0.36.0') {
+    implementation('dev.langchain4j:langchain4j-open-ai:0.36.2') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
@@ -346,11 +347,11 @@ dependencies {
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
     }
-    implementation('dev.langchain4j:langchain4j-google-ai-gemini:0.36.0') {
+    implementation('dev.langchain4j:langchain4j-google-ai-gemini:0.36.2') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
     }
-    implementation('dev.langchain4j:langchain4j-hugging-face:0.36.0') {
+    implementation('dev.langchain4j:langchain4j-hugging-face:0.36.2') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
@@ -367,7 +368,7 @@ dependencies {
         exclude group: 'org.jetbrains.kotlin', module: 'kotlin-stdlib-jdk8'
     }
     // GemxFX also (transitively) depends on kotlin
-    implementation 'org.jetbrains.kotlin:kotlin-stdlib-jdk8:2.0.21'
+    implementation 'org.jetbrains.kotlin:kotlin-stdlib-jdk8:2.1.0'
     // endregion
 
     implementation 'commons-io:commons-io:2.18.0'
@@ -376,9 +377,9 @@ dependencies {
     implementation 'io.github.adr:e-adr:2.0.0-SNAPSHOT'
 
     implementation 'io.zonky.test:embedded-postgres:2.1.0'
-    implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.0.0')
+    implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.2.0')
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.177'
+    testImplementation 'io.github.classgraph:classgraph:4.8.179'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.11.3'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.11.3'
 

buildres/linux/jabref.spec

@@ -4,8 +4,17 @@ Version: APPLICATION_VERSION
 Release: APPLICATION_RELEASE
 License: APPLICATION_LICENSE_TYPE
 Vendor: APPLICATION_VENDOR
-Prefix: %{dirname:APPLICATION_DIRECTORY}
+
+%if "xAPPLICATION_URL" != "x"
+URL: APPLICATION_URL
+%endif
+
+%if "xAPPLICATION_PREFIX" != "x"
+Prefix: APPLICATION_PREFIX
+%endif
+
 Provides: APPLICATION_PACKAGE
+
 %if "xAPPLICATION_GROUP" != "x"
 Group: APPLICATION_GROUP
 %endif
@@ -16,14 +25,20 @@ Autoreq: 0
 Requires: PACKAGE_DEFAULT_DEPENDENCIES PACKAGE_CUSTOM_DEPENDENCIES
 %endif
 
-#avoid ARCH subfolder
-%define _rpmfilename %%{NAME}-%%{VERSION}-%%{RELEASE}.%%{ARCH}.rpm
-
 #comment line below to enable effective jar compression
 #it could easily get your package size from 40 to 15Mb but
 #build time will substantially increase and it may require unpack200/system java to install
 %define __jar_repack %{nil}
 
+# on RHEL we got unwanted improved debugging enhancements
+%define _build_id_links none
+
+%define package_filelist %{_builddir}/%{name}.files
+%define app_filelist %{_builddir}/%{name}.app.files
+%define filesystem_filelist %{_builddir}/%{name}.filesystem.files
+
+%define default_filesystem / /opt /usr /usr/bin /usr/lib /usr/local /usr/local/bin /usr/local/lib
+
 %description
 APPLICATION_DESCRIPTION
 
@@ -37,33 +52,58 @@ APPLICATION_DESCRIPTION
 rm -rf %{buildroot}
 install -d -m 755 %{buildroot}APPLICATION_DIRECTORY
 cp -r %{_sourcedir}APPLICATION_DIRECTORY/* %{buildroot}APPLICATION_DIRECTORY
+if [ "$(echo %{_sourcedir}/lib/systemd/system/*.service)" != '%{_sourcedir}/lib/systemd/system/*.service' ]; then
+  install -d -m 755 %{buildroot}/lib/systemd/system
+  cp %{_sourcedir}/lib/systemd/system/*.service %{buildroot}/lib/systemd/system
+fi
 %if "xAPPLICATION_LICENSE_FILE" != "x"
   %define license_install_file %{_defaultlicensedir}/%{name}-%{version}/%{basename:APPLICATION_LICENSE_FILE}
-  install -d -m 755 %{buildroot}%{dirname:%{license_install_file}}
-  install -m 644 APPLICATION_LICENSE_FILE %{buildroot}%{license_install_file}
+  install -d -m 755 "%{buildroot}%{dirname:%{license_install_file}}"
+  install -m 644 "APPLICATION_LICENSE_FILE" "%{buildroot}%{license_install_file}"
+%endif
+(cd %{buildroot} && find . -path ./lib/systemd -prune -o -type d -print) | sed -e 's/^\.//' -e '/^$/d' | sort > %{app_filelist}
+{ rpm -ql filesystem || echo %{default_filesystem}; } | sort > %{filesystem_filelist}
+comm -23 %{app_filelist} %{filesystem_filelist} > %{package_filelist}
+sed -i -e 's/.*/%dir "&"/' %{package_filelist}
+(cd %{buildroot} && find . -not -type d) | sed -e 's/^\.//' -e 's/.*/"&"/' >> %{package_filelist}
+%if "xAPPLICATION_LICENSE_FILE" != "x"
+  sed -i -e 's|"%{license_install_file}"||' -e '/^$/d' %{package_filelist}
 %endif
 
-%files
+%files -f %{package_filelist}
 %if "xAPPLICATION_LICENSE_FILE" != "x"
-  %license %{license_install_file}
-  %{dirname:%{license_install_file}}
+  %license "%{license_install_file}"
 %endif
-# If installation directory for the application is /a/b/c, we want only root
-# component of the path (/a) in the spec file to make sure all subdirectories
-# are owned by the package.
-%(echo APPLICATION_DIRECTORY | sed -e "s|\(^/[^/]\{1,\}\).*$|\1|")
 
 %post
+package_type=rpm
+LAUNCHER_AS_SERVICE_SCRIPTS
+DESKTOP_COMMANDS_INSTALL
+LAUNCHER_AS_SERVICE_COMMANDS_INSTALL
 # Install the native-messaging host script for firefox/chrome/chromium
 install -D -m0755 /opt/jabref/lib/native-messaging-host/firefox/org.jabref.jabref.json /usr/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json
 install -D -m0755 /opt/jabref/lib/native-messaging-host/chromium/org.jabref.jabref.json /etc/chromium/native-messaging-hosts/org.jabref.jabref.json
 install -D -m0755 /opt/jabref/lib/native-messaging-host/chromium/org.jabref.jabref.json /etc/opt/chrome/native-messaging-hosts/org.jabref.jabref.json
 # Trigger an auto-install of the browser addon for chrome/chromium browsers
 install -D -m0644 /opt/jabref/lib/native-messaging-host/chromium/bifehkofibaamoeaopjglfkddgkijdlh.json /opt/google/chrome/extensions/bifehkofibaamoeaopjglfkddgkijdlh.json
 install -D -m0644 /opt/jabref/lib/native-messaging-host/chromium/bifehkofibaamoeaopjglfkddgkijdlh.json /usr/share/google-chrome/extensions/bifehkofibaamoeaopjglfkddgkijdlh.json
-DESKTOP_COMMANDS_INSTALL
+
+
+%pre
+package_type=rpm
+COMMON_SCRIPTS
+LAUNCHER_AS_SERVICE_SCRIPTS
+if [ "$1" -gt 1 ]; then
+  :; LAUNCHER_AS_SERVICE_COMMANDS_UNINSTALL
+fi
 
 %preun
+package_type=rpm
+COMMON_SCRIPTS
+DESKTOP_SCRIPTS
+LAUNCHER_AS_SERVICE_SCRIPTS
+DESKTOP_COMMANDS_UNINSTALL
+LAUNCHER_AS_SERVICE_COMMANDS_UNINSTALL
 # Remove the native-messaging hosts script only if relative to the deb package
 for NATIVE_MESSAGING_JSON in "/usr/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json"\
                      "/etc/chromium/native-messaging-hosts/org.jabref.jabref.json"\
@@ -75,7 +115,6 @@ done
 # Remove the auto-install triggers of the browser addon for chrom/chromium
 rm -f /opt/google/chrome/extensions/bifehkofibaamoeaopjglfkddgkijdlh.json || true
 rm -f /usr/share/google-chrome/extensions/bifehkofibaamoeaopjglfkddgkijdlh.json || true
-DESKTOP_SCRIPTS
-DESKTOP_COMMANDS_UNINSTALL
+
 
 %clean

docs/decisions/0034-use-citation-key-for-grouping-chat-messages.md

@@ -7,25 +7,25 @@ parent: Decision Records
 
 ## Context and Problem Statement
 
-Because we store chat messages not inside a BIB entry in `.bib` filecc, the chats file is represented as a map to
-BIB entry and a list of messages. We need to specify the key of this map. Turns out, it is not that easy.
+As we store chat messages not inside a BibTeX entry in `.bib` file, the chats file is represented as a map to
+BibTeX entry and a list of messages. We need to specify the key of this map. Turns out, it is not that easy.
 
 ## Decision Drivers
 
-* The key should exist for every BIB entry
-* The key should be unique along other BIB entries in one library file
-* The key should not change at run-time, between launches of JabRef, and should be cross-platform (most important)
+* The key should exist for every BibTeX entry
+* The key should be unique along other BibTeX entries in one library file
+* It is assumed that the key does not change at run-time, between launches of JabRef, and should be cross-platform (most important)
 
 ## Considered Options
 
 * `BibEntry` Java object
 * `BibEntry`'s `id`
-* `BibEntry`'s Citation key
+* `BibEntry`'s citation key
 * `BibEntry`'s `ShareId`
 
 ## Decision Outcome
 
-Chosen option: "`BibEntry`'s Citation key", because this is the only choice that complains to the third point in Decision Drivers.
+Chosen option: "`BibEntry`'s citation key", because this is the only choice that complies to the third point in Decision Drivers.
 
 ### Positive Consequences
 
@@ -50,11 +50,11 @@ This identifier is created on each load of a library (and not stored permanently
 
 Very bad, for the same reasons as `BibEntry` Java object.
 
-### `BibEntry`'s Citation key
+### `BibEntry`'s citation key
 
 * Good, because it is cross-platform, stable (meaning stays the same across launches of JabRef)
 * Bad, because it is not guaranteed that citation key exists on `BibEntry`, and that it is unique across other
-`BibEntriy`'s' in the library
+BibTeX entries in the library
 
 ### `BibEntry`'s `ShareId`
 
@@ -67,3 +67,5 @@ This approach cannot be used here, because there is no server running which we c
 ## More Information
 
 Refer to [issue #160](https://github.com/JabRef/jabref/issues/160) in JabRef main repository
+
+[ADR-038](0038-use-entryId-for-bibentries.md) takes another option, because it re-generates the index at each start of JabRef.

docs/decisions/0036-use-textarea-for-chat-content.md

@@ -3,7 +3,7 @@ nav_order: 0036
 parent: Decision Records
 ---
 
-# Use TextArea for Chat Message Content
+# Use `TextArea` for Chat Message Content
 
 ## Context and Problem Statement
 
@@ -41,7 +41,7 @@ which for now we value more than Markdown rendering.
 
 ### Use a third-party package
 
-There seems to be only one package for JavaFX that provides a ready-to-use UI node for Markdown rendering.
+There seems to be [only one package](https://github.com/JPro-one/markdown-javafx-renderer) for JavaFX that provides a ready-to-use UI node for Markdown rendering.
 
 * Good, because it is easy to implement
 * Good, because it renders Markdown
@@ -77,8 +77,10 @@ There seems to be only one package for JavaFX that provides a ready-to-use UI no
 
 ## More Information
 
+This ADR is highly linked to [ADR-0042](./0042-use-webview-for-summarization-content.md).
+
 Actually we used an `ExpandingTextArea` from `GemsFX` package so the content can occupy
 as much space as it needs in the `ScrollPane`.
 
 About the selection and copying, this goes down to fundamental issue from JavaFX.
-`Text` and `Label` cannot be selected by any means.
+`Text` and `Label` as a whole or a part [cannot be selected and/or copied](https://bugs.openjdk.org/browse/JDK-8091644).

docs/decisions/0042-use-webview-for-summarization-content.md

@@ -0,0 +1,37 @@
+---
+nav_order: 0042
+parent: Decision Records
+---
+
+# Use `WebView` for Chat Message Content
+
+## Context and Problem Statement
+
+This decision record concerns the UI component that is used for rendering the content of AI summaries.
+
+## Decision Drivers
+
+Same as in [ADR-0036](./0036-use-textarea-for-chat-content.md).
+
+## Considered Options
+
+Same as in [ADR-0036](./0036-use-textarea-for-chat-content.md).
+
+## Decision Outcome
+
+Chosen option: "Use `WebView`".
+
+Some of the options does not support selecting and copying of text. Some options do not render Markdown.
+
+However, in contrary to [ADR-0036](./0036-use-textarea-for-chat-content.md), we chose here a `WebView`, instead of `TextArea`, because there is only one summary content in UI (when user switches entries, no new components are added, rather old ones are *rebinding* to new entry). It would hurt the performance if we used `WebView` for messages, as there could be a lot of messages in one chat.
+
+## Pros and Cons of the Options
+
+Same as in [ADR-0036](./0036-use-textarea-for-chat-content.md).
+
+## More Information
+
+This ADR is highly linked to [ADR-0036](./0036-use-textarea-for-chat-content.md).
+
+About the selection and copying, this goes down to fundamental issue from JavaFX.
+`Text` and `Label` as a whole or a part [cannot be selected and/or copied](https://bugs.openjdk.org/browse/JDK-8091644).