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

* upstream/main: (31 commits)
  Citavi Importer - Import all knowledge items (JabRef#9043)
  Fixed table update in eft preferences (JabRef#9051)
  Keep EOL setting at backups (JabRef#9048)
  ExternalFileTypes singleton refactor (JabRef#9044)
  Fix dead link (JabRef#9047)
  Fix performance regresssion (JabRef#9045)
  Update javafx to 18.02
  import citavi knowledge items (JabRef#9033)
  Fix .gitattributes for CHANGELOG.md
  [GSOC22] - B - Implement merging fields in the three way merge UI (JabRef#9022)
  [GSOC22] - A - Implement a fully functional three way merge UI (JabRef#8945)
  Change button label from "Return to JabRef" to "Return to library" (JabRef#9039)
  Bump postgresql from 42.4.0 to 42.4.1 (JabRef#9036)
  Bump org.javamodularity.moduleplugin from 1.8.11 to 1.8.12 (JabRef#9037)
  Bump slf4j-api from 2.0.0-alpha7 to 2.0.0-beta1 (JabRef#9035)
  Bump slf4j-api from 2.0.0-alpha7 to 2.0.0-beta1 in /buildSrc (JabRef#9038)
  Update Gradle Wrapper from 7.5 to 7.5.1. (JabRef#9034)
  Refactor of DOI import failure dialog, import format reader and clipboard manager (JabRef#8839)
  Snapcraft and issue template
  Show development information\n\n+semver: minor
  ...

.gitattributes

@@ -13,5 +13,9 @@ gradlew text eol=lf
 # .bib files have to be written using OS specific line endings to enable our tests working
 *.bib text !eol
 
-# disable after a release
-CHANGELOG.md merge=union
+# Citavi needs to be LF line ending
+# This overwrites the setting of "*.bib"
+Citavi*.bib eol=lf
+
+# disable after a release (otherwise, duplicate CHANGELOG.md entries will be generated)
+# CHANGELOG.md merge=union

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -12,7 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.6 (latest release)"
+        - "5.7 (latest release)"
         - "3.8.2"
         - Latest development branch build (please note build date below)
         - Other (please describe below)

CHANGELOG.md

@@ -11,6 +11,30 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+### Changed
+
+- 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 changed the button label from "Return to JabRef" to "Return to library" to better indicate the purpose of the action.
+
+### Fixed
+
+- The [HtmlToLaTeXFormatter](https://docs.jabref.org/finding-sorting-and-cleaning-entries/saveactions#html-to-latex) keeps single `<` characters.
+- We fixed a performance regression when opening large libraries [#9041](https://github.com/JabRef/jabref/issues/9041)
+
+### Removed
+
+
+
+
+
+
+
+
+## [5.7] - 2022-08-05
+
+### Added
+
 - 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)
@@ -43,6 +67,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- We fixed an issue where the user could not rate an entry in the main table when an entry was not yet ranked. [#5842](https://github.com/JabRef/jabref/issues/5842)
 - 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)
@@ -68,15 +93,6 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - We removed the social media buttons for our Twitter and Facebook pages. [#8774](https://github.com/JabRef/jabref/issues/8774)
 
-
-
-
-
-
-
-
-
-
 ## [5.6] - 2022-04-25
 
 ### Added
@@ -847,7 +863,8 @@ The changelog of JabRef 4.x is available at the [v4.3.1 tag](https://github.com/
 The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
 The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).
 
-[Unreleased]: https://github.com/JabRef/jabref/compare/v5.6...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v5.7...HEAD
+[5.7]: https://github.com/JabRef/jabref/compare/v5.6...v5.7
 [5.6]: https://github.com/JabRef/jabref/compare/v5.5...v5.6
 [5.5]: https://github.com/JabRef/jabref/compare/v5.4...v5.5
 [5.4]: https://github.com/JabRef/jabref/compare/v5.3...v5.4

build.gradle

@@ -10,7 +10,7 @@ plugins {
 
     id 'me.champeau.gradle.jmh' version '0.5.3'
 
-    id 'org.javamodularity.moduleplugin' version '1.8.11'
+    id 'org.javamodularity.moduleplugin' version '1.8.12'
 
     id 'org.openjfx.javafxplugin' version '0.0.13'
 
@@ -99,7 +99,7 @@ dependencyLocking {
 }
 
 javafx {
-    version = "18.0.1"
+    version = "18.0.2"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -148,7 +148,7 @@ dependencies {
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.6'
 
-    implementation 'org.postgresql:postgresql:42.4.0'
+    implementation 'org.postgresql:postgresql:42.4.1'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -181,7 +181,7 @@ dependencies {
     implementation 'org.jsoup:jsoup:1.15.1'
     implementation 'com.konghq:unirest-java:3.13.10'
 
-    implementation 'org.slf4j:slf4j-api:2.0.0-alpha7'
+    implementation 'org.slf4j:slf4j-api:2.0.0-beta1'
     implementation "org.tinylog:tinylog-api:2.4.1"
     implementation "org.tinylog:slf4j-tinylog:2.4.1"
     implementation "org.tinylog:tinylog-impl:2.4.1"

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:2.0.0-alpha7'
+    implementation 'org.slf4j:slf4j-api:2.0.0-beta1'
 }
 
 sourceSets{

buildres/csl/csl-styles/dependent/liver-transplantation.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-US">
+  <info>
+    <title>Liver Transplantation</title>
+    <id>http://www.zotero.org/styles/liver-transplantation</id>
+    <link href="http://www.zotero.org/styles/liver-transplantation" rel="self"/>
+    <link href="http://www.zotero.org/styles/vancouver" rel="independent-parent"/>
+    <link href="https://aasldpubs.onlinelibrary.wiley.com/hub/journal/15276473/about/author-guidelines" rel="documentation"/>
+    <category citation-format="numeric"/>
+    <category field="medicine"/>
+    <issn>1527-6473</issn>
+    <issn>1527-6465</issn>
+    <updated>2022-08-03T21:58:08+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/food-and-agriculture-organization-of-the-united-nations.csl

@@ -31,7 +31,7 @@
     <category field="science"/>
     <category field="social_science"/>
     <summary>This style is created to meet the citation and bibliographical requirements of FAOSTYLE, and has been tested with Zotero and Mendeley. Last update: February 2022.</summary>
-    <updated>2022-02-02T16:03:38+00:00</updated>
+    <updated>2022-08-02T08:28:31+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>
   <!-- Locale settings for English. Settings for other languages could be added later to this section. -->
@@ -180,6 +180,20 @@
       </else>
     </choose>
   </macro>
+  <macro name="event-title">
+    <choose>
+      <!-- TODO: We expect "event-title" to be used,
+           but processors and applications may not be updated yet.
+           This macro ensures that either "event" or "event-title" can be accpeted.
+           Remove if procesor logic and application adoption can handle this. -->
+      <if variable="event-title">
+        <text variable="event-title"/>
+      </if>
+      <else>
+        <text variable="event"/>
+      </else>
+    </choose>
+  </macro>
   <!-- in-line citation: (author, date) -->
   <citation disambiguate-add-year-suffix="true" collapse="year" et-al-min="4" et-al-use-first="1">
     <sort>
@@ -298,7 +312,7 @@
                 <text variable="title"/>
                 <group delimiter=" ">
                   <text term="presented at"/>
-                  <text variable="event" suffix=","/>
+                  <text macro="event-title" suffix=","/>
                   <date form="text" variable="issued" suffix=","/>
                   <text macro="publisher-and-place"/>
                 </group>
@@ -310,7 +324,7 @@
                 <text macro="in-and-container"/>
                 <text variable="collection-title"/>
                 <group delimiter=", " suffix=".">
-                  <text variable="event"/>
+                  <text macro="event-title"/>
                   <text variable="publisher-place"/>
                   <text variable="publisher"/>
                   <!-- Not using macro "publisher-and-place" here because event date needs to be appended and the suffix "." of the macro would appear. -->

docs/decisions/0001-use-crowdin-for-translations.md

@@ -13,7 +13,7 @@ The JabRef UI is offered in multiple languages. It should be easy for translator
 * Use [Crowdin](http://crowdin.com/)
 * Use [popeye](https://github.com/JabRef/popeye)
 * Use [Lingohub](https://lingohub.com/)
-* Keep current GitHub flow. See the [Step-by-step guide](https://docs.jabref.org/faq/how-to-translate-the-ui).
+* Keep current GitHub flow. See the [Step-by-step guide](https://docs.jabref.org/contributing/how-to-translate-the-ui).
 
 ## Decision Outcome
 

external-libraries.md

@@ -267,13 +267,6 @@ URL:     https://github.com/jhalterman/typetools
 License: Apache-2.0
 ```
 
-```yaml
-Id:      org.antlr:antlr-runtime
-Project: ANTLR 3
-URL:     http://www.antlr3.org/
-License: BSD-3-Clause
-```
-
 ```yaml
 Id:      org.antlr:antlr4-runtime
 Project: ANTLR 4
@@ -282,16 +275,9 @@ License: BSD-3-Clause
 ```
 
 ```yaml
-Id:      org.apache.commons:commons-csv
+Id:      org.apache.commons:*
 Project: Apache Commons CSV
-URL:     https://commons.apache.org/proper/commons-csv/
-License: Apache-2.0
-```
-
-```yaml
-Id:      org.apache.commons:commons-lang3
-Project: Apache Commons Lang
-URL:     https://commons.apache.org/proper/commons-lang/
+URL:     https://commons.apache.org/
 License: Apache-2.0
 ```
 
@@ -566,29 +552,30 @@ de.saxsys:mvvmfx:1.8.0
 de.undercouch:citeproc-java:3.0.0-alpha.6
 eu.lestard:doc-annotations:0.2
 info.debatty:java-string-similarity:2.0.0
-io.github.java-diff-utils:java-diff-utils:4.11
+io.github.java-diff-utils:java-diff-utils:4.12
 jakarta.annotation:jakarta.annotation-api:1.3.5
 jakarta.xml.bind:jakarta.xml.bind-api:3.0.1
 net.harawata:appdirs:1.2.1
 net.java.dev.jna:jna-platform:5.6.0
 net.java.dev.jna:jna:5.6.0
 net.jcip:jcip-annotations:1.0
 net.jodah:typetools:0.6.1
-org.antlr:antlr-runtime:3.5.3
 org.antlr:antlr4-runtime:4.9.3
 org.apache.commons:commons-csv:1.9.0
 org.apache.commons:commons-lang3:3.12.0
+org.apache.commons:commons-text:1.9
 org.apache.httpcomponents:httpasyncclient:4.1.5
 org.apache.httpcomponents:httpclient:4.5.13
 org.apache.httpcomponents:httpcore-nio:4.4.13
 org.apache.httpcomponents:httpcore:4.4.13
 org.apache.httpcomponents:httpmime:4.5.13
-org.apache.lucene:lucene-analysis-common:9.2.0
-org.apache.lucene:lucene-core:9.2.0
-org.apache.lucene:lucene-highlighter:9.2.0
-org.apache.lucene:lucene-queries:9.2.0
-org.apache.lucene:lucene-queryparser:9.2.0
-org.apache.lucene:lucene-sandbox:9.2.0
+org.apache.lucene:lucene-analysis-common:9.3.0
+org.apache.lucene:lucene-core:9.3.0
+org.apache.lucene:lucene-highlighter:9.3.0
+org.apache.lucene:lucene-memory:9.3.0
+org.apache.lucene:lucene-queries:9.3.0
+org.apache.lucene:lucene-queryparser:9.3.0
+org.apache.lucene:lucene-sandbox:9.3.0
 org.apache.pdfbox:fontbox:3.0.0-RC1
 org.apache.pdfbox:pdfbox:3.0.0-RC1
 org.apache.pdfbox:xmpbox:3.0.0-RC1
@@ -612,8 +599,8 @@ org.jsoup:jsoup:1.15.1
 org.kordamp.ikonli:ikonli-core:12.3.1
 org.kordamp.ikonli:ikonli-javafx:12.3.1
 org.kordamp.ikonli:ikonli-materialdesign2-pack:12.3.1
-org.libreoffice:libreoffice:7.3.4
-org.libreoffice:unoloader:7.3.4
+org.libreoffice:libreoffice:7.3.5
+org.libreoffice:unoloader:7.3.5
 org.mariadb.jdbc:mariadb-java-client:2.7.6
 org.openjfx:javafx-base:18.0.1
 org.openjfx:javafx-controls:18.0.1

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionSha256Sum=cb87f222c5585bd46838ad4db78463a5c5f3d336e5e2b98dc7c0c586527351c2
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.5-bin.zip
+distributionSha256Sum=f6b8596b10cce501591e92f229816aa4046424f3b24d771751b06779d58c8ec4
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

snap/snapcraft.yaml

@@ -57,7 +57,7 @@ environment:
 parts:
   jabref:
     plugin: dump
-    source: https://builds.jabref.org/main/JabRef-5.7-portable_linux.tar.gz
+    source: https://builds.jabref.org/main/JabRef-5.8-portable_linux.tar.gz
     stage-packages:
       - x11-utils
     override-build: |

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -15,7 +15,6 @@
 
 import org.jabref.gui.Globals;
 import org.jabref.gui.externalfiles.AutoSetFileLinksUtil;
-import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.logic.JabRefException;
 import org.jabref.logic.bibtex.FieldWriterPreferences;
@@ -640,8 +639,7 @@ private void automaticallySetFileLinks(List<ParserResult> loaded) {
             AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(
                     parserResult.getDatabaseContext(),
                     preferencesService.getFilePreferences(),
-                    preferencesService.getAutoLinkPreferences(),
-                    ExternalFileTypes.getInstance());
+                    preferencesService.getAutoLinkPreferences());
             util.linkAssociatedFiles(database.getEntries(), new NamedCompound(""));
         }
     }