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

* upstream/main: (46 commits) New Crowdin updates (#8349) Bump pdfbox from 2.0.24 to 2.0.25 (#8345) Bump fontbox from 2.0.24 to 2.0.25 (#8348) Bump xmlunit-core from 2.8.3 to 2.8.4 (#8347) Bump tika-core from 2.1.0 to 2.2.0 (#8346) Added missing executable bindings to various commands (#8342) Update Gradle Wrapper from 7.3.1 to 7.3.2. (#8343) Fix issues with writing metadata to pdfs (#8332) add tinylog test (#8339) Tinylog (#8226) Don't register any database changes to the indexer while dropping a file (#8334) Fix ACM fetcher (#8338) Squashed 'buildres/csl/csl-styles/' changes from 3bb4b5f..60bf7d5 Exception shouldn't happen when pasting an entry with a publication date-range of form yyyy-yyyy (#8247) Refactor Sidepane logic (#8202) New translations JabRef_en.properties (Japanese) (#8331) Bump bcprov-jdk15on from 1.69 to 1.70 (#8333) Update Controlsfx to 11.1.1 (#8330) Update citeproc (#8329) Bump classgraph from 4.8.137 to 4.8.138 (#8327) ... # Conflicts: # build.gradle
JabRef · Dec 20, 2021 · 2762345 · 2762345
2 parents 21749cd + 1cb83e8
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -4,7 +4,7 @@ updates:
   directory: "/"
   schedule:
     interval: weekly
-  open-pull-requests-limit: 10
+  open-pull-requests-limit: 15
   labels:
   - "type: dependencies"
   ignore:
@@ -14,12 +14,6 @@ updates:
   - dependency-name: com.microsoft.azure:applicationinsights-logging-log4j2
     versions:
     - ">= 2.5.a" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
-  - dependency-name: de.jensd:fontawesomefx-materialdesignfont
-    versions:
-    - "> 1.7.22-4" # Strange versioning format
-  - dependency-name: org.fxmisc.richtext:richtextfx
-    versions:
-    - "< 0.10.6" # Blocked by https://github.com/FXMisc/RichTextFX/issues/967, wait for new release
 - package-ecosystem: "github-actions"
   directory: "/"
   schedule:

diff --git a/.github/outdatedDependencies.md b/.github/outdatedDependencies.md
diff --git a/.github/workflows/check-outdated-dependencies.yml b/.github/workflows/check-outdated-dependencies.yml
diff --git a/.idea/runConfigurations/JabRef_Main.xml b/.idea/runConfigurations/JabRef_Main.xml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -41,6 +41,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We reworked the export order in the preferences and the save order in the library preferences. You can now set more than three sort criteria in your library preferences. [#7935](https://github.com/JabRef/jabref/pull/7935)
 - The metadata-to-pdf actions now also embeds the bibfile to the PDF. [#8037](https://github.com/JabRef/jabref/pull/8037)
 - The snap was updated to use the core20 base and to use lzo compression for better startup performance [#8109](https://github.com/JabRef/jabref/pull/8109)
+- We moved the union/intersection view button in the group sidepane to the left of the other controls. [#8202](https://github.com/JabRef/jabref/pull/8202)
 - We improved the Drag and Drop behavior in the "Customize Entry Types" Dialog [#6338](https://github.com/JabRef/jabref/issues/6338)
 - When determining the URL of an ArXiV eprint, the URL now points to the version [#8149](https://github.com/JabRef/jabref/pull/8149)
 - We Included all standard fields with citation key when exporting to Old OpenOffice/LibreOffice Calc Format [#8176](https://github.com/JabRef/jabref/pull/8176)
@@ -52,15 +53,20 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We trim white space and non-ASCII characters from DOI [#8127](https://github.com/JabRef/jabref/issues/8127)
 - The duplicate checker now inspects other fields in case no difference in the required and optional fields are found.
 - We reworked the library properties dialog and integrated the `Library > Preamble`, `Library > Citation key pattern` and `Library > String constants dialogs` [#8264](https://github.com/JabRef/jabref/pulls/8264)
+- We improved the startup time of JabRef by switching from the logging library `log4j2` to `tinylog` [#8007](https://github.com/JabRef/jabref/issues/8007)
 
 ### Fixed
 
+- We fixed an issue where an exception occurred when pasting an entry with a publication date-range of the form 1910/1917 [#7864](https://github.com/JabRef/jabref/issues/7864)
+- We fixed an issue where an exception occured when a preview style was edited and afterwards another preview style selected. [#8280](https://github.com/JabRef/jabref/issues/8280)
 - We fixed an issue where the actions to move a file to a directory were incorrectly disabled. [#7908](https://github.com/JabRef/jabref/issues/7908)
 - We fixed an issue where an exception occurred when a linked online file was edited in the entry editor [#8008](https://github.com/JabRef/jabref/issues/8008)
 - We fixed an issue when checking for a new version when JabRef is used behind a corporate proxy. [#7884](https://github.com/JabRef/jabref/issues/7884)
 - We fixed some icons that were drawn in the wrong color when JabRef used a custom theme. [#7853](https://github.com/JabRef/jabref/issues/7853)
 - We fixed an issue where the `Aux file` on `Edit group` doesn't support relative sub-directories path to import. [#7719](https://github.com/JabRef/jabref/issues/7719).
 - We fixed an issue where it was impossible to add or modify groups. [#7912](https://github.com/JabRef/jabref/pull/793://github.com/JabRef/jabref/pull/7921)
+- We fixed an issue about the visible side pane components being out of sync with the view menu. [#8115](https://github.com/JabRef/jabref/issues/8115)
+- We fixed an issue where the side pane would not close when all its components were closed. [#8082]((https://github.com/JabRef/jabref/issues/8082))
 - We fixed an issue where exported entries from a Citavi bib containing URLs could not be imported [#7892](https://github.com/JabRef/jabref/issues/7882)
 - We fixed an issue where the icons in the search bar had the same color, toggled as well as untoggled. [#8014](https://github.com/JabRef/jabref/pull/8014)
 - We fixed an issue where typing an invalid UNC path into the "Main file directory" text field caused an error. [#8107](https://github.com/JabRef/jabref/issues/8107)
@@ -69,15 +75,20 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed "The library has been modified by another program" showing up when line breaks change [#4877](https://github.com/JabRef/jabref/issues/4877)
 - The default directory of the "LaTeX Citations" tab is now the directory of the currently opened database (and not the directory chosen at the last open file dialog or the last database save) [koppor#538](https://github.com/koppor/jabref/issues/538)
 - When writing a bib file, the `NegativeArraySizeException` should not occur [#8231](https://github.com/JabRef/jabref/issues/8231) [#8265](https://github.com/JabRef/jabref/issues/8265)
+- We fixed an issue where some menu entries were available without entries selected. [#4795](https://github.com/JabRef/jabref/issues/4795)
 - We fixed an issue where right-clicking on a tab and selecting close will close the focused tab even if it is not the tab we right-clicked [#8193](https://github.com/JabRef/jabref/pull/8193)
 - We fixed an issue where selecting a citation style in the preferences would sometimes produce an exception [#7860](https://github.com/JabRef/jabref/issues/7860)
 - We fixed an issue where an exception would occur when clicking on a DOI link in the preview pane [#7706](https://github.com/JabRef/jabref/issues/7706)
+- We fixed an issue where XMP and embedded BibTeX export would not work [#8278](https://github.com/JabRef/jabref/issues/8278)
+- We fixed an issue where the XMP and embedded BibTeX import of a file containing multiple schemas failed [#8278](https://github.com/JabRef/jabref/issues/8278)
+- We fixed an issue where writing embedded BibTeX import fails due to write protection or bibtex already being present [#8332](https://github.com/JabRef/jabref/pull/8332)
+- We fixed an issue where pdf-paths and the pdf-indexer could get out of sync [#8182](https://github.com/JabRef/jabref/issues/8182)
+- We fixed an issue where Status-Logger error messages appeared during the startup of JabRef [#5475](https://github.com/JabRef/jabref/issues/5475)
 
 ### Removed
 
 - We removed two orphaned preferences options [#8164](https://github.com/JabRef/jabref/pull/8164)
-
-
+- We removed the functionality of the `--debug` commandline options. Use the java command line switch `-Dtinylog.level=debug` for debug output instead. [#8226](https://github.com/JabRef/jabref/pull/8226)
 
 
 

diff --git a/build.gradle b/build.gradle
@@ -14,8 +14,6 @@ plugins {
 
     id 'me.champeau.gradle.jmh' version '0.5.3'
 
-    id 'com.github.ben-manes.versions' version '0.39.0'
-
     id 'org.javamodularity.moduleplugin' version '1.8.10'
 
     id 'org.openjfx.javafxplugin' version '0.0.10'
@@ -118,21 +116,21 @@ dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     implementation fileTree(dir: 'lib', includes: ['*.jar'])
 
-    implementation 'org.apache.pdfbox:pdfbox:2.0.24'
-    implementation 'org.apache.pdfbox:fontbox:2.0.24'
+    implementation 'org.apache.pdfbox:pdfbox:2.0.25'
+    implementation 'org.apache.pdfbox:fontbox:2.0.25'
     implementation 'org.apache.pdfbox:xmpbox:2.0.24'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
-    implementation 'com.h2database:h2-mvstore:1.4.200'
+    implementation 'com.h2database:h2-mvstore:2.0.202'
 
-    implementation group: 'org.apache.tika', name: 'tika-core', version: '2.1.0'
+    implementation group: 'org.apache.tika', name: 'tika-core', version: '2.2.0'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk15on:1.69'
+    implementation 'org.bouncycastle:bcprov-jdk15on:1.70'
 
     implementation 'commons-cli:commons-cli:1.5.0'
 
-    implementation 'org.libreoffice:libreoffice:7.2.2'
+    implementation 'org.libreoffice:libreoffice:7.2.3'
     implementation 'org.libreoffice:unoloader:7.2.2'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.11'
@@ -151,7 +149,7 @@ dependencies {
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.4'
 
-    implementation 'org.postgresql:postgresql:42.2.24'
+    implementation 'org.postgresql:postgresql:42.3.1'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -175,20 +173,17 @@ dependencies {
     implementation 'org.fxmisc.richtext:richtextfx:0.10.7'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     implementation 'com.jfoenix:jfoenix:9.0.10'
-    implementation 'org.controlsfx:controlsfx:11.1.0'
+    implementation 'org.controlsfx:controlsfx:11.1.1'
 
     implementation 'org.jsoup:jsoup:1.14.3'
     implementation 'com.konghq:unirest-java:3.13.4'
 
     implementation 'org.slf4j:slf4j-api:2.0.0-alpha5'
-    implementation group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
-    implementation group: 'org.apache.logging.log4j', name: 'log4j-slf4j18-impl', version: '3.0.0-SNAPSHOT'
-    implementation group: 'org.apache.logging.log4j', name: 'log4j-plugins', version: '3.0.0-SNAPSHOT'
-    implementation group: 'org.apache.logging.log4j', name: 'log4j-api', version: '3.0.0-SNAPSHOT'
-    implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
-    annotationProcessor group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
+    implementation "org.tinylog:tinylog-api:2.4.1"
+    implementation "org.tinylog:slf4j-tinylog:2.4.1"
+    implementation "org.tinylog:tinylog-impl:2.4.1"
 
-    implementation 'de.undercouch:citeproc-java:3.0.0-alpha.2'
+    implementation 'de.undercouch:citeproc-java:3.0.0-alpha.3'
 
     implementation group: 'jakarta.activation', name: 'jakarta.activation-api', version: '1.2.1'
     implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
@@ -213,15 +208,14 @@ dependencies {
     implementation("com.apollographql.apollo3:apollo-runtime:3.0.0-beta04")
     implementation("com.apollographql.apollo3:apollo-rx3-support:3.0.0-beta04")
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.137'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.8.1'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.8.1'
+    testImplementation 'io.github.classgraph:classgraph:4.8.138'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.12.2'
     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:4.1.0'
-    testImplementation 'org.xmlunit:xmlunit-core:2.8.3'
+    testImplementation 'org.xmlunit:xmlunit-core:2.8.4'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.8.3'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.22.0'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.22.0'
@@ -233,46 +227,6 @@ dependencies {
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
 }
 
-dependencyUpdates {
-    outputFormatter = "json"
-}
-
-// We have some dependencies which cannot be updated due to various reasons.
-dependencyUpdates.resolutionStrategy {
-    componentSelection { rules ->
-        rules.all { ComponentSelection selection ->
-            boolean rejected = ['alpha', 'snapshot', 'beta', 'rc', 'cr', 'm', 'preview', 'b', 'ea'].any { qualifier ->
-                selection.candidate.version ==~ /(?i).*[.-]$qualifier[.\d-+]*/
-            }
-            if (rejected) {
-                selection.reject('Release candidate')
-            }
-        }
-        rules.withModule("org.javamodularity.moduleplugin:org.javamodularity.moduleplugin.gradle.plugin") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /1.6.0/) {
-                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5270")
-            }
-        }
-        rules.withModule("com.microsoft.azure:applicationinsights-core") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.5.0/ || selection.candidate.version ==~ /2.5.1/) {
-                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5596")
-            }
-        }
-        rules.withModule("com.microsoft.azure:applicationinsights-logging-log4j2") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.5.0/ || selection.candidate.version ==~ /2.5.1/) {
-                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5596")
-            }
-        }
-    }
-}
-
-task checkOutdatedDependencies(dependsOn: dependencyUpdates) {
-    doLast {
-        def dependencyReport = new JsonSlurper().parseText(new File("build/dependencyUpdates/report.json").text)
-        assert dependencyReport.outdated.count == 0: "There are outdated dependencies in build.gradle!\n Run ./gradlew dependencyUpdates to see which"
-    }
-}
-
 clean {
     delete "src/main/generated"
     delete "src-gen"
@@ -634,14 +588,9 @@ jlink {
         requires 'com.sun.xml.fastinfoset'
         requires 'com.sun.xml.txw2'
         requires 'org.slf4j'
-        uses 'org.apache.logging.log4j.util.PropertySource'
-        uses 'org.apache.logging.log4j.core.util.WatchEventService'
-        uses 'org.apache.logging.log4j.plugins.processor.PluginService'
         uses 'org.controlsfx.glyphfont.GlyphFont'
         uses 'com.airhacks.afterburner.views.ResourceLocator'
-        uses 'org.apache.logging.log4j.message.ThreadDumpMessage.ThreadInfoFactory'
         uses 'com.airhacks.afterburner.injection.PresenterFactory'
-        uses 'org.apache.logging.log4j.spi.Provider'
         uses 'org.mariadb.jdbc.credential.CredentialPlugin'
         uses 'org.mariadb.jdbc.authentication.AuthenticationPlugin'
         uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'
@@ -650,16 +599,11 @@ jlink {
         uses 'org.eclipse.jgit.lib.GpgSigner'
         uses 'javax.xml.bind.JAXBContextFactory'
         provides 'org.apache.lucene.codecs.DocValuesFormat' with 'org.apache.lucene.codecs.lucene80.Lucene80DocValuesFormat'
-        provides 'javax.annotation.processing.Processor' with 'org.apache.logging.log4j.plugins.processor.PluginProcessor'
         provides 'org.controlsfx.glyphfont.GlyphFont' with 'org.controlsfx.glyphfont.FontAwesome'
-        provides 'org.apache.logging.log4j.message.ThreadDumpMessage.ThreadInfoFactory' with 'org.apache.logging.log4j.core.message.ExtendedThreadInfoFactory'
         provides 'org.mariadb.jdbc.tls.TlsSocketPlugin' with 'org.mariadb.jdbc.internal.protocol.tls.DefaultTlsSocketPlugin'
         provides 'com.microsoft.applicationinsights.core.dependencies.io.grpc.ServerProvider' with 'com.microsoft.applicationinsights.core.dependencies.io.grpc.netty.shaded.io.grpc.netty.NettyServerProvider'
         provides 'com.microsoft.applicationinsights.core.dependencies.io.grpc.NameResolverProvider' with 'com.microsoft.applicationinsights.core.dependencies.io.grpc.internal.DnsNameResolverProvider'
-        provides 'org.apache.logging.log4j.util.PropertySource' with 'org.apache.logging.log4j.util.EnvironmentPropertySource',
-                'org.apache.logging.log4j.util.SystemPropertiesPropertySource'
         provides 'java.sql.Driver' with 'org.postgresql.Driver'
-        provides 'org.apache.logging.log4j.plugins.processor.PluginService' with 'org.apache.logging.log4j.plugins.convert.plugins.Log4jPlugins'
         provides 'org.mariadb.jdbc.authentication.AuthenticationPlugin' with 'org.mariadb.jdbc.internal.com.send.authentication.CachingSha2PasswordPlugin',
                 'org.mariadb.jdbc.internal.com.send.authentication.ClearPasswordPlugin',
                 'org.mariadb.jdbc.internal.com.send.authentication.Ed25519PasswordPlugin',
@@ -671,8 +615,6 @@ jlink {
         provides 'org.mariadb.jdbc.credential.CredentialPlugin' with 'org.mariadb.jdbc.credential.aws.AwsIamCredentialPlugin',
                 'org.mariadb.jdbc.credential.env.EnvCredentialPlugin',
                 'org.mariadb.jdbc.credential.system.PropertiesCredentialPlugin'
-        provides 'org.slf4j.spi.SLF4JServiceProvider' with 'org.apache.logging.slf4j.SLF4JServiceProvider'
-        provides 'org.apache.logging.log4j.spi.Provider' with 'org.apache.logging.log4j.core.impl.Log4jProvider'
         provides 'java.security.Provider' with 'org.bouncycastle.jce.provider.BouncyCastleProvider',
                 'org.bouncycastle.pqc.jcajce.provider.BouncyCastlePQCProvider'
         provides 'com.microsoft.applicationinsights.core.dependencies.io.grpc.ManagedChannelProvider' with 'com.microsoft.applicationinsights.core.dependencies.io.grpc.netty.shaded.io.grpc.netty.NettyChannelProvider'

diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
@@ -6,9 +6,9 @@ repositories {
 }
 
 dependencies {
-    implementation 'com.h2database:h2-mvstore:1.4.200'
-    implementation 'org.apache.commons:commons-csv:1.8'
-    implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
+    implementation 'com.h2database:h2-mvstore:2.0.202'
+    implementation 'org.apache.commons:commons-csv:1.9.0'
+    implementation 'org.slf4j:slf4j-api:2.0.0-alpha5'
 }
 
 sourceSets{