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Merge remote-tracking branch 'upstream/main' into fixUrlLink
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* upstream/main:
  Bump guava from 31.0.1-jre to 31.1-jre (#8543)
  Bump org.beryx.jlink from 2.24.4 to 2.25.0 (#8548)
  Bump postgresql from 42.3.2 to 42.3.3 (#8546)
  Bump richtextfx from 0.10.7 to 0.10.9 (#8547)
  Bump archunit-junit5-engine from 0.22.0 to 0.23.1 (#8545)
  Bump actions/checkout from 2 to 3 (#8542)
  Squashed 'buildres/csl/csl-styles/' changes from eb97405..8f69d4e
  Bump classgraph from 4.8.139 to 4.8.141 (#8535)
  Bump archunit-junit5-api from 0.22.0 to 0.23.1 (#8536)
  issue(8448): allow URL with + sign in entry tabs (#8508)
  Add initial telemetry development documentation (#8530)
  Add existing "Remote storage" to index
  Disable telemetry client due to incompatibilites with jakarta (#8526)
  Update to jakarta xml everywhere and update PDFbox (#8521)
  Bump flexmark-ext-gfm-tasklist from 0.62.2 to 0.64.0 (#8515)
  Bump xmlunit-core from 2.8.4 to 2.9.0 (#8519)
  Bump org.openjfx.javafxplugin from 0.0.11 to 0.0.12 (#8518)
  Bump mockito-core from 4.3.0 to 4.3.1 (#8520)
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Siedlerchr committed Mar 7, 2022
2 parents 48c44a5 + 3c381bb commit e21e236
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Showing 60 changed files with 5,836 additions and 1,111 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/check-links.yaml
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Expand Up @@ -13,7 +13,7 @@ jobs:
markdown-link-check:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- uses: gaurav-nelson/github-action-markdown-link-check@v1
with:
use-quiet-mode: 'yes'
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4 changes: 2 additions & 2 deletions .github/workflows/deployment.yml
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Expand Up @@ -51,7 +51,7 @@ jobs:
name: Create installer and portable version for ${{ matrix.displayName }}
steps:
- name: Fetch all history for all tags and branches
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Install GitVersion
Expand Down Expand Up @@ -152,7 +152,7 @@ jobs:
env:
BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
- name: Checkout source
uses: actions/checkout@v2
uses: actions/checkout@v3
- name: Fetch all history for all tags and branches
run: git fetch --prune --unshallow
- name: Install GitVersion
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2 changes: 1 addition & 1 deletion .github/workflows/gource.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: 'Checkout'
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Determine dates
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2 changes: 1 addition & 1 deletion .github/workflows/refresh-csl-subtrees.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
if: github.repository == 'JabRef/jabref'
steps:
- name: Checkout source
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
ref: main
fetch-depth: 0
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2 changes: 1 addition & 1 deletion .github/workflows/refresh-journal-lists.yml
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Expand Up @@ -10,7 +10,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Fetch all history for all tags and branches
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
ref: main
persist-credentials: false
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2 changes: 1 addition & 1 deletion .github/workflows/snap.yml
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Expand Up @@ -30,7 +30,7 @@ jobs:
env:
SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
- name: Checkout source
uses: actions/checkout@v2
uses: actions/checkout@v3
# The image relies on https://builds.jabref.org/master/JabRef-5.0-portable_linux.tar.gz^
# See snap/snapcraft.yml for details
- name: Run snapcraft build
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2 changes: 1 addition & 1 deletion .github/workflows/tests-fetchers.yml
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Expand Up @@ -37,7 +37,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout source
uses: actions/checkout@v2
uses: actions/checkout@v3
- name: Set up JDK
uses: actions/setup-java@v2
with:
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12 changes: 6 additions & 6 deletions .github/workflows/tests.yml
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Expand Up @@ -26,7 +26,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout source
uses: actions/checkout@v2
uses: actions/checkout@v3
- name: Set up JDK
uses: actions/setup-java@v2
with:
Expand All @@ -50,7 +50,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout source
uses: actions/checkout@v2
uses: actions/checkout@v3
- name: Set up JDK
uses: actions/setup-java@v2
with:
Expand Down Expand Up @@ -82,7 +82,7 @@ jobs:
options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
steps:
- name: Checkout source
uses: actions/checkout@v2
uses: actions/checkout@v3
- name: Set up JDK
uses: actions/setup-java@v2
with:
Expand Down Expand Up @@ -116,7 +116,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout source
uses: actions/checkout@v2
uses: actions/checkout@v3
- name: Set up JDK
uses: actions/setup-java@v2
with:
Expand Down Expand Up @@ -154,7 +154,7 @@ jobs:
env:
SNAPCRAFT_LOGIN_FILE: ${{ secrets.CODECOV_TOKEN }}
- name: Checkout source
uses: actions/checkout@v2
uses: actions/checkout@v3
- name: Set up JDK
uses: actions/setup-java@v2
with:
Expand All @@ -174,5 +174,5 @@ jobs:
name: "Validate Gradle Wrapper"
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- uses: gradle/wrapper-validation-action@v1
2 changes: 1 addition & 1 deletion .github/workflows/update-gradle-wrapper.yml
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Expand Up @@ -10,7 +10,7 @@ jobs:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- name: Update Gradle Wrapper
uses: gradle-update/update-gradle-wrapper-action@v1
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -25,6 +25,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We fixed an issue where an exception could occur when saving the preferences [#7614](https://github.com/JabRef/jabref/issues/7614)
- We fixed an issue where "Copy DOI url" in the right-click menu of the Entry List would just copy the DOI and not the DOI url. [#8389](https://github.com/JabRef/jabref/issues/8389)
- We fixed an issue where opening the console from the drop-down menu would cause an exception. [#8466](https://github.com/JabRef/jabref/issues/8466)
- We fixed an issue where pasting a URL was replacing + signs by spaces making the URL unreachable. [#8448](https://github.com/JabRef/jabref/issues/8448)

### Removed

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41 changes: 20 additions & 21 deletions build.gradle
Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,9 @@ plugins {

id 'org.javamodularity.moduleplugin' version '1.8.10'

id 'org.openjfx.javafxplugin' version '0.0.11'
id 'org.openjfx.javafxplugin' version '0.0.12'

id 'org.beryx.jlink' version '2.24.4'
id 'org.beryx.jlink' version '2.25.0'

// nicer test outputs during running and completion
// Homepage: https://github.com/radarsh/gradle-test-logger-plugin
Expand Down Expand Up @@ -114,9 +114,9 @@ dependencies {
// Include all jar-files in the 'lib' folder as dependencies
implementation fileTree(dir: 'lib', includes: ['*.jar'])

implementation 'org.apache.pdfbox:pdfbox:2.0.25'
implementation 'org.apache.pdfbox:fontbox:2.0.25'
implementation 'org.apache.pdfbox:xmpbox:2.0.25'
implementation 'org.apache.pdfbox:pdfbox:3.0.0-RC1'
implementation 'org.apache.pdfbox:fontbox:3.0.0-RC1'
implementation 'org.apache.pdfbox:xmpbox:3.0.0-RC1'

implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
implementation 'com.h2database:h2-mvstore:2.1.210'
Expand Down Expand Up @@ -147,14 +147,14 @@ dependencies {

implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.5'

implementation 'org.postgresql:postgresql:42.3.2'
implementation 'org.postgresql:postgresql:42.3.3'

implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
// causing module issues
exclude module: 'oraclepki'
}

implementation ('com.google.guava:guava:31.0.1-jre') {
implementation ('com.google.guava:guava:31.1-jre') {
// TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
exclude module: "jsr305"
}
Expand All @@ -168,7 +168,7 @@ dependencies {
implementation 'de.saxsys:mvvmfx:1.8.0'
implementation 'com.tobiasdiez:easybind:2.2'
implementation 'org.fxmisc.flowless:flowless:0.6.8'
implementation 'org.fxmisc.richtext:richtextfx:0.10.7'
implementation 'org.fxmisc.richtext:richtextfx:0.10.9'
implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
implementation 'com.jfoenix:jfoenix:9.0.10'
implementation 'org.controlsfx:controlsfx:11.1.1'
Expand All @@ -183,9 +183,9 @@ dependencies {

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'
implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.2'
// jakarta.activation is already depdency of glassfish
implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '3.0.1'
implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'

implementation ('com.github.tomtung:latex2unicode_2.12:0.2.6') {
exclude module: 'fastparse_2.12'
Expand All @@ -198,27 +198,29 @@ dependencies {

implementation 'com.vladsch.flexmark:flexmark:0.62.2'
implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.64.0'
implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.62.2'
implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.64.0'

implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'

testImplementation 'io.github.classgraph:classgraph:4.8.139'
testImplementation 'io.github.classgraph:classgraph:4.8.141'
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:4.3.0'
testImplementation 'org.xmlunit:xmlunit-core:2.8.4'
testImplementation 'org.mockito:mockito-core:4.3.1'
testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.22.0'
testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.22.0'
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.hamcrest:hamcrest-library:2.2"

checkstyle 'com.puppycrawl.tools:checkstyle:9.3'
xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
// 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'
}

clean {
Expand Down Expand Up @@ -555,8 +557,6 @@ jlink {
requires 'jdk.security.jgss'
requires 'jdk.xml.dom'
requires 'com.google.gson'
requires 'com.sun.xml.fastinfoset'
requires 'com.sun.xml.txw2'
requires 'org.slf4j'
uses 'org.controlsfx.glyphfont.GlyphFont'
uses 'com.airhacks.afterburner.views.ResourceLocator'
Expand All @@ -567,7 +567,6 @@ jlink {
uses 'org.mariadb.jdbc.LocalInfileInterceptor'
uses 'org.eclipse.jgit.transport.SshSessionFactory'
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 'org.controlsfx.glyphfont.GlyphFont' with 'org.controlsfx.glyphfont.FontAwesome'
provides 'org.mariadb.jdbc.tls.TlsSocketPlugin' with 'org.mariadb.jdbc.internal.protocol.tls.DefaultTlsSocketPlugin'
Expand Down
4 changes: 2 additions & 2 deletions buildres/csl/csl-styles/american-journal-of-archaeology.csl
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
<issn>0002-9114</issn>
<eissn>1939-828X</eissn>
<summary>The American Journal of Archaeology style</summary>
<updated>2021-11-12T14:22:00+00:00</updated>
<updated>2022-02-27T11:00:00+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>
Expand Down Expand Up @@ -262,7 +262,7 @@
<text macro="container-prefix" suffix=" "/>
</if>
</choose>
<text variable="container-title" font-style="italic"/>
<text variable="container-title" text-case="title" font-style="italic"/>
</macro>
<macro name="publisher">
<group>
Expand Down
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