Merge remote-tracking branch 'upstream/master' into writebackupToTemp

* upstream/master: (55 commits) Rename menus citation style in preview style (#6899) Fix for some Unicode characters in citation keys (#6938) Add missing authors Fix a fetcher test for the ShortDOIService (#6945) Fixes Shared Database: Changes filtering in CoarseChangeFilter to attribute property (#6868) Changed default value of "search and store files relative to bibtex file" to true (#6928) Replace comment by just a failure (#6943) Fix: in entry types editor selected field is not removed after first click (#6941) Fix remove actions for entry types in the editor (#6933) Always use Java 15 (#6929) Update DevDocs: workaround for issues with local openjfx maven libraries (#6931) Fixes bugs in the `regex` cite key pattern modifier (#6893) Add missing author Readability for citation key patterns (#6706) Add new author Reset to master and add default case to switch (#6847) Bump mockito-core from 3.5.10 to 3.5.11 (#6924) Bump byte-buddy-parent from 1.10.14 to 1.10.15 (#6923) Bump org.beryx.jlink from 2.21.4 to 2.22.0 (#6925) Bump xmpbox from 2.0.20 to 2.0.21 (#6926) ... # Conflicts: # src/main/java/org/jabref/logic/util/DelayTaskThrottler.java
JabRef · Sep 26, 2020 · e2186e7 · e2186e7
2 parents 83240fd + deb2f20
commit e2186e7
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diff --git a/.Rhistory b/.Rhistory
diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -16,7 +16,7 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.9.0
+        uses: pascalgn/automerge-action@v0.10.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "squash"

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -55,18 +55,10 @@ jobs:
       - name: Run GitVersion
         id: gitversion
         uses: gittools/actions/gitversion/execute@v0.9.4
-      - name: Set up Adotptopen JDK mac
-        uses: joschi/setup-jdk@v2
-        with:
-          # reason: https://bugs.openjdk.java.net/browse/JDK-8238184
-          java-version: 15
-          release_type: ea
-        if: matrix.os == 'macos-latest'
-      - name: Set up JDK for linux and windows
+      - name: Set up JDK
         uses: actions/setup-java@v1
         with:
-          java-version: 14
-        if: matrix.os != 'macos-latest'
+          java-version: 15
       - name: Restore gradle cache
         uses: actions/cache@master
         with:
@@ -109,17 +101,17 @@ jobs:
         if: matrix.os == 'macos-latest' && github.ref == 'refs/heads/master'
         shell: bash
         run: |
-          REQUEST_UUID=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')
-          while xcrun altool --notarization-info "$REQUEST_UUID" -u ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} -p  ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
+          REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')
+          while xcrun altool --notarization-info "$REQUEST_UUID_DMG" -u ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} -p  ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
             echo "Verification in progress..."
             sleep 30
           done
           xcrun stapler staple "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
           spctl -vvv --assess --type exec build/distribution/JabRef.app
           codesign -vvv --deep --strict "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
           codesign -dvv "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
-          REQUEST_UUID=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg" | grep RequestUUID | awk '{print $3}')
-          while xcrun altool --notarization-info "$REQUEST_UUID" -u ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} -p  ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
+          REQUEST_UUID_PKG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "W2PU6LW5U5" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg" | grep RequestUUID | awk '{print $3}')
+          while xcrun altool --notarization-info "$REQUEST_UUID_PKG" -u ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} -p  ${{ secrets.OSX_NOTARIZATION_APP_PWD }} | grep "Status: in progress" > /dev/null; do
             echo "Verification in progress..."
             sleep 30
           done

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -235,7 +235,7 @@ jobs:
         with:
           # full checkout needed for authors generation
           fetch-depth: 0
-      - name: "Check AUTHORS"
+      - name: "All authors of this PR listed in AUTHORS"
         id: authors_check
         shell: bash
         run: |
@@ -245,19 +245,16 @@ jobs:
           set +o pipefail
           added=$(git diff HEAD --no-ext-diff --unified=0 -a --no-prefix | egrep "^\+[^+]" | sed "s/^\+//")
           if [ -z "$added" ]; then
-            echo "::set-output name=newauthor::false"
             echo "No authors added"
             exit 0
           fi
-          message="The JabRef maintainers will add the following name to the [AUTHORS file](https://github.com/JabRef/jabref/blob/master/CONTRIBUTING.md#author-credits). In case you want to use a different one, please comment here and [adjust your name in your git configuration](https://docs.github.com/en/github/using-git/setting-your-username-in-git) for future commits.%0A%0A\`\`\`%0A${added//$'\n'/'%0A'}%0A\`\`\`%0A"
-          echo "::set-output name=message::$message"
-          echo "::set-output name=newauthor::true"
-          echo "New authors found"
-      - name: Comment PR
-        uses: unsplash/comment-on-pr@master
-        if: steps.authors_check.outputs.newauthor == 'true'
-        env:
-          GITHUB_TOKEN: ${{ secrets.GH_TOKEN_COMMENT_ON_PR }}
-        with:
-          msg: "${{ steps.authors_check.outputs.message }}"
-          check_for_duplicate_msg: true
+          echo "Authors found in this PR not listed in the AUTHORS file."
+          echo
+          echo "The JabRef maintainers will add the following name to the AUTHORS file"
+          echo
+          echo -e "$added"
+          echo
+          echo "In case you want to use a different one, please comment here and adjust your name in your git configuration for future commits"
+          echo
+          echo "Background: Information about the AUTHORS file can be found at https://github.com/JabRef/jabref/blob/master/CONTRIBUTING.md#author-credits"
+          exit 1
diff --git a/.mailmap b/.mailmap
@@ -47,6 +47,7 @@ Frédéric Darboux <Frederic.Darboux@orleans.inra.fr>
 Frédéric Darboux <Frederic.Darboux@orleans.inra.fr> <fdar@users.sourceforge.net>
 Frédéric Darboux <Frederic.Darboux@orleans.inra.fr> <mlep@users.noreply.github.com>
 Frédéric Darboux <Frederic.Darboux@orleans.inra.fr> <mlep@github.com>
+Frédéric Darboux <frederic.darboux@inrae.fr>
 Florian Straßer <strassfn@studi.informatik.uni-stuttgart.de>
 Gregor Herrmann <gregoa@debian.org>
 Hakan Duran <ehakanduran@gmail.com> hakova <ehakanduran@gmail.com>
@@ -211,3 +212,4 @@ Tianjian Lei <185049857@qq.com> <leitianjian@outlook.com>
 Muhammad Arsalan Badar <arsalan_badar@intuit.com>
 ZhouSky <11711923@mail.sustech.edu.cn>
 Vincent Gagnon <vincentgagnon53@gmail.com>
+Tom Warnke <Toromtomtom@users.noreply.github.com>
diff --git a/.markdownlint.yml b/.markdownlint.yml
@@ -13,6 +13,9 @@ MD013: false
 MD026:
   punctuation: ".,;:!"
 
+# not supported by gitbook
+MD031: false
+
 MD033:
   # we have <a> tags with ids and superscript
   allowed_elements: ['a', 'sup']
diff --git a/AUTHORS b/AUTHORS
@@ -119,6 +119,7 @@ Ethan Harris
 Fabian Bauer
 Fabian Bieker
 Fabiani Giovanni
+Fabio Marcos
 Fabrice Dessaint
 Fancy Zhang
 Fedor Bezrukov
@@ -181,6 +182,7 @@ John Relph
 John Zedlewski
 Jonas Lähnemann
 Jonas Moosmann
+Jonatan Asketorp
 Jonathan Powell
 Jong-Ho Shinn
 Jorge Tornero
@@ -250,6 +252,7 @@ MhhhxX
 Michael Beckmann
 Michael Falkenthal
 Michael Lass
+Michael Mauersberger
 Michael McCann
 Michael Schwarmi
 Michael Spiegel
@@ -278,6 +281,7 @@ Nikita Borovikov
 Niklas Schmitt
 nikmilpv
 NikodemKch
+Nikolaus Koopmann
 Nils Streijffert
 Niv Ierushalmi
 Nivedha Sunderraj
@@ -374,6 +378,7 @@ Tobias Boceck
 Tobias Bouschen
 Tobias Denkinger
 Tobias Diez
+Tom Warnke
 Tomás Morales de Luna
 Tony K
 Toralf Senger

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,18 +22,28 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - JabRef now offers journal lists from <https://abbrv.jabref.org>. JabRef the lists which use a dot inside the abbreviations. [#5749](https://github.com/JabRef/jabref/pull/5749)
 - We removed two useless preferences in the groups preferences dialog. [#6836](https://github.com/JabRef/jabref/pull/6836)
 - Synchronization of SpecialFields to keywords is now disabled by default. [#6621](https://github.com/JabRef/jabref/issues/6621)
-- JabRef no longer opens the entry editor with the first entry on startup [6855](https://github.com/JabRef/jabref/issues/6855)
+- JabRef no longer opens the entry editor with the first entry on startup [#6855](https://github.com/JabRef/jabref/issues/6855)
+- We completed the rebranding of `bibtexkey` as `citationkey` which was started in JabRef 5.1.
+- JabRef no longer opens the entry editor with the first entry on startup [#6855](https://github.com/JabRef/jabref/issues/6855)
+- Fetch by ID: (long) "SAO/NASA Astrophysics Data System" replaced by (short) "SAO/NASA ADS" [#6876](https://github.com/JabRef/jabref/pull/6876)
+- We changed the title of the window "Manage field names and content" to have the same title as the corresponding menu item [#6895](https://github.com/JabRef/jabref/pull/6895)
+- We renamed the menus "View -> Previous citation style" and "View -> Next citation style" into "View -> Previous preview style" and "View -> Next preview style" and renamed the "Preview" style to "Customized preview style". [#6899](https://github.com/JabRef/jabref/pull/6899)
+- We changed the default preference option "Search and store files relative to library file location" to on, as this seems to be a more intuitive behaviour. [#6863](https://github.com/JabRef/jabref/issues/6863)
+- Improved detection of "short" DOIs [6880](https://github.com/JabRef/jabref/issues/6880)
 
 ### Fixed
 
 - We fixed an issue changing the icon link_variation_off that is not meaningful. [#6834][https://github.com/JabRef/jabref/issues/6834]
 - We fixed an issue where the `.sav` file was not deleted upon exiting JabRef. [#6109](https://github.com/JabRef/jabref/issues/6109)
 - We fixed a linked identifier icon inconsistency. [#6705](https://github.com/JabRef/jabref/issues/6705)
 - We fixed the wrong behavior that font size changes are not reflected in dialogs. [#6039](https://github.com/JabRef/jabref/issues/6039)
+- We fixed an issue where the sort order of the entry table was reset after a restart of JabRef. [#6898](https://github.com/JabRef/jabref/pull/6898)
+- We fixed an issue where no longer a warning was displayed when inserting references into LibreOffice with an invalid "ReferenceParagraphFormat". [#6907](https://github.com/JabRef/jabref/pull/60907).
+- We fixed an issue where a selected field was not removed after the first click in the custom entry types dialog [#6934](https://github.com/JabRef/jabref/issues/6934)
+- We fixed an issue where a remove icon was shown for standard entry types in the custom entry types dialog [6906](https://github.com/JabRef/jabref/issues/6906)
 
 ### Removed
 
-
 ## [5.1] – 2020-08-30
 
 ### Added

diff --git a/build.gradle b/build.gradle
@@ -13,10 +13,10 @@ plugins {
     id 'application'
     id "com.simonharrer.modernizer" version '2.1.0-1'
     id 'me.champeau.gradle.jmh' version '0.5.1'
-    id 'com.github.ben-manes.versions' version '0.29.0'
+    id 'com.github.ben-manes.versions' version '0.33.0'
     id 'org.javamodularity.moduleplugin' version '1.7.0'
     id 'org.openjfx.javafxplugin' version '0.0.9'
-    id 'org.beryx.jlink' version '2.21.3'
+    id 'org.beryx.jlink' version '2.22.0'
 
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
@@ -105,9 +105,9 @@ dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     implementation fileTree(dir: 'lib', includes: ['*.jar'])
 
-    implementation 'org.apache.pdfbox:pdfbox:2.0.20'
-    implementation 'org.apache.pdfbox:fontbox:2.0.20'
-    implementation 'org.apache.pdfbox:xmpbox:2.0.20'
+    implementation 'org.apache.pdfbox:pdfbox:2.0.21'
+    implementation 'org.apache.pdfbox:fontbox:2.0.21'
+    implementation 'org.apache.pdfbox:xmpbox:2.0.21'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.8'
     implementation 'com.h2database:h2-mvstore:1.4.200'
@@ -137,7 +137,7 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.8-1'
     implementation 'org.antlr:antlr4-runtime:4.8-1'
 
-    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.6.1') {
+    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.6.2') {
         exclude group: 'org.apache.lucene', module: 'lucene-sandbox'
     }
 
@@ -199,15 +199,15 @@ dependencies {
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.62.2'
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.62.2'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.89'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.6.2'
-    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.6.2'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.6.2'
+    testImplementation 'io.github.classgraph:classgraph:4.8.90'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.7.0'
+    testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.0'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.7.0'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.14'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.15'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testImplementation 'org.mockito:mockito-core:3.5.7'
+    testImplementation 'org.mockito:mockito-core:3.5.11'
     testImplementation 'org.xmlunit:xmlunit-core:2.7.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.7.0'
     testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.14.1'
@@ -216,7 +216,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.36'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.36.1'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
     jython 'org.python:jython-standalone:2.7.2'
 }

diff --git a/docs/.gitbook/assets/eclipse-create-run-config (1) (1).png b/docs/.gitbook/assets/eclipse-create-run-config (1) (1).png
diff --git a/docs/.gitbook/assets/grafik (1).png b/docs/.gitbook/assets/grafik (1).png
diff --git a/docs/.gitbook/assets/grafik.png b/docs/.gitbook/assets/grafik.png
diff --git a/docs/.gitbook/assets/intellij-gradle-config-ignore-buildSrc (2).png b/docs/.gitbook/assets/intellij-gradle-config-ignore-buildSrc (2).png
diff --git a/docs/README.md b/docs/README.md
@@ -1,6 +1,6 @@
 # Overview on Developing
 
-This page presents all development informatation around JabRef.
+This page presents all development information around JabRef.
 
 ## Starting point for newcomers
 
@@ -37,23 +37,11 @@ Without jlink, it is not possible to generate a fat jar any more. During develop
 
 Diagram showing aspects of groups: [Groups.uml](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/Groups.uml).
 
-## Decision Records
+## Architectural Decision Records
 
-This log lists the decisions for JabRef.
+[Architectural decisions for JabRef](adr.md) are recorded.
 
-* [ADR-0000](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0000-use-markdown-architectural-decision-records.md) - Use Markdown Architectural Decision Records
-* [ADR-0001](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0001-use-crowdin-for-translations.md) - Use Crowdin for translations
-* [ADR-0002](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0002-use-slf4j-for-logging.md) - Use slf4j together with log4j2 for logging
-* [ADR-0003](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0003-use-gradle-as-build-tool.md) - Use Gradle as build tool
-* [ADR-0004](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0004-use-mariadb-connector.md) - Use MariaDB Connector
-* [ADR-0005](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0005-fully-support-utf8-only-for-latex-files.md) - Fully Support UTF-8 Only For LaTeX Files
-* [ADR-0006](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0006-only-translated-strings-in-language-file.md) - Only translated strings in language file
-* [ADR-0007](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0007-human-readable-changelog.md) - Provide a human-readable changelog
-* [ADR-0008](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0008-use-public-final-instead-of-getters.md) - Use public final instead of getters to offer access to immutable variables
-* [ADR-0009](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0009-use-plain-junit5-for-testing.md) - Use Plain JUnit5 for advanced test assertions
-* [ADR-0010](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/0010-use-h2-as-internal-database.md) - Use H2 as Internal SQL Database
-
-For new ADRs, please use [template.md](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/template.md) as basis. More information on MADR is available at [https://adr.github.io/madr/](https://adr.github.io/madr/). General information about architectural decision records is available at [https://adr.github.io/](https://adr.github.io/).
+For new ADRs, please use [template.md](https://github.com/JabRef/jabref/tree/3b3716b1e05a0d3273c886e102a8efe5e96472e0/docs/adr/template.md) as basis. More information on MADR is available at [https://adr.github.io/madr/](https://adr.github.io/madr/). General information about architectural decision records is available at [https://adr.github.io/](https://adr.github.io/). Add them to the [list of architectural decision records](adr.md).
 
 ## FAQ