Merge remote-tracking branch 'upstream/main' into jdk17

* upstream/main: (45 commits)
  Squashed 'buildres/csl/csl-styles/' changes from ec4a4c0..176997d (#7910)
  Update citeproc-java to 3.0.0-alpha.2 (#7911)
  Search in PDF Files (#2838)
  Removed references to apache commons logging (#7907)
  Oobranch c : ootext and rangesort (#7788)
  Bump jackson-datatype-jsr310 from 2.12.3 to 2.12.4 (#7901)
  fix markdownlint
  Bump jackson-dataformat-yaml from 2.12.3 to 2.12.4 (#7899)
  Bump postgresql from 42.2.22 to 42.2.23 (#7902)
  Bump classgraph from 4.8.109 to 4.8.110 (#7900)
  Bump gittools/actions from 0.9.9 to 0.9.10 (#7898)
  Bump flowless from 0.6.3 to 0.6.4 (#7903)
  Bump jsoup from 1.13.1 to 1.14.1 (#7904)
  Bump tika-core from 1.26 to 1.27 (#7897)
  Try even more empty lines to provoke conflicts in CHANGELOG.md after a release
  Fix position in CHANGELOG.md
  Add corporate proxy workaround for Version.getAllAvailableVersions() (#7890)
  Update to Java 16 in build.gradle (#7892)
  Preparing Changelog for the next release cycle
  New development cycle
  ...

# Conflicts:
#	gradle/wrapper/gradle-wrapper.properties

.github/workflows/check-outdated-dependencies.yml

@@ -14,7 +14,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 14
+          java-version: 16
           distribution: 'adopt'
       - name: Look for outdated dependencies
         run: ./gradlew -q checkOutdatedDependencies

.github/workflows/deployment.yml

@@ -10,6 +10,8 @@ on:
       - 'docs/**'
       - 'src/test/**'
       - 'README.md'
+    tags:
+       - '*'
   pull_request:
     paths-ignore:
       - 'docs/**'
@@ -51,12 +53,12 @@ jobs:
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].9
+        uses: gittools/actions/gitversion/[email protected].10
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].9
+        uses: gittools/actions/gitversion/[email protected].10
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -103,7 +105,7 @@ jobs:
           jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type pkg --vendor JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
           productsign --sign "Developer ID Installer: JabRef e.V. (6792V39SK3)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Notarize dmg and pkg installer
-        if: matrix.os == 'macos-latest' && github.ref == 'refs/heads/main'
+        if: matrix.os == 'macos-latest' && startsWith(github.ref, 'refs/tags/') 
         shell: bash
         run: |
           REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "6792V39SK3" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')
@@ -160,12 +162,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].9
+        uses: gittools/actions/gitversion/[email protected].10
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].9
+        uses: gittools/actions/gitversion/[email protected].10
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

.github/workflows/refresh-journal-lists.yml

@@ -18,7 +18,8 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 14
+          java-version: 16
+          distribution: 'adopt'
       - uses: actions/cache@v1
         name: Restore gradle wrapper
         with:

.github/workflows/tests-fetchers.yml

@@ -36,7 +36,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 14
+          java-version: 16
           distribution: 'adopt'
       - uses: actions/cache@v2
         name: Restore gradle cache

CHANGELOG.md

@@ -11,6 +11,114 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+- We added a fulltext search feature. [#2838](https://github.com/JabRef/jabref/pull/2838)
+
+### Changed
+
+### Fixed
+
+- 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)
+
+### Removed
+
+
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+## [5.3] – 2021-07-05
+
+### Added
+
 - We added a progress counter to the title bar in Possible Duplicates dialog window. [#7366](https://github.com/JabRef/jabref/issues/7366)
 - We added new "Customization" tab to the preferences which includes option to choose a custom address for DOI access. [#7337](https://github.com/JabRef/jabref/issues/7337)
 - We added zbmath to the public databases from which the bibliographic information of an existing entry can be updated. [#7437](https://github.com/JabRef/jabref/issues/7437)
@@ -24,6 +132,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added two new fields to track the creation and most recent modification date and time for each entry. [koppor#130](https://github.com/koppor/jabref/issues/130)
 - We added a feature that allows the user to copy highlighted text in the preview window. [#6962](https://github.com/JabRef/jabref/issues/6962)
 - We added a feature that allows you to create new BibEntry via paste arxivId [#2292](https://github.com/JabRef/jabref/issues/2292)
+- We added support for conducting automated and systematic literature search across libraries and git support for persistence [#369](https://github.com/koppor/jabref/issues/369)
 - We added a add group functionality at the bottom of the side pane. [#4682](https://github.com/JabRef/jabref/issues/4682)
 - We added a feature that allows the user to choose whether to trust the target site when unable to find a valid certification path from the file download site. [#7616](https://github.com/JabRef/jabref/issues/7616)
 - We added a feature that allows the user to open all linked files of multiple selected entries by "Open file" option. [#6966](https://github.com/JabRef/jabref/issues/6966)
@@ -116,6 +225,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where duplicate files (both file names and contents are the same) is downloaded and add to linked files [#6197](https://github.com/JabRef/jabref/issues/6197)
 - We fixed an issue where changing the appearance of the preview tab did not trigger a restart warning. [#5464](https://github.com/JabRef/jabref/issues/5464)
 - We fixed an issue where editing "Custom preview style" triggers exception. [#7526](https://github.com/JabRef/jabref/issues/7526)
+- We fixed the [SAO/NASA Astrophysics Data System](https://docs.jabref.org/collect/import-using-online-bibliographic-database#sao-nasa-astrophysics-data-system) fetcher. [#7867](https://github.com/JabRef/jabref/pull/7867)
 - We fixed an issue where a title with multiple applied formattings in EndNote was not imported correctly [forum#2734](https://discourse.jabref.org/t/importing-endnote-label-field-to-jabref-from-xml-file/2734)
 - We fixed an issue where a `report` in EndNote was imported as `article` [forum#2734](https://discourse.jabref.org/t/importing-endnote-label-field-to-jabref-from-xml-file/2734)
 - We fixed an issue where the field `publisher` in EndNote was not imported in JabRef [forum#2734](https://discourse.jabref.org/t/importing-endnote-label-field-to-jabref-from-xml-file/2734)
@@ -607,11 +717,12 @@ 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/v5.2...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v5.3...HEAD
+[5.3]: https://github.com/JabRef/jabref/compare/v5.2...v5.3
 [5.2]: https://github.com/JabRef/jabref/compare/v5.1...v5.2
 [5.1]: https://github.com/JabRef/jabref/compare/v5.0...v5.1
 [5.0]: https://github.com/JabRef/jabref/compare/v5.0-beta...v5.0
 [5.0-beta]: https://github.com/JabRef/jabref/compare/v5.0-alpha...v5.0-beta
 [5.0-alpha]: https://github.com/JabRef/jabref/compare/v4.3...v5.0-alpha
 
-<!-- markdownlint-disable-file MD024 MD033 -->
+<!-- markdownlint-disable-file MD012 MD024 MD033 -->

build.gradle

@@ -123,7 +123,7 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.8'
     implementation 'com.h2database:h2-mvstore:1.4.200'
 
-    implementation group: 'org.apache.tika', name: 'tika-core', version: '1.26'
+    implementation group: 'org.apache.tika', name: 'tika-core', version: '1.27'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk15on:1.69'
@@ -142,18 +142,14 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.9.2'
     implementation 'org.antlr:antlr4-runtime:4.9.2'
 
-    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.9.0') {
-        exclude group: 'org.apache.lucene', module: 'lucene-sandbox'
-    }
-
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.12.0.202106070339-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.12.3'
-    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.12.3'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.12.4'
+    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.12.4'
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.3'
 
-    implementation 'org.postgresql:postgresql:42.2.22'
+    implementation 'org.postgresql:postgresql:42.2.23'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -173,24 +169,24 @@ dependencies {
     implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.2'
-    implementation 'org.fxmisc.flowless:flowless:0.6.3'
+    implementation 'org.fxmisc.flowless:flowless:0.6.4'
     implementation 'org.fxmisc.richtext:richtextfx:0.10.6'
     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.jsoup:jsoup:1.13.1'
+    implementation 'org.jsoup:jsoup:1.14.1'
     implementation 'com.konghq:unirest-java:3.11.11'
 
-    implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
+    implementation 'org.slf4j:slf4j-api:2.0.0-alpha2'
     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 'de.undercouch:citeproc-java:3.0.0-alpha.1'
+    implementation 'de.undercouch:citeproc-java:3.0.0-alpha.2'
 
     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'
@@ -209,19 +205,21 @@ 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:4.8.108'
+    implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
+
+    testImplementation 'io.github.classgraph:classgraph:4.8.110'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.7.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.7.2'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.11.5'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.11.6'
     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:3.11.2'
     testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
-    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.19.0'
-    testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.19.0'
+    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.20.0'
+    testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.20.0'
     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"
@@ -649,7 +647,6 @@ 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.apache.commons.logging.LogFactory' with 'org.apache.logging.log4j.jcl.LogFactoryImpl'
         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',

buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationLoader.java

@@ -25,9 +25,12 @@ public static JournalAbbreviationRepository loadRepository(JournalAbbreviationPr
         JournalAbbreviationRepository repository;
         // Initialize with built-in list
         try {
-            Path tempJournalList = Files.createTempDirectory("journal").resolve("journalList.mv");
+            Path tempDir = Files.createTempDirectory("jabref-journal");
+            Path tempJournalList = tempDir.resolve("journalList.mv");
             Files.copy(JournalAbbreviationRepository.class.getResourceAsStream("/journals/journalList.mv"), tempJournalList);
             repository = new JournalAbbreviationRepository(tempJournalList);
+            tempDir.toFile().deleteOnExit();
+            tempJournalList.toFile().deleteOnExit();
         } catch (IOException e) {
             LOGGER.error("Error while copying journal list", e);
             return null;

buildSrc/src/main/groovy/org/jabref/build/JournalAbbreviationConverter.groovy

@@ -27,7 +27,6 @@ abstract class JournalAbbreviationConverter extends DefaultTask {
             MVMap<String, String> abbreviationToFull = store.openMap("AbbreviationToFull")
 
             inputDir.getAsFileTree().filter({ File f -> f.name.endsWith(".csv") }).getFiles().each { file ->
-                duplicatesStrategy = DuplicatesStrategy.EXCLUDE
 
                 def abbreviations = JournalAbbreviationLoader.readJournalListFromFile(file.toPath())
                 fullToAbbreviation.putAll(

buildres/csl/csl-locales/locales-pl-PL.xml

@@ -7,6 +7,9 @@
     <translator>
       <name>Michal</name>
     </translator>
+    <translator>
+      <name>Pendzoncymisio</name>
+    </translator>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
     <updated>2012-07-04T23:31:02+00:00</updated>
   </info>
@@ -22,7 +25,7 @@
     <date-part name="year"/>
   </date>
   <terms>
-    <term name="accessed">udostępniono</term>
+    <term name="accessed">dostęp</term>
     <term name="and">i</term>
     <term name="and others">i inni</term>
     <term name="anonymous">anonim</term>

buildres/csl/csl-styles/Gemfile.lock

@@ -20,7 +20,7 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.7.0)
+    addressable (2.8.0)
       public_suffix (>= 2.0.2, < 5.0)
     citeproc (1.0.10)
       namae (~> 1.0)

buildres/csl/csl-styles/acta-anaesthesiologica-scandinavica.csl

@@ -155,13 +155,10 @@
   </citation>
   <bibliography second-field-align="flush">
     <layout>
-<<<<<<< HEAD
       <group delimiter=". " suffix=". ">
         <text variable="citation-number"/>
-=======
       <text variable="citation-number" suffix=". "/>
       <group delimiter=". " suffix=". ">
->>>>>>> dbb93e7d9be410a475814d5ae49aef83ce158191
         <text macro="author"/>
         <text macro="title"/>
       </group>