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

* upstream/main: (37 commits) Update database context in state manager after loading (JabRef#9450) Bump classgraph from 4.8.151 to 4.8.152 (JabRef#9448) Bump appleboy/ssh-action from 0.1.5 to 0.1.6 (JabRef#9443) Bump Pendect/action-rsyncer from 1.1.0 to 2.0.0 (JabRef#9444) Bump jackson-dataformat-yaml from 2.14.0 to 2.14.1 (JabRef#9445) Bump unirest-java from 3.14.0 to 3.14.1 (JabRef#9447) Bump postgresql from 42.5.0 to 42.5.1 (JabRef#9446) New Crowdin updates (JabRef#9435) Return absolute path in case an absolute one is given (JabRef#9433) New Crowdin updates (JabRef#9434) Fix for issue: right click menu 6601 (JabRef#9271) Fix modernizer and refactor protected terms (JabRef#9427) Observable Preferences (OpenOffice) (JabRef#9422) Allow users to review backup changes before restoring them or merge them selectively (JabRef#9311) Bump slf4j-api from 2.0.4 to 2.0.5 (JabRef#9428) Bump archunit-junit5-api from 1.0.0 to 1.0.1 (JabRef#9429) Bump jackson-datatype-jsr310 from 2.14.0 to 2.14.1 (JabRef#9430) Bump lucene-highlighter from 9.4.1 to 9.4.2 (JabRef#9431) Fix weird checkbox styling (JabRef#9425) New translations JabRef_en.properties (Italian) (JabRef#9424) ...
MaryJml · Dec 13, 2022 · ab54f7e · ab54f7e
2 parents dc8cf5c + 513d3aa
commit ab54f7e
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diff --git a/.github/workflows/cleanup_pr.yml b/.github/workflows/cleanup_pr.yml
@@ -14,9 +14,9 @@ jobs:
         shell: bash
         run: |
           if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
-            echo "secretspresent=false" >> $GITHUB_OUTPUT
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo "secretspresent=true" >> $GITHUB_OUTPUT
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -26,8 +26,8 @@ jobs:
         run: |
           echo "branch=${{ github.event.pull_request.head.ref }}" >> $GITHUB_OUTPUT
       - name: Delete folder on builds.jabref.org
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: appleboy/ssh-action@v0.1.5
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: appleboy/ssh-action@v0.1.6
         with:
           script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
           host: build-upload.jabref.org

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -55,9 +55,9 @@ jobs:
         shell: bash
         run: |
           if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
-            echo "secretspresent=false" >> $GITHUB_OUTPUT
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo "secretspresent=true" >> $GITHUB_OUTPUT
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -79,29 +79,29 @@ jobs:
           distribution: 'temurin'
           cache: 'gradle'
       - name: Setup OSX key chain on OSX
-        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         uses: apple-actions/import-codesign-certs@v1
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           keychain-password: jabref
       - name: Setup OSX key chain on OSX for app id cert
-        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         uses: apple-actions/import-codesign-certs@v1
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           create-keychain: false
           keychain-password: jabref
       - name: Build runtime image
-        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
-        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
       - name: Resign app image for OSX and build dmg
-        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
           codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
@@ -112,7 +112,7 @@ jobs:
           jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ 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 }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Notarize dmg and pkg installer
-        if: (matrix.os == 'macos-latest') && startsWith(github.ref, 'refs/tags/') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && startsWith(github.ref, 'refs/tags/') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
           REQUEST_UUID_DMG=$(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 $3}')
@@ -133,15 +133,17 @@ jobs:
           rm "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg"
           mv "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg"
       - name: Package application image
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: ${{ matrix.archivePortable }}
       - name: Rename files
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: pwsh
         run: |
-          get-childitem -Path build/distribution/*
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
       - name: Upload to GitHub workflow artifacts store
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         uses: actions/upload-artifact@v3
         with:
           name: JabRef-${{ matrix.displayName }}
@@ -158,42 +160,49 @@ jobs:
         shell: bash
         run: |
           if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
-            echo "secretspresent=false" >> $GITHUB_OUTPUT
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo "secretspresent=true" >> $GITHUB_OUTPUT
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Checkout source
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/checkout@v3
       - name: Fetch all history for all tags and branches
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         run: git fetch --prune --unshallow
       - name: Install GitVersion
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: gittools/actions/gitversion/setup@v0.9.15
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         id: gitversion
         uses: gittools/actions/gitversion/execute@v0.9.15
       - name: Get linux binaries
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/download-artifact@master
         with:
           name: JabRef-linux
           path: build/distribution
       - name: Get windows binaries
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/download-artifact@master
         with:
           name: JabRef-windows
           path: build/distribution
       - name: Get macOS binaries
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/download-artifact@master
         with:
           name: JabRef-macOS
           path: build/distribution/
       - name: Deploy to builds.jabref.org
         id: deploy
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: Pendect/action-rsyncer@v1.1.0
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: Pendect/action-rsyncer@v2.0.0
         env:
           DEPLOY_KEY: ${{ secrets.buildJabRefPrivateKey }}
           BRANCH: ${{ steps.gitversion.outputs.branchName }}

diff --git a/.github/workflows/snap.yml b/.github/workflows/snap.yml
@@ -23,9 +23,9 @@ jobs:
         shell: bash
         run: |
           if [ "$SNAPCRAFT_LOGIN_FILE" == "" ]; then
-            echo "secretspresent=false" >> $GITHUB_OUTPUT
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo "secretspresent=true" >> $GITHUB_OUTPUT
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
@@ -39,7 +39,7 @@ jobs:
         with:
           snapcraft-args: "--debug"
       - name: Upload snap
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: snapcore/action-publish@v1
         with:
           store_login: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -150,9 +150,9 @@ jobs:
         shell: bash
         run: |
           if [ "$CODECOV_TOKEN" == "" ]; then
-            echo "secretspresent=false" >> $GITHUB_OUTPUT
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo "secretspresent=true" >> $GITHUB_OUTPUT
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.CODECOV_TOKEN }}
@@ -165,7 +165,7 @@ jobs:
           distribution: 'temurin'
           cache: 'gradle'
       - name: Update test coverage metrics
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport && bash <(curl -s https://codecov.io/bash);
         env:
           CI: "true"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -56,6 +56,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added HTML and Markdown files to Find Unlinked Files and removed BibTeX.[koppor#547](https://github.com/koppor/jabref/issues/547)
 - We changed the messages after importing unlinked local files to past tense. [koppor#548](https://github.com/koppor/jabref/issues/548)
 - We fixed an issue where the wrong icon for a successful import of a bib entry was shown [#9308](https://github.com/JabRef/jabref/pull/9308)
+- We modified the Change case sub-menus and their corresponding tips (displayed when you stay long over the menu) to properly reflect exemplified cases. [#9339](https://github.com/Jabref/jabref/issues/9339)
 
 ### Fixed
 
@@ -85,6 +86,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue with the message that is displayed when fetcher returns an empty list of entries for given query. [#9195](https://github.com/JabRef/jabref/issues/9195)
 - We fixed an issue where an exception was not logged correctly. [koppor#627](https://github.com/JabRef/koppor/issues/627)
 - We fixed an issue where hitting enter on the search field within the preferences dialog closed the dialog. [koppor#630](https://github.com/koppor/jabref/issues/630)
+- We fixed an issue where a user could not open an attached file in a new unsaved library. [#9386](https://github.com/JabRef/jabref/issues/9386)
 - We fixed a typo within a connection error message. [koppor#625](https://github.com/koppor/jabref/issues/625)
 - We fixed an issue where the 'close dialog' key binding was not closing the Preferences dialog. [#8888](https://github.com/jabref/jabref/issues/8888)
 - We fixed an issue where editing entry's "date" field in library mode "biblatex" causes an uncaught exception. [#8747](https://github.com/JabRef/jabref/issues/8747)

diff --git a/build.gradle b/build.gradle
@@ -116,10 +116,10 @@ dependencies {
     implementation 'org.apache.pdfbox:xmpbox:3.0.0-RC1'
 
     implementation 'org.apache.lucene:lucene-core:9.4.1'
-    implementation 'org.apache.lucene:lucene-queryparser:9.4.1'
+    implementation 'org.apache.lucene:lucene-queryparser:9.4.2'
     implementation 'org.apache.lucene:lucene-queries:9.4.1'
-    implementation 'org.apache.lucene:lucene-analysis-common:9.4.1'
-    implementation 'org.apache.lucene:lucene-highlighter:9.4.1'
+    implementation 'org.apache.lucene:lucene-analysis-common:9.4.2'
+    implementation 'org.apache.lucene:lucene-highlighter:9.4.2'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0'
@@ -143,12 +143,12 @@ dependencies {
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.3.0.202209071007-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.14.0'
-    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.14.0'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.14.1'
+    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.14.1'
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.7'
 
-    implementation 'org.postgresql:postgresql:42.5.0'
+    implementation 'org.postgresql:postgresql:42.5.1'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -176,9 +176,9 @@ dependencies {
     implementation 'org.controlsfx:controlsfx:11.1.2'
 
     implementation 'org.jsoup:jsoup:1.15.3'
-    implementation 'com.konghq:unirest-java:3.13.13'
+    implementation 'com.konghq:unirest-java:3.14.1'
 
-    implementation 'org.slf4j:slf4j-api:2.0.4'
+    implementation 'org.slf4j:slf4j-api:2.0.5'
     implementation "org.tinylog:tinylog-api:2.5.0"
     implementation "org.tinylog:slf4j-tinylog:2.5.0"
     implementation "org.tinylog:tinylog-impl:2.5.0"
@@ -204,15 +204,15 @@ dependencies {
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.151'
+    testImplementation 'io.github.classgraph:classgraph:4.8.152'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.9.1'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.9.1'
 
     testImplementation 'org.mockito:mockito-core:4.9.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
-    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.0.0'
-    testImplementation 'com.tngtech.archunit:archunit-junit5-api:1.0.0'
+    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.0.1'
+    testImplementation 'com.tngtech.archunit:archunit-junit5-api:1.0.1'
     testImplementation "org.testfx:testfx-core:4.0.16-alpha"
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"

diff --git a/buildSrc/build.gradle b/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:2.0.4'
+    implementation 'org.slf4j:slf4j-api:2.0.5'
 }
 
 sourceSets{