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

* upstream/main: (104 commits) update test getPart (#8610) Add ControlHelper truncateString tests comments (#8612) Allow using custom SSL certificates (#8583) Fix protectedTerms not stored due to weaklistener (#8609) Fix changelog and version parsing (#8578) Creating more unit tests for NumericFieldComparatorTest (#8604) Fix merge entries dialog exceeding screen size (#8599) StringUtilTest new test for method GetPart (#8594) Use unkown entry type Add semantic scholar (#8575) Add research gate (#8580) fix import of unlinked files (#8444) (#8582) Missed l10n for fetcher fix (#8597) Fix some fetcher test (#8595) Bump slf4j-api from 2.0.0-alpha6 to 2.0.0-alpha7 in /buildSrc (#8589) Bump ikonli-materialdesign2-pack from 12.3.0 to 12.3.1 (#8591) Bump gittools/actions from 0.9.11 to 0.9.13 (#8587) Bump mockito-core from 4.3.1 to 4.4.0 (#8588) Bump flowless from 0.6.8 to 0.6.9 (#8590) Bump ikonli-javafx from 12.3.0 to 12.3.1 (#8592) ... # Conflicts: # src/main/java/org/jabref/gui/EntryTypeViewModel.java
JabRef · Mar 27, 2022 · a7eb2f3 · a7eb2f3
2 parents f64206a + ee88e7f
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diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
@@ -1,6 +1,6 @@
 # These are supported funding model platforms
 
-github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
+github: JabRef
 patreon: # Patreon user account
 open_collective: # Replace with a single Open Collective username
 ko_fi: # Replace with a single Ko-fi username

diff --git a/.github/workflows/check-links.yaml b/.github/workflows/check-links.yaml
@@ -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'

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -51,21 +51,21 @@ 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
-        uses: gittools/actions/gitversion/setup@v0.9.11
+        uses: gittools/actions/gitversion/setup@v0.9.13
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.11
+        uses: gittools/actions/gitversion/execute@v0.9.13
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Setup OSX key chain on OSX
         if: matrix.os == 'macos-latest'
@@ -152,16 +152,16 @@ 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
-        uses: gittools/actions/gitversion/setup@v0.9.11
+        uses: gittools/actions/gitversion/setup@v0.9.13
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.11
+        uses: gittools/actions/gitversion/execute@v0.9.13
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

diff --git a/.github/workflows/gource.yml b/.github/workflows/gource.yml
@@ -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

diff --git a/.github/workflows/refresh-csl-subtrees.yml b/.github/workflows/refresh-csl-subtrees.yml
@@ -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

diff --git a/.github/workflows/refresh-journal-lists.yml b/.github/workflows/refresh-journal-lists.yml
@@ -10,16 +10,16 @@ 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
           fetch-depth: 0
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Update journal lists
         run: |

diff --git a/.github/workflows/snap.yml b/.github/workflows/snap.yml
@@ -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

diff --git a/.github/workflows/tests-fetchers.yml b/.github/workflows/tests-fetchers.yml
@@ -37,12 +37,12 @@ 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:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Run fetcher tests
         run: ./gradlew fetcherTest

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -26,12 +26,12 @@ 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:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Run check style reporter
         uses: nikitasavinov/checkstyle-action@master
@@ -50,12 +50,12 @@ 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:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Run tests
         run: xvfb-run --auto-servernum ./gradlew check -x checkstyleJmh -x checkstyleMain -x checkstyleTest
@@ -82,12 +82,12 @@ 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:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Run tests on PostgreSQL
         run: ./gradlew databaseTest --rerun-tasks
@@ -116,12 +116,12 @@ 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:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Run GUI tests
         run: xvfb-run --auto-servernum ./gradlew guiTest
@@ -154,12 +154,12 @@ 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:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Update test coverage metrics
         if: ${{ steps.checksecrets.outputs.secretspresent }}
@@ -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
diff --git a/.github/workflows/update-gradle-wrapper.yml b/.github/workflows/update-gradle-wrapper.yml
@@ -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

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,16 +11,40 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+- We added an extra option when right-clicking an entry in the Entry List to copy either the DOI or the DOI url.
+- We added a new section to network preferences to allow using custom SSL certificates [#8126](https://github.com/JabRef/jabref/issues/8126)
+- We improved the version check to take also beta version into account and now redirect to the right changelog for the version
+- We added two new web and fulltext fetchers: SemanticScholar and ResearchGate
+
 ### Changed
 
+- We changed the list of CSL styles to those that support formatting bibliographies [#8421](https://github.com/JabRef/jabref/issues/8421) [citeproc-java#116](https://github.com/michel-kraemer/citeproc-java/issues/116)
+- The CSL preview styles now also support displaying data from cross references entries that are linked via the `crossref` field [#7378](https://github.com/JabRef/jabref/issues/7378)
+- We made the Search button in Web Search wider. We also skewed the panel titles to the left [#8397](https://github.com/JabRef/jabref/issues/8397)
+- We introduced a preference to disable fulltext indexing [#8468](https://github.com/JabRef/jabref/issues/8468)
+- When exporting entries, the encoding is always UTF-8
+- When embedding BibTeX data into a PDF, the encoding is always UTF-8
+
 ### Fixed
 
+- We fixed an issue where custom "Protected terms" files were missing after a restart of JabRef [#8608](https://github.com/JabRef/jabref/issues/8608)
+- We fixed an issue where JabRef could not start due to a missing directory for the fulltex index [#8579](https://github.com/JabRef/jabref/issues/8579)
+- We fixed an issue where long article numbers in the `pages` field would cause an exception and preventing the citation style to display [#8381](https://github.com/JabRef/jabref/issues/8381), [citeproc-java](https://github.com/michel-kraemer/citeproc-java/issues/114)
+- We fixed an issue where online links in the file field were not detected correctly and could produce an exception [#8150](https://github.com/JabRef/jabref/issues/8510)
 - 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 when reading non-UTF-8 encoded. When no encoding header is present, the encoding is now detected from the file content (and the preference option is disregarded) [#8417](https://github.com/JabRef/jabref/issues/8417)
+- 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)
+- We fixed an issue where creating subsidiary files from aux files created with some versions of biblatex would produce incorrect results. [#8513](https://github.com/JabRef/jabref/issues/8513)
+- We fixed an issue where opening the changelog from withing JabRef led to a 404 error [#8563](https://github.com/JabRef/jabref/issues/8563)
+- We fixed an issue where not all found unlinked local files were imported correctly due to some race condition. [#8444](https://github.com/JabRef/jabref/issues/8444)
+- We fixed an issue where Merge entries dialog exceeds screen boundaries.
 
 ### Removed
 
-
-
+- We removed the option to copy CSL Citation styles data as `XSL_FO`, `ASCIIDOC`, and `RTF` as these have not been working since a long time and are no longer supported in the external library used for processing the styles [#7378](https://github.com/JabRef/jabref/issues/7378)
+- We removed the option to configure the default encoding. The default encoding is now hard-coded to the modern UTF-8 encoding.
 
 
 
@@ -44,6 +68,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We moved the search box in preview preferences closer to the available citation styles list. [#8370](https://github.com/JabRef/jabref/pull/8370)
 - Changing the preference to show the preview panel as a separate tab now has effect without restarting JabRef. [#8370](https://github.com/JabRef/jabref/pull/8370)
 - We enabled switching themes in JabRef without the need to restart JabRef. [#7335](https://github.com/JabRef/jabref/pull/7335)
+- We added support for the field `day`, `rights`, `coverage` and `language` when reading XMP data in Dublin Core format. [#8491](https://github.com/JabRef/jabref/issues/8491)
 
 ### Fixed
 
@@ -57,6 +82,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where someone could add a duplicate field in the customize entry type dialog. [#8194](https://github.com/JabRef/jabref/issues/8194)
 - We fixed a typo in the library properties tab: "String constants". There, one can configure [BibTeX string constants](https://docs.jabref.org/advanced/strings).
 - We fixed an issue when writing a non-UTF-8 encoded file: The header is written again. [#8417](https://github.com/JabRef/jabref/issues/8417)
+- We fixed an issue where folder creation during systemic literature review failed due to an illegal fetcher name. [#8552](https://github.com/JabRef/jabref/pull/8552)
 
 ## [5.4] - 2021-12-20