Merge remote-tracking branch 'upstream/main' into fix-10424

* upstream/main: App semantic scholar api key to properties (#10656) Replace cache: gradle with "odern" gradle-build-action (#10657) Clean up test code (#10658) Bump org.openrewrite.rewrite from 6.4.0 to 6.5.4 (#10650) Bump com.puppycrawl.tools:checkstyle from 10.12.4 to 10.12.5 (#10654) Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml (#10653) Bump com.github.Dansoftowner:jSystemThemeDetector from 3.6 to 3.8 Remove comments - don't work on forks
JabRef · Nov 26, 2023 · b9b4da0 · b9b4da0
2 parents 5a820a7 + 43364b8
commit b9b4da0
Show file tree

Hide file tree

Showing 32 changed files with 145 additions and 156 deletions.
diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -63,7 +63,6 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
       - name: Clean up keychain
         run: |
          security delete-keychain signing_temp.keychain ${{runner.temp}}/keychain/notarization.keychain || true
@@ -85,6 +84,8 @@ jobs:
           mkdir ${{runner.temp}}/keychain
           security create-keychain -p jabref ${{runner.temp}}/keychain/notarization.keychain
           security set-keychain-settings ${{runner.temp}}/keychain/notarization.keychain
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Prepare merged jars and modules dir (macOS)
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir
       - name: Build dmg (macOS)

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -94,7 +94,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Prepare merged jars and modules dir (macOS)
         if: (matrix.os == 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'NO')
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir

diff --git a/.github/workflows/refresh-journal-lists.yml b/.github/workflows/refresh-journal-lists.yml
@@ -32,7 +32,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Check whether journal-list.mv can be generated (the "real" generation is done inside JabRef's build process)
         run: |
           ./gradlew generateJournalListMV

diff --git a/.github/workflows/tests-fetchers.yml b/.github/workflows/tests-fetchers.yml
@@ -50,7 +50,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run fetcher tests
         run: ./gradlew fetcherTest
         env:

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -39,30 +39,17 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
       - name: Run checkstyle reporter
         uses: nikitasavinov/checkstyle-action@master
         with:
           reporter: github-pr-review
           github_token: ${{ secrets.GITHUB_TOKEN }}
           checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
           checkstyle_version: '10.3'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run checkstyle using gradle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              Your code currently does not meet JabRef's code guidelines.
-              We use [Checkstyle](https://checkstyle.sourceforge.io/) to identify issues.
-              The tool reviewdog already placed comments on GitHub to indicate the places. See the tab "Files" in you PR.
-              Please carefully follow [the setup guide for the codestyle](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
-              Afterwards, please run checkstyle locally and fix the issues.
-
-
-              More information on code quality in JabRef is available at <https://devdocs.jabref.org/getting-into-the-code/development-strategy.html>.
-          comment_tag: checkstyle
   openrewrite:
     name: OpenRewrite
     runs-on: ubuntu-latest
@@ -77,23 +64,11 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run OpenRewrite
         run: |
           ./gradlew rewriteDryRun
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              Your code currently does not meet JabRef's code guidelines.
-              We use [OpenRewrite](https://docs.openrewrite.org/) to ensure "modern" Java coding practices.
-              The issues found can be **automatically fixed**.
-              Please execute the gradle task *`rewriteRun`*, check the results, commit, and push.
-
-
-              You can check the detailed error output at the tab "Checks", section "Tests" (on the left), subsection "OpenRewrite".
-          comment_tag: openrewrite
   modernizer:
     name: Modernizer
     runs-on: ubuntu-latest
@@ -108,24 +83,13 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run modernizer
         run: |
           # enable failing of this task if modernizer complains
           sed -i "s/failOnViolations = false/failOnViolations = true/" build.gradle
           ./gradlew modernizer
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              Your code currently does not meet JabRef's code guidelines.
-              We use [Gradle Modernizer Plugin](https://github.com/andygoossens/gradle-modernizer-plugin#gradle-modernizer-plugin) to ensure "modern" Java coding practices.
-              Please fix the detected errors, commit, and push.
-
-
-              You can check the detailed error output at the tab "Checks", section "Tests" (on the left), subsection "Modernizer".
-          comment_tag: modernizer
   markdown:
     name: Markdown
     runs-on: ubuntu-latest
@@ -141,17 +105,6 @@ jobs:
           globs: |
             *.md
             docs/**/*.md
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              You modified Markdown (*.md) files.
-              To ensure consistent styling, we have [markdown-lint](https://github.com/DavidAnson/markdownlint) in place.
-              [Markdown lint's rules](https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md#rules) help to keep our Markdown files consistent within this repository and consistent with the Markdown files outside here.
-
-              You can check the detailed error output at the tab "Checks", section "Tests" (on the left), subsection "Markdown".
-          comment_tag: markdown
   changelog:
     name: CHANGELOG.md
     runs-on: ubuntu-latest
@@ -198,14 +151,6 @@ jobs:
           diff \
             <(git show origin/main:CHANGELOG.md | clparse --format=json --separator=– - | jq '.releases[] | select(.version != null)') \
             <(git show HEAD:CHANGELOG.md | clparse --format=json --separator=– - | jq '.releases[] | select(.version != null)')
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              While the PR was in progress, JabRef released a new version.
-              You have to merge `upstream/main` and move your entry in `CHANGELOG.md` to section `## [Unreleased]`.
-          comment_tag: changelog-unreleased-only
   tests:
     name: Unit tests
     runs-on: ubuntu-latest
@@ -220,7 +165,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run tests
         run: xvfb-run --auto-servernum ./gradlew check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
         env:
@@ -255,7 +201,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run tests on PostgreSQL
         run: ./gradlew databaseTest --rerun-tasks
         env:
@@ -292,7 +239,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Run GUI tests
         run: xvfb-run --auto-servernum ./gradlew guiTest
         env:
@@ -336,7 +284,8 @@ jobs:
         with:
           java-version: 21.0.1
           distribution: 'liberica'
-          cache: 'gradle'
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
       - name: Update test coverage metrics
         if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport

diff --git a/build.gradle b/build.gradle
@@ -27,7 +27,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.4.0'
+    id 'org.openrewrite.rewrite' version '6.5.4'
 }
 
 // Enable following for debugging
@@ -144,7 +144,7 @@ dependencies {
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.7.0.202309050840-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.15.3'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.16.0'
     implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.15.3'
 
     implementation 'com.fasterxml:aalto-xml:1.3.2'
@@ -180,7 +180,7 @@ dependencies {
     }
 
     implementation 'org.controlsfx:controlsfx:11.2.0'
-    implementation 'com.github.Dansoftowner:jSystemThemeDetector:3.6'
+    implementation 'com.github.Dansoftowner:jSystemThemeDetector:3.8'
 
     implementation 'org.jsoup:jsoup:1.16.2'
     implementation 'com.konghq:unirest-java:3.14.5'
@@ -248,12 +248,12 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.12.4'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.12.5'
     // 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'
 
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.4.1"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.5.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")
@@ -277,7 +277,8 @@ processResources {
                 "astrophysicsDataSystemAPIKey": System.getenv('AstrophysicsDataSystemAPIKey') ? System.getenv('AstrophysicsDataSystemAPIKey') : '',
                 "ieeeAPIKey": System.getenv('IEEEAPIKey') ? System.getenv('IEEEAPIKey') : '',
                 "scienceDirectApiKey": System.getenv('SCIENCEDIRECTAPIKEY') ? System.getenv('SCIENCEDIRECTAPIKEY') : '',
-                "biodiversityHeritageApiKey": System.getenv('BiodiversityHeritageApiKey') ? System.getenv('BiodiversityHeritageApiKey') : ''
+                "biodiversityHeritageApiKey": System.getenv('BiodiversityHeritageApiKey') ? System.getenv('BiodiversityHeritageApiKey') : '',
+                "semanticScholarApiKey": System.getenv('SemanticScholarApiKey') ? System.getenv("SemanticScholarApiKey") : ''
         )
         filteringCharset = 'UTF-8'
     }

diff --git a/buildSrc/src/main/groovy/org/jabref/build/xjc/XjcTask.groovy b/buildSrc/src/main/groovy/org/jabref/build/xjc/XjcTask.groovy
@@ -103,8 +103,9 @@ class XjcTask extends DefaultTask {
     }
 
     private void updateOutput() {
-        if (outputDirectory != null && javaPackage != null)
-        outputs.dir(new File(getOutputDirectory(), packageAsPath(javaPackage)))
+        if (outputDirectory != null && javaPackage != null) {
+            outputs.dir(new File(getOutputDirectory(), packageAsPath(javaPackage)))
+        }
     }
 
     private static String packageAsPath(String pkg) {

diff --git a/docs/code-howtos/fetchers.md b/docs/code-howtos/fetchers.md
@@ -5,15 +5,16 @@ parent: Code Howtos
 
 Fetchers are the implementation of the [search using online services](https://docs.jabref.org/collect/import-using-online-bibliographic-database). Some fetchers require API keys to get them working. To get the fetchers running in a JabRef development setup, the keys need to be placed in the respective environment variable. The following table lists the respective fetchers, where to get the key from and the environment variable where the key has to be placed.
 
-| Service                                                                                                                                              | Key Source                                                                                                     | Environment Variable           | Rate Limit                       |
-|:-----------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------|--------------------------------|----------------------------------|
-| [IEEEXplore](https://docs.jabref.org/collect/import-using-online-bibliographic-database#ieeexplore)                                                  | [IEEE Xplore API portal](https://developer.ieee.org)                                                           | `IEEEAPIKey`                   | 200 calls/day                    |
-| [MathSciNet](http://www.ams.org/mathscinet)                                                                                                          | (none)                                                                                                         | (none)                         | Depending on the current network |
-| [SAO/NASA Astrophysics Data System](https://docs.jabref.org/collect/import-using-online-bibliographic-database#sao-nasa-astrophysics-data-system)    | [ADS UI](https://ui.adsabs.harvard.edu/user/settings/token)                                                    | `AstrophysicsDataSystemAPIKey` | 5000 calls/day                   |
-| [ScienceDirect](https://www.sciencedirect.com)                                                                                                       |                                                                                                                | `ScienceDirectApiKey`          |                                  |
-| [Springer Nature](https://docs.jabref.org/collect/import-using-online-bibliographic-database#springer)                                               | [Springer Nature API Portal](https://dev.springernature.com)                                                   | `SpringerNatureAPIKey`         | 5000 calls/day                   |
-| [Zentralblatt Math](https://www.zbmath.org)                                                                                                          | (none)                                                                                                         | (none)                         | Depending on the current network |
-| [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/)                                                                                | [Biodiversitylibrary](https://about.biodiversitylibrary.org/tools-and-services/developer-and-data-tools/#APIs) | `BiodiversityHeritageApiKey`   |  -                               |
+| Service                                                                                                                                           | Key Source                                                                                                     | Environment Variable           | Rate Limit                       |
+|:--------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------|--------------------------------|----------------------------------|
+| [IEEEXplore](https://docs.jabref.org/collect/import-using-online-bibliographic-database#ieeexplore)                                               | [IEEE Xplore API portal](https://developer.ieee.org)                                                           | `IEEEAPIKey`                   | 200 calls/day                    |
+| [MathSciNet](http://www.ams.org/mathscinet)                                                                                                       | (none)                                                                                                         | (none)                         | Depending on the current network |
+| [SAO/NASA Astrophysics Data System](https://docs.jabref.org/collect/import-using-online-bibliographic-database#sao-nasa-astrophysics-data-system) | [ADS UI](https://ui.adsabs.harvard.edu/user/settings/token)                                                    | `AstrophysicsDataSystemAPIKey` | 5000 calls/day                   |
+| [ScienceDirect](https://www.sciencedirect.com)                                                                                                    |                                                                                                                | `ScienceDirectApiKey`          |                                  |
+| [SemanticScholar](https://www.semanticscholar.org/)                                                                                               | <https://www.semanticscholar.org/product/api#api-key-form>                                                     | `SemanticScholarApiKey`        |                                  |
+| [Springer Nature](https://docs.jabref.org/collect/import-using-online-bibliographic-database#springer)                                            | [Springer Nature API Portal](https://dev.springernature.com)                                                   | `SpringerNatureAPIKey`         | 5000 calls/day                   |
+| [Zentralblatt Math](https://www.zbmath.org)                                                                                                       | (none)                                                                                                         | (none)                         | Depending on the current network |
+| [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/)                                                                             | [Biodiversitylibrary](https://about.biodiversitylibrary.org/tools-and-services/developer-and-data-tools/#APIs) | `BiodiversityHeritageApiKey`   | -                                |
 
 "Depending on the current network" means that it depends on whether your request is routed through a network having paid access. For instance, some universities have subscriptions to MathSciNet.
 
@@ -72,7 +73,7 @@ springerNatureAPIKey=${springerNatureAPIKey}
 In `build.gradle`, these variables are filled:
 
 ```groovy
-"springerNatureAPIKey": System.getenv('SpringerNatureAPIKey')
+"springerNatureAPIKey" : System.getenv('SpringerNatureAPIKey')
 ```
 
 The `BuildInfo` class reads from that file.