Merge branch 'JabRef:main' into fix-issue-10506

.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)

.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

.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

.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:

.github/workflows/tests.yml

@@ -39,14 +39,15 @@ 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
   openrewrite:
@@ -63,7 +64,8 @@ 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
@@ -81,7 +83,8 @@ 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
@@ -162,7 +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:
@@ -197,7 +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:
@@ -234,7 +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:
@@ -278,7 +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

build.gradle

@@ -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'
     }

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.

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java

@@ -83,7 +83,7 @@ public CitationRelationsTab(EntryEditorPreferences preferences, DialogService di
         setText(Localization.lang("Citation relations"));
         setTooltip(new Tooltip(Localization.lang("Show articles related by citation")));
 
-        this.bibEntryRelationsRepository = new BibEntryRelationsRepository(new SemanticScholarFetcher(),
+        this.bibEntryRelationsRepository = new BibEntryRelationsRepository(new SemanticScholarFetcher(preferencesService.getImporterPreferences()),
                 new BibEntryRelationsCache());
     }
 

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/semanticscholar/SemanticScholarFetcher.java

@@ -7,14 +7,25 @@
 import java.util.List;
 
 import org.jabref.logic.importer.FetcherException;
+import org.jabref.logic.importer.ImporterPreferences;
+import org.jabref.logic.importer.fetcher.CustomizableKeyFetcher;
 import org.jabref.logic.net.URLDownload;
+import org.jabref.logic.util.BuildInfo;
 import org.jabref.model.entry.BibEntry;
 
 import com.google.gson.Gson;
 
-public class SemanticScholarFetcher implements CitationFetcher {
+public class SemanticScholarFetcher implements CitationFetcher, CustomizableKeyFetcher {
     private static final String SEMANTIC_SCHOLAR_API = "https://api.semanticscholar.org/graph/v1/";
 
+    private static final String API_KEY = new BuildInfo().semanticScholarApiKey;
+
+    private final ImporterPreferences importerPreferences;
+
+    public SemanticScholarFetcher(ImporterPreferences importerPreferences) {
+        this.importerPreferences = importerPreferences;
+    }
+
     @Override
     public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
         if (entry.getDOI().isPresent()) {
@@ -24,17 +35,20 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
                     .append("/citations")
                     .append("?fields=").append("title,authors,year,citationCount,referenceCount")
                     .append("&limit=1000");
-
             try {
                 URL citationsUrl = URI.create(urlBuilder.toString()).toURL();
-
                 URLDownload urlDownload = new URLDownload(citationsUrl);
+
+                String apiKey = getApiKey();
+                if (!apiKey.isEmpty()) {
+                    urlDownload.addHeader("x-api-key", apiKey);
+                }
                 CitationsResponse citationsResponse = new Gson()
                         .fromJson(urlDownload.asString(), CitationsResponse.class);
 
                 return citationsResponse.getData()
-                            .stream().filter(citationDataItem -> citationDataItem.getCitingPaper() != null)
-                            .map(citationDataItem -> citationDataItem.getCitingPaper().toBibEntry()).toList();
+                                        .stream().filter(citationDataItem -> citationDataItem.getCitingPaper() != null)
+                                        .map(citationDataItem -> citationDataItem.getCitingPaper().toBibEntry()).toList();
             } catch (IOException e) {
                 throw new RuntimeException(e);
             }
@@ -50,19 +64,23 @@ public List<BibEntry> searchCiting(BibEntry entry) {
                     .append("paper/")
                     .append("DOI:").append(entry.getDOI().get().getDOI())
                     .append("/references")
-                    .append("?fields=").append("title,authors,year,citationCount,referenceCount")
+                    .append("?fields=")
+                    .append("title,authors,year,citationCount,referenceCount")
                     .append("&limit=1000");
             try {
                 URL referencesUrl = URI.create(urlBuilder.toString()).toURL();
-
                 URLDownload urlDownload = new URLDownload(referencesUrl);
+                String apiKey = getApiKey();
+                if (!apiKey.isEmpty()) {
+                    urlDownload.addHeader("x-api-key", apiKey);
+                }
                 ReferencesResponse referencesResponse = new Gson()
                         .fromJson(urlDownload.asString(), ReferencesResponse.class);
 
                 return referencesResponse.getData()
-                             .stream()
-                             .filter(citationDataItem -> citationDataItem.getCitedPaper() != null)
-                             .map(referenceDataItem -> referenceDataItem.getCitedPaper().toBibEntry()).toList();
+                                         .stream()
+                                         .filter(citationDataItem -> citationDataItem.getCitedPaper() != null)
+                                         .map(referenceDataItem -> referenceDataItem.getCitedPaper().toBibEntry()).toList();
             } catch (IOException e) {
                 throw new RuntimeException(e);
             }
@@ -75,4 +93,8 @@ public List<BibEntry> searchCiting(BibEntry entry) {
     public String getName() {
         return "Semantic Scholar Citations Fetcher";
     }
+
+    private String getApiKey() {
+        return importerPreferences.getApiKey(getName()).orElse(API_KEY);
+    }
 }

src/main/java/org/jabref/logic/util/BuildInfo.java

@@ -28,6 +28,7 @@ public final class BuildInfo {
     public final String minRequiredJavaVersion;
     public final boolean allowJava9;
     public final String biodiversityHeritageApiKey;
+    public final String semanticScholarApiKey;
 
     public BuildInfo() {
         this("/build.properties");
@@ -57,14 +58,15 @@ public BuildInfo(String path) {
         minRequiredJavaVersion = properties.getProperty("minRequiredJavaVersion", "1.8");
         allowJava9 = "true".equals(properties.getProperty("allowJava9", "true"));
         biodiversityHeritageApiKey = BuildInfo.getValue(properties, "biodiversityHeritageApiKey", "36b910b6-2eb3-46f2-b64c-9abc149925ba");
+        semanticScholarApiKey = BuildInfo.getValue(properties, "semanticScholarApiKey", "");
     }
 
     private static String getValue(Properties properties, String key, String defaultValue) {
         String result = Optional.ofNullable(properties.getProperty(key))
                                 // workaround unprocessed build.properties file --> just remove the reference to some variable used in build.gradle
                                 .map(value -> value.replaceAll("\\$\\{.*\\}", ""))
                                 .orElse("");
-        if (!"".equals(result)) {
+        if (!result.isEmpty()) {
             return result;
         }
         return defaultValue;

src/main/resources/build.properties

@@ -6,4 +6,4 @@ springerNatureAPIKey=${springerNatureAPIKey}
 astrophysicsDataSystemAPIKey=${astrophysicsDataSystemAPIKey}
 ieeeAPIKey=${ieeeAPIKey}
 biodiversityHeritageApiKey=${biodiversityHeritageApiKey}
-
+semanticScholarApiKey=${semanticScholarApiKey}