KPMP-5467_upgrade-to-java21

.classpath

@@ -1,9 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" output="bin/main" path="src/main/java">
+	<classpathentry kind="src" output="bin/test" path="src/test/java">
 		<attributes>
-			<attribute name="gradle_scope" value="main"/>
-			<attribute name="gradle_used_by_scope" value="main,test"/>
+			<attribute name="gradle_scope" value="test"/>
+			<attribute name="gradle_used_by_scope" value="test"/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="src" output="bin/main" path="src/main/resources">
@@ -12,14 +13,13 @@
 			<attribute name="gradle_used_by_scope" value="main,test"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="bin/test" path="src/test/java">
+	<classpathentry kind="src" output="bin/main" path="src/main/java">
 		<attributes>
-			<attribute name="gradle_scope" value="test"/>
-			<attribute name="gradle_used_by_scope" value="test"/>
-			<attribute name="test" value="true"/>
+			<attribute name="gradle_scope" value="main"/>
+			<attribute name="gradle_used_by_scope" value="main,test"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8/"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-21/"/>
 	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
 	<classpathentry kind="output" path="bin/default"/>
 </classpath>

.github/workflows/build-gradle-project.yml

@@ -21,12 +21,12 @@ jobs:
         uses: actions/checkout@v3
       - uses: actions/setup-java@v3
         with:
-          java-version: '8'
+          java-version: '21'
           distribution: 'temurin'
       - name: Setup Gradle
         uses: gradle/gradle-build-action@v2
         with:
-          gradle-version: 7.4
+          gradle-version: 8.5
 
       - name: Login to Docker Hub
         uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a

Dockerfile

@@ -1,7 +1,7 @@
-FROM alpine:3.19.1
+FROM --platform=linux/amd64 alpine:3.19.1
 
 RUN apk update
-RUN apk add openjdk8
+RUN apk add openjdk21
 
 VOLUME /tmp
 ARG DEPENDENCY=target/dependency

build.gradle

@@ -3,50 +3,54 @@ buildscript {
         mavenCentral()
     }
     dependencies {
-        classpath("org.springframework.boot:spring-boot-gradle-plugin:2.6.3")
+        classpath("org.springframework.boot:spring-boot-gradle-plugin:3.2.5")
     }
 }
 
 plugins {
-    id 'com.palantir.docker' version '0.22.1'
+    id 'com.palantir.docker' version '0.35.0'
+    id 'org.springframework.boot' version '3.2.5'
 }
 
 group = 'kingstonduo'
+version = '300'
 
 apply plugin: 'java'
 apply plugin: 'eclipse'
 apply plugin: 'idea'
 apply plugin: 'org.springframework.boot'
 apply plugin: 'io.spring.dependency-management'
 
-jar {
-    baseName='pegasus-data'
-    version= '2.5.0'
-}
 
 repositories {
     mavenCentral()
 }
 
-sourceCompatibility = 1.8
-targetCompatibility = 1.8
+sourceCompatibility = '21'
+targetCompatibility = '21'
 
 dependencies {
+
     implementation 'org.springframework.boot:spring-boot-starter-web'
     implementation 'org.springframework.boot:spring-boot-starter-data-jpa'
     implementation 'org.springframework.boot:spring-boot-starter-test'
-    implementation 'org.springframework:spring-test:5.0.5.RELEASE'
-    implementation 'commons-io:commons-io:2.6'
-    implementation 'mysql:mysql-connector-java:8.0.15'
-    implementation 'org.apache.commons:commons-compress:1.17'
-    implementation 'org.apache.commons:commons-text:1.7'
+
+    implementation 'commons-io:commons-io:2.16.1'
+    implementation 'com.mysql:mysql-connector-j:9.0.0'
+    implementation 'org.apache.commons:commons-compress:1.26.2'
+    implementation 'org.apache.commons:commons-text:1.12.0'
     implementation 'com.graphql-java:graphql-spring-boot-starter:5.0.2'
     implementation 'com.graphql-java:graphiql-spring-boot-starter:5.0.2'
     implementation 'com.graphql-java:graphql-java-tools:5.2.4'
-    testImplementation 'org.mockito:mockito-core'
-    testImplementation 'org.springframework.boot:spring-boot-starter-test:2.2.0.RELEASE'
+    implementation 'org.springframework.graphql:spring-graphql'
     implementation 'org.springframework.boot:spring-boot-starter-cache'
     implementation 'com.hazelcast:hazelcast-all:4.2.5'
+
+    testImplementation('org.mockito:mockito-junit-jupiter:3.12.4')
+    testImplementation 'org.springframework.boot:spring-boot-starter-test'
+    testImplementation 'org.springframework:spring-test:5.2.25.RELEASE'
+    testImplementation 'org.mockito:mockito-core'
+
 }
 
 springBoot {
@@ -75,15 +79,15 @@ def getCurrentGitBranch() {
       } catch (e) {
         }
         if (gitBranch == "develop" || gitBranch == "master"){
-          return jar.version
+          return project.version
         }else{
           return gitBranch
         }
     }
 }
 
 docker {
-    name "kingstonduo/${jar.baseName}:" + getCurrentGitBranch()
+    name "kingstonduo/pegasus-data:" + getCurrentGitBranch()
     copySpec.from(tasks.unpack.outputs).into("dependency")
     buildArgs(['DEPENDENCY': "dependency"])
 }

gradle/wrapper/gradle-wrapper.properties

@@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-all.zip

src/main/java/org/kpmp/Application.java

@@ -24,7 +24,7 @@ public WebMvcConfigurer corsConfigurer() {
 		return new WebMvcConfigurer() {
 			@Override
 			public void addCorsMappings(CorsRegistry registry) {
-				registry.addMapping("/graphql").allowedOrigins("http://localhost:3000");
+				registry.addMapping("/graphql").allowedOrigins("*");
 			}
 		};
 	}

src/main/java/org/kpmp/Query.java → src/main/java/org/kpmp/QueryController.java

@@ -29,12 +29,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Component;
+import org.springframework.graphql.data.method.annotation.Argument;
+import org.springframework.graphql.data.method.annotation.QueryMapping;
+import org.springframework.stereotype.Controller;
 
 import com.coxautodev.graphql.tools.GraphQLQueryResolver;
 
-@Component
-public class Query implements GraphQLQueryResolver {
+@Controller
+public class QueryController implements GraphQLQueryResolver {
 
 	private AutocompleteService autocompleteService;
 	private CellTypeService cellTypeService;
@@ -46,11 +48,11 @@ public class Query implements GraphQLQueryResolver {
 
 	private RPExpressionDataService rpExpressionDataService;
 	private ParticipantService participantService;
-  private AtlasMessageService atlasMessageService;
-	private Logger logger = LoggerFactory.getLogger(Query.class);
+    private AtlasMessageService atlasMessageService;
+	private Logger logger = LoggerFactory.getLogger(QueryController.class);
 
 	@Autowired
-	public Query(AutocompleteService autocompleteService, CellTypeService cellTypeService,
+	public QueryController(AutocompleteService autocompleteService, CellTypeService cellTypeService,
 			UmapDataService umapService, GeneExpressionSummaryService geneExpressionSummaryService,
 			DataSummaryService dataSummaryService, ClusterHierarchyService clusterHierarchyService,
 			RTExpressionDataService rtExpressionDataService, RPExpressionDataService rpExpressionDataService,
@@ -68,16 +70,19 @@ public Query(AutocompleteService autocompleteService, CellTypeService cellTypeSe
         this.atlasMessageService = atlasMessageService;
 	}
 
-	public List<AutocompleteResult> autocomplete(String searchTerm) throws IOException, Exception {
+    @QueryMapping
+	public List<AutocompleteResult> autocomplete(@Argument String searchTerm) throws IOException, Exception {
 		return autocompleteService.query(searchTerm);
 	}
 
-	public CellTypeHierarchy getCellTypeHierarchy() throws IOException {
+    @QueryMapping
+	public CellTypeHierarchy cellTypeHierarchy() throws IOException {
 		return cellTypeService.getCellTypeHierarchy();
 	}
 
-	public List<? extends GeneExpressionSummary> geneExpressionSummary(String dataType, String geneSymbol,
-			String cellType, String tissueType) throws IOException {
+    @QueryMapping
+	public List<? extends GeneExpressionSummary> geneExpressionSummary(@Argument String dataType, @Argument String geneSymbol,
+        @Argument String cellType, @Argument String tissueType) throws IOException {
 		List<? extends GeneExpressionSummary> results = new ArrayList<>();
 		if (cellType.isEmpty()) {
 			results = geneExpressionSummaryService.getByDataTypeTissueTypeAndGene(dataType, geneSymbol, tissueType);
@@ -88,11 +93,13 @@ public List<? extends GeneExpressionSummary> geneExpressionSummary(String dataTy
 		return results;
 	}
 
-	public List<ClusterHierarchy> getClusterHieararchies(String cellType) throws IOException {
+    @QueryMapping
+	public List<ClusterHierarchy> getClusterHieararchies(@Argument String cellType) throws IOException {
 		return clusterHierarchyService.findClustersByCellType(cellType);
 	}
 
-	public PlotData getUmapPlotData(String dataType, String geneSymbol, String tissueType) throws Exception {
+    @QueryMapping
+	public PlotData getUmapPlotData(@Argument String dataType, @Argument String geneSymbol, @Argument String tissueType) throws Exception {
 		try {
 			return umapService.getPlotData(dataType, geneSymbol, tissueType);
 		} catch (Exception e) {
@@ -101,6 +108,7 @@ public PlotData getUmapPlotData(String dataType, String geneSymbol, String tissu
 		}
 	}
 
+    @QueryMapping
 	public List<DataTypeSummary> getDataTypeSummaryInformation() throws Exception {
 		try {
 			return geneExpressionSummaryService.getDataTypeSummaryInformation();
@@ -110,6 +118,7 @@ public List<DataTypeSummary> getDataTypeSummaryInformation() throws Exception {
 		}
 	}
 
+    @QueryMapping
 	public List<DataTypeSummary> getSummaryData() throws Exception {
 		try {
 			return dataSummaryService.getSummaryData();
@@ -119,7 +128,8 @@ public List<DataTypeSummary> getSummaryData() throws Exception {
 		}
 	}
 
-	public List<String> dataTypesForConcept(String geneSymbol, String clusterName) throws Exception {
+    @QueryMapping
+	public List<String> dataTypesForConcept(@Argument String geneSymbol, @Argument String clusterName) throws Exception {
 		if (geneSymbol != null && !geneSymbol.isEmpty()) {
 			return geneExpressionSummaryService.findDataTypesByGene(geneSymbol);
 		} else if (clusterName != null && !clusterName.isEmpty()) {
@@ -129,7 +139,8 @@ public List<String> dataTypesForConcept(String geneSymbol, String clusterName) t
 
 	}
 
-	public RTExpressionByTissueType getRTGeneExpressionByTissue(String comparisonType, String geneSymbol)
+    @QueryMapping
+	public RTExpressionByTissueType getRTGeneExpressionByTissue(@Argument String comparisonType, @Argument String geneSymbol)
 			throws Exception {
 		try {
 			return rtExpressionDataService.getByComparisonTypeAndGeneSymbolPerTissue(comparisonType, geneSymbol);
@@ -139,7 +150,8 @@ public RTExpressionByTissueType getRTGeneExpressionByTissue(String comparisonTyp
 		}
 	}
 
-	public RPExpressionByTissueType getRPGeneExpressionByTissueAndProtein(String geneSymbol, String protein) throws Exception {
+    @QueryMapping
+	public RPExpressionByTissueType getRPGeneExpressionByTissueAndProtein(@Argument String geneSymbol, @Argument String protein) throws Exception {
 		try {
 			return rpExpressionDataService.getByGeneSymbolAndProteinPerTissue(geneSymbol, protein);
 		} catch (Exception e) {
@@ -148,7 +160,8 @@ public RPExpressionByTissueType getRPGeneExpressionByTissueAndProtein(String gen
 		}
 	}
 
-	public List<? extends RTExpressionData> getRTGeneExpressionByStructure(String structure) throws Exception {
+    @QueryMapping
+	public List<? extends RTExpressionData> getRTGeneExpressionByStructure(@Argument String structure) throws Exception {
 		try {
 			return rtExpressionDataService.getByStructure(structure);
 		} catch (Exception e) {
@@ -157,15 +170,18 @@ public List<? extends RTExpressionData> getRTGeneExpressionByStructure(String st
 		}
 	}
 
-	public List<RPExpressionData> getRPGeneExpressionByStructure(String structure) throws Exception {
+    @QueryMapping
+	public List<RPExpressionData> getRPGeneExpressionByStructure(@Argument String structure) throws Exception {
 		try {
 			return rpExpressionDataService.getByStructure(structure);
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			throw e;
 		}
 	}
-	public List<RPAccessionGroup> getRPGeneExpressionByTissue(String geneSymbol)
+
+    @QueryMapping
+	public List<RPAccessionGroup> getRPGeneExpressionByTissue(@Argument String geneSymbol)
 			throws Exception {
 		try {
 			return rpExpressionDataService.getByGeneSymbolPerTissue(geneSymbol);
@@ -175,35 +191,40 @@ public List<RPAccessionGroup> getRPGeneExpressionByTissue(String geneSymbol)
 		}
 	}
 
-	public ParticipantDataTypeSummary getDataTypeInformationByParticipant(String redcapId) {
+    @QueryMapping
+	public ParticipantDataTypeSummary getDataTypeInformationByParticipant(@Argument String redcapId) {
 		return participantService.getExperimentCounts(redcapId);
 	}
 
-	public ParticipantRepoDataTypeSummary getRepoDataTypeInformationByParticipant(String redcapId) {
+    @QueryMapping
+	public ParticipantRepoDataTypeSummary getRepoDataTypeInformationByParticipant(@Argument String redcapId) {
 		return participantService.getDataTypeCounts(redcapId);
 	}
 
-	public ParticipantSummaryDataset participantSummaryDataset(String redcap_id) throws Exception {
+    @QueryMapping
+	public ParticipantSummaryDataset participantSummaryDataset(@Argument String redcapId) throws Exception {
 		try {
-			return participantService.getParticipantSummaryDataset(redcap_id);
+			return participantService.getParticipantSummaryDataset(redcapId);
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			ParticipantSummaryDataset emptyResult = new ParticipantSummaryDataset();
-			emptyResult.setRedcapId(redcap_id);
+			emptyResult.setRedcapId(redcapId);
 
 			return emptyResult;
 		}
 	}
 
-	public ParticipantRepoDataTypeInformation getTotalParticipantFilesCount(String redcap_id) throws Exception {
+    @QueryMapping
+	public ParticipantRepoDataTypeInformation getTotalParticipantFilesCount(@Argument String redcapId) throws Exception {
 		try {
-			return this.participantService.getTotalFilesCount(redcap_id);
+			return this.participantService.getTotalFilesCount(redcapId);
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			throw e;
 		}
 	}
 
+    @QueryMapping
 	public List<ParticipantTissueTypeSummary> getTissueTypeSummaryData() throws Exception {
 		try {
 			return participantService.getTissueData();
@@ -213,6 +234,7 @@ public List<ParticipantTissueTypeSummary> getTissueTypeSummaryData() throws Exce
 		}
 	}
 
+    @QueryMapping
 	public AtlasRepoSummaryResult getAtlasSummaryRows() throws Exception {
 		try {
 			return dataSummaryService.getAtlasRepoSummary();
@@ -222,6 +244,7 @@ public AtlasRepoSummaryResult getAtlasSummaryRows() throws Exception {
 		}
 	}
 
+    @QueryMapping
     public List<AtlasMessage> getAtlasMessages() throws Exception {
         try{
             return atlasMessageService.getAtlasMessage();
@@ -231,7 +254,8 @@ public List<AtlasMessage> getAtlasMessages() throws Exception {
         }
     }
 
-	public List<ParticipantRepoDataTypeInformation> getExperimentalStrategyCountsByParticipant(String redcapId) {
+    @QueryMapping
+	public List<ParticipantRepoDataTypeInformation> getExperimentalStrategyCountsByParticipant(@Argument String redcapId) {
 		return participantService.getExperimentalStrategyCountsByParticipant(redcapId);
 	}
 }

src/main/java/org/kpmp/atlasMessage/AtlasMessage.java

@@ -3,9 +3,9 @@
 import java.io.Serializable;
 import java.util.Date;
 
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Id;
+import jakarta.persistence.Table;
 
 @Entity
 @Table(name = "atlas_messages")