From f0372ef810ee170ad793011e187f859a5728cf23 Mon Sep 17 00:00:00 2001 From: rlreamy <34109594+rlreamy@users.noreply.github.com> Date: Tue, 9 Jul 2024 10:14:27 -0400 Subject: [PATCH 01/11] Update build.gradle --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 8263f04..dbc689e 100755 --- a/build.gradle +++ b/build.gradle @@ -21,7 +21,7 @@ apply plugin: 'io.spring.dependency-management' jar { baseName='pegasus-data' - version= '2.4.0' + version= '2.5.0' } repositories { From 0c3fa824788c98df9f12f2c8916d9e9794b21e51 Mon Sep 17 00:00:00 2001 From: rlreamy <34109594+rlreamy@users.noreply.github.com> Date: Tue, 9 Jul 2024 10:15:11 -0400 Subject: [PATCH 02/11] Update build-gradle-project.yml --- .github/workflows/build-gradle-project.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-gradle-project.yml b/.github/workflows/build-gradle-project.yml index 5c35cb8..44877ec 100644 --- a/.github/workflows/build-gradle-project.yml +++ b/.github/workflows/build-gradle-project.yml @@ -6,7 +6,7 @@ on: jobs: build-gradle-project: env: - IMAGE_TAG: 2.4.0 + IMAGE_TAG: 2.5.0 runs-on: ubuntu-latest steps: - name: Get branch names From 8e143674921431ddea680fbbd3f3fcfbbbf50d8c Mon Sep 17 00:00:00 2001 From: rlreamy <34109594+rlreamy@users.noreply.github.com> Date: Tue, 9 Jul 2024 10:16:21 -0400 Subject: [PATCH 03/11] Update changelog.md --- changelog.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/changelog.md b/changelog.md index 106497c..ecf2264 100644 --- a/changelog.md +++ b/changelog.md @@ -1,6 +1,13 @@ # Changelog -## Release 2.4 [unreleased] +## Release 2.5 + +### Breaking changes + +### Non-breaking changes + +------ +## Release 2.4 (released 07/08/2024) Brief summary of what's in this release: - added a total column to show total number of files for a grouping (needed back end because total includes groups not shown on atlas home page or explorer home page) From 28aed7cac0dd75e246bc93b543207a6c300e1042 Mon Sep 17 00:00:00 2001 From: rlreamy <34109594+rlreamy@users.noreply.github.com> Date: Tue, 9 Jul 2024 10:19:59 -0400 Subject: [PATCH 04/11] Update changelog.md --- changelog.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/changelog.md b/changelog.md index ecf2264..f9e8347 100644 --- a/changelog.md +++ b/changelog.md @@ -1,10 +1,13 @@ # Changelog -## Release 2.5 +## Release 2.5 (unreleased) +Brief summary of what's in this release: ### Breaking changes +Breaking changes include any database updates needed, if we need to edit any files on system (like .env or certs, etc). Things that are outside of the code itself that need changed for the system to work. ### Non-breaking changes +Just a place to keep track of things that have changed in the code that we may want to pay special attention to when smoke testing, etc. ------ ## Release 2.4 (released 07/08/2024) From 59c6769ad3392c06d0563f2f2c3b5ab180a2e7a3 Mon Sep 17 00:00:00 2001 From: dert1129 Date: Wed, 24 Jul 2024 10:56:24 -0400 Subject: [PATCH 05/11] First pass at java 21 upgrade --- .classpath | 16 ++++---- Dockerfile | 4 +- build.gradle | 38 ++++++++++--------- gradle/wrapper/gradle-wrapper.properties | 2 +- src/main/java/org/kpmp/Application.java | 2 +- src/main/java/org/kpmp/Query.java | 30 +++++++++++++-- .../org/kpmp/atlasMessage/AtlasMessage.java | 6 +-- src/main/java/org/kpmp/cellType/CellType.java | 14 +++---- .../org/kpmp/cellType/CellTypeSynonym.java | 16 ++++---- .../cellTypeSummary/ClusterHierarchy.java | 10 ++--- src/main/java/org/kpmp/cluster/Cluster.java | 6 +-- .../kpmp/dataSummary/DataSummaryValue.java | 8 ++-- .../ExperimentalStrategyValue.java | 8 ++-- .../java/org/kpmp/errors/ErrorController.java | 2 +- src/main/java/org/kpmp/file/ARFileInfo.java | 6 +-- .../kpmp/geneExpression/RPExpressionData.java | 8 ++-- .../RTExpressionDataAllSegments.java | 8 ++-- .../geneExpression/RTExpressionDataGTI.java | 8 ++-- .../kpmp/geneExpression/SCExpressionData.java | 11 +++--- .../kpmp/geneExpression/SNExpressionData.java | 8 ++-- .../RPParticipantValue.java | 2 +- .../RTParticipantValue.java | 10 ++--- ...AGeneExpressionExpressionSummaryValue.java | 12 +++--- .../singleCell/SCRNAParticipantValue.java | 10 ++--- ...AGeneExpressionExpressionSummaryValue.java | 12 +++--- .../singleNucleus/SNRNAParticipantValue.java | 10 ++--- .../java/org/kpmp/logging/LoggingService.java | 2 +- .../kpmp/participant/ParticipantRepoData.java | 6 +-- .../ParticipantSummaryDataset.java | 8 ++-- .../kpmp/participant/SingleCellMetadata.java | 8 ++-- .../participant/SingleNucleusMetadata.java | 8 ++-- .../participant/SpatialViewerDataType.java | 8 ++-- src/main/java/org/kpmp/umap/SCMetadata.java | 10 ++--- src/main/java/org/kpmp/umap/SNMetadata.java | 10 ++--- src/main/resources/application.properties | 6 +-- .../knowledge_environment.graphqls | 34 ++++++++--------- src/test/java/org/kpmp/DataTypeEnumTest.java | 4 +- .../java/org/kpmp/FullDataTypeEnumTest.java | 4 +- src/test/java/org/kpmp/OmicsTypeEnumTest.java | 4 +- src/test/java/org/kpmp/QueryTest.java | 16 ++++---- .../org/kpmp/RTComparisonTypeEnumTest.java | 4 +- .../java/org/kpmp/TissueTypeEnumTest.java | 4 +- .../atlasMessage/AtlasMessageServiceTest.java | 2 +- .../kpmp/cellType/CellTypeHierarchyTest.java | 12 +++--- .../kpmp/cellType/CellTypeServiceTest.java | 12 +++--- .../cellType/CellTypeStructureRegionTest.java | 14 +++---- .../CellTypeStructureSubregionTest.java | 12 +++--- .../java/org/kpmp/cellType/CellTypeTest.java | 10 ++--- .../ClusterHierarchyIdTest.java | 10 ++--- .../ClusterHierarchyServiceTest.java | 10 ++--- .../cellTypeSummary/ClusterHierarchyTest.java | 12 +++--- .../org/kpmp/cluster/ClusterServiceTest.java | 12 +++--- .../java/org/kpmp/cluster/ClusterTest.java | 12 +++--- .../AtlasRepoSummaryResultTest.java | 12 +++--- .../dataSummary/AtlasRepoSummaryRowTest.java | 12 +++--- .../AtlasRepositoryLinkInformationTest.java | 10 ++--- .../dataSummary/DataSummaryServiceTest.java | 12 +++--- .../kpmp/dataSummary/DataTypeSummaryTest.java | 12 +++--- .../ExperimentalStrategyIdTest.java | 10 ++--- .../ExperimentalStrategyValueTest.java | 10 ++--- .../org/kpmp/errors/ErrorControllerTest.java | 12 +++--- .../org/kpmp/errors/FrontEndErrorTest.java | 12 +++--- .../org/kpmp/file/ARFileInfoServiceTest.java | 2 +- .../java/org/kpmp/file/ARFileInfoTest.java | 2 +- .../java/org/kpmp/gene/GeneServiceTest.java | 12 +++--- .../java/org/kpmp/gene/MyGeneInfoHitTest.java | 12 +++--- .../org/kpmp/gene/MyGeneInfoResultTest.java | 12 +++--- .../ExpressionDataServiceTest.java | 12 +++--- .../geneExpression/RPAccessionGroupTest.java | 10 ++--- .../RPExpressionByTissueTypeTest.java | 10 ++--- .../RPExpressionDataServiceTest.java | 10 ++--- .../geneExpression/RPExpressionDataTest.java | 10 ++--- .../RTExpressionByTissueTypeTest.java | 10 ++--- .../RTExpressionDataAllSegmentsTest.java | 2 +- .../RTExpressionDataGTITest.java | 3 +- .../RTExpressionDataServiceTest.java | 10 ++--- .../geneExpression/SCExpressionDataTest.java | 12 +++--- .../geneExpression/SNExpressionDataTest.java | 12 +++--- .../GeneExpressionIdTest.java | 12 +++--- .../GeneExpressionSummaryServiceTest.java | 12 +++--- .../ParticipantIdTest.java | 12 +++--- .../SCRNAGeneExpressionSummaryValueTest.java | 12 +++--- .../SCRNAParticipantValueTest.java | 12 +++--- .../SNRNAGeneExpressionSummaryValueTest.java | 12 +++--- .../SNRNAParticipantValueTest.java | 12 +++--- .../ParticipantDataTypeSummaryTest.java | 12 +++--- .../participant/ParticipantRepoDataTest.java | 12 +++--- ...articipantRepoDataTypeInformationTest.java | 12 +++--- .../ParticipantRepoDataTypeSummaryTest.java | 12 +++--- .../participant/ParticipantServiceTest.java | 14 +++---- .../ParticipantTissueTypeSummaryTest.java | 12 +++--- .../participant/SingleCellMetadataTest.java | 12 +++--- .../SingleNucleusMetadataTest.java | 12 +++--- .../SpatialViewerDataTypeTest.java | 12 +++--- .../java/org/kpmp/umap/FeatureDataTest.java | 12 +++--- src/test/java/org/kpmp/umap/PlotDataTest.java | 12 +++--- .../org/kpmp/umap/ReferenceClusterTest.java | 12 +++--- .../java/org/kpmp/umap/SCMetadataTest.java | 10 ++--- .../java/org/kpmp/umap/SNMetadataTest.java | 10 ++--- .../org/kpmp/umap/UmapDataServiceTest.java | 12 +++--- 100 files changed, 527 insertions(+), 499 deletions(-) rename src/main/resources/{ => graphql}/knowledge_environment.graphqls (90%) diff --git a/.classpath b/.classpath index f00842b..7b824e4 100755 --- a/.classpath +++ b/.classpath @@ -1,9 +1,10 @@ - + - - + + + @@ -12,14 +13,13 @@ - + - - - + + - + diff --git a/Dockerfile b/Dockerfile index 559051d..e609593 100755 --- a/Dockerfile +++ b/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 diff --git a/build.gradle b/build.gradle index dbc689e..6606052 100755 --- a/build.gradle +++ b/build.gradle @@ -3,15 +3,17 @@ 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' @@ -19,34 +21,36 @@ 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 { @@ -75,7 +79,7 @@ def getCurrentGitBranch() { } catch (e) { } if (gitBranch == "develop" || gitBranch == "master"){ - return jar.version + return project.version }else{ return gitBranch } @@ -83,7 +87,7 @@ def getCurrentGitBranch() { } docker { - name "kingstonduo/${jar.baseName}:" + getCurrentGitBranch() + name "kingstonduo/pegasus-data:" + getCurrentGitBranch() copySpec.from(tasks.unpack.outputs).into("dependency") buildArgs(['DEPENDENCY': "dependency"]) } diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 534a9cb..e985136 100755 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/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 diff --git a/src/main/java/org/kpmp/Application.java b/src/main/java/org/kpmp/Application.java index 8b858c4..d6afb2a 100755 --- a/src/main/java/org/kpmp/Application.java +++ b/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("*"); } }; } diff --git a/src/main/java/org/kpmp/Query.java b/src/main/java/org/kpmp/Query.java index b3cf843..fe496fb 100755 --- a/src/main/java/org/kpmp/Query.java +++ b/src/main/java/org/kpmp/Query.java @@ -29,11 +29,13 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.graphql.data.method.annotation.QueryMapping; import org.springframework.stereotype.Component; +import org.springframework.stereotype.Controller; import com.coxautodev.graphql.tools.GraphQLQueryResolver; -@Component +@Controller public class Query implements GraphQLQueryResolver { private AutocompleteService autocompleteService; @@ -46,7 +48,7 @@ public class Query implements GraphQLQueryResolver { private RPExpressionDataService rpExpressionDataService; private ParticipantService participantService; - private AtlasMessageService atlasMessageService; + private AtlasMessageService atlasMessageService; private Logger logger = LoggerFactory.getLogger(Query.class); @Autowired @@ -68,14 +70,17 @@ public Query(AutocompleteService autocompleteService, CellTypeService cellTypeSe this.atlasMessageService = atlasMessageService; } + @QueryMapping public List autocomplete(String searchTerm) throws IOException, Exception { return autocompleteService.query(searchTerm); } - public CellTypeHierarchy getCellTypeHierarchy() throws IOException { + @QueryMapping + public CellTypeHierarchy cellTypeHierarchy() throws IOException { return cellTypeService.getCellTypeHierarchy(); } + @QueryMapping public List geneExpressionSummary(String dataType, String geneSymbol, String cellType, String tissueType) throws IOException { List results = new ArrayList<>(); @@ -88,10 +93,12 @@ public List geneExpressionSummary(String dataTy return results; } + @QueryMapping public List getClusterHieararchies(String cellType) throws IOException { return clusterHierarchyService.findClustersByCellType(cellType); } + @QueryMapping public PlotData getUmapPlotData(String dataType, String geneSymbol, String tissueType) throws Exception { try { return umapService.getPlotData(dataType, geneSymbol, tissueType); @@ -101,6 +108,7 @@ public PlotData getUmapPlotData(String dataType, String geneSymbol, String tissu } } + @QueryMapping public List getDataTypeSummaryInformation() throws Exception { try { return geneExpressionSummaryService.getDataTypeSummaryInformation(); @@ -110,6 +118,7 @@ public List getDataTypeSummaryInformation() throws Exception { } } + @QueryMapping public List getSummaryData() throws Exception { try { return dataSummaryService.getSummaryData(); @@ -119,6 +128,7 @@ public List getSummaryData() throws Exception { } } + @QueryMapping public List dataTypesForConcept(String geneSymbol, String clusterName) throws Exception { if (geneSymbol != null && !geneSymbol.isEmpty()) { return geneExpressionSummaryService.findDataTypesByGene(geneSymbol); @@ -129,6 +139,7 @@ public List dataTypesForConcept(String geneSymbol, String clusterName) t } + @QueryMapping public RTExpressionByTissueType getRTGeneExpressionByTissue(String comparisonType, String geneSymbol) throws Exception { try { @@ -139,6 +150,7 @@ public RTExpressionByTissueType getRTGeneExpressionByTissue(String comparisonTyp } } + @QueryMapping public RPExpressionByTissueType getRPGeneExpressionByTissueAndProtein(String geneSymbol, String protein) throws Exception { try { return rpExpressionDataService.getByGeneSymbolAndProteinPerTissue(geneSymbol, protein); @@ -148,6 +160,7 @@ public RPExpressionByTissueType getRPGeneExpressionByTissueAndProtein(String gen } } + @QueryMapping public List getRTGeneExpressionByStructure(String structure) throws Exception { try { return rtExpressionDataService.getByStructure(structure); @@ -157,6 +170,7 @@ public List getRTGeneExpressionByStructure(String st } } + @QueryMapping public List getRPGeneExpressionByStructure(String structure) throws Exception { try { return rpExpressionDataService.getByStructure(structure); @@ -165,6 +179,8 @@ public List getRPGeneExpressionByStructure(String structure) t throw e; } } + + @QueryMapping public List getRPGeneExpressionByTissue(String geneSymbol) throws Exception { try { @@ -175,14 +191,17 @@ public List getRPGeneExpressionByTissue(String geneSymbol) } } + @QueryMapping public ParticipantDataTypeSummary getDataTypeInformationByParticipant(String redcapId) { return participantService.getExperimentCounts(redcapId); } + @QueryMapping public ParticipantRepoDataTypeSummary getRepoDataTypeInformationByParticipant(String redcapId) { return participantService.getDataTypeCounts(redcapId); } + @QueryMapping public ParticipantSummaryDataset participantSummaryDataset(String redcap_id) throws Exception { try { return participantService.getParticipantSummaryDataset(redcap_id); @@ -195,6 +214,7 @@ public ParticipantSummaryDataset participantSummaryDataset(String redcap_id) thr } } + @QueryMapping public ParticipantRepoDataTypeInformation getTotalParticipantFilesCount(String redcap_id) throws Exception { try { return this.participantService.getTotalFilesCount(redcap_id); @@ -204,6 +224,7 @@ public ParticipantRepoDataTypeInformation getTotalParticipantFilesCount(String r } } + @QueryMapping public List getTissueTypeSummaryData() throws Exception { try { return participantService.getTissueData(); @@ -213,6 +234,7 @@ public List 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 getAtlasMessages() throws Exception { try{ return atlasMessageService.getAtlasMessage(); @@ -231,6 +254,7 @@ public List getAtlasMessages() throws Exception { } } + @QueryMapping public List getExperimentalStrategyCountsByParticipant(String redcapId) { return participantService.getExperimentalStrategyCountsByParticipant(redcapId); } diff --git a/src/main/java/org/kpmp/atlasMessage/AtlasMessage.java b/src/main/java/org/kpmp/atlasMessage/AtlasMessage.java index 1e0cd8b..fb37292 100644 --- a/src/main/java/org/kpmp/atlasMessage/AtlasMessage.java +++ b/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") diff --git a/src/main/java/org/kpmp/cellType/CellType.java b/src/main/java/org/kpmp/cellType/CellType.java index 0e872f5..f81ac15 100755 --- a/src/main/java/org/kpmp/cellType/CellType.java +++ b/src/main/java/org/kpmp/cellType/CellType.java @@ -5,13 +5,13 @@ import java.util.List; import java.util.Set; -import javax.annotation.Nullable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.FetchType; -import javax.persistence.Id; -import javax.persistence.OneToMany; -import javax.persistence.Table; +import jakarta.annotation.Nullable; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.FetchType; +import jakarta.persistence.Id; +import jakarta.persistence.OneToMany; +import jakarta.persistence.Table; import org.apache.commons.lang3.builder.HashCodeBuilder; diff --git a/src/main/java/org/kpmp/cellType/CellTypeSynonym.java b/src/main/java/org/kpmp/cellType/CellTypeSynonym.java index f33f904..2d59594 100755 --- a/src/main/java/org/kpmp/cellType/CellTypeSynonym.java +++ b/src/main/java/org/kpmp/cellType/CellTypeSynonym.java @@ -2,14 +2,14 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.FetchType; -import javax.persistence.Id; -import javax.persistence.IdClass; -import javax.persistence.JoinColumn; -import javax.persistence.ManyToOne; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.FetchType; +import jakarta.persistence.Id; +import jakarta.persistence.IdClass; +import jakarta.persistence.JoinColumn; +import jakarta.persistence.ManyToOne; +import jakarta.persistence.Table; @Entity @Table(name = "celltype_synonym") diff --git a/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java b/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java index 4a26dd2..c633a9f 100755 --- a/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java +++ b/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java @@ -2,11 +2,11 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.IdClass; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.IdClass; +import jakarta.persistence.Table; import org.springframework.lang.Nullable; diff --git a/src/main/java/org/kpmp/cluster/Cluster.java b/src/main/java/org/kpmp/cluster/Cluster.java index 1982e8a..cddf521 100755 --- a/src/main/java/org/kpmp/cluster/Cluster.java +++ b/src/main/java/org/kpmp/cluster/Cluster.java @@ -1,8 +1,8 @@ package org.kpmp.cluster; -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 = "cluster") diff --git a/src/main/java/org/kpmp/dataSummary/DataSummaryValue.java b/src/main/java/org/kpmp/dataSummary/DataSummaryValue.java index 476517c..6f555ba 100755 --- a/src/main/java/org/kpmp/dataSummary/DataSummaryValue.java +++ b/src/main/java/org/kpmp/dataSummary/DataSummaryValue.java @@ -2,10 +2,10 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; import org.springframework.lang.Nullable; diff --git a/src/main/java/org/kpmp/dataSummary/ExperimentalStrategyValue.java b/src/main/java/org/kpmp/dataSummary/ExperimentalStrategyValue.java index 99d0887..7cb2bed 100644 --- a/src/main/java/org/kpmp/dataSummary/ExperimentalStrategyValue.java +++ b/src/main/java/org/kpmp/dataSummary/ExperimentalStrategyValue.java @@ -2,10 +2,10 @@ import java.io.Serializable; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.IdClass; -import javax.persistence.Table; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.IdClass; +import jakarta.persistence.Table; @Entity @Table(name = "repository_summary_v") diff --git a/src/main/java/org/kpmp/errors/ErrorController.java b/src/main/java/org/kpmp/errors/ErrorController.java index 93fbdc0..4f0c951 100755 --- a/src/main/java/org/kpmp/errors/ErrorController.java +++ b/src/main/java/org/kpmp/errors/ErrorController.java @@ -1,6 +1,6 @@ package org.kpmp.errors; -import javax.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletRequest; import org.kpmp.logging.LoggingService; import org.springframework.beans.factory.annotation.Autowired; diff --git a/src/main/java/org/kpmp/file/ARFileInfo.java b/src/main/java/org/kpmp/file/ARFileInfo.java index 80141c4..aba0b97 100644 --- a/src/main/java/org/kpmp/file/ARFileInfo.java +++ b/src/main/java/org/kpmp/file/ARFileInfo.java @@ -1,8 +1,8 @@ package org.kpmp.file; -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 = "ar_file_info") diff --git a/src/main/java/org/kpmp/geneExpression/RPExpressionData.java b/src/main/java/org/kpmp/geneExpression/RPExpressionData.java index 0b67b29..8865b40 100755 --- a/src/main/java/org/kpmp/geneExpression/RPExpressionData.java +++ b/src/main/java/org/kpmp/geneExpression/RPExpressionData.java @@ -1,9 +1,9 @@ package org.kpmp.geneExpression; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; @Entity @Table(name = "rp_expression") diff --git a/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java b/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java index da63cbf..c598fd9 100755 --- a/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java +++ b/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java @@ -2,10 +2,10 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; @Entity @Table(name = "rt_segments") diff --git a/src/main/java/org/kpmp/geneExpression/RTExpressionDataGTI.java b/src/main/java/org/kpmp/geneExpression/RTExpressionDataGTI.java index 2b99c90..ffcf28f 100755 --- a/src/main/java/org/kpmp/geneExpression/RTExpressionDataGTI.java +++ b/src/main/java/org/kpmp/geneExpression/RTExpressionDataGTI.java @@ -2,10 +2,10 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; @Entity @Table(name = "rt_gti") diff --git a/src/main/java/org/kpmp/geneExpression/SCExpressionData.java b/src/main/java/org/kpmp/geneExpression/SCExpressionData.java index 7a738ff..9b40ab0 100755 --- a/src/main/java/org/kpmp/geneExpression/SCExpressionData.java +++ b/src/main/java/org/kpmp/geneExpression/SCExpressionData.java @@ -2,14 +2,15 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; - import org.json.JSONException; import org.json.JSONObject; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; + + @Entity @Table(name = "sc_feature_data") class SCExpressionData implements Serializable { diff --git a/src/main/java/org/kpmp/geneExpression/SNExpressionData.java b/src/main/java/org/kpmp/geneExpression/SNExpressionData.java index 1e21871..aaba6bf 100755 --- a/src/main/java/org/kpmp/geneExpression/SNExpressionData.java +++ b/src/main/java/org/kpmp/geneExpression/SNExpressionData.java @@ -2,10 +2,10 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; import org.json.JSONException; import org.json.JSONObject; diff --git a/src/main/java/org/kpmp/geneExpressionSummary/regionalProteomics/RPParticipantValue.java b/src/main/java/org/kpmp/geneExpressionSummary/regionalProteomics/RPParticipantValue.java index c36dbba..8f93eda 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/regionalProteomics/RPParticipantValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/regionalProteomics/RPParticipantValue.java @@ -3,7 +3,7 @@ import org.kpmp.geneExpressionSummary.Participant; import org.kpmp.geneExpressionSummary.ParticipantId; -import javax.persistence.*; +import jakarta.persistence.*; import java.io.Serializable; @Entity diff --git a/src/main/java/org/kpmp/geneExpressionSummary/regionalTranscriptomics/RTParticipantValue.java b/src/main/java/org/kpmp/geneExpressionSummary/regionalTranscriptomics/RTParticipantValue.java index e14162a..9cfb53c 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/regionalTranscriptomics/RTParticipantValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/regionalTranscriptomics/RTParticipantValue.java @@ -5,11 +5,11 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.IdClass; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.IdClass; +import jakarta.persistence.Table; @Entity @Table(name = "rt_participant_tissue_v") diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAGeneExpressionExpressionSummaryValue.java b/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAGeneExpressionExpressionSummaryValue.java index cd4e971..0daa17b 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAGeneExpressionExpressionSummaryValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAGeneExpressionExpressionSummaryValue.java @@ -3,12 +3,12 @@ import java.beans.Transient; import java.io.Serializable; -import javax.annotation.Nullable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.IdClass; -import javax.persistence.Table; +import jakarta.annotation.Nullable; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.IdClass; +import jakarta.persistence.Table; import org.apache.commons.lang3.builder.EqualsBuilder; import org.apache.commons.lang3.builder.HashCodeBuilder; diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAParticipantValue.java b/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAParticipantValue.java index d5a6e26..9557dc8 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAParticipantValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAParticipantValue.java @@ -4,11 +4,11 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.IdClass; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.IdClass; +import jakarta.persistence.Table; @Entity @Table(name = "sn_participant_tissue_v") diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAGeneExpressionExpressionSummaryValue.java b/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAGeneExpressionExpressionSummaryValue.java index 294b99c..37c5d43 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAGeneExpressionExpressionSummaryValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAGeneExpressionExpressionSummaryValue.java @@ -2,12 +2,12 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.IdClass; -import javax.persistence.Table; -import javax.persistence.Transient; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.IdClass; +import jakarta.persistence.Table; +import jakarta.persistence.Transient; import org.kpmp.DataTypeEnum; import org.kpmp.geneExpressionSummary.GeneExpressionId; diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAParticipantValue.java b/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAParticipantValue.java index c6a0d3f..49f7fd0 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAParticipantValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAParticipantValue.java @@ -5,11 +5,11 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.IdClass; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.IdClass; +import jakarta.persistence.Table; @Entity @Table(name = "sn_participant_tissue_v") diff --git a/src/main/java/org/kpmp/logging/LoggingService.java b/src/main/java/org/kpmp/logging/LoggingService.java index 57597c0..5404392 100755 --- a/src/main/java/org/kpmp/logging/LoggingService.java +++ b/src/main/java/org/kpmp/logging/LoggingService.java @@ -1,6 +1,6 @@ package org.kpmp.logging; -import javax.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletRequest; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/org/kpmp/participant/ParticipantRepoData.java b/src/main/java/org/kpmp/participant/ParticipantRepoData.java index 7bd6443..880aa77 100644 --- a/src/main/java/org/kpmp/participant/ParticipantRepoData.java +++ b/src/main/java/org/kpmp/participant/ParticipantRepoData.java @@ -1,8 +1,8 @@ package org.kpmp.participant; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; @Entity diff --git a/src/main/java/org/kpmp/participant/ParticipantSummaryDataset.java b/src/main/java/org/kpmp/participant/ParticipantSummaryDataset.java index c90a5a0..ff79979 100755 --- a/src/main/java/org/kpmp/participant/ParticipantSummaryDataset.java +++ b/src/main/java/org/kpmp/participant/ParticipantSummaryDataset.java @@ -2,10 +2,10 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; @Entity @Table(name = "participant") diff --git a/src/main/java/org/kpmp/participant/SingleCellMetadata.java b/src/main/java/org/kpmp/participant/SingleCellMetadata.java index 6dc4c08..237c29c 100755 --- a/src/main/java/org/kpmp/participant/SingleCellMetadata.java +++ b/src/main/java/org/kpmp/participant/SingleCellMetadata.java @@ -2,10 +2,10 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; @Entity @Table(name = "sc_metadata") diff --git a/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java b/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java index 417e59c..4b151c6 100755 --- a/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java +++ b/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java @@ -2,10 +2,10 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; @Entity @Table(name = "sn_metadata") diff --git a/src/main/java/org/kpmp/participant/SpatialViewerDataType.java b/src/main/java/org/kpmp/participant/SpatialViewerDataType.java index 44f2985..9e3ce85 100755 --- a/src/main/java/org/kpmp/participant/SpatialViewerDataType.java +++ b/src/main/java/org/kpmp/participant/SpatialViewerDataType.java @@ -2,10 +2,10 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; @Entity @Table(name = "sv_data_type_v") diff --git a/src/main/java/org/kpmp/umap/SCMetadata.java b/src/main/java/org/kpmp/umap/SCMetadata.java index dff6125..63f6cfb 100755 --- a/src/main/java/org/kpmp/umap/SCMetadata.java +++ b/src/main/java/org/kpmp/umap/SCMetadata.java @@ -2,11 +2,11 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; -import javax.persistence.Transient; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; +import jakarta.persistence.Transient; @Entity @Table(name = "sc_umap_point_v") diff --git a/src/main/java/org/kpmp/umap/SNMetadata.java b/src/main/java/org/kpmp/umap/SNMetadata.java index 7e2a5d4..3eabf27 100755 --- a/src/main/java/org/kpmp/umap/SNMetadata.java +++ b/src/main/java/org/kpmp/umap/SNMetadata.java @@ -2,11 +2,11 @@ import java.io.Serializable; -import javax.persistence.Column; -import javax.persistence.Entity; -import javax.persistence.Id; -import javax.persistence.Table; -import javax.persistence.Transient; +import jakarta.persistence.Column; +import jakarta.persistence.Entity; +import jakarta.persistence.Id; +import jakarta.persistence.Table; +import jakarta.persistence.Transient; @Entity @Table(name = "sn_umap_point_v") diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties index f6d43aa..d995322 100755 --- a/src/main/resources/application.properties +++ b/src/main/resources/application.properties @@ -2,14 +2,14 @@ spring.datasource.url=jdbc:mysql://${MYSQL_HOST}:3306/knowledge_environment spring.datasource.username=${MYSQL_USER} spring.datasource.password=${MYSQL_PASSWORD} spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver -spring.jpa.database-platform=org.hibernate.dialect.MySQL5InnoDBDialect +spring.jpa.database-platform=org.hibernate.dialect.MySQLDialect spring.main.allow-bean-definition-overriding=true graphql.servlet.exception-handlers-enabled=true spring.jpa.show_sql=false -spring.jpa.properties.hibernate.dialect = org.hibernate.dialect.MySQL5Dialect +spring.jpa.properties.hibernate.dialect = org.hibernate.dialect.MySQLDialect server.port=3030 spring.jpa.properties.hibernate.jdbc.time_zone=America/Detroit - +spring.graphql.graphiql.enabled=true experiment.label.clinicalStudyData=Clinical Study Data experiment.label.biomarkers=Biomarkers diff --git a/src/main/resources/knowledge_environment.graphqls b/src/main/resources/graphql/knowledge_environment.graphqls similarity index 90% rename from src/main/resources/knowledge_environment.graphqls rename to src/main/resources/graphql/knowledge_environment.graphqls index 5287985..4bd6d24 100755 --- a/src/main/resources/knowledge_environment.graphqls +++ b/src/main/resources/graphql/knowledge_environment.graphqls @@ -36,11 +36,11 @@ type AtlasRepoSummaryResult { } type AtlasRepoSummaryRow { - akiCount: Long - ckdCount: Long - hrtCount: Long - dmrCount: Long - totalCount: Long + akiCount: Int + ckdCount: Int + hrtCount: Int + dmrCount: Int + totalCount: Int omicsType: String linkInformation: AtlasRepositoryLinkInformation } @@ -51,10 +51,10 @@ type AtlasRepositoryLinkInformation { } type ParticipantTissueTypeSummary { - akiCount: Long - ckdCount: Long - hrtCount: Long - dmrCount: Long + akiCount: Int + ckdCount: Int + hrtCount: Int + dmrCount: Int } type ParticipantDataTypeSummary { @@ -64,7 +64,7 @@ type ParticipantDataTypeSummary { type ParticipantDataTypeInformation { dataType: String - count: Long + count: Int isAggregatedData: Boolean } @@ -74,7 +74,7 @@ type ParticipantRepoDataTypeSummary { type ParticipantRepoDataTypeInformation { dataType: String - count: Long + count: Int linkInformation: AtlasRepositoryLinkInformation } @@ -82,12 +82,12 @@ type DataTypeSummaryInformation { omicsType: String dataType: String dataTypeShort: String - akiCount: Long - ckdCount: Long - hrtCount: Long - dmrCount: Long - totalCount: Long - participantCount: Long + akiCount: Int + ckdCount: Int + hrtCount: Int + dmrCount: Int + totalCount: Int + participantCount: Int } diff --git a/src/test/java/org/kpmp/DataTypeEnumTest.java b/src/test/java/org/kpmp/DataTypeEnumTest.java index 9b87d33..57bbe80 100755 --- a/src/test/java/org/kpmp/DataTypeEnumTest.java +++ b/src/test/java/org/kpmp/DataTypeEnumTest.java @@ -1,8 +1,8 @@ package org.kpmp; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.Test; +import org.junit.jupiter.api.Test; public class DataTypeEnumTest { diff --git a/src/test/java/org/kpmp/FullDataTypeEnumTest.java b/src/test/java/org/kpmp/FullDataTypeEnumTest.java index f27f455..28af352 100755 --- a/src/test/java/org/kpmp/FullDataTypeEnumTest.java +++ b/src/test/java/org/kpmp/FullDataTypeEnumTest.java @@ -1,8 +1,8 @@ package org.kpmp; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.Test; +import org.junit.jupiter.api.Test; public class FullDataTypeEnumTest { diff --git a/src/test/java/org/kpmp/OmicsTypeEnumTest.java b/src/test/java/org/kpmp/OmicsTypeEnumTest.java index b4e6e94..15ae3ac 100755 --- a/src/test/java/org/kpmp/OmicsTypeEnumTest.java +++ b/src/test/java/org/kpmp/OmicsTypeEnumTest.java @@ -1,8 +1,8 @@ package org.kpmp; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.Test; +import org.junit.jupiter.api.Test; public class OmicsTypeEnumTest { diff --git a/src/test/java/org/kpmp/QueryTest.java b/src/test/java/org/kpmp/QueryTest.java index ea3afde..00d39aa 100755 --- a/src/test/java/org/kpmp/QueryTest.java +++ b/src/test/java/org/kpmp/QueryTest.java @@ -1,7 +1,7 @@ package org.kpmp; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.fail; +import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.api.Assertions.fail; import static org.mockito.ArgumentMatchers.any; import static org.mockito.Mockito.mock; import static org.mockito.Mockito.times; @@ -15,9 +15,9 @@ import java.util.Date; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.atlasMessage.AtlasMessage; import org.kpmp.atlasMessage.AtlasMessageService; import org.kpmp.autocomplete.AutocompleteResult; @@ -77,7 +77,7 @@ public class QueryTest { @Mock private RPExpressionDataService rpExpressionDataService; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); query = new Query(autocompleteService, cellTypeService, umapDataService, geneExpressionService, @@ -85,7 +85,7 @@ public void setUp() throws Exception { participantService, atlasMessageService); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); query = null; @@ -124,7 +124,7 @@ public void testGetCellTypeHierarchy() throws Exception { CellTypeHierarchy expectedResult = new CellTypeHierarchy(); when(cellTypeService.getCellTypeHierarchy()).thenReturn(expectedResult); - assertEquals(expectedResult, query.getCellTypeHierarchy()); + assertEquals(expectedResult, query.cellTypeHierarchy()); } @SuppressWarnings({ "rawtypes", "unchecked" }) diff --git a/src/test/java/org/kpmp/RTComparisonTypeEnumTest.java b/src/test/java/org/kpmp/RTComparisonTypeEnumTest.java index f4cee0a..47cd2ab 100755 --- a/src/test/java/org/kpmp/RTComparisonTypeEnumTest.java +++ b/src/test/java/org/kpmp/RTComparisonTypeEnumTest.java @@ -1,8 +1,8 @@ package org.kpmp; -import org.junit.Test; +import org.junit.jupiter.api.Test; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; public class RTComparisonTypeEnumTest { diff --git a/src/test/java/org/kpmp/TissueTypeEnumTest.java b/src/test/java/org/kpmp/TissueTypeEnumTest.java index 680d310..3cb79c9 100755 --- a/src/test/java/org/kpmp/TissueTypeEnumTest.java +++ b/src/test/java/org/kpmp/TissueTypeEnumTest.java @@ -1,8 +1,8 @@ package org.kpmp; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.Test; +import org.junit.jupiter.api.Test; public class TissueTypeEnumTest { diff --git a/src/test/java/org/kpmp/atlasMessage/AtlasMessageServiceTest.java b/src/test/java/org/kpmp/atlasMessage/AtlasMessageServiceTest.java index ae21f72..097f996 100644 --- a/src/test/java/org/kpmp/atlasMessage/AtlasMessageServiceTest.java +++ b/src/test/java/org/kpmp/atlasMessage/AtlasMessageServiceTest.java @@ -1,6 +1,6 @@ package org.kpmp.atlasMessage; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.when; import java.text.SimpleDateFormat; diff --git a/src/test/java/org/kpmp/cellType/CellTypeHierarchyTest.java b/src/test/java/org/kpmp/cellType/CellTypeHierarchyTest.java index f0570a3..ac85344 100755 --- a/src/test/java/org/kpmp/cellType/CellTypeHierarchyTest.java +++ b/src/test/java/org/kpmp/cellType/CellTypeHierarchyTest.java @@ -1,24 +1,24 @@ package org.kpmp.cellType; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class CellTypeHierarchyTest { private CellTypeHierarchy hierarchy; - @Before + @BeforeEach public void setUp() throws Exception { hierarchy = new CellTypeHierarchy(); } - @After + @AfterEach public void tearDown() throws Exception { hierarchy = null; } diff --git a/src/test/java/org/kpmp/cellType/CellTypeServiceTest.java b/src/test/java/org/kpmp/cellType/CellTypeServiceTest.java index 47bf377..3190a94 100755 --- a/src/test/java/org/kpmp/cellType/CellTypeServiceTest.java +++ b/src/test/java/org/kpmp/cellType/CellTypeServiceTest.java @@ -1,13 +1,13 @@ package org.kpmp.cellType; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.when; import java.util.ArrayList; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -17,14 +17,14 @@ public class CellTypeServiceTest { private CellTypeRepository cellTypeRepo; private CellTypeService service; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); service = new CellTypeService(cellTypeRepo); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); service = null; diff --git a/src/test/java/org/kpmp/cellType/CellTypeStructureRegionTest.java b/src/test/java/org/kpmp/cellType/CellTypeStructureRegionTest.java index 76b0361..861af28 100755 --- a/src/test/java/org/kpmp/cellType/CellTypeStructureRegionTest.java +++ b/src/test/java/org/kpmp/cellType/CellTypeStructureRegionTest.java @@ -1,25 +1,25 @@ package org.kpmp.cellType; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertTrue; +import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.api.Assertions.assertTrue; import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class CellTypeStructureRegionTest { private CellTypeStructureRegion region; - @Before + @BeforeEach public void setUp() throws Exception { region = new CellTypeStructureRegion("region1"); } - @After + @AfterEach public void tearDown() throws Exception { region = null; } diff --git a/src/test/java/org/kpmp/cellType/CellTypeStructureSubregionTest.java b/src/test/java/org/kpmp/cellType/CellTypeStructureSubregionTest.java index bea2616..482e372 100755 --- a/src/test/java/org/kpmp/cellType/CellTypeStructureSubregionTest.java +++ b/src/test/java/org/kpmp/cellType/CellTypeStructureSubregionTest.java @@ -1,18 +1,18 @@ package org.kpmp.cellType; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class CellTypeStructureSubregionTest { - @Before + @BeforeEach public void setUp() throws Exception { } - @After + @AfterEach public void tearDown() throws Exception { } diff --git a/src/test/java/org/kpmp/cellType/CellTypeTest.java b/src/test/java/org/kpmp/cellType/CellTypeTest.java index 73b69ac..218e5a9 100755 --- a/src/test/java/org/kpmp/cellType/CellTypeTest.java +++ b/src/test/java/org/kpmp/cellType/CellTypeTest.java @@ -8,20 +8,20 @@ import java.util.List; import java.util.Set; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class CellTypeTest { private CellType cellType; - @Before + @BeforeEach public void setUp() { cellType = new CellType(); } - @After + @AfterEach public void tearDown() { cellType = null; } diff --git a/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyIdTest.java b/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyIdTest.java index 298ee3f..49891fe 100755 --- a/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyIdTest.java +++ b/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyIdTest.java @@ -2,20 +2,20 @@ import static org.junit.jupiter.api.Assertions.assertEquals; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ClusterHierarchyIdTest { private ClusterHierarchyId id; - @Before + @BeforeEach public void setUp() throws Exception { id = new ClusterHierarchyId(); } - @After + @AfterEach public void tearDown() throws Exception { id = null; } diff --git a/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyServiceTest.java b/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyServiceTest.java index a46778c..18f5957 100755 --- a/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyServiceTest.java +++ b/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyServiceTest.java @@ -8,9 +8,9 @@ import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.DataTypeEnum; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -21,13 +21,13 @@ public class ClusterHierarchyServiceTest { private ClusterHiearchyRepository clusterHierarchyRepo; private ClusterHierarchyService service; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); service = new ClusterHierarchyService(clusterHierarchyRepo); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); service = null; diff --git a/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyTest.java b/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyTest.java index 18b33b6..cde5bf9 100755 --- a/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyTest.java +++ b/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyTest.java @@ -1,21 +1,21 @@ package org.kpmp.cellTypeSummary; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ClusterHierarchyTest { private ClusterHierarchy clusterHierarchy; - @Before + @BeforeEach public void setUp() throws Exception { clusterHierarchy = new ClusterHierarchy(); } - @After + @AfterEach public void tearDown() throws Exception { clusterHierarchy = null; } diff --git a/src/test/java/org/kpmp/cluster/ClusterServiceTest.java b/src/test/java/org/kpmp/cluster/ClusterServiceTest.java index 5e23bec..7f2470a 100755 --- a/src/test/java/org/kpmp/cluster/ClusterServiceTest.java +++ b/src/test/java/org/kpmp/cluster/ClusterServiceTest.java @@ -1,14 +1,14 @@ package org.kpmp.cluster; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.when; import java.util.Arrays; import java.util.Map; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -18,13 +18,13 @@ public class ClusterServiceTest { private ClusterRepository clusterRepo; private ClusterService service; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); service = new ClusterService(clusterRepo); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); service = null; diff --git a/src/test/java/org/kpmp/cluster/ClusterTest.java b/src/test/java/org/kpmp/cluster/ClusterTest.java index ad1920d..c924352 100755 --- a/src/test/java/org/kpmp/cluster/ClusterTest.java +++ b/src/test/java/org/kpmp/cluster/ClusterTest.java @@ -1,21 +1,21 @@ package org.kpmp.cluster; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ClusterTest { private Cluster cluster; - @Before + @BeforeEach public void setUp() throws Exception { cluster = new Cluster(); } - @After + @AfterEach public void tearDown() throws Exception { cluster = null; } diff --git a/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryResultTest.java b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryResultTest.java index 51a7d66..02095a4 100644 --- a/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryResultTest.java +++ b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryResultTest.java @@ -1,12 +1,12 @@ package org.kpmp.dataSummary; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.mockito.Mock; public class AtlasRepoSummaryResultTest { @@ -15,12 +15,12 @@ public class AtlasRepoSummaryResultTest { @Mock private List summaryRows; - @Before + @BeforeEach public void setUp() throws Exception { result = new AtlasRepoSummaryResult(); } - @After + @AfterEach public void tearDown() throws Exception { result = null; } diff --git a/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryRowTest.java b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryRowTest.java index 74e5450..5ce58e3 100644 --- a/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryRowTest.java +++ b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryRowTest.java @@ -1,11 +1,11 @@ package org.kpmp.dataSummary; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.mock; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -15,13 +15,13 @@ public class AtlasRepoSummaryRowTest { AtlasRepositoryLinkInformation linkInformation; private AtlasRepoSummaryRow row; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); row = new AtlasRepoSummaryRow("omicsType", linkInformation); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); row = null; diff --git a/src/test/java/org/kpmp/dataSummary/AtlasRepositoryLinkInformationTest.java b/src/test/java/org/kpmp/dataSummary/AtlasRepositoryLinkInformationTest.java index 7ec48e7..f9339d1 100644 --- a/src/test/java/org/kpmp/dataSummary/AtlasRepositoryLinkInformationTest.java +++ b/src/test/java/org/kpmp/dataSummary/AtlasRepositoryLinkInformationTest.java @@ -2,18 +2,18 @@ import static org.junit.jupiter.api.Assertions.assertEquals; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class AtlasRepositoryLinkInformationTest { - @Before + @BeforeEach public void setUp() throws Exception { } - @After + @AfterEach public void tearDown() throws Exception { } diff --git a/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java b/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java index d80b38a..49361af 100755 --- a/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java +++ b/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java @@ -1,15 +1,15 @@ package org.kpmp.dataSummary; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.when; import java.util.Arrays; import java.util.List; import java.util.ArrayList; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.DataTypeEnum; import org.kpmp.FullDataTypeEnum; import org.kpmp.TissueTypeEnum; @@ -27,7 +27,7 @@ public class DataSummaryServiceTest { @Mock private ARFileInfoService fileInfoService; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); dataSummaryService = new DataSummaryService(dataSummaryRepository, atlasRepoSummaryRepository, fileInfoService); @@ -36,7 +36,7 @@ public void setUp() throws Exception { ReflectionTestUtils.setField(dataSummaryService, "BIOMARKER", "Biomarker"); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); dataSummaryService = null; diff --git a/src/test/java/org/kpmp/dataSummary/DataTypeSummaryTest.java b/src/test/java/org/kpmp/dataSummary/DataTypeSummaryTest.java index 33d73c4..0e8823e 100755 --- a/src/test/java/org/kpmp/dataSummary/DataTypeSummaryTest.java +++ b/src/test/java/org/kpmp/dataSummary/DataTypeSummaryTest.java @@ -1,10 +1,10 @@ package org.kpmp.dataSummary; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.DataTypeEnum; import org.kpmp.FullDataTypeEnum; import org.kpmp.OmicsTypeEnum; @@ -13,7 +13,7 @@ public class DataTypeSummaryTest { private DataTypeSummary datasetSummary; - @Before + @BeforeEach public void setUp() { datasetSummary = new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), @@ -21,7 +21,7 @@ public void setUp() { Long.valueOf(2), Long.valueOf(4), Long.valueOf(6), Long.valueOf(7), Long.valueOf(8)); } - @After + @AfterEach public void tearDown() { datasetSummary = null; } diff --git a/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyIdTest.java b/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyIdTest.java index d9d80ac..51e5242 100644 --- a/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyIdTest.java +++ b/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyIdTest.java @@ -2,20 +2,20 @@ import static org.junit.jupiter.api.Assertions.assertEquals; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ExperimentalStrategyIdTest { private ExperimentalStrategyId id; - @Before + @BeforeEach public void setUp() throws Exception { id = new ExperimentalStrategyId(); } - @After + @AfterEach public void tearDown() throws Exception { id = null; } diff --git a/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyValueTest.java b/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyValueTest.java index b2b3346..a4b6f1b 100644 --- a/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyValueTest.java +++ b/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyValueTest.java @@ -2,20 +2,20 @@ import static org.junit.jupiter.api.Assertions.assertEquals; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ExperimentalStrategyValueTest { private ExperimentalStrategyValue value; - @Before + @BeforeEach public void setUp() throws Exception { value = new ExperimentalStrategyValue(); } - @After + @AfterEach public void tearDown() throws Exception { value = null; } diff --git a/src/test/java/org/kpmp/errors/ErrorControllerTest.java b/src/test/java/org/kpmp/errors/ErrorControllerTest.java index 8297df7..77f4d8a 100755 --- a/src/test/java/org/kpmp/errors/ErrorControllerTest.java +++ b/src/test/java/org/kpmp/errors/ErrorControllerTest.java @@ -3,11 +3,11 @@ import static org.mockito.Mockito.mock; import static org.mockito.Mockito.verify; -import javax.servlet.http.HttpServletRequest; +import jakarta.servlet.http.HttpServletRequest; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.logging.LoggingService; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -18,13 +18,13 @@ public class ErrorControllerTest { private LoggingService logger; private ErrorController controller; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); controller = new ErrorController(logger); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); } diff --git a/src/test/java/org/kpmp/errors/FrontEndErrorTest.java b/src/test/java/org/kpmp/errors/FrontEndErrorTest.java index 84b618c..6bf86fc 100755 --- a/src/test/java/org/kpmp/errors/FrontEndErrorTest.java +++ b/src/test/java/org/kpmp/errors/FrontEndErrorTest.java @@ -1,21 +1,21 @@ package org.kpmp.errors; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class FrontEndErrorTest { private FrontEndError error; - @Before + @BeforeEach public void setup() { error = new FrontEndError(); } - @After + @AfterEach public void tearDown() { error = null; } diff --git a/src/test/java/org/kpmp/file/ARFileInfoServiceTest.java b/src/test/java/org/kpmp/file/ARFileInfoServiceTest.java index 81d1470..22c9848 100644 --- a/src/test/java/org/kpmp/file/ARFileInfoServiceTest.java +++ b/src/test/java/org/kpmp/file/ARFileInfoServiceTest.java @@ -1,6 +1,6 @@ package org.kpmp.file; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.when; import org.junit.jupiter.api.AfterEach; diff --git a/src/test/java/org/kpmp/file/ARFileInfoTest.java b/src/test/java/org/kpmp/file/ARFileInfoTest.java index 10eac04..297e872 100644 --- a/src/test/java/org/kpmp/file/ARFileInfoTest.java +++ b/src/test/java/org/kpmp/file/ARFileInfoTest.java @@ -1,6 +1,6 @@ package org.kpmp.file; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.BeforeEach; diff --git a/src/test/java/org/kpmp/gene/GeneServiceTest.java b/src/test/java/org/kpmp/gene/GeneServiceTest.java index a160b02..9b7a122 100755 --- a/src/test/java/org/kpmp/gene/GeneServiceTest.java +++ b/src/test/java/org/kpmp/gene/GeneServiceTest.java @@ -1,6 +1,6 @@ package org.kpmp.gene; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.junit.jupiter.api.Assertions.fail; import static org.mockito.ArgumentMatchers.any; import static org.mockito.Mockito.doReturn; @@ -14,9 +14,9 @@ import java.util.List; import org.apache.commons.io.IOUtils; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.MockitoAnnotations; @@ -28,13 +28,13 @@ public class GeneServiceTest { @Mock HttpURLConnection connection; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); geneService = new GeneService(); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); geneService = null; diff --git a/src/test/java/org/kpmp/gene/MyGeneInfoHitTest.java b/src/test/java/org/kpmp/gene/MyGeneInfoHitTest.java index ebe0244..08d1b7f 100755 --- a/src/test/java/org/kpmp/gene/MyGeneInfoHitTest.java +++ b/src/test/java/org/kpmp/gene/MyGeneInfoHitTest.java @@ -1,24 +1,24 @@ package org.kpmp.gene; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class MyGeneInfoHitTest { private MyGeneInfoHit myGeneInfoHit; - @Before + @BeforeEach public void setUp() throws Exception { myGeneInfoHit = new MyGeneInfoHit(); } - @After + @AfterEach public void tearDown() throws Exception { myGeneInfoHit = null; } diff --git a/src/test/java/org/kpmp/gene/MyGeneInfoResultTest.java b/src/test/java/org/kpmp/gene/MyGeneInfoResultTest.java index c9d8649..b692b64 100755 --- a/src/test/java/org/kpmp/gene/MyGeneInfoResultTest.java +++ b/src/test/java/org/kpmp/gene/MyGeneInfoResultTest.java @@ -1,10 +1,10 @@ package org.kpmp.gene; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import java.util.Arrays; import java.util.List; @@ -14,12 +14,12 @@ public class MyGeneInfoResultTest { private MyGeneInfoResult myGeneInfoResult; - @Before + @BeforeEach public void setUp() throws Exception { myGeneInfoResult = new MyGeneInfoResult(); } - @After + @AfterEach public void tearDown() throws Exception { myGeneInfoResult = null; } diff --git a/src/test/java/org/kpmp/geneExpression/ExpressionDataServiceTest.java b/src/test/java/org/kpmp/geneExpression/ExpressionDataServiceTest.java index 2030703..55ee0a0 100755 --- a/src/test/java/org/kpmp/geneExpression/ExpressionDataServiceTest.java +++ b/src/test/java/org/kpmp/geneExpression/ExpressionDataServiceTest.java @@ -1,15 +1,15 @@ package org.kpmp.geneExpression; -import static org.junit.Assert.fail; +import static org.junit.jupiter.api.Assertions.fail; import static org.junit.jupiter.api.Assertions.assertEquals; import static org.mockito.Mockito.mock; import static org.mockito.Mockito.when; import org.json.JSONException; import org.json.JSONObject; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -21,13 +21,13 @@ public class ExpressionDataServiceTest { private SCExpressionDataRepository scRepo; private SNSCExpressionDataService service; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); service = new SNSCExpressionDataService(snRepo, scRepo); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); service = null; diff --git a/src/test/java/org/kpmp/geneExpression/RPAccessionGroupTest.java b/src/test/java/org/kpmp/geneExpression/RPAccessionGroupTest.java index 70015f9..317c87b 100755 --- a/src/test/java/org/kpmp/geneExpression/RPAccessionGroupTest.java +++ b/src/test/java/org/kpmp/geneExpression/RPAccessionGroupTest.java @@ -1,8 +1,8 @@ package org.kpmp.geneExpression; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import static org.junit.jupiter.api.Assertions.assertEquals; @@ -10,12 +10,12 @@ public class RPAccessionGroupTest { private RPAccessionGroup rpAccessionGroup; - @Before + @BeforeEach public void setUp() throws Exception { rpAccessionGroup = new RPAccessionGroup(); } - @After + @AfterEach public void tearDown() throws Exception { rpAccessionGroup = null; } diff --git a/src/test/java/org/kpmp/geneExpression/RPExpressionByTissueTypeTest.java b/src/test/java/org/kpmp/geneExpression/RPExpressionByTissueTypeTest.java index e83b25b..5f8d8a9 100644 --- a/src/test/java/org/kpmp/geneExpression/RPExpressionByTissueTypeTest.java +++ b/src/test/java/org/kpmp/geneExpression/RPExpressionByTissueTypeTest.java @@ -6,20 +6,20 @@ import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class RPExpressionByTissueTypeTest { private RPExpressionByTissueType rpExpression; - @Before + @BeforeEach public void setUp() throws Exception { rpExpression = new RPExpressionByTissueType(); } - @After + @AfterEach public void tearDown() throws Exception { rpExpression = null; } diff --git a/src/test/java/org/kpmp/geneExpression/RPExpressionDataServiceTest.java b/src/test/java/org/kpmp/geneExpression/RPExpressionDataServiceTest.java index dab2141..fbabdc2 100755 --- a/src/test/java/org/kpmp/geneExpression/RPExpressionDataServiceTest.java +++ b/src/test/java/org/kpmp/geneExpression/RPExpressionDataServiceTest.java @@ -2,9 +2,9 @@ import static org.junit.jupiter.api.Assertions.assertEquals; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.TissueTypeEnum; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -22,13 +22,13 @@ public class RPExpressionDataServiceTest { RPExpressionDataService rpExpressionDataService; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); rpExpressionDataService = new RPExpressionDataService(rpExpressionDataRepository); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); rpExpressionDataService = null; diff --git a/src/test/java/org/kpmp/geneExpression/RPExpressionDataTest.java b/src/test/java/org/kpmp/geneExpression/RPExpressionDataTest.java index 062b41f..beaf4e7 100755 --- a/src/test/java/org/kpmp/geneExpression/RPExpressionDataTest.java +++ b/src/test/java/org/kpmp/geneExpression/RPExpressionDataTest.java @@ -1,8 +1,8 @@ package org.kpmp.geneExpression; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import static org.junit.jupiter.api.Assertions.assertEquals; @@ -10,12 +10,12 @@ public class RPExpressionDataTest { private RPExpressionData rpExpressionData; - @Before + @BeforeEach public void setUp() throws Exception { rpExpressionData = new RPExpressionData(); } - @After + @AfterEach public void tearDown() throws Exception { rpExpressionData = null; } diff --git a/src/test/java/org/kpmp/geneExpression/RTExpressionByTissueTypeTest.java b/src/test/java/org/kpmp/geneExpression/RTExpressionByTissueTypeTest.java index e4f7e33..2f4d7c3 100755 --- a/src/test/java/org/kpmp/geneExpression/RTExpressionByTissueTypeTest.java +++ b/src/test/java/org/kpmp/geneExpression/RTExpressionByTissueTypeTest.java @@ -5,20 +5,20 @@ import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class RTExpressionByTissueTypeTest { private RTExpressionByTissueType rtExpressionByTissueType; - @Before + @BeforeEach public void setUp() throws Exception { rtExpressionByTissueType = new RTExpressionByTissueType(); } - @After + @AfterEach public void tearDown() throws Exception { rtExpressionByTissueType = null; } diff --git a/src/test/java/org/kpmp/geneExpression/RTExpressionDataAllSegmentsTest.java b/src/test/java/org/kpmp/geneExpression/RTExpressionDataAllSegmentsTest.java index 94fbcc3..dfc474f 100755 --- a/src/test/java/org/kpmp/geneExpression/RTExpressionDataAllSegmentsTest.java +++ b/src/test/java/org/kpmp/geneExpression/RTExpressionDataAllSegmentsTest.java @@ -1,6 +1,6 @@ package org.kpmp.geneExpression; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.BeforeEach; diff --git a/src/test/java/org/kpmp/geneExpression/RTExpressionDataGTITest.java b/src/test/java/org/kpmp/geneExpression/RTExpressionDataGTITest.java index fb89396..9fa71b4 100755 --- a/src/test/java/org/kpmp/geneExpression/RTExpressionDataGTITest.java +++ b/src/test/java/org/kpmp/geneExpression/RTExpressionDataGTITest.java @@ -2,7 +2,6 @@ import static org.junit.jupiter.api.Assertions.assertEquals; -import org.junit.Assert; import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -84,7 +83,7 @@ void setSegmentName() { @Test void setAdjPVal() { rtExpressionDataGTI.setAdjPVal(123.456); - Assert.assertEquals(123.456, rtExpressionDataGTI.getAdjPVal(), 0.001); + assertEquals(123.456, rtExpressionDataGTI.getAdjPVal(), 0.001); } diff --git a/src/test/java/org/kpmp/geneExpression/RTExpressionDataServiceTest.java b/src/test/java/org/kpmp/geneExpression/RTExpressionDataServiceTest.java index 6384d48..248992b 100755 --- a/src/test/java/org/kpmp/geneExpression/RTExpressionDataServiceTest.java +++ b/src/test/java/org/kpmp/geneExpression/RTExpressionDataServiceTest.java @@ -6,9 +6,9 @@ import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.TissueTypeEnum; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -21,14 +21,14 @@ public class RTExpressionDataServiceTest { private RTExpressionDataGTIRepository rtExpressionDataGTIRepository; private RTExpressionDataService rtExpressionDataService; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); rtExpressionDataService = new RTExpressionDataService(rtExpressionDataAllSegmentsRepository, rtExpressionDataGTIRepository); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); rtExpressionDataService = null; diff --git a/src/test/java/org/kpmp/geneExpression/SCExpressionDataTest.java b/src/test/java/org/kpmp/geneExpression/SCExpressionDataTest.java index 0bdb4c0..c71f2a1 100755 --- a/src/test/java/org/kpmp/geneExpression/SCExpressionDataTest.java +++ b/src/test/java/org/kpmp/geneExpression/SCExpressionDataTest.java @@ -1,22 +1,22 @@ package org.kpmp.geneExpression; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import org.json.JSONObject; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class SCExpressionDataTest { private SCExpressionData data; - @Before + @BeforeEach public void setUp() throws Exception { data = new SCExpressionData(); } - @After + @AfterEach public void tearDown() throws Exception { data = null; } diff --git a/src/test/java/org/kpmp/geneExpression/SNExpressionDataTest.java b/src/test/java/org/kpmp/geneExpression/SNExpressionDataTest.java index 455a115..80afe5e 100755 --- a/src/test/java/org/kpmp/geneExpression/SNExpressionDataTest.java +++ b/src/test/java/org/kpmp/geneExpression/SNExpressionDataTest.java @@ -1,22 +1,22 @@ package org.kpmp.geneExpression; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import org.json.JSONObject; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class SNExpressionDataTest { private SNExpressionData data; - @Before + @BeforeEach public void setUp() throws Exception { data = new SNExpressionData(); } - @After + @AfterEach public void tearDown() throws Exception { data = null; } diff --git a/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionIdTest.java b/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionIdTest.java index 472a2e1..f0f5be7 100755 --- a/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionIdTest.java +++ b/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionIdTest.java @@ -1,21 +1,21 @@ package org.kpmp.geneExpressionSummary; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; public class GeneExpressionIdTest { private GeneExpressionId geneExpressionId; - @Before + @BeforeEach public void setUp() { geneExpressionId = new GeneExpressionId(); } - @After + @AfterEach public void tearDown() { geneExpressionId = null; } diff --git a/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java b/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java index e788e8f..bbf5a28 100755 --- a/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java +++ b/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java @@ -1,6 +1,6 @@ package org.kpmp.geneExpressionSummary; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.verify; import static org.mockito.Mockito.when; @@ -8,9 +8,9 @@ import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.DataTypeEnum; import org.kpmp.dataSummary.DataTypeSummary; import org.kpmp.geneExpression.RPExpressionDataRepository; @@ -48,7 +48,7 @@ public class GeneExpressionSummaryServiceTest { @Mock private RPParticipantRepository rpParticipantRepository; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); geneExpressionService = new GeneExpressionSummaryService( @@ -57,7 +57,7 @@ public void setUp() throws Exception { rtParticipantRepository, rtExpressionDataAllSegmentsRepository, rpExpressionDataRepository, rpParticipantRepository); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); geneExpressionService = null; diff --git a/src/test/java/org/kpmp/geneExpressionSummary/ParticipantIdTest.java b/src/test/java/org/kpmp/geneExpressionSummary/ParticipantIdTest.java index c7c2082..7b55f77 100755 --- a/src/test/java/org/kpmp/geneExpressionSummary/ParticipantIdTest.java +++ b/src/test/java/org/kpmp/geneExpressionSummary/ParticipantIdTest.java @@ -1,21 +1,21 @@ package org.kpmp.geneExpressionSummary; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; public class ParticipantIdTest { private ParticipantId participantId; - @Before + @BeforeEach public void setUp() { participantId = new ParticipantId(); } - @After + @AfterEach public void tearDown() { participantId = null; } diff --git a/src/test/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionSummaryValueTest.java b/src/test/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionSummaryValueTest.java index 40711e2..82d5e95 100755 --- a/src/test/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionSummaryValueTest.java +++ b/src/test/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionSummaryValueTest.java @@ -1,22 +1,22 @@ package org.kpmp.geneExpressionSummary; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.geneExpressionSummary.singleCell.SCRNAGeneExpressionExpressionSummaryValue; public class SCRNAGeneExpressionSummaryValueTest { private SCRNAGeneExpressionExpressionSummaryValue scrnaGeneExpressionValue; - @Before + @BeforeEach public void setUp() throws Exception { scrnaGeneExpressionValue = new SCRNAGeneExpressionExpressionSummaryValue(); } - @After + @AfterEach public void tearDown() throws Exception { scrnaGeneExpressionValue = null; } diff --git a/src/test/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValueTest.java b/src/test/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValueTest.java index 214ee2c..feebfc6 100755 --- a/src/test/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValueTest.java +++ b/src/test/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValueTest.java @@ -1,22 +1,22 @@ package org.kpmp.geneExpressionSummary; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.geneExpressionSummary.singleCell.SCRNAParticipantValue; public class SCRNAParticipantValueTest { SCRNAParticipantValue scrnaParticipantValue; - @Before + @BeforeEach public void setUp() throws Exception { scrnaParticipantValue = new SCRNAParticipantValue(); } - @After + @AfterEach public void tearDown() throws Exception { scrnaParticipantValue = null; } diff --git a/src/test/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionSummaryValueTest.java b/src/test/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionSummaryValueTest.java index 118e05c..2451fa7 100755 --- a/src/test/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionSummaryValueTest.java +++ b/src/test/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionSummaryValueTest.java @@ -1,22 +1,22 @@ package org.kpmp.geneExpressionSummary; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionExpressionSummaryValue; public class SNRNAGeneExpressionSummaryValueTest { SNRNAGeneExpressionExpressionSummaryValue snrnaGeneExpressionValue; - @Before + @BeforeEach public void setUp() throws Exception { snrnaGeneExpressionValue = new SNRNAGeneExpressionExpressionSummaryValue(); } - @After + @AfterEach public void tearDown() throws Exception { snrnaGeneExpressionValue = null; } diff --git a/src/test/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValueTest.java b/src/test/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValueTest.java index 3dbed99..7371cb1 100755 --- a/src/test/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValueTest.java +++ b/src/test/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValueTest.java @@ -1,22 +1,22 @@ package org.kpmp.geneExpressionSummary; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAParticipantValue; public class SNRNAParticipantValueTest { SNRNAParticipantValue snrnaParticipantValue; - @Before + @BeforeEach public void setUp() throws Exception { snrnaParticipantValue = new SNRNAParticipantValue(); } - @After + @AfterEach public void tearDown() throws Exception { snrnaParticipantValue = null; } diff --git a/src/test/java/org/kpmp/participant/ParticipantDataTypeSummaryTest.java b/src/test/java/org/kpmp/participant/ParticipantDataTypeSummaryTest.java index 557cddb..203d007 100755 --- a/src/test/java/org/kpmp/participant/ParticipantDataTypeSummaryTest.java +++ b/src/test/java/org/kpmp/participant/ParticipantDataTypeSummaryTest.java @@ -1,25 +1,25 @@ package org.kpmp.participant; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.mock; import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ParticipantDataTypeSummaryTest { private ParticipantDataTypeSummary summary; - @Before + @BeforeEach public void setUp() throws Exception { summary = new ParticipantDataTypeSummary(); } - @After + @AfterEach public void tearDown() throws Exception { summary = null; } diff --git a/src/test/java/org/kpmp/participant/ParticipantRepoDataTest.java b/src/test/java/org/kpmp/participant/ParticipantRepoDataTest.java index 4cb1c08..d8f885b 100644 --- a/src/test/java/org/kpmp/participant/ParticipantRepoDataTest.java +++ b/src/test/java/org/kpmp/participant/ParticipantRepoDataTest.java @@ -1,21 +1,21 @@ package org.kpmp.participant; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.mock; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ParticipantRepoDataTest { private ParticipantRepoData participantRepoData; - @Before + @BeforeEach public void setUp() throws Exception { participantRepoData = new ParticipantRepoData(); } - @After + @AfterEach public void tearDown() throws Exception { participantRepoData = null; } diff --git a/src/test/java/org/kpmp/participant/ParticipantRepoDataTypeInformationTest.java b/src/test/java/org/kpmp/participant/ParticipantRepoDataTypeInformationTest.java index cc769a8..9e435ba 100644 --- a/src/test/java/org/kpmp/participant/ParticipantRepoDataTypeInformationTest.java +++ b/src/test/java/org/kpmp/participant/ParticipantRepoDataTypeInformationTest.java @@ -1,23 +1,23 @@ package org.kpmp.participant; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.mock; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.dataSummary.AtlasRepositoryLinkInformation; public class ParticipantRepoDataTypeInformationTest { private ParticipantRepoDataTypeInformation info; - @Before + @BeforeEach public void setUp() throws Exception { info = new ParticipantRepoDataTypeInformation("abc", 1, mock(AtlasRepositoryLinkInformation.class)); } - @After + @AfterEach public void tearDown() throws Exception { info = null; } diff --git a/src/test/java/org/kpmp/participant/ParticipantRepoDataTypeSummaryTest.java b/src/test/java/org/kpmp/participant/ParticipantRepoDataTypeSummaryTest.java index 0892198..0bdab78 100644 --- a/src/test/java/org/kpmp/participant/ParticipantRepoDataTypeSummaryTest.java +++ b/src/test/java/org/kpmp/participant/ParticipantRepoDataTypeSummaryTest.java @@ -1,25 +1,25 @@ package org.kpmp.participant; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.mock; import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ParticipantRepoDataTypeSummaryTest { private ParticipantRepoDataTypeSummary summary; - @Before + @BeforeEach public void setUp() throws Exception { summary = new ParticipantRepoDataTypeSummary(); } - @After + @AfterEach public void tearDown() throws Exception { summary = null; } diff --git a/src/test/java/org/kpmp/participant/ParticipantServiceTest.java b/src/test/java/org/kpmp/participant/ParticipantServiceTest.java index f7cb616..52b2e98 100755 --- a/src/test/java/org/kpmp/participant/ParticipantServiceTest.java +++ b/src/test/java/org/kpmp/participant/ParticipantServiceTest.java @@ -1,16 +1,16 @@ package org.kpmp.participant; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.fail; +import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.api.Assertions.fail; import static org.mockito.Mockito.verify; import static org.mockito.Mockito.when; import java.util.Arrays; import java.util.List; import org.kpmp.TissueTypeEnum; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.dataSummary.DataSummaryRepository; import org.kpmp.geneExpressionSummary.regionalProteomics.RPParticipantRepository; import org.kpmp.geneExpressionSummary.regionalTranscriptomics.RTParticipantRepository; @@ -39,14 +39,14 @@ public class ParticipantServiceTest { @Mock private RPParticipantRepository rpParticipantRepository; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); participantService = new ParticipantService(dataSummaryRepo, svTypeRepo, scMetadataRepo, snMetadataRepo, rtParticipantRepo, participantSummaryDatasetRepository, rpParticipantRepository,fileByParticipantRepo); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); participantService = null; diff --git a/src/test/java/org/kpmp/participant/ParticipantTissueTypeSummaryTest.java b/src/test/java/org/kpmp/participant/ParticipantTissueTypeSummaryTest.java index 61d5965..3810fad 100644 --- a/src/test/java/org/kpmp/participant/ParticipantTissueTypeSummaryTest.java +++ b/src/test/java/org/kpmp/participant/ParticipantTissueTypeSummaryTest.java @@ -1,19 +1,19 @@ package org.kpmp.participant; -import static org.junit.Assert.assertEquals; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.*; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ParticipantTissueTypeSummaryTest { private ParticipantTissueTypeSummary tissueSummary; - @Before + @BeforeEach public void setUp() { tissueSummary = new ParticipantTissueTypeSummary(Long.valueOf(4), Long.valueOf(5), Long.valueOf(6), Long.valueOf(7)); } - @After + @AfterEach public void tearDown() { tissueSummary = null; } diff --git a/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java b/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java index dbea114..715d8f4 100755 --- a/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java +++ b/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java @@ -1,21 +1,21 @@ package org.kpmp.participant; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class SingleCellMetadataTest { private SingleCellMetadata scMetadata; - @Before + @BeforeEach public void setUp() throws Exception { scMetadata = new SingleCellMetadata(); } - @After + @AfterEach public void tearDown() throws Exception { scMetadata = null; } diff --git a/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java b/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java index 2c62101..9b3420a 100755 --- a/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java +++ b/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java @@ -1,21 +1,21 @@ package org.kpmp.participant; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class SingleNucleusMetadataTest { private SingleNucleusMetadata snMetadata; - @Before + @BeforeEach public void setUp() throws Exception { snMetadata = new SingleNucleusMetadata(); } - @After + @AfterEach public void tearDown() throws Exception { snMetadata = null; } diff --git a/src/test/java/org/kpmp/participant/SpatialViewerDataTypeTest.java b/src/test/java/org/kpmp/participant/SpatialViewerDataTypeTest.java index d42162d..551190d 100755 --- a/src/test/java/org/kpmp/participant/SpatialViewerDataTypeTest.java +++ b/src/test/java/org/kpmp/participant/SpatialViewerDataTypeTest.java @@ -1,21 +1,21 @@ package org.kpmp.participant; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class SpatialViewerDataTypeTest { private SpatialViewerDataType type; - @Before + @BeforeEach public void setUp() throws Exception { type = new SpatialViewerDataType(); } - @After + @AfterEach public void tearDown() throws Exception { type = null; } diff --git a/src/test/java/org/kpmp/umap/FeatureDataTest.java b/src/test/java/org/kpmp/umap/FeatureDataTest.java index cbae157..3989d41 100755 --- a/src/test/java/org/kpmp/umap/FeatureDataTest.java +++ b/src/test/java/org/kpmp/umap/FeatureDataTest.java @@ -1,25 +1,25 @@ package org.kpmp.umap; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class FeatureDataTest { private FeatureData featureData; private static double DOUBLE_PRECISION = 0.000001d; - @Before + @BeforeEach public void setUp() throws Exception { featureData = new FeatureData(); } - @After + @AfterEach public void tearDown() throws Exception { featureData = null; } diff --git a/src/test/java/org/kpmp/umap/PlotDataTest.java b/src/test/java/org/kpmp/umap/PlotDataTest.java index 559813b..b716e9a 100755 --- a/src/test/java/org/kpmp/umap/PlotDataTest.java +++ b/src/test/java/org/kpmp/umap/PlotDataTest.java @@ -1,13 +1,13 @@ package org.kpmp.umap; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import java.util.ArrayList; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.mockito.Mock; public class PlotDataTest { @@ -18,12 +18,12 @@ public class PlotDataTest { private List referenceData; private PlotData plotData; - @Before + @BeforeEach public void setUp() throws Exception { plotData = new PlotData(referenceData, featureData); } - @After + @AfterEach public void tearDown() throws Exception { plotData = null; } diff --git a/src/test/java/org/kpmp/umap/ReferenceClusterTest.java b/src/test/java/org/kpmp/umap/ReferenceClusterTest.java index 721438d..0b49891 100755 --- a/src/test/java/org/kpmp/umap/ReferenceClusterTest.java +++ b/src/test/java/org/kpmp/umap/ReferenceClusterTest.java @@ -1,25 +1,25 @@ package org.kpmp.umap; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import java.util.Arrays; import java.util.List; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ReferenceClusterTest { private ReferenceCluster cluster; private static double DOUBLE_PRECISION = 0.000001d; - @Before + @BeforeEach public void setUp() throws Exception { cluster = new ReferenceCluster("clusterAbbrev", "color"); } - @After + @AfterEach public void tearDown() throws Exception { cluster = null; } diff --git a/src/test/java/org/kpmp/umap/SCMetadataTest.java b/src/test/java/org/kpmp/umap/SCMetadataTest.java index b4983b8..e58c686 100755 --- a/src/test/java/org/kpmp/umap/SCMetadataTest.java +++ b/src/test/java/org/kpmp/umap/SCMetadataTest.java @@ -2,21 +2,21 @@ import static org.junit.jupiter.api.Assertions.assertEquals; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class SCMetadataTest { private static double DOUBLE_PRECISION = 0.000001d; private SCMetadata point; - @Before + @BeforeEach public void setUp() throws Exception { point = new SCMetadata(); } - @After + @AfterEach public void tearDown() throws Exception { point = null; } diff --git a/src/test/java/org/kpmp/umap/SNMetadataTest.java b/src/test/java/org/kpmp/umap/SNMetadataTest.java index b8b8505..85e49b7 100755 --- a/src/test/java/org/kpmp/umap/SNMetadataTest.java +++ b/src/test/java/org/kpmp/umap/SNMetadataTest.java @@ -2,21 +2,21 @@ import static org.junit.jupiter.api.Assertions.assertEquals; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class SNMetadataTest { private static double DOUBLE_PRECISION = 0.000001d; private SNMetadata point; - @Before + @BeforeEach public void setUp() throws Exception { point = new SNMetadata(); } - @After + @AfterEach public void tearDown() throws Exception { point = null; } diff --git a/src/test/java/org/kpmp/umap/UmapDataServiceTest.java b/src/test/java/org/kpmp/umap/UmapDataServiceTest.java index 920ed34..74c89ad 100755 --- a/src/test/java/org/kpmp/umap/UmapDataServiceTest.java +++ b/src/test/java/org/kpmp/umap/UmapDataServiceTest.java @@ -1,15 +1,15 @@ package org.kpmp.umap; -import static org.junit.Assert.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.when; import java.util.Arrays; import java.util.List; import org.json.JSONObject; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.AfterEach; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.kpmp.geneExpression.SNSCExpressionDataService; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -26,13 +26,13 @@ public class UmapDataServiceTest { private static double DOUBLE_PRECISION = 0.000001d; - @Before + @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); service = new UmapDataService(scMetadataRepository, snMetadataRepository, expressionDataService); } - @After + @AfterEach public void tearDown() throws Exception { MockitoAnnotations.openMocks(this).close(); service = null; From 373f9cd5b70c6a65ce2a18a5e3108d30c69b16f2 Mon Sep 17 00:00:00 2001 From: dert1129 Date: Wed, 24 Jul 2024 13:27:15 -0400 Subject: [PATCH 06/11] update more code to work with java21 --- .github/workflows/build-gradle-project.yml | 4 +- src/main/java/org/kpmp/Query.java | 40 +++++++------- .../autocomplete/AutocompleteService.java | 54 +++++++++++-------- .../org/kpmp/cellType/CellTypeRepository.java | 4 +- .../kpmp/participant/ParticipantService.java | 1 + .../ParticipantSummaryDatasetRepository.java | 3 +- 6 files changed, 59 insertions(+), 47 deletions(-) diff --git a/.github/workflows/build-gradle-project.yml b/.github/workflows/build-gradle-project.yml index 44877ec..d0db8b0 100644 --- a/.github/workflows/build-gradle-project.yml +++ b/.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 diff --git a/src/main/java/org/kpmp/Query.java b/src/main/java/org/kpmp/Query.java index fe496fb..a2f6bf7 100755 --- a/src/main/java/org/kpmp/Query.java +++ b/src/main/java/org/kpmp/Query.java @@ -29,6 +29,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.graphql.data.method.annotation.Argument; import org.springframework.graphql.data.method.annotation.QueryMapping; import org.springframework.stereotype.Component; import org.springframework.stereotype.Controller; @@ -71,7 +72,7 @@ public Query(AutocompleteService autocompleteService, CellTypeService cellTypeSe } @QueryMapping - public List autocomplete(String searchTerm) throws IOException, Exception { + public List autocomplete(@Argument String searchTerm) throws IOException, Exception { return autocompleteService.query(searchTerm); } @@ -81,8 +82,8 @@ public CellTypeHierarchy cellTypeHierarchy() throws IOException { } @QueryMapping - public List geneExpressionSummary(String dataType, String geneSymbol, - String cellType, String tissueType) throws IOException { + public List geneExpressionSummary(@Argument String dataType, @Argument String geneSymbol, + @Argument String cellType, @Argument String tissueType) throws IOException { List results = new ArrayList<>(); if (cellType.isEmpty()) { results = geneExpressionSummaryService.getByDataTypeTissueTypeAndGene(dataType, geneSymbol, tissueType); @@ -94,12 +95,12 @@ public List geneExpressionSummary(String dataTy } @QueryMapping - public List getClusterHieararchies(String cellType) throws IOException { + public List getClusterHieararchies(@Argument String cellType) throws IOException { return clusterHierarchyService.findClustersByCellType(cellType); } @QueryMapping - public PlotData getUmapPlotData(String dataType, String geneSymbol, String tissueType) throws Exception { + public PlotData getUmapPlotData(@Argument String dataType, @Argument String geneSymbol, @Argument String tissueType) throws Exception { try { return umapService.getPlotData(dataType, geneSymbol, tissueType); } catch (Exception e) { @@ -129,7 +130,7 @@ public List getSummaryData() throws Exception { } @QueryMapping - public List dataTypesForConcept(String geneSymbol, String clusterName) throws Exception { + public List dataTypesForConcept(@Argument String geneSymbol, @Argument String clusterName) throws Exception { if (geneSymbol != null && !geneSymbol.isEmpty()) { return geneExpressionSummaryService.findDataTypesByGene(geneSymbol); } else if (clusterName != null && !clusterName.isEmpty()) { @@ -140,7 +141,7 @@ public List dataTypesForConcept(String geneSymbol, String clusterName) t } @QueryMapping - public RTExpressionByTissueType getRTGeneExpressionByTissue(String comparisonType, String geneSymbol) + public RTExpressionByTissueType getRTGeneExpressionByTissue(@Argument String comparisonType, @Argument String geneSymbol) throws Exception { try { return rtExpressionDataService.getByComparisonTypeAndGeneSymbolPerTissue(comparisonType, geneSymbol); @@ -151,7 +152,7 @@ public RTExpressionByTissueType getRTGeneExpressionByTissue(String comparisonTyp } @QueryMapping - public RPExpressionByTissueType getRPGeneExpressionByTissueAndProtein(String geneSymbol, String protein) throws Exception { + public RPExpressionByTissueType getRPGeneExpressionByTissueAndProtein(@Argument String geneSymbol, @Argument String protein) throws Exception { try { return rpExpressionDataService.getByGeneSymbolAndProteinPerTissue(geneSymbol, protein); } catch (Exception e) { @@ -161,7 +162,7 @@ public RPExpressionByTissueType getRPGeneExpressionByTissueAndProtein(String gen } @QueryMapping - public List getRTGeneExpressionByStructure(String structure) throws Exception { + public List getRTGeneExpressionByStructure(@Argument String structure) throws Exception { try { return rtExpressionDataService.getByStructure(structure); } catch (Exception e) { @@ -171,7 +172,7 @@ public List getRTGeneExpressionByStructure(String st } @QueryMapping - public List getRPGeneExpressionByStructure(String structure) throws Exception { + public List getRPGeneExpressionByStructure(@Argument String structure) throws Exception { try { return rpExpressionDataService.getByStructure(structure); } catch (Exception e) { @@ -181,7 +182,7 @@ public List getRPGeneExpressionByStructure(String structure) t } @QueryMapping - public List getRPGeneExpressionByTissue(String geneSymbol) + public List getRPGeneExpressionByTissue(@Argument String geneSymbol) throws Exception { try { return rpExpressionDataService.getByGeneSymbolPerTissue(geneSymbol); @@ -192,32 +193,33 @@ public List getRPGeneExpressionByTissue(String geneSymbol) } @QueryMapping - public ParticipantDataTypeSummary getDataTypeInformationByParticipant(String redcapId) { + public ParticipantDataTypeSummary getDataTypeInformationByParticipant(@Argument String redcapId) { return participantService.getExperimentCounts(redcapId); } @QueryMapping - public ParticipantRepoDataTypeSummary getRepoDataTypeInformationByParticipant(String redcapId) { + public ParticipantRepoDataTypeSummary getRepoDataTypeInformationByParticipant(@Argument String redcapId) { return participantService.getDataTypeCounts(redcapId); } @QueryMapping - public ParticipantSummaryDataset participantSummaryDataset(String redcap_id) throws Exception { + public ParticipantSummaryDataset participantSummaryDataset(@Argument String redcapId) throws Exception { + logger.info(redcapId); 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; } } @QueryMapping - public ParticipantRepoDataTypeInformation getTotalParticipantFilesCount(String redcap_id) throws Exception { + 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; @@ -255,7 +257,7 @@ public List getAtlasMessages() throws Exception { } @QueryMapping - public List getExperimentalStrategyCountsByParticipant(String redcapId) { + public List getExperimentalStrategyCountsByParticipant(@Argument String redcapId) { return participantService.getExperimentalStrategyCountsByParticipant(redcapId); } } \ No newline at end of file diff --git a/src/main/java/org/kpmp/autocomplete/AutocompleteService.java b/src/main/java/org/kpmp/autocomplete/AutocompleteService.java index f0d65e6..75f840c 100755 --- a/src/main/java/org/kpmp/autocomplete/AutocompleteService.java +++ b/src/main/java/org/kpmp/autocomplete/AutocompleteService.java @@ -59,33 +59,41 @@ public List convertCellTypesToAutocompleteResults(List autocompleteResults = new ArrayList<>(); List idsAdded = new ArrayList<>(); - for (CellType cellType : cellTypeListNoDupes) { - autocompleteResults.add(new AutocompleteResult(cellType.getCellType(), null, - Integer.toString(cellType.getCellTypeId()), TYPE_CELL_TYPE, cellType.getSynonymStringList())); - idsAdded.add(cellType.getCellTypeId()); - } + if (cellTypeListNoDupes != null){ + for (CellType cellType : cellTypeListNoDupes) { + autocompleteResults.add(new AutocompleteResult(cellType.getCellType(), null, + Integer.toString(cellType.getCellTypeId()), TYPE_CELL_TYPE, cellType.getSynonymStringList())); + idsAdded.add(cellType.getCellTypeId()); + } + } List subregionHits = new ArrayList<>(); - for (CellType subregion : subregions) { - - if (!(subregionHits.contains(subregion.getStructureSubregion()) - || idsAdded.contains(subregion.getCellTypeId()))) { - autocompleteResults.add(new AutocompleteResult(subregion.getStructureSubregion(), null, - Integer.toString(subregion.getCellTypeId()), TYPE_CELL_TYPE, null)); - subregionHits.add(subregion.getStructureSubregion()); - idsAdded.add(subregion.getCellTypeId()); - } - } + if (subregions != null){ + for (CellType subregion : subregions) { + + if (!(subregionHits.contains(subregion.getStructureSubregion()) + || idsAdded.contains(subregion.getCellTypeId()))) { + autocompleteResults.add(new AutocompleteResult(subregion.getStructureSubregion(), null, + Integer.toString(subregion.getCellTypeId()), TYPE_CELL_TYPE, null)); + subregionHits.add(subregion.getStructureSubregion()); + idsAdded.add(subregion.getCellTypeId()); + } + } + } + List regionHits = new ArrayList<>(); - for (CellType region : regions) { - if (!(regionHits.contains(region.getStructureRegion()) || idsAdded.contains(region.getCellTypeId()))) { - autocompleteResults.add(new AutocompleteResult(region.getStructureRegion(), null, - Integer.toString(region.getCellTypeId()), TYPE_CELL_TYPE, null)); - regionHits.add(region.getStructureRegion()); - idsAdded.add(region.getCellTypeId()); - } - } + if(regions != null){ + for (CellType region : regions) { + if (!(regionHits.contains(region.getStructureRegion()) || idsAdded.contains(region.getCellTypeId()))) { + autocompleteResults.add(new AutocompleteResult(region.getStructureRegion(), null, + Integer.toString(region.getCellTypeId()), TYPE_CELL_TYPE, null)); + regionHits.add(region.getStructureRegion()); + idsAdded.add(region.getCellTypeId()); + } + } + } + autocompleteResults.sort(new Comparator() { @Override diff --git a/src/main/java/org/kpmp/cellType/CellTypeRepository.java b/src/main/java/org/kpmp/cellType/CellTypeRepository.java index 0fc449b..81668fa 100755 --- a/src/main/java/org/kpmp/cellType/CellTypeRepository.java +++ b/src/main/java/org/kpmp/cellType/CellTypeRepository.java @@ -12,9 +12,9 @@ public interface CellTypeRepository extends CrudRepository { @Cacheable("cellTypeContainingOrSynonymContaining") - @Query(value = "SELECT ct.*, cs.* " + " FROM cell_type ct " + @Query(value = "SELECT ct.cell_type_id, ct.structure_region, ct.structure_subregion, ct.cell_type, ct.release_ver, ct.release_sunset, ct.cell_type_order, cs.cell_type_synonym " + " FROM cell_type ct " + " JOIN celltype_synonym cs ON (ct.cell_type_id = cs.cell_type_id AND cs.cell_type_synonym LIKE %:searchTerm%) " - + " UNION " + " SELECT ct.*, cs.* " + " FROM cell_type ct " + + " UNION " + " SELECT ct.cell_type_id, ct.structure_region, ct.structure_subregion, ct.cell_type, ct.release_ver, ct.release_sunset, ct.cell_type_order, cs.cell_type_synonym " + " FROM cell_type ct " + " LEFT JOIN celltype_synonym cs ON ct.cell_type_id = cs.cell_type_id " + " WHERE ct.cell_type LIKE %:searchTerm% ", nativeQuery = true) List findByCellTypeContainingOrSynonymContaining(@Param("searchTerm") String searchTerm); diff --git a/src/main/java/org/kpmp/participant/ParticipantService.java b/src/main/java/org/kpmp/participant/ParticipantService.java index 137dd8b..62a6e31 100755 --- a/src/main/java/org/kpmp/participant/ParticipantService.java +++ b/src/main/java/org/kpmp/participant/ParticipantService.java @@ -59,6 +59,7 @@ public ParticipantService(DataSummaryRepository dataSummaryRepo, SpatialViewerTy } public ParticipantSummaryDataset getParticipantSummaryDataset(String redcapId) { + logger.info(participantSummaryDatasetRepository.findByRedcapId(redcapId).toString()); return participantSummaryDatasetRepository.findByRedcapId(redcapId); } diff --git a/src/main/java/org/kpmp/participant/ParticipantSummaryDatasetRepository.java b/src/main/java/org/kpmp/participant/ParticipantSummaryDatasetRepository.java index 6862bf6..fab74f2 100755 --- a/src/main/java/org/kpmp/participant/ParticipantSummaryDatasetRepository.java +++ b/src/main/java/org/kpmp/participant/ParticipantSummaryDatasetRepository.java @@ -10,7 +10,8 @@ public interface ParticipantSummaryDatasetRepository extends CrudRepository { @Cacheable("participantByRedcap") - ParticipantSummaryDataset findByRedcapId(@Param("redcap_id") String redcapId); + @Query(value = "select * from participant where redcap_id= :redcapId", nativeQuery = true) + ParticipantSummaryDataset findByRedcapId(@Param("redcapId") String redcapId); @Cacheable("partipantByTissueType") @Query(value = "select count(*) from participant where tissue_type= :tissue_type", nativeQuery = true) From 33cc8b241aaecb3bba251453d7522b76a3559940 Mon Sep 17 00:00:00 2001 From: dert1129 Date: Wed, 24 Jul 2024 13:31:49 -0400 Subject: [PATCH 07/11] remove unused code --- src/main/java/org/kpmp/Query.java | 1 - src/main/java/org/kpmp/dataSummary/DataSummaryService.java | 3 --- .../java/org/kpmp/participant/ParticipantRepoDataTest.java | 1 - 3 files changed, 5 deletions(-) diff --git a/src/main/java/org/kpmp/Query.java b/src/main/java/org/kpmp/Query.java index a2f6bf7..e78db95 100755 --- a/src/main/java/org/kpmp/Query.java +++ b/src/main/java/org/kpmp/Query.java @@ -31,7 +31,6 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.graphql.data.method.annotation.Argument; import org.springframework.graphql.data.method.annotation.QueryMapping; -import org.springframework.stereotype.Component; import org.springframework.stereotype.Controller; import com.coxautodev.graphql.tools.GraphQLQueryResolver; diff --git a/src/main/java/org/kpmp/dataSummary/DataSummaryService.java b/src/main/java/org/kpmp/dataSummary/DataSummaryService.java index 3e479be..03add0c 100755 --- a/src/main/java/org/kpmp/dataSummary/DataSummaryService.java +++ b/src/main/java/org/kpmp/dataSummary/DataSummaryService.java @@ -25,9 +25,6 @@ public class DataSummaryService { private String BIOMARKERS; @Value("${experiment.category.biomarker}") private String BIOMARKER; - - private static final String CONTROLLED_ACCESS = "controlled"; - private static final String OPEN_ACCESS = "open"; private DataSummaryRepository dataSummaryRepository; private AtlasRepoSummaryRepository repoSummaryRepository; diff --git a/src/test/java/org/kpmp/participant/ParticipantRepoDataTest.java b/src/test/java/org/kpmp/participant/ParticipantRepoDataTest.java index d8f885b..6d4dcf0 100644 --- a/src/test/java/org/kpmp/participant/ParticipantRepoDataTest.java +++ b/src/test/java/org/kpmp/participant/ParticipantRepoDataTest.java @@ -1,7 +1,6 @@ package org.kpmp.participant; import static org.junit.jupiter.api.Assertions.*; -import static org.mockito.Mockito.mock; import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.BeforeEach; From 7bc37ef434cc37144dac899a7a9b4687c4a9e46d Mon Sep 17 00:00:00 2001 From: dert1129 Date: Wed, 24 Jul 2024 13:34:58 -0400 Subject: [PATCH 08/11] rename Query.java to QueryController.java --- src/main/java/org/kpmp/{Query.java => QueryController.java} | 6 +++--- src/main/java/org/kpmp/gene/GeneService.java | 4 ++-- .../org/kpmp/{QueryTest.java => QueryControllerTest.java} | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-) rename src/main/java/org/kpmp/{Query.java => QueryController.java} (97%) rename src/test/java/org/kpmp/{QueryTest.java => QueryControllerTest.java} (98%) diff --git a/src/main/java/org/kpmp/Query.java b/src/main/java/org/kpmp/QueryController.java similarity index 97% rename from src/main/java/org/kpmp/Query.java rename to src/main/java/org/kpmp/QueryController.java index e78db95..d187176 100755 --- a/src/main/java/org/kpmp/Query.java +++ b/src/main/java/org/kpmp/QueryController.java @@ -36,7 +36,7 @@ import com.coxautodev.graphql.tools.GraphQLQueryResolver; @Controller -public class Query implements GraphQLQueryResolver { +public class QueryController implements GraphQLQueryResolver { private AutocompleteService autocompleteService; private CellTypeService cellTypeService; @@ -49,10 +49,10 @@ public class Query implements GraphQLQueryResolver { private RPExpressionDataService rpExpressionDataService; private ParticipantService participantService; private AtlasMessageService atlasMessageService; - private Logger logger = LoggerFactory.getLogger(Query.class); + 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, diff --git a/src/main/java/org/kpmp/gene/GeneService.java b/src/main/java/org/kpmp/gene/GeneService.java index ed16a67..6f58dfe 100755 --- a/src/main/java/org/kpmp/gene/GeneService.java +++ b/src/main/java/org/kpmp/gene/GeneService.java @@ -11,7 +11,7 @@ import java.util.Collections; import java.util.List; -import org.kpmp.Query; +import org.kpmp.QueryController; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.cache.annotation.Cacheable; @@ -23,7 +23,7 @@ @Service public class GeneService { - private Logger logger = LoggerFactory.getLogger(Query.class); + private Logger logger = LoggerFactory.getLogger(QueryController.class); static final String GET_MY_GENE_INFO_QUERY_SYMBOL = "http://mygene.info/v3/query?q=symbol:%s%%2A&species=9606&fields=symbol,name,taxid,entrezgene,alias&size=100"; static final String GET_MY_GENE_INFO_QUERY_ALIAS = "http://mygene.info/v3/query?q=alias:%s%%2A%%20NOT%%20symbol:%s%%2A&species=9606&fields=symbol,name,taxid,entrezgene,alias&size=100"; diff --git a/src/test/java/org/kpmp/QueryTest.java b/src/test/java/org/kpmp/QueryControllerTest.java similarity index 98% rename from src/test/java/org/kpmp/QueryTest.java rename to src/test/java/org/kpmp/QueryControllerTest.java index 00d39aa..a8df14c 100755 --- a/src/test/java/org/kpmp/QueryTest.java +++ b/src/test/java/org/kpmp/QueryControllerTest.java @@ -50,7 +50,7 @@ import org.mockito.Mock; import org.mockito.MockitoAnnotations; -public class QueryTest { +public class QueryControllerTest { @Mock private CellTypeService cellTypeService; @@ -60,7 +60,7 @@ public class QueryTest { private GeneExpressionSummaryService geneExpressionService; @Mock private DataSummaryService dataSummaryService; - private Query query; + private QueryController query; @Mock private UmapDataService umapDataService; @Mock @@ -80,7 +80,7 @@ public class QueryTest { @BeforeEach public void setUp() throws Exception { MockitoAnnotations.openMocks(this); - query = new Query(autocompleteService, cellTypeService, umapDataService, geneExpressionService, + query = new QueryController(autocompleteService, cellTypeService, umapDataService, geneExpressionService, dataSummaryService, clusterHierarchyService, rtExpressionDataService, rpExpressionDataService, participantService, atlasMessageService); } From 7eaf206b6d9453ba2da1761384cc8c1dfdbe35ef Mon Sep 17 00:00:00 2001 From: dert1129 Date: Wed, 24 Jul 2024 13:41:25 -0400 Subject: [PATCH 09/11] remove debug logging --- src/main/java/org/kpmp/QueryController.java | 1 - src/main/java/org/kpmp/participant/ParticipantService.java | 1 - 2 files changed, 2 deletions(-) diff --git a/src/main/java/org/kpmp/QueryController.java b/src/main/java/org/kpmp/QueryController.java index d187176..37ac1a5 100755 --- a/src/main/java/org/kpmp/QueryController.java +++ b/src/main/java/org/kpmp/QueryController.java @@ -203,7 +203,6 @@ public ParticipantRepoDataTypeSummary getRepoDataTypeInformationByParticipant(@A @QueryMapping public ParticipantSummaryDataset participantSummaryDataset(@Argument String redcapId) throws Exception { - logger.info(redcapId); try { return participantService.getParticipantSummaryDataset(redcapId); } catch (Exception e) { diff --git a/src/main/java/org/kpmp/participant/ParticipantService.java b/src/main/java/org/kpmp/participant/ParticipantService.java index 62a6e31..137dd8b 100755 --- a/src/main/java/org/kpmp/participant/ParticipantService.java +++ b/src/main/java/org/kpmp/participant/ParticipantService.java @@ -59,7 +59,6 @@ public ParticipantService(DataSummaryRepository dataSummaryRepo, SpatialViewerTy } public ParticipantSummaryDataset getParticipantSummaryDataset(String redcapId) { - logger.info(participantSummaryDatasetRepository.findByRedcapId(redcapId).toString()); return participantSummaryDatasetRepository.findByRedcapId(redcapId); } From 99478d5f8f3ab976f45f9dca7f445e986ddd5ee9 Mon Sep 17 00:00:00 2001 From: dert1129 Date: Mon, 29 Jul 2024 10:52:52 -0400 Subject: [PATCH 10/11] fix env for develop branch --- .github/workflows/build-gradle-project.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-gradle-project.yml b/.github/workflows/build-gradle-project.yml index d0db8b0..f60d069 100644 --- a/.github/workflows/build-gradle-project.yml +++ b/.github/workflows/build-gradle-project.yml @@ -41,7 +41,7 @@ jobs: - name: Push to Docker Hub if branch is develop if: steps.branch-names.outputs.current_branch == 'develop' run: | - docker push "kingstonduo/pegasus-data:$IMAGE_TAG" + docker push "kingstonduo/pegasus-data:${{env.IMAGE_TAG}}" - name: Push to Docker Hub if branch is not develop if: steps.branch-names.outputs.current_branch != 'develop' From c2d0bb516ca52da571a84ab6bd1167b44c612453 Mon Sep 17 00:00:00 2001 From: dert1129 Date: Mon, 29 Jul 2024 12:49:01 -0400 Subject: [PATCH 11/11] update pegasus-data version in build.gradle file --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 6606052..009551e 100755 --- a/build.gradle +++ b/build.gradle @@ -13,7 +13,7 @@ plugins { } group = 'kingstonduo' -version = '300' +version = '2.5.0' apply plugin: 'java' apply plugin: 'eclipse'