diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index c0e2b3b..ab982bf 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,4 +1,4 @@ -image: maven:3.3.9-jdk-8 +image: maven:3.9-eclipse-temurin-21-alpine variables: MAVEN_CLI_OPTS: "-s .m2/settings.xml --batch-mode" diff --git a/pom.xml b/pom.xml index 28880a4..6348841 100644 --- a/pom.xml +++ b/pom.xml @@ -4,14 +4,14 @@ uk.ac.ebi.pride.archive pride-mongodb-repo - 1.0.9-SNAPSHOT + 1.0.10-SNAPSHOT jar PRIDE MongoDB repository org.springframework.boot spring-boot-starter-parent - 2.0.1.RELEASE + 3.3.3 + + de.flapdoodle.embed + de.flapdoodle.embed.mongo + 3.5.4 + test @@ -84,6 +97,13 @@ spring-boot-starter-data-mongodb + + + org.mongodb + mongodb-driver-sync + 4.9.1 + + com.fasterxml.jackson jackson-base @@ -122,7 +142,6 @@ org.hibernate.validator hibernate-validator - 6.1.5.Final test @@ -141,7 +160,6 @@ org.projectlombok lombok - 1.18.24 @@ -238,6 +256,35 @@ org.apache.maven.plugins maven-source-plugin + + org.openrewrite.maven + rewrite-maven-plugin + 5.39.0 + + true + + org.openrewrite.java.spring.boot3.UpgradeSpringBoot_3_3 + + + + + org.openrewrite.recipe + rewrite-spring + 5.17.0 + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.8.1 + + true + + -parameters + + + diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideProject.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideProject.java index 53f03be..a359504 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideProject.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideProject.java @@ -1,6 +1,9 @@ package uk.ac.ebi.pride.mongodb.archive.model.projects; -import lombok.*; +import lombok.AccessLevel; +import lombok.AllArgsConstructor; +import lombok.Data; +import lombok.Getter; import lombok.experimental.SuperBuilder; import org.bson.types.ObjectId; import org.springframework.data.annotation.Id; @@ -46,6 +49,7 @@ public MongoPrideProject() { * Project Accession in PRIDE **/ @Indexed(unique = true, name = PrideArchiveField.ACCESSION) + @Field(value = PrideArchiveField.ACCESSION) protected String accession; /** diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideReanalysisProject.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideReanalysisProject.java index 2fa9c37..28873c8 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideReanalysisProject.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideReanalysisProject.java @@ -1,6 +1,7 @@ package uk.ac.ebi.pride.mongodb.archive.model.projects; -import lombok.*; +import lombok.Builder; +import lombok.Data; import org.bson.types.ObjectId; import org.springframework.data.annotation.Id; import org.springframework.data.mongodb.core.index.Indexed; diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/files/PrideFileMongoRepositoryImpl.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/files/PrideFileMongoRepositoryImpl.java index b1e8347..2683e4c 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/files/PrideFileMongoRepositoryImpl.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/files/PrideFileMongoRepositoryImpl.java @@ -10,7 +10,7 @@ import org.springframework.data.mongodb.core.MongoTemplate; import org.springframework.data.mongodb.core.query.Criteria; import org.springframework.data.mongodb.core.query.Query; -import org.springframework.data.repository.support.PageableExecutionUtils; +import org.springframework.data.support.PageableExecutionUtils; import uk.ac.ebi.pride.archive.dataprovider.common.Triple; import uk.ac.ebi.pride.mongodb.archive.model.PrideArchiveField; import uk.ac.ebi.pride.mongodb.archive.model.files.MongoPrideFile; diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/msruns/PrideMSRunMongoRepositoryImpl.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/msruns/PrideMSRunMongoRepositoryImpl.java index 09d5646..072b1ec 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/msruns/PrideMSRunMongoRepositoryImpl.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/msruns/PrideMSRunMongoRepositoryImpl.java @@ -8,7 +8,7 @@ import org.springframework.data.mongodb.core.MongoTemplate; import org.springframework.data.mongodb.core.query.Criteria; import org.springframework.data.mongodb.core.query.Query; -import org.springframework.data.repository.support.PageableExecutionUtils; +import org.springframework.data.support.PageableExecutionUtils; import uk.ac.ebi.pride.archive.dataprovider.common.Triple; import uk.ac.ebi.pride.mongodb.archive.model.PrideArchiveField; import uk.ac.ebi.pride.mongodb.archive.model.msrun.MongoPrideMSRun; diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/ImportedProjectMongoRepositoryCustomImpl.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/ImportedProjectMongoRepositoryCustomImpl.java index e5d5657..66ce401 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/ImportedProjectMongoRepositoryCustomImpl.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/ImportedProjectMongoRepositoryCustomImpl.java @@ -1,13 +1,12 @@ package uk.ac.ebi.pride.mongodb.archive.repo.projects; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.data.domain.Page; import org.springframework.data.domain.Pageable; import org.springframework.data.mongodb.core.MongoTemplate; import org.springframework.data.mongodb.core.query.Criteria; import org.springframework.data.mongodb.core.query.Query; -import org.springframework.data.repository.support.PageableExecutionUtils; +import org.springframework.data.support.PageableExecutionUtils; import uk.ac.ebi.pride.mongodb.archive.model.PrideArchiveField; import uk.ac.ebi.pride.mongodb.archive.model.projects.MongoImportedProject; @@ -21,7 +20,6 @@ public class ImportedProjectMongoRepositoryCustomImpl implements ImportedProject private final MongoTemplate mongoTemplate; - @Autowired public ImportedProjectMongoRepositoryCustomImpl(@Qualifier("archiveMongoTemplate") MongoTemplate mongoTemplate) { this.mongoTemplate = mongoTemplate; } diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideAnalysisMongoRepositoryImpl.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideAnalysisMongoRepositoryImpl.java index 49c6120..f758699 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideAnalysisMongoRepositoryImpl.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideAnalysisMongoRepositoryImpl.java @@ -7,7 +7,7 @@ import org.springframework.data.mongodb.core.MongoOperations; import org.springframework.data.mongodb.core.MongoTemplate; import org.springframework.data.mongodb.core.query.Query; -import org.springframework.data.repository.support.PageableExecutionUtils; +import org.springframework.data.support.PageableExecutionUtils; import uk.ac.ebi.pride.archive.dataprovider.common.Triple; import uk.ac.ebi.pride.mongodb.archive.model.projects.MongoPrideAnalysis; import uk.ac.ebi.pride.mongodb.utils.PrideMongoUtils; diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideProjectMongoRepository.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideProjectMongoRepository.java index 9e0af97..500267a 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideProjectMongoRepository.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideProjectMongoRepository.java @@ -3,6 +3,7 @@ import org.bson.types.ObjectId; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.data.mongodb.repository.Query; +import org.springframework.data.repository.query.Param; import org.springframework.stereotype.Repository; import uk.ac.ebi.pride.mongodb.archive.model.PrideArchiveField; import uk.ac.ebi.pride.mongodb.archive.model.projects.MongoPrideProject; diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideProjectMongoRepositoryCustomImpl.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideProjectMongoRepositoryCustomImpl.java index 28dd647..5630375 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideProjectMongoRepositoryCustomImpl.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/repo/projects/PrideProjectMongoRepositoryCustomImpl.java @@ -1,13 +1,12 @@ package uk.ac.ebi.pride.mongodb.archive.repo.projects; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.data.domain.Page; import org.springframework.data.domain.Pageable; import org.springframework.data.mongodb.core.MongoTemplate; import org.springframework.data.mongodb.core.query.Criteria; import org.springframework.data.mongodb.core.query.Query; -import org.springframework.data.repository.support.PageableExecutionUtils; +import org.springframework.data.support.PageableExecutionUtils; import uk.ac.ebi.pride.mongodb.archive.model.PrideArchiveField; import uk.ac.ebi.pride.mongodb.archive.model.projects.MongoPrideProject; @@ -21,7 +20,6 @@ public class PrideProjectMongoRepositoryCustomImpl implements PrideProjectMongoR private final MongoTemplate mongoTemplate; - @Autowired public PrideProjectMongoRepositoryCustomImpl(@Qualifier("archiveMongoTemplate") MongoTemplate mongoTemplate) { this.mongoTemplate = mongoTemplate; } diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/assays/PrideAssayMongoService.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/assays/PrideAssayMongoService.java index bc131d9..fe69b00 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/assays/PrideAssayMongoService.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/assays/PrideAssayMongoService.java @@ -1,7 +1,6 @@ package uk.ac.ebi.pride.mongodb.archive.service.assays; import lombok.extern.slf4j.Slf4j; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.data.mongodb.core.MongoOperations; import org.springframework.stereotype.Service; import uk.ac.ebi.pride.archive.dataprovider.common.Triple; @@ -30,7 +29,6 @@ public class PrideAssayMongoService { final PrideAssayMongoRepository assayRepository; - @Autowired public PrideAssayMongoService(PrideAssayMongoRepository assayRepository) { this.assayRepository = assayRepository; } diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/files/PrideFileMongoService.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/files/PrideFileMongoService.java index c7b26c7..b99cb2e 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/files/PrideFileMongoService.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/files/PrideFileMongoService.java @@ -43,7 +43,6 @@ public void setMongoOperations(MongoTemplate mongoTemplate) { this.mongoOperations = mongoTemplate; } - @Autowired public PrideFileMongoService(PrideFileMongoRepository fileRepository, PrideMSRunMongoRepository msRunMongoRepository) { this.fileRepository = fileRepository; this.msRunMongoRepository = msRunMongoRepository; diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/msruns/PrideMsRunMongoService.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/msruns/PrideMsRunMongoService.java index 55443eb..567694a 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/msruns/PrideMsRunMongoService.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/msruns/PrideMsRunMongoService.java @@ -41,7 +41,6 @@ public class PrideMsRunMongoService implements IMSRunService { OntologyCacheService ontologyCacheService; - @Autowired public PrideMsRunMongoService(PrideMSRunMongoRepository msRunRepository) { this.msRunRepository = msRunRepository; try { diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/ImportedProjectMongoService.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/ImportedProjectMongoService.java index 4dfb1b1..2985ce3 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/ImportedProjectMongoService.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/ImportedProjectMongoService.java @@ -2,7 +2,6 @@ import lombok.extern.slf4j.Slf4j; import org.bson.types.ObjectId; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.data.domain.Page; import org.springframework.data.domain.Pageable; import org.springframework.stereotype.Service; @@ -28,7 +27,6 @@ public class ImportedProjectMongoService { final ImportedProjectMongoRepository repository; final PrideAssayMongoRepository assayMongoRepository; - @Autowired public ImportedProjectMongoService(ImportedProjectMongoRepository repository, PrideAssayMongoRepository assayMongoRepository) { this.repository = repository; this.assayMongoRepository = assayMongoRepository; @@ -41,7 +39,7 @@ public ImportedProjectMongoService(ImportedProjectMongoRepository repository, Pr * @return MongoImportedProject */ public Optional insert(MongoImportedProject project) { - if (!repository.findByAccession(project.getAccession()).isPresent()) { + if (repository.findByAccession(project.getAccession()).isEmpty()) { project = repository.save(project); log.info("A new project has been saved into MongoDB database with Accession -- " + project.getAccession()); } else @@ -196,7 +194,7 @@ public boolean deleteByAccession(String accession) { public void saveAssays(List mongoAssays) { mongoAssays.forEach(x -> { Optional currentAssay = assayMongoRepository.findPrideAssayByAccession(x.getAccession()); - if (!currentAssay.isPresent()) + if (currentAssay.isEmpty()) assayMongoRepository.save(x); else { updateAssay(currentAssay.get(), x); diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideAnalysisMongoService.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideAnalysisMongoService.java index bc14e91..6283b3c 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideAnalysisMongoService.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideAnalysisMongoService.java @@ -1,7 +1,6 @@ package uk.ac.ebi.pride.mongodb.archive.service.projects; import lombok.extern.slf4j.Slf4j; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import uk.ac.ebi.pride.mongodb.archive.repo.projects.PrideAnalysisMongoRepository; @@ -18,7 +17,6 @@ public class PrideAnalysisMongoService { // @Autowired // private MongoOperations mongo; - @Autowired public PrideAnalysisMongoService(PrideAnalysisMongoRepository repository) { this.repository = repository; } diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideProjectMongoService.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideProjectMongoService.java index ffc2726..fe6af8c 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideProjectMongoService.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideProjectMongoService.java @@ -2,7 +2,6 @@ import lombok.extern.slf4j.Slf4j; import org.bson.types.ObjectId; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.data.domain.Page; import org.springframework.data.domain.Pageable; import org.springframework.stereotype.Service; @@ -33,7 +32,6 @@ public class PrideProjectMongoService { final PrideProjectMongoRepository repository; final PrideAssayMongoRepository assayMongoRepository; - @Autowired public PrideProjectMongoService(PrideProjectMongoRepository repository, PrideAssayMongoRepository assayMongoRepository) { this.repository = repository; this.assayMongoRepository = assayMongoRepository; @@ -46,7 +44,7 @@ public PrideProjectMongoService(PrideProjectMongoRepository repository, PrideAss * @return MongoPrideProject */ public Optional insert(MongoPrideProject project) { - if (!repository.findByAccession(project.getAccession()).isPresent()) { + if (repository.findByAccession(project.getAccession()).isEmpty()) { project = repository.save(project); log.info("A new project has been saved into MongoDB database with Accession -- " + project.getAccession()); } else @@ -201,7 +199,7 @@ public boolean deleteByAccession(String accession) { public void saveAssays(List mongoAssays) { mongoAssays.forEach(x -> { Optional currentAssay = assayMongoRepository.findPrideAssayByAccession(x.getAccession()); - if (!currentAssay.isPresent()) + if (currentAssay.isEmpty()) assayMongoRepository.save(x); else { updateAssay(currentAssay.get(), x); diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideReanalysisMongoService.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideReanalysisMongoService.java index efd626f..43d1a52 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideReanalysisMongoService.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/projects/PrideReanalysisMongoService.java @@ -2,7 +2,6 @@ import lombok.extern.slf4j.Slf4j; import org.bson.types.ObjectId; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import uk.ac.ebi.pride.mongodb.archive.model.projects.MongoPrideReanalysisProject; import uk.ac.ebi.pride.mongodb.archive.repo.projects.PrideReanalysisMongoRepository; @@ -25,7 +24,6 @@ public class PrideReanalysisMongoService { final PrideReanalysisMongoRepository repository; - @Autowired public PrideReanalysisMongoService(PrideReanalysisMongoRepository repository) { this.repository = repository; } diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/samples/PrideSampleMongoService.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/samples/PrideSampleMongoService.java index 091d637..03021c7 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/samples/PrideSampleMongoService.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/samples/PrideSampleMongoService.java @@ -3,7 +3,6 @@ import lombok.extern.slf4j.Slf4j; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import uk.ac.ebi.pride.archive.dataprovider.sample.ISampleMSRunRow; import uk.ac.ebi.pride.archive.dataprovider.sample.SampleProvider; @@ -37,7 +36,6 @@ public class PrideSampleMongoService { /** Logger use to query and filter the data **/ private static final Logger LOGGER = LoggerFactory.getLogger(PrideSampleMongoService.class); - @Autowired public PrideSampleMongoService(PrideMongoExperimentalDesign prideMongoExperimentalDesign) { this.prideMongoExperimentalDesign = prideMongoExperimentalDesign; } diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/stats/PeptidomeStatsMongoService.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/stats/PeptidomeStatsMongoService.java index 0aa6aba..718aaf1 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/stats/PeptidomeStatsMongoService.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/stats/PeptidomeStatsMongoService.java @@ -1,7 +1,6 @@ package uk.ac.ebi.pride.mongodb.archive.service.stats; import lombok.extern.slf4j.Slf4j; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import uk.ac.ebi.pride.mongodb.archive.model.stats.MongoPeptidomeStats; import uk.ac.ebi.pride.mongodb.archive.repo.stats.PeptidomeStatsMongoRepository; @@ -14,7 +13,6 @@ public class PeptidomeStatsMongoService { final PeptidomeStatsMongoRepository repository; - @Autowired public PeptidomeStatsMongoService(PeptidomeStatsMongoRepository repository) { this.repository = repository; } diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/stats/PrideStatsMongoService.java b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/stats/PrideStatsMongoService.java index d9ad736..b26d69f 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/stats/PrideStatsMongoService.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/archive/service/stats/PrideStatsMongoService.java @@ -1,7 +1,6 @@ package uk.ac.ebi.pride.mongodb.archive.service.stats; import lombok.extern.slf4j.Slf4j; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import uk.ac.ebi.pride.archive.dataprovider.common.Tuple; import uk.ac.ebi.pride.mongodb.archive.model.stats.MongoPrideStats; @@ -29,7 +28,6 @@ public class PrideStatsMongoService { final PrideStatsMongoRepository repository; - @Autowired public PrideStatsMongoService(PrideStatsMongoRepository repository) { this.repository = repository; } @@ -73,7 +71,7 @@ public Optional updateSubmissionCountStats(Date date, PrideStat Optional stats = findStatsBydate(date); MongoPrideStats currentStats; - if(!stats.isPresent()){ + if(stats.isEmpty()){ Map>> submissionCounts = new HashMap<>(); submissionCounts.put(prideStatsKeysConstants.statsKey, submissionCount); MongoPrideStats mongoPrideStats = MongoPrideStats.builder() @@ -102,7 +100,7 @@ public Optional updateSubmissionComplexStats(Date date, PrideSt Optional stats = findStatsBydate(date); MongoPrideStats currentStats; - if(!stats.isPresent()){ + if(stats.isEmpty()){ Map submissionCounts = new HashMap<>(); submissionCounts.put(prideStatsKeysConstants.statsKey, submissionCount); MongoPrideStats mongoPrideStats = MongoPrideStats.builder() diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/configs/AbstractPrideMongoConfiguration.java b/src/main/java/uk/ac/ebi/pride/mongodb/configs/AbstractPrideMongoConfiguration.java index b942e8d..32f8740 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/configs/AbstractPrideMongoConfiguration.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/configs/AbstractPrideMongoConfiguration.java @@ -1,37 +1,44 @@ package uk.ac.ebi.pride.mongodb.configs; import com.mongodb.*; -import org.springframework.data.mongodb.MongoDbFactory; -import org.springframework.data.mongodb.config.AbstractMongoConfiguration; -import org.springframework.data.mongodb.core.SimpleMongoDbFactory; +import com.mongodb.client.MongoClient; +import com.mongodb.client.MongoClients; +import org.springframework.context.annotation.Bean; +import org.springframework.data.mongodb.MongoDatabaseFactory; +import org.springframework.data.mongodb.core.MongoTemplate; +import org.springframework.data.mongodb.core.SimpleMongoClientDatabaseFactory; + /** * This Abstract class is used to Configure all the connections to Spring. * @author ypriverol */ -public abstract class AbstractPrideMongoConfiguration extends AbstractMongoConfiguration { +public abstract class AbstractPrideMongoConfiguration { - @Override - public MongoClient mongoClient() { - MongoClient mongoClient = configureMachineFromURI(getMongoURI()); - return mongoClient; + @Bean + public MongoTemplate mongoTemplate() { + return new MongoTemplate(mongoDbFactory()); } - @Override - public MongoDbFactory mongoDbFactory(){ - return new SimpleMongoDbFactory(mongoClient(), getDatabaseName()); + @Bean + public MongoDatabaseFactory mongoDbFactory(){ + return new SimpleMongoClientDatabaseFactory(mongoClient(), getDatabaseName()); } + @Bean + public MongoClient mongoClient() { + return configureMachineFromURI(getMongoURI()); + } - /** - * This method create a connection from an URI - * @param uri URI in String format - * @return MongoClient - */ - public MongoClient configureMachineFromURI(String uri){ - MongoClientURI clientURI = new MongoClientURI(uri); - return new MongoClient(clientURI); + public MongoClient configureMachineFromURI(String uri) { + ConnectionString connectionString = new ConnectionString(uri); + MongoClientSettings settings = MongoClientSettings.builder() + .applyConnectionString(connectionString) + .build(); + return MongoClients.create(settings); } public abstract String getMongoURI(); + + public abstract String getDatabaseName(); } diff --git a/src/main/java/uk/ac/ebi/pride/mongodb/configs/ArchiveMongoConfig.java b/src/main/java/uk/ac/ebi/pride/mongodb/configs/ArchiveMongoConfig.java index c3f0e0c..c8da4dc 100644 --- a/src/main/java/uk/ac/ebi/pride/mongodb/configs/ArchiveMongoConfig.java +++ b/src/main/java/uk/ac/ebi/pride/mongodb/configs/ArchiveMongoConfig.java @@ -1,9 +1,11 @@ package uk.ac.ebi.pride.mongodb.configs; +import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.ComponentScan; import org.springframework.context.annotation.Configuration; +import org.springframework.context.annotation.Primary; import org.springframework.data.mongodb.core.MongoTemplate; import org.springframework.data.mongodb.repository.config.EnableMongoRepositories; import org.springframework.transaction.annotation.EnableTransactionManagement; @@ -21,41 +23,18 @@ public class ArchiveMongoConfig extends AbstractPrideMongoConfiguration { @Value("${mongodb.project.database}") private String mongoProjectDatabase; - @Value("${mongodb.project.app.user}") - private String user; - - @Value("${mongodb.project.app.password}") - private String password; - - @Value("${mongodb.project.app.authenticationDatabase}") - private String authenticationDatabse; - - @Value("${mongodb.projects.replicate.hosts}") - private String mongoHosts; - - @Value("${mongodb.projects.replicate.ports}") - private String mongoPorts; - - @Value("${mongodb.project.app.machine.port}") - private String port; - - @Value("${mongo.single.machine}") - private String singleMachine; - - @Value("${mongodb.projects.single.machine.host}") - private String mongoHost; - @Value("${mongodb.projects.machine.uri}") private String mongoURI; - @Override - @Bean(name = "archiveMongoTemplate") + @Primary + @Bean + @Qualifier("archiveMongoTemplate") public MongoTemplate mongoTemplate() { - return new MongoTemplate(super.mongoDbFactory()); + return super.mongoTemplate(); } @Override - protected String getDatabaseName() { + public String getDatabaseName() { return mongoProjectDatabase; } diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/ArchiveOracleConfig.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/ArchiveOracleConfig.java index 6dfffb7..b9ab980 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/ArchiveOracleConfig.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/ArchiveOracleConfig.java @@ -5,6 +5,7 @@ import org.springframework.boot.context.properties.ConfigurationProperties; import org.springframework.boot.jdbc.DataSourceBuilder; import org.springframework.boot.orm.jpa.EntityManagerFactoryBuilder; +import org.springframework.boot.sql.init.dependency.DependsOnDatabaseInitialization; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.ComponentScan; import org.springframework.context.annotation.Configuration; @@ -14,7 +15,7 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean; import org.springframework.transaction.annotation.EnableTransactionManagement; -import javax.persistence.EntityManagerFactory; +import jakarta.persistence.EntityManagerFactory; import javax.sql.DataSource; /** @@ -43,6 +44,7 @@ public LocalContainerEntityManagerFactoryBean entityManagerFactory(EntityManager } @Bean(name = "oracleTransactionManager") + @DependsOnDatabaseInitialization public JpaTransactionManager jpaTransactionManager( @Qualifier("oracleEntityManagerFactory") EntityManagerFactory entityManagerFactory) { return new JpaTransactionManager(entityManagerFactory); diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideMongoLocalhostConfig.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideMongoLocalhostConfig.java index 94a1166..d72f9bb 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideMongoLocalhostConfig.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideMongoLocalhostConfig.java @@ -1,11 +1,11 @@ package uk.ac.ebi.pride.mongodb.archive.config; -import com.mongodb.MongoClient; +import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.ComponentScan; import org.springframework.context.annotation.Configuration; -import org.springframework.data.mongodb.config.AbstractMongoConfiguration; -import org.springframework.data.mongodb.core.mapping.MongoMappingContext; +import org.springframework.data.mongodb.core.MongoTemplate; import org.springframework.data.mongodb.repository.config.EnableMongoRepositories; +import uk.ac.ebi.pride.mongodb.configs.AbstractPrideMongoConfiguration; /** * This code is licensed under the Apache License, Version 2.0 (the @@ -22,21 +22,22 @@ @ComponentScan(basePackages = {"uk.ac.ebi.pride.mongodb.archive.service", "uk.ac.ebi.pride.utilities.ols.web.service.cache"}) @EnableMongoRepositories(basePackages = {"uk.ac.ebi.pride.mongodb.archive.repo"}) @Configuration -public class PrideMongoLocalhostConfig extends AbstractMongoConfiguration { +public class PrideMongoLocalhostConfig extends AbstractPrideMongoConfiguration { + @Override - public MongoMappingContext mongoMappingContext() - throws ClassNotFoundException { - return super.mongoMappingContext(); + @Bean(name = "archiveMongoTestTemplate") + public MongoTemplate mongoTemplate() { + return super.mongoTemplate(); } @Override - protected String getDatabaseName() { - return "prideDB"; + public String getMongoURI() { + return "localhost" + ":" + "27017"; } @Override - public MongoClient mongoClient() { - return new MongoClient("localhost" + ":" + "27017"); + public String getDatabaseName() { + return "prideDB"; } } diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideProjectFongoTestConfig.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideProjectFongoTestConfig.java index d4d9dda..6ec6ae0 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideProjectFongoTestConfig.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideProjectFongoTestConfig.java @@ -1,35 +1,73 @@ package uk.ac.ebi.pride.mongodb.archive.config; +// +//import com.github.fakemongo.Fongo; +//import com.mongodb.MongoClient; +//import org.springframework.context.annotation.Bean; +//import org.springframework.context.annotation.ComponentScan; +//import org.springframework.context.annotation.Configuration; +//import org.springframework.data.mongodb.config.AbstractMongoConfiguration; +//import org.springframework.data.mongodb.repository.config.EnableMongoRepositories; +// +///** +// * Test Configuration for Mongo PRIDE Projects using the fongo {@link Fongo} library. +// * +// * @author ypriverol +// */ +// +//@ComponentScan(basePackages = "uk.ac.ebi.pride.mongodb.archive.service") +//@EnableMongoRepositories(basePackages = {"uk.ac.ebi.pride.mongodb.archive.repo"}) +//@Configuration +//public class PrideProjectFongoTestConfig extends AbstractMongoConfiguration{ +// +// @Override +// protected String getDatabaseName() { +// return "mongo-unit-test"; +// } +// +// @Bean +// @Override +// public MongoClient mongoClient() { +// return new Fongo("mongo-test").getMongo(); +// } +//} +// +// +// -import com.github.fakemongo.Fongo; -import com.mongodb.MongoClient; +import com.mongodb.client.MongoClients; +import com.mongodb.client.MongoClient; +import de.flapdoodle.embed.mongo.distribution.Version; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.ComponentScan; import org.springframework.context.annotation.Configuration; -import org.springframework.data.mongodb.config.AbstractMongoConfiguration; +import org.springframework.data.mongodb.core.MongoTemplate; +import org.springframework.data.mongodb.core.SimpleMongoClientDatabaseFactory; +import de.flapdoodle.embed.mongo.MongodExecutable; +import de.flapdoodle.embed.mongo.MongodStarter; +import de.flapdoodle.embed.mongo.config.MongodConfig; +import de.flapdoodle.embed.mongo.config.Net; +import de.flapdoodle.embed.process.runtime.Network; import org.springframework.data.mongodb.repository.config.EnableMongoRepositories; -/** - * Test Configuration for Mongo PRIDE Projects using the fongo {@link Fongo} library. - * - * @author ypriverol - */ - @ComponentScan(basePackages = "uk.ac.ebi.pride.mongodb.archive.service") @EnableMongoRepositories(basePackages = {"uk.ac.ebi.pride.mongodb.archive.repo"}) @Configuration -public class PrideProjectFongoTestConfig extends AbstractMongoConfiguration{ +public class PrideProjectFongoTestConfig { - @Override - protected String getDatabaseName() { - return "mongo-unit-test"; - } + private MongodExecutable mongodExecutable; @Bean - @Override - public MongoClient mongoClient() { - return new Fongo("mongo-test").getMongo(); - } -} - + public MongoTemplate mongoTemplate() throws Exception { + MongodStarter starter = MongodStarter.getDefaultInstance(); + MongodConfig mongodConfig = MongodConfig.builder() + .version(Version.Main.PRODUCTION) + .net(new Net(27017, Network.localhostIsIPv6())) + .build(); + mongodExecutable = starter.prepare(mongodConfig); + mongodExecutable.start(); + MongoClient mongoClient = MongoClients.create("mongodb://localhost:27017"); + return new MongoTemplate(new SimpleMongoClientDatabaseFactory(mongoClient, "test")); + } +} diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideProjectsHttpTestConfig.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideProjectsHttpTestConfig.java index 9e9b99f..8c9bd9a 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideProjectsHttpTestConfig.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/config/PrideProjectsHttpTestConfig.java @@ -17,78 +17,14 @@ public class PrideProjectsHttpTestConfig extends AbstractPrideMongoConfiguration @Value("${mongodb.project.database}") private String mongoProjectDatabase; - @Value("${mongodb.project.app.user}") - private String user; - - @Value("${mongodb.project.app.password}") - private String password; - - @Value("${mongodb.project.app.authenticationDatabase}") - private String authenticationDatabse; - - @Value("${mongodb.projects.replicate.hosts}") - private String mongoHosts; - - @Value("${mongodb.projects.replicate.ports}") - private String mongoPorts; - - @Value("${mongodb.project.app.machine.port}") - private String port; - - @Value("${mongo.single.machine}") - private String singleMachine; - - @Value("${mongodb.projects.single.machine.host}") - private String mongoHost; - @Value("${mongodb.projects.machine.uri}") private String mongoURI; @Override - protected String getDatabaseName() { + public String getDatabaseName() { return mongoProjectDatabase; } -// @Override -// public String getUser() { -// return user; -// } -// -// @Override -// public String getPassword() { -// return password; -// } -// -// @Override -// public String getAuthenticationDatabse() { -// return authenticationDatabse; -// } -// -// @Override -// public String getMongoHosts() { -// return mongoHosts; -// } -// -// @Override -// public String getMongoPorts() { -// return mongoPorts; -// } -// -// @Override -// public String getPort() { -// return port; -// } -// -// @Override -// public String getSingleMachine() { -// return singleMachine; -// } -// -// @Override -// public String getMongoHost() { -// return mongoHost; -// } - @Override public String getMongoURI() { return mongoURI; diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/PrideFieldEnumTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/PrideFieldEnumTest.java index c943efd..887bd94 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/PrideFieldEnumTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/PrideFieldEnumTest.java @@ -1,7 +1,7 @@ package uk.ac.ebi.pride.mongodb.archive.model; -import org.junit.Assert; -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; /** * This code is licensed under the Apache License, Version 2.0 (the @@ -22,6 +22,6 @@ public void prideFieldEnumTest(){ for(PrideFieldEnum prideFieldEnum: PrideFieldEnum.values()) System.out.println(prideFieldEnum.toString()); - Assert.assertTrue(PrideFieldEnum.values().length > 0); + Assertions.assertTrue(PrideFieldEnum.values().length > 0); } } \ No newline at end of file diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/files/MongoPrideFileTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/files/MongoPrideFileTest.java index 751d41c..58a21c0 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/files/MongoPrideFileTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/files/MongoPrideFileTest.java @@ -1,7 +1,7 @@ package uk.ac.ebi.pride.mongodb.archive.model.files; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import uk.ac.ebi.pride.archive.dataprovider.param.CvParamProvider; import uk.ac.ebi.pride.archive.dataprovider.param.CvParam; import uk.ac.ebi.pride.archive.dataprovider.utils.ProjectFileCategoryConstants; @@ -24,7 +24,7 @@ public class MongoPrideFileTest { MongoPrideFile file; - @Before + @BeforeEach public void setUp() { CvParamProvider cvCategory = ProjectFileCategoryConstants.RAW.getCv(); diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideAnalysisTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideAnalysisTest.java index 166f64a..8dafe33 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideAnalysisTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideAnalysisTest.java @@ -1,8 +1,8 @@ package uk.ac.ebi.pride.mongodb.archive.model.projects; -import org.junit.Assert; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; /** * This code is licensed under the Apache License, Version 2.0 (the @@ -19,7 +19,7 @@ public class MongoPrideAnalysisTest { MongoPrideAnalysis project; - @Before + @BeforeEach public void setUp() { project = MongoPrideAnalysis.builder().accession("RPX000001").build(); @@ -28,6 +28,6 @@ public void setUp() { @Test public void mongoAnalysisTest(){ System.out.println(project.toString()); - Assert.assertTrue(project.accession.equalsIgnoreCase("RPX000001")); + Assertions.assertTrue(project.accession.equalsIgnoreCase("RPX000001")); } } \ No newline at end of file diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideProjectTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideProjectTest.java index 3a7b3a7..59dd145 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideProjectTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/projects/MongoPrideProjectTest.java @@ -1,7 +1,7 @@ package uk.ac.ebi.pride.mongodb.archive.model.projects; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import java.util.Collection; import java.util.Collections; @@ -21,7 +21,7 @@ public class MongoPrideProjectTest { MongoPrideProject project; - @Before + @BeforeEach public void setUp() { Collection tags = Collections.singleton("Metaproteomics"); diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/reference/MongoReferenceTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/reference/MongoReferenceTest.java index 4cee85e..1fbb71d 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/reference/MongoReferenceTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/model/reference/MongoReferenceTest.java @@ -1,8 +1,8 @@ package uk.ac.ebi.pride.mongodb.archive.model.reference; -import org.junit.Assert; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import uk.ac.ebi.pride.archive.dataprovider.reference.Reference; /** @@ -20,7 +20,7 @@ public class MongoReferenceTest { Reference ref; - @Before + @BeforeEach public void setUp() { ref = new Reference("Uszkoreit, Julian, et al. \"PIA: An intuitive protein inference engine with a web-based user interface.\" Journal of proteome research 14.7 (2015): 2988-2997.",25938255,"10.1021/acs.jproteome.5b00121"); @@ -29,7 +29,7 @@ public void setUp() { @Test public void mongReferenceTest(){ System.out.println(ref.toString()); - Assert.assertEquals(25938255, ref.getPubmedId()); + Assertions.assertEquals(25938255, ref.getPubmedId()); } @Test diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/fongo/projects/PrideFongoProjectServiceTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/fongo/projects/PrideFongoProjectServiceTest.java index aef51e7..f310220 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/fongo/projects/PrideFongoProjectServiceTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/fongo/projects/PrideFongoProjectServiceTest.java @@ -1,12 +1,10 @@ package uk.ac.ebi.pride.mongodb.archive.service.fongo.projects; -import org.junit.Assert; -import org.junit.Before; -import org.junit.Test; -import org.junit.runner.RunWith; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.context.SpringBootTest; -import org.springframework.test.context.junit4.SpringRunner; import uk.ac.ebi.pride.archive.dataprovider.common.Triple; import uk.ac.ebi.pride.archive.dataprovider.common.Tuple; import uk.ac.ebi.pride.archive.dataprovider.param.CvParamProvider; @@ -37,7 +35,6 @@ */ -@RunWith(SpringRunner.class) @SpringBootTest(classes = {PrideProjectFongoTestConfig.class}) public class PrideFongoProjectServiceTest { @@ -50,7 +47,7 @@ public class PrideFongoProjectServiceTest { @Autowired PrideMsRunMongoService prideMsRunMongoService; - @Before + @BeforeEach public void setUp(){ } @@ -79,7 +76,7 @@ private Submission readSubmission() throws SubmissionFileException, URISyntaxExc @Test public void importPrideProject() throws SubmissionFileException, URISyntaxException { Optional project = prideProjectService.insert(TestUtils.parseProject(readSubmission())); - Assert.assertTrue(project.get() + Assertions.assertTrue(project.get() .getAccession().equalsIgnoreCase("PXD000003")); } @@ -109,7 +106,7 @@ public void importPrideProjectWithFiles() throws SubmissionFileException, URISyn }).collect(Collectors.toList()); List> filesInserted= prideFileMongoService.insertAllFilesAndMsRuns(mongoFiles,null); - Assert.assertEquals(mongoFiles.size(), dataFiles.size()); + Assertions.assertEquals(mongoFiles.size(), dataFiles.size()); List> fileRelations = new ArrayList<>(); for(DataFile dataFile: dataFiles){ @@ -123,7 +120,7 @@ public void importPrideProjectWithFiles() throws SubmissionFileException, URISyn } project = prideProjectService.updateFileRelations(project.get().getAccession(),fileRelations); - Assert.assertEquals(600, project.get().getSubmittedFileRelations().size()); + Assertions.assertEquals(600, project.get().getSubmittedFileRelations().size()); @@ -148,7 +145,7 @@ public void updateTypeOfRawMSRun() throws SubmissionFileException, URISyntaxExce }).collect(Collectors.toList()); List> filesInserted= prideFileMongoService.insertAllFilesAndMsRuns(mongoFiles,null); - Assert.assertEquals(mongoFiles.size(), dataFiles.size()); + Assertions.assertEquals(mongoFiles.size(), dataFiles.size()); for(MongoPrideFile prideFile: prideFileMongoService.findFilesByProjectAccession(project.get().getAccession())){ if(prideFile.getFileCategory().getAccession().equalsIgnoreCase(ProjectFileCategoryConstants.RAW.getCv().getAccession())){ @@ -158,7 +155,7 @@ public void updateTypeOfRawMSRun() throws SubmissionFileException, URISyntaxExce } List msRuns = prideMsRunMongoService.getMSRunsByProject(project.get().getAccession()); - Assert.assertEquals(150, msRuns.size()); + Assertions.assertEquals(150, msRuns.size()); diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/fongo/stats/PrideStatsMongoServiceTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/fongo/stats/PrideStatsMongoServiceTest.java index b3655e4..8bb0713 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/fongo/stats/PrideStatsMongoServiceTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/fongo/stats/PrideStatsMongoServiceTest.java @@ -1,11 +1,9 @@ package uk.ac.ebi.pride.mongodb.archive.service.fongo.stats; -import org.junit.Assert; -import org.junit.Test; -import org.junit.runner.RunWith; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.context.SpringBootTest; -import org.springframework.test.context.junit4.SpringRunner; import uk.ac.ebi.pride.archive.dataprovider.common.Tuple; import uk.ac.ebi.pride.mongodb.archive.config.PrideProjectFongoTestConfig; import uk.ac.ebi.pride.mongodb.archive.model.stats.MongoPrideStats; @@ -27,7 +25,6 @@ */ -@RunWith(SpringRunner.class) @SpringBootTest(classes = {PrideProjectFongoTestConfig.class}) public class PrideStatsMongoServiceTest { @@ -66,7 +63,7 @@ public void findStatsBydate() { insertDataset(); Optional findDatasets = service.findStatsBydate(date); findDatasets.ifPresent(mongoPrideStats -> System.out.println(mongoPrideStats.getEstimationDate())); - Assert.assertTrue(findDatasets.isPresent()); + Assertions.assertTrue(findDatasets.isPresent()); } @@ -77,7 +74,7 @@ public void updateSubmissionCountStats() { service.updateSubmissionCountStats(date, PrideStatsKeysConstants.SUBMISSIONS_PER_YEAR, monthlySubmissions); Optional findDatasets = service.findStatsBydate(date); findDatasets.ifPresent(mongoPrideStats -> System.out.println(mongoPrideStats.getSubmissionsCount().size())); - Assert.assertEquals(5, findDatasets.get().getSubmissionsCount().get(PrideStatsKeysConstants.SUBMISSIONS_PER_YEAR.getStatsKey()).size()); + Assertions.assertEquals(5, findDatasets.get().getSubmissionsCount().get(PrideStatsKeysConstants.SUBMISSIONS_PER_YEAR.getStatsKey()).size()); } @Test @@ -92,7 +89,7 @@ public void findLastGeneratedStats() { if(findDatasets != null) System.out.println(findDatasets.getEstimationDate()); assert findDatasets != null; - Assert.assertEquals(4, Objects.requireNonNull(findDatasets).getSubmissionsCount().get(PrideStatsKeysConstants.SUBMISSIONS_PER_YEAR.getStatsKey()).size()); + Assertions.assertEquals(4, Objects.requireNonNull(findDatasets).getSubmissionsCount().get(PrideStatsKeysConstants.SUBMISSIONS_PER_YEAR.getStatsKey()).size()); } } \ No newline at end of file diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/integration/projects/PrideFileMongoServiceTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/integration/projects/PrideFileMongoServiceTest.java index 1d7a3a1..67db7eb 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/integration/projects/PrideFileMongoServiceTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/integration/projects/PrideFileMongoServiceTest.java @@ -1,15 +1,13 @@ package uk.ac.ebi.pride.mongodb.archive.service.integration.projects; -import org.junit.Assert; -import org.junit.Ignore; -import org.junit.Test; -import org.junit.runner.RunWith; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.context.SpringBootTest; import org.springframework.data.domain.Page; import org.springframework.data.domain.PageRequest; import org.springframework.test.context.TestPropertySource; -import org.springframework.test.context.junit4.SpringRunner; import uk.ac.ebi.pride.archive.dataprovider.param.CvParam; import uk.ac.ebi.pride.archive.dataprovider.utils.MSFileTypeConstants; import uk.ac.ebi.pride.archive.repo.repos.file.ProjectFile; @@ -35,7 +33,6 @@ * * @author ypriverol */ -@RunWith(SpringRunner.class) @SpringBootTest(classes = {PrideProjectFongoTestConfig.class, ArchiveOracleConfig.class}) @TestPropertySource(locations = "classpath:application-test.properties") public class PrideFileMongoServiceTest { @@ -49,7 +46,7 @@ public class PrideFileMongoServiceTest { @Autowired ProjectRepository oracleProjectRepository; - @Ignore + @Disabled @Test public void save() { MongoPrideFile file = MongoPrideFile @@ -59,7 +56,7 @@ public void save() { } @Test - @Ignore + @Disabled public void searchFilesTest(){ insertFilesSave(); String filterRaw = "fileCategory.value==RESULT"; @@ -128,7 +125,7 @@ private void insertFilesSave(){ } ); - Assert.assertEquals(400, prideFileMongoService.count()); + Assertions.assertEquals(400, prideFileMongoService.count()); } @@ -165,7 +162,7 @@ private void insertFilesInBatchSave(){ prideFileMongoService.insertAllFilesAndMsRuns(mongoPrideFiles,null); }); - Assert.assertEquals(1200, prideFileMongoService.count()); + Assertions.assertEquals(1200, prideFileMongoService.count()); } } \ No newline at end of file diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/localhost/projects/PrideLocalhostProjectServiceTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/localhost/projects/PrideLocalhostProjectServiceTest.java index 578c0bc..ad4dea7 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/localhost/projects/PrideLocalhostProjectServiceTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/localhost/projects/PrideLocalhostProjectServiceTest.java @@ -1,13 +1,11 @@ package uk.ac.ebi.pride.mongodb.archive.service.localhost.projects; import com.fasterxml.jackson.databind.ObjectMapper; -import org.junit.Assert; -import org.junit.Before; -import org.junit.Test; -import org.junit.runner.RunWith; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.context.SpringBootTest; -import org.springframework.test.context.junit4.SpringRunner; import uk.ac.ebi.pride.archive.dataprovider.common.Triple; import uk.ac.ebi.pride.archive.dataprovider.common.Tuple; import uk.ac.ebi.pride.archive.dataprovider.param.CvParam; @@ -40,7 +38,6 @@ */ -@RunWith(SpringRunner.class) @SpringBootTest(classes = {PrideMongoLocalhostConfig.class, ArchiveOracleConfig.class}) public class PrideLocalhostProjectServiceTest { @@ -54,7 +51,7 @@ public class PrideLocalhostProjectServiceTest { PrideMsRunMongoService prideMsRunMongoService; - @Before + @BeforeEach public void setup(){ // prideProjectService.deleteAll(); // prideFileMongoService.deleteAll(); @@ -94,7 +91,7 @@ private MSRunJson readMSrunMetadata() throws URISyntaxException, IOException { @Test public void importPrideProject() throws SubmissionFileException, URISyntaxException { Optional project = prideProjectService.insert(TestUtils.parseProject(readSubmission())); - Assert.assertTrue(project.get() + Assertions.assertTrue(project.get() .getAccession().equalsIgnoreCase("PXD000003")); } @@ -125,7 +122,7 @@ public void importPrideProjectWithFiles() throws SubmissionFileException, URISyn }).collect(Collectors.toList()); List> filesInserted= prideFileMongoService.insertAllFilesAndMsRuns(mongoFiles,null); - Assert.assertEquals(mongoFiles.size(), dataFiles.size()); + Assertions.assertEquals(mongoFiles.size(), dataFiles.size()); List> fileRelations = new ArrayList<>(); for(DataFile dataFile: dataFiles){ @@ -139,7 +136,7 @@ public void importPrideProjectWithFiles() throws SubmissionFileException, URISyn } project = prideProjectService.updateFileRelations(project.get().getAccession(),fileRelations); - Assert.assertEquals(600, project.get().getSubmittedFileRelations().size()); + Assertions.assertEquals(600, project.get().getSubmittedFileRelations().size()); @@ -164,7 +161,7 @@ public void updateTypeOfRawMSRun() throws SubmissionFileException, URISyntaxExce }).collect(Collectors.toList()); List> filesInserted= prideFileMongoService.insertAllFilesAndMsRuns(mongoFiles,null); - Assert.assertEquals(mongoFiles.size(), dataFiles.size()); + Assertions.assertEquals(mongoFiles.size(), dataFiles.size()); MSRunJson msRunJson = readMSrunMetadata(); @@ -190,7 +187,7 @@ public void updateTypeOfRawMSRun() throws SubmissionFileException, URISyntaxExce } List msRuns = prideMsRunMongoService.getMSRunsByProject(project.get().getAccession()); - Assert.assertEquals(150, msRuns.size()); + Assertions.assertEquals(150, msRuns.size()); } /** diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/mockito/PridePeptideEvidenceMongoServiceTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/mockito/PridePeptideEvidenceMongoServiceTest.java index 786817b..69689c6 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/mockito/PridePeptideEvidenceMongoServiceTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/mockito/PridePeptideEvidenceMongoServiceTest.java @@ -1,14 +1,11 @@ package uk.ac.ebi.pride.mongodb.archive.service.mockito; -import org.junit.runner.RunWith; import org.springframework.boot.test.context.SpringBootTest; -import org.springframework.test.context.junit4.SpringRunner; import uk.ac.ebi.pride.mongodb.archive.config.PrideProjectFongoTestConfig; /** * @author ypriverol */ -@RunWith(SpringRunner.class) @SpringBootTest(classes = {PrideProjectFongoTestConfig.class}) public class PridePeptideEvidenceMongoServiceTest { diff --git a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/stats/CategoryStatsTest.java b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/stats/CategoryStatsTest.java index 03c32b6..a710990 100644 --- a/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/stats/CategoryStatsTest.java +++ b/src/test/java/uk/ac/ebi/pride/mongodb/archive/service/stats/CategoryStatsTest.java @@ -1,8 +1,8 @@ package uk.ac.ebi.pride.mongodb.archive.service.stats; -import org.junit.Assert; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import uk.ac.ebi.pride.archive.dataprovider.common.Tuple; /** @@ -20,7 +20,7 @@ public class CategoryStatsTest { CategoryStats stats; - @Before + @BeforeEach public void setUp() { stats = CategoryStats .builder() @@ -31,7 +31,7 @@ public void setUp() { @Test public void CategoryTest(){ System.out.println(stats.toString()); - Assert.assertEquals(new Tuple<>("Number od Submissions", 30000), stats.getCategory()); + Assertions.assertEquals(new Tuple<>("Number od Submissions", 30000), stats.getCategory()); } @Test diff --git a/src/test/resources/application-test.properties b/src/test/resources/application-test.properties index af9abe0..46c41e1 100644 --- a/src/test/resources/application-test.properties +++ b/src/test/resources/application-test.properties @@ -11,14 +11,14 @@ spring.datasource.oracle.driver.class.name=@pride.archive.repo.jdbc.driver@ # Configuration for MongoDB mongodb.project.database=@maven.spring.pridedb.datasource.mongo.db@ -mongodb.project.app.user=@maven.spring.pridedb.datasource.mongo.user@ -mongodb.project.app.password=@maven.spring.pridedb.datasource.mongo.password@ -mongodb.project.app.authenticationDatabase=@maven.spring.pridedb.datasource.mongo.authenticationDatabase@ -mongodb.projects.replicate.hosts=@maven.spring.pridedb.datasource.mongo.replicate.hosts@ -mongodb.projects.replicate.ports=@maven.spring.pridedb.datasource.mongo.replicate.ports@ -mongodb.project.app.machine.port=@maven.spring.pridedb.datasource.mongo.single.machine.port@ -mongo.single.machine=@maven.spring.pridedb.datasource.mongo.single.machine@ -mongodb.projects.single.machine.host=@maven.spring.pridedb.datasource.mongo.single.machine.host@ +#mongodb.project.app.user=@maven.spring.pridedb.datasource.mongo.user@ +#mongodb.project.app.password=@maven.spring.pridedb.datasource.mongo.password@ +#mongodb.project.app.authenticationDatabase=@maven.spring.pridedb.datasource.mongo.authenticationDatabase@ +#mongodb.projects.replicate.hosts=@maven.spring.pridedb.datasource.mongo.replicate.hosts@ +#mongodb.projects.replicate.ports=@maven.spring.pridedb.datasource.mongo.replicate.ports@ +#mongodb.project.app.machine.port=@maven.spring.pridedb.datasource.mongo.single.machine.port@ +#mongo.single.machine=@maven.spring.pridedb.datasource.mongo.single.machine@ +#mongodb.projects.single.machine.host=@maven.spring.pridedb.datasource.mongo.single.machine.host@ mongodb.projects.machine.uri=@maven.spring.pridedb.datasource.mongo.machine.uri@ #Configure Default Database