Spring boot upgrade 3.3

.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"

pom.xml

@@ -4,14 +4,14 @@
 
     <groupId>uk.ac.ebi.pride.archive</groupId>
     <artifactId>pride-mongodb-repo</artifactId>
-    <version>1.0.9-SNAPSHOT</version>
+    <version>1.0.10-SNAPSHOT</version>
     <packaging>jar</packaging>
     <name>PRIDE MongoDB repository</name>
 
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.0.1.RELEASE</version>
+        <version>3.3.3</version>
     </parent>
 
     <!-- This project requires several maven profiles to build and run correctly.
@@ -24,6 +24,7 @@
 
     <properties>
         <archive.data.provider.api.version>1.0.1-SNAPSHOT</archive.data.provider.api.version>
+        <maven.compiler.release>17</maven.compiler.release>
         <uk.ac.ebi.pride.architectural-pride-tdd.version>1.0.4-SNAPSHOT</uk.ac.ebi.pride.architectural-pride-tdd.version>
         <uk.ac.ebi.pride.architectural-pride-spring.version>1.0.0-SNAPSHOT</uk.ac.ebi.pride.architectural-pride-spring.version>
         <uk.ac.ebi.pride.px-submission-core.version>2.0.18</uk.ac.ebi.pride.px-submission-core.version>
@@ -41,17 +42,14 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-core</artifactId>
-            <version>${jackson.version}</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-annotations</artifactId>
-            <version>${jackson.version}</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>${jackson.version}</version>
         </dependency>
 
 
@@ -76,6 +74,21 @@
             <version>${uk.ac.ebi.pride.architectural-pride-tdd.version}</version>
             <type>pom</type>
             <scope>test</scope>
+            <exclusions>
+                <exclusion>
+                    <groupId>junit</groupId>
+                    <artifactId>junit</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
+
+        <!-- EmbedMongo for in-memory MongoDB instances  as Fongo deprecated-->
+        <dependency>
+            <groupId>de.flapdoodle.embed</groupId>
+            <artifactId>de.flapdoodle.embed.mongo</artifactId>
+            <version>3.5.4</version>
+            <scope>test</scope>
         </dependency>
 
         <!-- MongoDB and Lombok -->
@@ -84,6 +97,13 @@
             <artifactId>spring-boot-starter-data-mongodb</artifactId>
         </dependency>
 
+        <!-- MongoDB Java Driver -->
+        <dependency>
+            <groupId>org.mongodb</groupId>
+            <artifactId>mongodb-driver-sync</artifactId>
+            <version>4.9.1</version>
+        </dependency>
+
         <dependency>
             <groupId>com.fasterxml.jackson</groupId>
             <artifactId>jackson-base</artifactId>
@@ -122,7 +142,6 @@
         <dependency>
             <groupId>org.hibernate.validator</groupId>
             <artifactId>hibernate-validator</artifactId>
-            <version>6.1.5.Final</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -141,7 +160,6 @@
         <dependency>
             <groupId>org.projectlombok</groupId>
             <artifactId>lombok</artifactId>
-            <version>1.18.24</version>
         </dependency>
 
         <dependency>
@@ -238,6 +256,35 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-source-plugin</artifactId>
             </plugin>
+            <plugin>
+                <groupId>org.openrewrite.maven</groupId>
+                <artifactId>rewrite-maven-plugin</artifactId>
+                <version>5.39.0</version>
+                <configuration>
+                    <exportDatatables>true</exportDatatables>
+                    <activeRecipes>
+                        <recipe>org.openrewrite.java.spring.boot3.UpgradeSpringBoot_3_3</recipe>
+                    </activeRecipes>
+                </configuration>
+                <dependencies>
+                    <dependency>
+                        <groupId>org.openrewrite.recipe</groupId>
+                        <artifactId>rewrite-spring</artifactId>
+                        <version>5.17.0</version>
+                    </dependency>
+                </dependencies>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.8.1</version>
+                <configuration>
+                    <parameters>true</parameters>
+                    <compilerArgs>
+                        <arg>-parameters</arg>
+                    </compilerArgs>
+                </configuration>
+            </plugin>
         </plugins>
     </build>
 

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;
 
     /**

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;

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;

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;

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;
     }

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;

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;

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;
     }

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;
     }

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;

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 {

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<MongoImportedProject> 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<MongoPrideAssay> mongoAssays) {
         mongoAssays.forEach(x -> {
             Optional<MongoPrideAssay> currentAssay = assayMongoRepository.findPrideAssayByAccession(x.getAccession());
-            if (!currentAssay.isPresent())
+            if (currentAssay.isEmpty())
                 assayMongoRepository.save(x);
             else {
                 updateAssay(currentAssay.get(), x);

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;
     }

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<MongoPrideProject> 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<MongoPrideAssay> mongoAssays) {
         mongoAssays.forEach(x -> {
             Optional<MongoPrideAssay> currentAssay = assayMongoRepository.findPrideAssayByAccession(x.getAccession());
-            if (!currentAssay.isPresent())
+            if (currentAssay.isEmpty())
                 assayMongoRepository.save(x);
             else {
                 updateAssay(currentAssay.get(), x);

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;
     }

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;
     }