Merge pull request #683 from EBIBioSamples/dev

BSD software release 5.2.20
EBIBioSamples · Oct 30, 2023 · 2dde98e · 2dde98e
2 parents 02da9ed + 4f1bc66
commit 2dde98e
Show file tree

Hide file tree

Showing 201 changed files with 5,226 additions and 4,703 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,19 +1,22 @@
-image: docker:latest
+image: docker:stable
+services:
+  - docker:stable-dind
 
 variables:
   DEPLOY_PATH: ~/gitlab
 
 before_script:
   - echo $CI_BUILD_REF
   - echo $CI_PROJECT_DIR
+  - apk update && apk add git
 
 stages:
   - package
   - config
   - deploy
 
 maven-package:
-  image: openjdk:11
+  image: eclipse-temurin:17-jdk-alpine
   stage: package
   script:
     - './mvnw -q deploy -P embl-ebi -s ci_settings.xml -Dmaven.source.skip=true'
@@ -24,17 +27,18 @@ maven-package:
     - cp agents/uploadworkers/target/agents-uploadworkers-*.jar deployment/agents-uploadworkers.jar
     - cp pipelines/curation/target/pipelines-curation-*.jar deployment/pipelines-curation.jar
     - cp pipelines/ena/target/pipelines-ena-*.jar deployment/pipelines-ena.jar
+    - cp pipelines/ncbi-ena-link/target/pipelines-ncbi-ena-link-*.jar deployment/pipelines-ncbi-ena-link.jar
     - cp pipelines/sample-release/target/pipelines-sample-release-*.jar deployment/pipelines-sample-release.jar
     - cp pipelines/sample-post-release-action/target/pipelines-sample-post-release-action*.jar deployment/pipelines-sample-post-release-action.jar
     - cp pipelines/ncbi/target/pipelines-ncbi-*.jar deployment/pipelines-ncbi.jar
     - cp pipelines/reindex/target/pipelines-reindex-*.jar deployment/pipelines-reindex.jar
+    - cp pipelines/sample-transformation-dtol/target/pipelines-sample-transformation-dtol-*.jar deployment/pipelines-sample-transformation-dtol.jar
   artifacts:
     paths:
       - deployment
 #  when: manual
 
 clone-config-preproduction:
-  image: openjdk:11
   stage: config
   script:
     - git clone https://$BSD_INTERNAL_USER:$BSD_INTERNAL_PASS@gitlab.ebi.ac.uk/biosamples/biosamples-internal.git
@@ -50,7 +54,6 @@ clone-config-preproduction:
   when: manual
 
 clone-config-production:
-  image: openjdk:11
   stage: config
   script:
     - git clone https://$BSD_INTERNAL_USER:$BSD_INTERNAL_PASS@gitlab.ebi.ac.uk/biosamples/biosamples-internal.git

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM openjdk:8-jre-alpine
+FROM eclipse-temurin:17-jdk-alpine
 MAINTAINER EBI BioSamples <biosamples@ebi.ac.uk>
 
 COPY webapps/*/target/*.war webapps/*/target/*.jar agents/*/target/*.jar pipelines/*/target/*.jar integration/target/*.jar /

diff --git a/Dockerfile_Building b/Dockerfile_Building
@@ -4,7 +4,7 @@ RUN ls -la /tmp/*
 WORKDIR /tmp/
 RUN ./mvnw -U -P embl-ebi clean package -Dembedmongo.wait -pl !:pipelines-ena
 
-FROM openjdk:8-jre-alpine
+FROM eclipse-temurin:17-jdk-alpine
 MAINTAINER EBI BioSamples <biosamples@ebi.ac.uk>
 COPY --from=MAVEN_TOOL_CHAIN /tmp/webapps/*/target/*.war /tmp/agents/*/target/*.jar /tmp/pipelines/*/target/*.jar /tmp/integration/target/*.jar /
 

diff --git a/README.adoc b/README.adoc
@@ -28,8 +28,8 @@ This document provides information about the local installation, development env
 == Softwares
 
 * Git 2.17.1
-* Java 8
-* JDK 8
+* Java 17
+* JDK 17
 * Maven 3.6.3
 * Docker 18.6
 

diff --git a/RELEASE.adoc b/RELEASE.adoc
@@ -2,6 +2,15 @@
 :toc: auto
 
 This pages contains links to release notes for BioSamples for version 4.0.0 and higher. This release represents a comprehensive overhaul and therefore previous release notes are no longer applicable.
+[[v5.2.20]]
+== v5.2.30 Release notes
+* ERS accessioning in BioSamples
+* Java 17 and Spring Boot 2.5 upgrade
+
+[[v5.2.19]]
+== v5.2.19 Release notes
+* BioSamples client multi-threading fix
+
 [[v5.2.18]]
 == v5.2.18 Release notes
 

diff --git a/agents/pom.xml b/agents/pom.xml
@@ -9,7 +9,7 @@
 	<parent>
 		<groupId>uk.ac.ebi.biosamples</groupId>
 		<artifactId>biosamples</artifactId>
-		<version>5.2.19-RC3</version>
+		<version>5.2.21-SNAPSHOT</version>
 	</parent>
 
 	<modules>

diff --git a/agents/solr/pom.xml b/agents/solr/pom.xml
@@ -7,36 +7,36 @@
 	<parent>
 		<groupId>uk.ac.ebi.biosamples</groupId>
 		<artifactId>biosamples</artifactId>
-		<version>5.2.19-RC3</version>
+		<version>5.2.21-SNAPSHOT</version>
 		<relativePath>../../</relativePath>
 	</parent>
 
 	<dependencies>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>properties</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>models-solr</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>messaging</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>utils-ols</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 
 		<dependency>
 			<groupId>org.springframework.hateoas</groupId>
 			<artifactId>spring-hateoas</artifactId>
-			<version>1.2.0</version>
+			<version>1.3.4</version>
 		</dependency>
 		<dependency>
 			<groupId>com.github.ben-manes.caffeine</groupId>

diff --git a/agents/uploadworkers/pom.xml b/agents/uploadworkers/pom.xml
@@ -7,15 +7,15 @@
 	<parent>
 		<groupId>uk.ac.ebi.biosamples</groupId>
 		<artifactId>biosamples</artifactId>
-		<version>5.2.19-RC3</version>
+		<version>5.2.21-SNAPSHOT</version>
 		<relativePath>../../</relativePath>
 	</parent>
 
 	<dependencies>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>biosamples-spring-boot-starter</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
@@ -28,27 +28,27 @@
 		<dependency>
 			<groupId>org.springframework.hateoas</groupId>
 			<artifactId>spring-hateoas</artifactId>
-			<version>1.2.0</version>
+			<version>1.3.4</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>properties</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>utils-webapp</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>messaging</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>models-mongo</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>

diff --git a/agents/uploadworkers/src/main/java/uk/ac/ebi/biosamples/Application.java b/agents/uploadworkers/src/main/java/uk/ac/ebi/biosamples/Application.java
@@ -17,7 +17,6 @@
 import org.springframework.boot.autoconfigure.amqp.SimpleRabbitListenerContainerFactoryConfigurer;
 import org.springframework.context.annotation.Bean;
 import org.springframework.data.mongodb.core.MongoOperations;
-import uk.ac.ebi.biosamples.mongo.MongoProperties;
 import uk.ac.ebi.biosamples.mongo.repo.MongoSampleRepository;
 import uk.ac.ebi.biosamples.mongo.service.MongoAccessionService;
 import uk.ac.ebi.biosamples.mongo.service.MongoSampleToSampleConverter;
@@ -36,15 +35,15 @@
       TokenRepositoryRest.class
     })
 public class Application {
-  public static void main(String[] args) {
+  public static void main(final String[] args) {
     System.exit(SpringApplication.exit(SpringApplication.run(Application.class, args)));
   }
 
   @Bean("biosamplesFileUploadSubmissionContainerFactory")
   public SimpleRabbitListenerContainerFactory containerFactory(
-      SimpleRabbitListenerContainerFactoryConfigurer configurer,
-      ConnectionFactory connectionFactory) {
-    SimpleRabbitListenerContainerFactory factory = new SimpleRabbitListenerContainerFactory();
+      final SimpleRabbitListenerContainerFactoryConfigurer configurer,
+      final ConnectionFactory connectionFactory) {
+    final SimpleRabbitListenerContainerFactory factory = new SimpleRabbitListenerContainerFactory();
     factory.setConcurrentConsumers(5);
     factory.setMaxConcurrentConsumers(5);
     configurer.configure(factory, connectionFactory);
@@ -54,16 +53,14 @@ public SimpleRabbitListenerContainerFactory containerFactory(
 
   @Bean(name = "SampleAccessionService")
   public MongoAccessionService mongoSampleAccessionService(
-      MongoSampleRepository mongoSampleRepository,
-      SampleToMongoSampleConverter sampleToMongoSampleConverter,
-      MongoSampleToSampleConverter mongoSampleToSampleConverter,
-      MongoProperties mongoProperties,
-      MongoOperations mongoOperations) {
+      final MongoSampleRepository mongoSampleRepository,
+      final SampleToMongoSampleConverter sampleToMongoSampleConverter,
+      final MongoSampleToSampleConverter mongoSampleToSampleConverter,
+      final MongoOperations mongoOperations) {
     return new MongoAccessionService(
         mongoSampleRepository,
         sampleToMongoSampleConverter,
         mongoSampleToSampleConverter,
-        mongoProperties.getAccessionPrefix(),
         mongoOperations);
   }
 }
diff --git a/...oadworkers/src/main/java/uk/ac/ebi/biosamples/submission/FileUploadSubmissionService.java b/...oadworkers/src/main/java/uk/ac/ebi/biosamples/submission/FileUploadSubmissionService.java
@@ -47,17 +47,14 @@ public class FileUploadSubmissionService {
   private final Logger log = LoggerFactory.getLogger(getClass());
   private ValidationResult validationResult;
   private FileUploadUtils fileUploadUtils;
-
   @Autowired BioSamplesClient bioSamplesAapClient;
 
   @Autowired
   @Qualifier("WEBINCLIENT")
   BioSamplesClient bioSamplesWebinClient;
 
   @Autowired FileUploadStorageService fileUploadStorageService;
-
   @Autowired MongoFileUploadRepository mongoFileUploadRepository;
-
   @Autowired MongoSampleRepository mongoSampleRepository;
 
   @RabbitListener(

diff --git a/client/client/pom.xml b/client/client/pom.xml
@@ -11,8 +11,8 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
 				<configuration>
-					<source>8</source>
-					<target>8</target>
+					<source>17</source>
+					<target>17</target>
 				</configuration>
 			</plugin>
 		</plugins>
@@ -21,30 +21,30 @@
 	<parent>
 		<groupId>uk.ac.ebi.biosamples</groupId>
 		<artifactId>biosamples</artifactId>
-		<version>5.2.19-RC3</version>
+		<version>5.2.21-SNAPSHOT</version>
 		<relativePath>../../</relativePath>
 	</parent>
 
 	<dependencies>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>models-core</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>properties</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>utils-thread</artifactId>
-			<version>5.2.19-RC3</version>
+			<version>5.2.21-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.springframework.hateoas</groupId>
 			<artifactId>spring-hateoas</artifactId>
-			<version>1.2.0</version>
+			<version>1.3.4</version>
 		</dependency>
 		<!-- unmentioned requirements of hateoas -->
 		<dependency>
@@ -71,7 +71,7 @@
 		<dependency>
 			<groupId>org.projectlombok</groupId>
 			<artifactId>lombok</artifactId>
-			<version>1.18.2</version>
+			<version>1.18.22</version>
 			<scope>provided</scope>
 		</dependency>
 		<dependency>