WIP

- Migration complete

Makefile

@@ -5,7 +5,7 @@ TRIVY_VERSION ?= v0.41.0
 
 all:
 
-build-backend: build-metadata-db build-database-service build-query-service build-table-service build-identifier-service build-container-service build-discovery-service build-gateway-service build-metadata-service build-analyse-service build-user-service
+build-backend: build-metadata-db build-database-service build-query-service build-table-service build-identifier-service build-container-service build-metadata-service build-analyse-service build-user-service
 
 build-metadata-db:
 	mvn -f ./dbrepo-metadata-db/pom.xml clean install
@@ -22,12 +22,6 @@ build-container-service: build-metadata-db
 build-database-service: build-metadata-db
 	mvn -f ./dbrepo-database-service/pom.xml clean package -DskipTests
 
-build-discovery-service: build-metadata-db
-	mvn -f ./dbrepo-discovery-service/pom.xml clean package -DskipTests
-
-build-gateway-service: build-metadata-db
-	mvn -f ./dbrepo-gateway-service/pom.xml clean package -DskipTests
-
 build-query-service: build-metadata-db
 	mvn -f ./dbrepo-query-service/pom.xml clean package -DskipTests
 

dbrepo-container-service/Dockerfile

@@ -23,6 +23,8 @@ RUN mvn -q clean package -DskipTests
 FROM openjdk:17-alpine as runtime
 MAINTAINER Martin Weise <martin.weise@tuwien.ac.at>
 
+RUN apk --no-cache add bash
+
 ENV METADATA_DB=fda
 ENV METADATA_USERNAME=root
 ENV METADATA_PASSWORD=dbrepo

dbrepo-container-service/pom.xml

@@ -32,10 +32,6 @@
     </properties>
 
     <dependencies>
-        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-webflux</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-web</artifactId>

dbrepo-container-service/services/src/main/java/at/tuwien/config/JacksonConfig.java

@@ -19,7 +19,6 @@ public class JacksonConfig {
     @Bean
     public ObjectMapper objectMapper() throws JsonProcessingException {
         final ObjectMapper objectMapper = new ObjectMapper();
-        objectMapper.findAndRegisterModules();
         objectMapper.registerModule(new Jdk8Module());
         objectMapper.registerModule(new JavaTimeModule());
         objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);

dbrepo-database-service/Dockerfile

@@ -23,6 +23,8 @@ RUN mvn -q clean package -DskipTests
 FROM openjdk:17-alpine as runtime
 MAINTAINER Martin Weise <martin.weise@tuwien.ac.at>
 
+RUN apk --no-cache add bash
+
 ENV METADATA_DB=fda
 ENV METADATA_USERNAME=root
 ENV METADATA_PASSWORD=dbrepo

dbrepo-database-service/pom.xml

@@ -29,14 +29,11 @@
         <swagger.version>2.2.9</swagger.version>
         <jacoco.version>0.8.10</jacoco.version>
         <jwt.version>4.3.0</jwt.version>
-        <hibernate-c3po.version>5.6.3.Final</hibernate-c3po.version>
+        <c3p0.version>0.9.5.5</c3p0.version>
+        <c3p0-hibernate.version>6.2.2.Final</c3p0-hibernate.version>
     </properties>
 
     <dependencies>
-        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-webflux</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-web</artifactId>
@@ -93,6 +90,16 @@
             <version>${spring-cloud.version}</version>
         </dependency>
         <!-- Data Source -->
+        <dependency>
+            <groupId>com.mchange</groupId>
+            <artifactId>c3p0</artifactId>
+            <version>${c3p0.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.hibernate</groupId>
+            <artifactId>hibernate-c3p0</artifactId>
+            <version>${c3p0-hibernate.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jpa</artifactId>
@@ -121,11 +128,6 @@
             <version>${project.version}</version>
             <scope>compile</scope>
         </dependency>
-        <dependency>
-            <groupId>org.hibernate</groupId>
-            <artifactId>hibernate-c3p0</artifactId>
-            <version>${hibernate-c3po.version}</version>
-        </dependency>
         <!-- Testing -->
         <dependency>
             <groupId>org.springframework.boot</groupId>

dbrepo-database-service/services/src/main/java/at/tuwien/config/ElasticsearchConfig.java

@@ -22,10 +22,10 @@ public class ElasticsearchConfig {
     @Value("${spring.elasticsearch.uris}")
     private String elasticEndpoint;
 
-    @Value("${fda.elastic.username}")
+    @Value("${spring.elasticsearch.username}")
     private String elasticUsername;
 
-    @Value("${fda.elastic.password}")
+    @Value("${spring.elasticsearch.password}")
     private String elasticPassword;
 
     @Bean

dbrepo-database-service/services/src/main/java/at/tuwien/config/JacksonConfig.java

@@ -19,7 +19,6 @@ public class JacksonConfig {
     @Bean
     public ObjectMapper objectMapper() throws JsonProcessingException {
         final ObjectMapper objectMapper = new ObjectMapper();
-        objectMapper.findAndRegisterModules();
         objectMapper.registerModule(new Jdk8Module());
         objectMapper.registerModule(new JavaTimeModule());
         objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);

dbrepo-identifier-service/Dockerfile

@@ -3,7 +3,8 @@ FROM dbrepo-metadata-db:latest as dependency
 MAINTAINER Martin Weise <martin.weise@tuwien.ac.at>
 
 ###### SECOND STAGE ######
-FROM maven:slim as build
+FROM maven:3-openjdk-17 as build
+MAINTAINER Martin Weise <martin.weise@tuwien.ac.at>
 
 COPY ./pom.xml ./
 
@@ -20,7 +21,10 @@ COPY ./report ./report
 RUN mvn -q clean package -DskipTests
 
 ###### THIRD STAGE ######
-FROM openjdk:11-jre-slim as runtime
+FROM openjdk:17-alpine as runtime
+MAINTAINER Martin Weise <martin.weise@tuwien.ac.at>
+
+RUN apk --no-cache add bash
 
 ENV METADATA_DB=fda
 ENV METADATA_USERNAME=root

dbrepo-identifier-service/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.3.10.RELEASE</version>
+        <version>3.0.6</version>
     </parent>
 
     <groupId>at.tuwien</groupId>
@@ -23,24 +23,21 @@
     </modules>
 
     <properties>
-        <java.version>11</java.version>
-        <spring-cloud.version>3.0.1</spring-cloud.version>
-        <mapstruct.version>1.4.2.Final</mapstruct.version>
-        <swagger.version>2.1.7</swagger.version>
-        <springfox.version>3.0.0</springfox.version>
-        <jacoco.version>0.8.7</jacoco.version>
-        <javax-ws-rs.version>2.1.1</javax-ws-rs.version>
-        <maven-site.version>3.10.0</maven-site.version>
-        <docker.version>3.2.7</docker.version>
-        <commons-io.version>2.11.0</commons-io.version>
+        <java.version>17</java.version>
+        <spring-cloud.version>4.0.2</spring-cloud.version>
+        <mapstruct.version>1.5.5.Final</mapstruct.version>
+        <docker.version>3.3.0</docker.version>
+        <swagger.version>2.2.9</swagger.version>
+        <jacoco.version>0.8.10</jacoco.version>
         <jwt.version>4.3.0</jwt.version>
+        <hibernate-c3po.version>5.6.3.Final</hibernate-c3po.version>
+        <commons-io.version>2.11.0</commons-io.version>
+        <opencsv.version>5.7.1</opencsv.version>
+        <super-csv.version>2.4.0</super-csv.version>
+        <jsql.version>4.6</jsql.version>
     </properties>
 
     <dependencies>
-        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-webflux</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-web</artifactId>
@@ -110,12 +107,6 @@
             <artifactId>docker-java</artifactId>
             <version>${docker.version}</version>
             <scope>test</scope>
-            <exclusions>
-                <exclusion>
-                    <groupId>javax.ws.rs</groupId>
-                    <artifactId>jsr311-api</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>com.github.docker-java</groupId>
@@ -124,11 +115,6 @@
             <scope>test</scope>
         </dependency>
         <!-- Testing -->
-        <dependency>
-            <groupId>javax.ws.rs</groupId>
-            <artifactId>javax.ws.rs-api</artifactId>
-            <version>${javax-ws-rs.version}</version>
-        </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jpa</artifactId>

dbrepo-identifier-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java

@@ -4,7 +4,6 @@ import at.tuwien.api.error.ApiErrorDto;
 import at.tuwien.api.identifier.IdentifierCreateDto;
 import at.tuwien.api.identifier.IdentifierDto;
 import at.tuwien.api.identifier.IdentifierTypeDto;
-import at.tuwien.entities.database.DatabaseAccess;
 import at.tuwien.entities.identifier.Identifier;
 import at.tuwien.entities.user.User;
 import at.tuwien.exception.*;
@@ -27,8 +26,8 @@ import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.*;
 
-import javax.validation.Valid;
-import javax.validation.constraints.NotNull;
+import jakarta.validation.Valid;
+import jakarta.validation.constraints.NotNull;
 import java.security.Principal;
 import java.util.LinkedList;
 import java.util.List;

dbrepo-identifier-service/rest-service/src/main/java/at/tuwien/endpoints/PersistenceEndpoint.java

@@ -29,8 +29,8 @@ import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.*;
 
-import javax.validation.Valid;
-import javax.validation.constraints.NotNull;
+import jakarta.validation.Valid;
+import jakarta.validation.constraints.NotNull;
 import java.security.Principal;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;

dbrepo-identifier-service/rest-service/src/main/resources/application-local.yml

@@ -27,6 +27,10 @@ spring:
     virtual-host: dbrepo
     username: fda
     password: fda
+  elasticsearch:
+    password: elastic
+    username: elastic
+    uris: http://localhost:9200
 management.endpoints.web.exposure.include: health,info,prometheus
 server:
   port: 9096
@@ -46,7 +50,3 @@ fda:
   client_id: dbrepo-client
   gateway.endpoint: https://localhost
   website: https://localhost
\ No newline at end of file
-  elastic:
-    endpoint: localhost:9200
-    username: elastic
-    password: elastic
\ No newline at end of file

dbrepo-identifier-service/rest-service/src/main/resources/application.yml

@@ -27,6 +27,10 @@ spring:
     virtual-host: dbrepo
     username: "${BROKER_USERNAME}"
     password: "${BROKER_PASSWORD}"
+  elasticsearch:
+    password: "${ELASTIC_PASSWORD}"
+    username: elastic
+    uris: http://search-service:9200
 management.endpoints.web.exposure.include: health,info,prometheus
 server:
   port: 9096
@@ -46,7 +50,3 @@ fda:
   client_id: "${CLIENT_ID}"
   gateway.endpoint: "${GATEWAY_ENDPOINT}"
   website: "${WEBSITE}"
\ No newline at end of file
-  elastic:
-    endpoint: search-service:9200
-    username: elastic
-    password: "${ELASTIC_PASSWORD}"
\ No newline at end of file

dbrepo-identifier-service/rest-service/src/test/java/at/tuwien/endpoint/PersistenceEndpointUnitTest.java

@@ -75,7 +75,6 @@ public class PersistenceEndpointUnitTest extends BaseUnitTest {
     @Primary
     public ObjectMapper objectMapper() {
         final ObjectMapper objectMapper = new ObjectMapper();
-        objectMapper.findAndRegisterModules();
         objectMapper.registerModule(new Jdk8Module());
         objectMapper.registerModule(new JavaTimeModule());
         objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);

dbrepo-identifier-service/services/src/main/java/at/tuwien/auth/AuthTokenFilter.java

@@ -6,6 +6,10 @@ import com.auth0.jwt.JWT;
 import com.auth0.jwt.JWTVerifier;
 import com.auth0.jwt.algorithms.Algorithm;
 import com.auth0.jwt.interfaces.DecodedJWT;
+import jakarta.servlet.FilterChain;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
@@ -16,10 +20,6 @@ import org.springframework.security.web.authentication.WebAuthenticationDetailsS
 import org.springframework.util.StringUtils;
 import org.springframework.web.filter.OncePerRequestFilter;
 
-import javax.servlet.FilterChain;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.security.KeyFactory;
 import java.security.NoSuchAlgorithmException;

dbrepo-identifier-service/services/src/main/java/at/tuwien/config/ElasticsearchConfig.java

 package at.tuwien.config;
 
-import org.elasticsearch.client.RestHighLevelClient;
+import co.elastic.clients.elasticsearch.ElasticsearchClient;
+import co.elastic.clients.json.jackson.JacksonJsonpMapper;
+import co.elastic.clients.transport.ElasticsearchTransport;
+import co.elastic.clients.transport.rest_client.RestClientTransport;
+import lombok.extern.log4j.Log4j2;
+import org.apache.http.HttpHost;
+import org.apache.http.auth.AuthScope;
+import org.apache.http.auth.UsernamePasswordCredentials;
+import org.apache.http.client.CredentialsProvider;
+import org.apache.http.impl.client.BasicCredentialsProvider;
+import org.elasticsearch.client.RestClient;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.data.elasticsearch.client.ClientConfiguration;
-import org.springframework.data.elasticsearch.client.RestClients;
-import org.springframework.data.elasticsearch.core.ElasticsearchOperations;
-import org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate;
 
+@Log4j2
 @Configuration
 public class ElasticsearchConfig {
 
-    @Value("${fda.elastic.endpoint}")
+    @Value("${spring.elasticsearch.uris}")
     private String elasticEndpoint;
 
-    @Value("${fda.elastic.username}")
+    @Value("${spring.elasticsearch.username}")
     private String elasticUsername;
 
-    @Value("${fda.elastic.password}")
+    @Value("${spring.elasticsearch.password}")
     private String elasticPassword;
 
     @Bean
-    public RestHighLevelClient client() {
-        ClientConfiguration clientConfiguration = ClientConfiguration.builder()
-                .connectedTo(elasticEndpoint)
-                .withBasicAuth(elasticUsername, elasticPassword)
+    public ElasticsearchClient elasticsearchClient() {
+        log.debug("elastic endpoint={}", elasticEndpoint);
+        final CredentialsProvider credentialsProvider = new BasicCredentialsProvider();
+        credentialsProvider.setCredentials(AuthScope.ANY, new UsernamePasswordCredentials(elasticUsername, elasticPassword));
+        final RestClient restClient = RestClient.builder(HttpHost.create(elasticEndpoint))
+                .setHttpClientConfigCallback(httpClientBuilder -> httpClientBuilder
+                        .setDefaultCredentialsProvider(credentialsProvider))
                 .build();
-
-        return RestClients.create(clientConfiguration).rest();
+        ElasticsearchTransport transport = new RestClientTransport(
+                restClient, new JacksonJsonpMapper());
+        return new ElasticsearchClient(transport);
     }
 
-    @Bean
-    public ElasticsearchOperations elasticsearchTemplate() {
-        return new ElasticsearchRestTemplate(client());
-    }
 }
\ No newline at end of file

dbrepo-identifier-service/services/src/main/java/at/tuwien/config/JacksonConfig.java

@@ -21,7 +21,6 @@ public class JacksonConfig {
     @Primary
     public ObjectMapper objectMapper() throws JsonProcessingException {
         final ObjectMapper objectMapper = new ObjectMapper();
-        objectMapper.findAndRegisterModules();
         objectMapper.registerModule(new Jdk8Module());
         objectMapper.registerModule(new JavaTimeModule());
         objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);

dbrepo-identifier-service/services/src/main/java/at/tuwien/config/ReadyConfig.java

@@ -6,14 +6,12 @@ import org.springframework.boot.context.event.ApplicationReadyEvent;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.event.EventListener;
 
-import javax.validation.constraints.NotNull;
 import java.io.File;
 import java.io.IOException;
 
 @Configuration
 public class ReadyConfig {
 
-    @NotNull
     @Value("${fda.ready.path}")
     private String readyPath;
 

dbrepo-identifier-service/services/src/main/java/at/tuwien/config/TemplateConfig.java

@@ -2,7 +2,7 @@ package at.tuwien.config;
 
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
-import org.thymeleaf.spring5.SpringTemplateEngine;
+import org.thymeleaf.spring6.SpringTemplateEngine;
 import org.thymeleaf.templatemode.TemplateMode;
 import org.thymeleaf.templateresolver.ClassLoaderTemplateResolver;