Merge pull request #36 from DiSSCo/feature/new-data-model

Feature/new data model

pom.xml

@@ -6,7 +6,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.1.2</version>
+    <version>3.1.4</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
   <groupId>eu.dissco.core</groupId>
@@ -19,11 +19,11 @@
     <dwca-io.version>2.16</dwca-io.version>
     <commons-beanutils.version>1.9.4</commons-beanutils.version>
     <jaxb2-maven-plugin.version>3.1.0</jaxb2-maven-plugin.version>
-    <jakarta.activation-api.version>2.1.0</jakarta.activation-api.version>
-    <jakarta.xml.bind-api.version>4.0.0</jakarta.xml.bind-api.version>
-    <spring-kafka.version>3.0.10</spring-kafka.version>
+    <jakarta.activation-api.version>2.1.2</jakarta.activation-api.version>
+    <jakarta.xml.bind-api.version>4.0.1</jakarta.xml.bind-api.version>
+    <snappy-java.version>1.1.10.5</snappy-java.version>
     <mockito-inline.version>5.2.0</mockito-inline.version>
-    <testcontainers.version>1.17.5</testcontainers.version>
+    <testcontainers.version>1.19.0</testcontainers.version>
     <sonar.organization>dissco</sonar.organization>
     <sonar.host.url>https://sonarcloud.io</sonar.host.url>
     <sonar.coverage.jacoco.xmlReportPaths>../app-it/target/site/jacoco-aggregate/jacoco.xml
@@ -80,11 +80,11 @@
       <groupId>org.springframework.kafka</groupId>
       <artifactId>spring-kafka</artifactId>
     </dependency>
-    <!-- Overwrite kafka client snappy version as it contains high prio security issues (24-07-2023) -->
+    <!-- Overwrite kafka client snappy version as it contains high prio security issues (02-10-2023) -->
     <dependency>
       <groupId>org.xerial.snappy</groupId>
       <artifactId>snappy-java</artifactId>
-      <version>1.1.10.3</version>
+      <version>${snappy-java.version}</version>
     </dependency>
     <dependency>
       <groupId>org.springframework.boot</groupId>
@@ -273,6 +273,27 @@
           </dependency>
         </dependencies>
       </plugin>
+      <plugin>
+        <groupId>org.jsonschema2pojo</groupId>
+        <artifactId>jsonschema2pojo-maven-plugin</artifactId>
+        <version>1.2.1</version>
+        <configuration>
+          <sourceDirectory>${basedir}/src/main/resources/json-schema/</sourceDirectory>
+          <targetPackage>eu.dissco.core.translator.schema</targetPackage>
+          <generateBuilders>true</generateBuilders>
+          <includeDynamicBuilders>true</includeDynamicBuilders>
+          <includeAdditionalProperties>false</includeAdditionalProperties>
+        </configuration>
+        <executions>
+          <execution>
+            <goals>
+              <goal>
+                generate
+              </goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
     </plugins>
   </build>
 

src/main/java/eu/dissco/core/translator/Profiles.java

@@ -1,6 +1,7 @@
 package eu.dissco.core.translator;
 
 public class Profiles {
+
   public static final String BIOCASE = "biocase";
   public static final String DWCA = "dwca";
 

src/main/java/eu/dissco/core/translator/component/MappingComponent.java

@@ -6,6 +6,7 @@
 import jakarta.annotation.PostConstruct;
 import java.util.HashMap;
 import java.util.Map;
+import lombok.Getter;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.stereotype.Component;
@@ -18,14 +19,16 @@ public class MappingComponent {
   private final WebClientProperties properties;
   private final MappingRepository repository;
 
+  @Getter
   private final Map<String, String> fieldMappings = new HashMap<>();
+  @Getter
   private final Map<String, String> defaults = new HashMap<>();
 
   @PostConstruct
   void setup() throws DisscoRepositoryException {
     var objectNode = repository.retrieveMapping(properties.getSourceSystemId());
     var mappingObject = objectNode.get("mapping");
-    if (mappingObject != null){
+    if (mappingObject != null) {
       mappingObject.iterator().forEachRemaining(node -> node.fields()
           .forEachRemaining(field -> fieldMappings.put(field.getKey(), field.getValue().asText())));
     }
@@ -34,12 +37,4 @@ void setup() throws DisscoRepositoryException {
         .forEachRemaining(field -> defaults.put(field.getKey(), field.getValue().asText())));
   }
 
-  public Map<String, String> getFieldMappings() {
-    return fieldMappings;
-  }
-
-  public Map<String, String> getDefaultMappings() {
-    return defaults;
-  }
-
 }

src/main/java/eu/dissco/core/translator/component/RorComponent.java

@@ -17,7 +17,7 @@ public class RorComponent {
   private final WebClient webClient;
 
   @Cacheable("ror")
-  public String getRoRId(String ror) {
+  public String getRorName(String ror) {
     log.info("Requesting organisation details for organisation: {} with ror", ror);
     String url = "https://api.ror.org/organizations/" + ror;
     var response = webClient.get().uri(url).retrieve().bodyToMono(JsonNode.class)

src/main/java/eu/dissco/core/translator/configuration/ApplicationConfiguration.java

@@ -9,6 +9,7 @@
 
 @Configuration
 public class ApplicationConfiguration {
+
   public static final String DATE_STRING = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX";
 
   @Bean