Feature/refactoring

.github/workflows/codeql.yml

@@ -45,11 +45,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
-    - uses: actions/setup-java@v1
+    - uses: actions/setup-java@v3
       with:
-        java-version: 17
+        java-version: 21
+        distribution: temurin
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/maven.yml

@@ -19,13 +19,13 @@ jobs:
     name: Build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
-      - name: Set up JDK 17
+      - name: Set up JDK 21
         uses: actions/setup-java@v3
         with:
-          java-version: '17'
+          java-version: '21'
           distribution: 'temurin'
       - name: Cache SonarQube packages
         uses: actions/cache@v1

Infrastructure/templateImport.json

@@ -0,0 +1,14 @@
+{
+  "AWSTemplateFormatVersion": "2010-09-09",
+  "Description": "Import test",
+  "Resources": {
+    "ApplicationBackend": {
+      "Type": "AWS::ElasticBeanstalk::Application",
+      "DeletionPolicy": "Retain",
+      "Properties": {
+        "Description": "ApplicationBackend",
+        "ApplicationName": "fgai4h-oci-annotation-backend"
+      }
+    }
+  }
+}

documentation/Contributing.md

@@ -36,7 +36,10 @@ aws s3 ls --profile ai4h
 ```
 5. Get session ID from ~/.aws/cli/cache/<latest-file>
 Use the value from AccessKeyId, SecretAccessKey and SessionToken and set them in the environment variables.
-
+- AWS_ACCESS_KEY_ID=[AccessKeyId];
+- AWS_REGION=eu-central-1;
+- AWS_SECRET_ACCESS_KEY=[SecretAccessKey];
+- AWS_SESSION_TOKEN=[SessionToken];
 
 ## Getting Started
 

pom.xml

@@ -5,20 +5,21 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>3.0.4</version>
+        <version>3.2.5</version>
     </parent>
     <groupId>org.fgai4h</groupId>
     <artifactId>annotation</artifactId>
     <version>0.0.1-SNAPSHOT</version>
     <name>Annotation backend</name>
     <description>Annotation backend</description>
     <properties>
-        <java.version>17</java.version>
-        <maven.compiler.source>17</maven.compiler.source>
-        <maven.compiler.target>17</maven.compiler.target>
+        <java.version>21</java.version>
+        <maven.compiler.source>21</maven.compiler.source>
+        <maven.compiler.target>21</maven.compiler.target>
         <org.mapstruct.version>1.4.2.Final</org.mapstruct.version>
-        <org.projectlombok.version>1.18.24</org.projectlombok.version>
+        <org.projectlombok.version>1.18.32</org.projectlombok.version>
     </properties>
+
     <dependencyManagement>
         <dependencies>
             <dependency>
@@ -35,30 +36,36 @@
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-oauth2-resource-server</artifactId>
+            <version>3.2.5</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jpa</artifactId>
+            <version>3.2.5</version>
         </dependency>
 
         <dependency>
             <groupId>org.springframework.security</groupId>
             <artifactId>spring-security-oauth2-jose</artifactId>
+            <version>6.2.4</version>
         </dependency>
 
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-web</artifactId>
+            <version>3.2.5</version>
         </dependency>
 
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-hateoas</artifactId>
+            <version>3.2.5</version>
         </dependency>
 
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-actuator</artifactId>
+            <version>3.2.5</version>
         </dependency>
 
         <dependency>
@@ -134,6 +141,11 @@
             <artifactId>swagger-annotations</artifactId>
             <version>2.2.8</version>
         </dependency>
+        <dependency>
+            <groupId>com.google.code.findbugs</groupId>
+            <artifactId>jsr305</artifactId>
+            <version>3.0.2</version>
+        </dependency>
         <dependency>
             <groupId>org.mapstruct</groupId>
             <artifactId>mapstruct</artifactId>
@@ -145,6 +157,18 @@
             <version>3.12.0</version>
         </dependency>
 
+        <dependency>
+            <groupId>com.squareup.okhttp3</groupId>
+            <artifactId>okhttp</artifactId>
+            <version>4.12.0</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.squareup.okhttp3</groupId>
+            <artifactId>logging-interceptor</artifactId>
+            <version>4.12.0</version>
+        </dependency>
+
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
@@ -156,6 +180,42 @@
             <version>17.0.0</version>
             <scope>compile</scope>
         </dependency>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+            <version>2.10.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>io.gsonfire</groupId>
+            <artifactId>gson-fire</artifactId>
+            <version>1.9.0</version>
+        </dependency>
+
+        <dependency>
+            <groupId>javax.annotation</groupId>
+            <artifactId>javax.annotation-api</artifactId>
+            <version>1.3.2</version>
+        </dependency>
+
+        <dependency>
+            <groupId>io.swagger</groupId>
+            <artifactId>swagger-annotations</artifactId>
+            <version>1.6.14</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+            <version>5.10.1</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>javax.ws.rs</groupId>
+            <artifactId>javax.ws.rs-api</artifactId>
+            <version>2.1.1</version>
+        </dependency>
 
     </dependencies>
 
@@ -169,7 +229,7 @@
             <plugin>
                 <groupId>org.jacoco</groupId>
                 <artifactId>jacoco-maven-plugin</artifactId>
-                <version>0.8.8</version>
+                <version>0.8.11</version>
             </plugin>
             <plugin>
                 <groupId>org.springframework.boot</groupId>
@@ -187,7 +247,7 @@
                 <groupId>org.openapitools</groupId>
                 <artifactId>openapi-generator-maven-plugin</artifactId>
                 <!-- RELEASE_VERSION -->
-                <version>6.3.0</version>
+                <version>6.6.0</version>
                 <!-- /RELEASE_VERSION -->
                 <executions>
                     <execution>
@@ -217,10 +277,10 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.8.1</version>
+                <version>3.13.0</version>
                 <configuration>
-                    <source>1.8</source>
-                    <target>1.8</target>
+                    <source>21</source>
+                    <target>21</target>
                     <annotationProcessorPaths>
                         <path>
                             <groupId>org.mapstruct</groupId>

src/main/java/org/fgai4h/ap/DataSourceConfig.java

@@ -3,6 +3,8 @@
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.boot.jdbc.DataSourceBuilder;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -16,6 +18,8 @@
 @Profile("prod")
 public class DataSourceConfig {
 
+        private static final Logger LOGGER = LoggerFactory.getLogger(DataSourceConfig.class);
+
         @Bean
         public DataSource getDataSource() {
                 DataSourceBuilder dataSourceBuilder = DataSourceBuilder.create();
@@ -29,7 +33,7 @@ public DataSource getDataSource() {
                         dataSourceBuilder.password(secretsJson.get("password").textValue());
 
                 } catch (JsonProcessingException e) {
-                        e.printStackTrace();
+                        LOGGER.error("Error processing JSON", e);
                 }
 
                 return dataSourceBuilder.build();

src/main/java/org/fgai4h/ap/domain/campaign/entity/CampaignEntity.java

@@ -32,60 +32,71 @@ public class CampaignEntity implements Serializable {
     @Id
     @GeneratedValue(generator = "uuid2")
     @GenericGenerator(name = "uuid2", strategy = "uuid2")
-    @Column(columnDefinition = "BINARY(16)")
+
     private UUID campaignUUID;
 
     /**
      * The name for the campaign.
      */
     private String name;
+
     /**
      * The description for the campaign.
      */
     private String description;
+
     /**
      * The status of the campaign.
      */
     private String status;
+
     /**
      * The kind of annotation that is to be performed in the campaign.
      */
     private String annotationKind;
+
     /**
      * The tool that is to be used for annotation.
      */
     private String annotationTool;
+
     /**
-     * The model that is to be used for annotation.
+     * The pre annotation tool used to pre-process the annotations.
      */
     private String preAnnotationTool;
+
     /**
      * The model that is to be used for annotation.
      */
     private String preAnnotationModel;
+
     /**
      * The method that is to be used for annotation.
      */
     private String annotationMethod;
+
     /**
      * The instructions for annotation.
      */
     private String annotationInstructions;
+
     /**
      * The quality assurance for annotation.
      */
     private String qualityAssurance;
+
     /**
      * The kind of quality assurance that is to be performed in the campaign.
      */
     private Boolean isInstanceLabel;
+
     /**
      * The kind of quality assurance that is to be performed in the campaign.
      */
     private Integer minAnnotation;
 
     /**
-     * The class labels for the campaign.
+     * The annotation class labels for the campaign.
      */
     @OneToMany(mappedBy = "campaignEntity")
     private List<ClassLabelEntity> classLabels = new java.util.ArrayList<>();

src/main/java/org/fgai4h/ap/domain/campaign/entity/ClassLabelEntity.java

@@ -23,7 +23,7 @@ public class ClassLabelEntity implements Serializable
     @Id
     @GeneratedValue(generator = "uuid2")
     @GenericGenerator(name = "uuid2", strategy = "uuid2")
-    @Column(columnDefinition = "BINARY(16)")
+
     private UUID classLabelUUID;
 
     private String name;

src/main/java/org/fgai4h/ap/domain/campaign/model/CampaignModel.java

@@ -3,6 +3,7 @@
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonRootName;
 import lombok.*;
+
 import org.fgai4h.ap.domain.dataset.model.DatasetModel;
 import org.fgai4h.ap.domain.user.model.UserModel;
 import org.springframework.hateoas.RepresentationModel;
@@ -31,11 +32,15 @@ public class CampaignModel extends RepresentationModel<CampaignModel> {
     private List<UserModel> reviewers;
     private List<UserModel> supervisors;
     private List<ClassLabelModel> classLabels;
+
     private String annotationKind;
+
     private String annotationTool;
     private String preAnnotationTool;
     private String preAnnotationModel;
+
     private String annotationMethod;
+
     private String annotationInstructions;
     private String qualityAssurance;
     private Boolean isInstanceLabel;

src/main/java/org/fgai4h/ap/domain/campaign/service/CampaignService.java

@@ -101,7 +101,7 @@ public void generateTasks(UUID campaignId) {
             List<AnnotationTaskEntity> annotationTaskEntityList = new ArrayList<>();
             annotationTaskEntityList.add(annotationTaskRepository.save(AnnotationTaskEntity.builder()
                     .kind(campaign.getAnnotationKind())
-                    .title(campaign.getAnnotationKind())
+                    .title(String.valueOf(campaign.getAnnotationKind()))
                     .build()));
 
             for (int i = 0; i < objects.size(); i++) {

src/main/java/org/fgai4h/ap/domain/catalog/entity/DataAccessRequestEntity.java

@@ -25,7 +25,7 @@ public class DataAccessRequestEntity {
     @Id
     @GeneratedValue(generator = "uuid2")
     @GenericGenerator(name = "uuid2", strategy = "uuid2")
-    @Column(columnDefinition = "BINARY(16)")
+
     private UUID dataAccessRequestUUID;
 
     private LocalDateTime requestDate;

src/main/java/org/fgai4h/ap/domain/catalog/entity/DataCatalogEntity.java

@@ -22,7 +22,7 @@ public class DataCatalogEntity implements Serializable {
     @Id
     @GeneratedValue(generator = "uuid2")
     @GenericGenerator(name = "uuid2", strategy = "uuid2")
-    @Column(columnDefinition = "BINARY(16)")
+
     private UUID dataCatalogUUID;
 
     private String name;