Merge pull request #52 from Breeding-Insight/java-21-uuid

[BI-2497][BI-2498] Migrate to java 21 and UUID

Author: nickpalladino

Dockerfile

@@ -2,7 +2,7 @@
 # run container (dev): `docker run --name=brapi-test-server --network=bridge -p 8081:8081 -d brapicoordinatorselby/brapi-java-server`
 # run container (prod): `docker run --name=brapi-test-server --restart always --network=brapi_net -d brapicoordinatorselby/brapi-java-server`
 
-FROM adoptopenjdk/openjdk8
+FROM amazoncorretto:21
 
 EXPOSE 8080
 

README.md

@@ -8,6 +8,36 @@ This server implements all BrAPI calls. It is backed by a custom database with d
 
 Use [/calls](https://test-server.brapi.org/brapi/v1/call) (V1) or [/serverinfo](https://test-server.brapi.org/brapi/v2/serverinfo) (V2) to check the available endpoints.
 
+<<<<<<< HEAD
+=======
+## Prerequisites
+* Maven 3.9
+* Java 21
+* Postgres 17.2
+
+## Auth Configuration
+BrAPI has provided a [sample central authentication service for the test server](https://brapi.org/oauth).
+
+Here you can create a user and login to be presented with a token which can be used to make requests to your sample server implementation.
+
+Why offer auth? Apart from security concerns, you can utilize authentication with the BrAPI spec to deliver extra functionality
+tailored to what data you want your users to see.
+
+To utilize the sample central auth service, set the following properties in your `application.properties` file:
+```
+security.oidc_discovery_url=https://test-server.brapi.org/.well-known/openid-configuration
+security.issuer_urlhttps://auth.brapi.org/realms/brapi
+```
+
+If you are not using the sample BrAPI auth system, you must configure these variables properly with the endpoints they expect for your service.
+
+The [local authorization docker set up](#self-contained-authorization-implementation) has some details about how to find these values.
+
+For instructions on how to send the authentication token in your request, see [this section](#authenticating-a-request).
+
+For more information detailing the authentication of the BrAPI Test Server, more documentation with examples and diagrams
+can be found [here](https://plant-breeding-api.readthedocs.io/en/latest/docs/best_practices/Authentication.html)
+>>>>>>> e742f19 (Merge pull request #76 from plantbreeding/java-21-upgrade)
 ## Run
 
 ### Java IDE

docker-compose-dev.yaml

@@ -0,0 +1,21 @@
+services:
+  brapi-java-server-v2:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    ports:
+      - "8080:8080"
+      - "5005:5005"
+    depends_on:
+      - brapi-db
+    volumes:
+      - .\src\main\resources\properties\application.properties:/home/brapi/properties/application.properties
+  brapi-db:
+    image: postgres:17.2
+    environment:
+      POSTGRES_USER: brapi
+      POSTGRES_PASSWORD: password
+    volumes:
+      - /var/lib/postgresql/data
+    ports:
+      - "5433:5432"

docker-compose-local-auth.yaml

@@ -0,0 +1,61 @@
+services:
+  brapi-java-server-v2:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    ports:
+      - "8080:8080"
+      - "5005:5005"
+    depends_on:
+      - brapi-db
+    volumes:
+      - .\src\main\resources\properties\application.properties:/home/brapi/properties/application.properties
+  keycloak-brapi:
+    image: quay.io/keycloak/keycloak:latest
+    entrypoint: /opt/keycloak/bin/kc.sh start-dev
+    depends_on:
+      - keycloak-db
+    environment:
+      - KEYCLOAK_USER=admin
+      - KEYCLOAK_PASSWORD=admin
+      # The KC_HOSTNAME needs to be the same as the defined keycloak-brapi service in the compose file for a local setup.
+      # This allows the brapi app to talk to the keycloak container via the service name in the url, and sets up keycloak
+      # url defaults so that when brapi gets auth urls from keycloak it can still talk to it.
+      - KC_HOSTNAME=keycloak-brapi
+      - KC_DB=postgres
+      - KC_DB_URL=jdbc:postgresql://keycloak-db:5432/keycloak
+      - KC_DB_SCHEMA=public
+      - KC_DB_USERNAME=keycloak
+      - KC_DB_PASSWORD=password
+      - KC_HOSTNAME_STRICT=false
+      - KC_HOSTNAME_STRICT_HTTPS=false
+      - KC_HTTP_PORT=8008
+
+      - KC_LOG_LEVEL=info
+      - KC_METRICS_ENABLED=true
+      - KC_HEALTH_ENABLED=true
+      - KEYCLOAK_ADMIN=admin
+      - KEYCLOAK_ADMIN_PASSWORD=admin
+    ports:
+      - "8008:8008"
+  brapi-db:
+    image: postgres:17.2
+    environment:
+      POSTGRES_USER: brapi
+      POSTGRES_PASSWORD: password
+    volumes:
+      - brapi-data:/var/lib/postgresql/data
+    ports:
+      - "5433:5432"
+  keycloak-db:
+    image: postgres:17.2
+    volumes:
+      - keycloak-data:/var/lib/postgresql/data
+    environment:
+      POSTGRES_USER: keycloak
+      POSTGRES_PASSWORD: password
+    ports:
+      - "5434:5432"
+volumes:
+  keycloak-data:
+  brapi-data:

docker-compose.yaml

@@ -30,10 +30,10 @@ services:
       - KC_DB_USERNAME
       - KC_DB_PASSWORD
   postgres:
-    image: postgres:13
-    restart: unless-stopped
+    image: postgres:17.2
     volumes:
-      - /home/jenkins/brapi.org/brapi-test-server/data:/var/lib/postgresql/data
+      # Update this path with the path your pipeline tool expects
+      - /home/jenkins/brapi.org/brapi-test-server/17-2:/var/lib/postgresql/data
 networks:
     default:
         external:

pom.xml

@@ -14,18 +14,24 @@
 
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		<java.version>1.8</java.version>
-		<spring.version>2.5.12</spring.version>
-		<maven.compiler.source>1.8</maven.compiler.source>
-		<maven.compiler.target>1.8</maven.compiler.target>
-		<springfox-version>2.8.0</springfox-version>
+		<java.version>21</java.version>
+		<spring.version>3.4.0</spring.version>
+		<maven.compiler.source>21</maven.compiler.source>
+		<maven.compiler.target>21</maven.compiler.target>
+		<springfox-version>2.10.0</springfox-version>
+		<slf4j-version>2.0.16</slf4j-version>
 	</properties>
 
 	<dependencies>
 		<dependency>
-		    <groupId>org.flywaydb</groupId>
-		    <artifactId>flyway-core</artifactId>
-		    <version>7.7.3</version>
+			<groupId>org.flywaydb</groupId>
+			<artifactId>flyway-core</artifactId>
+			<version>11.0.1</version>
+		</dependency>
+		<dependency>
+			<groupId>org.flywaydb</groupId>
+			<artifactId>flyway-database-postgresql</artifactId>
+			<version>11.0.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.postgresql</groupId>
@@ -58,6 +64,11 @@
 			<artifactId>spring-boot-starter-security</artifactId>
 			<version>${spring.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-validation</artifactId>
+			<version>${spring.version}</version>
+		</dependency>
 		<dependency>
 			<groupId>io.jsonwebtoken</groupId>
 			<artifactId>jjwt</artifactId>
@@ -100,6 +111,11 @@
 			<artifactId>jackson-datatype-threetenbp</artifactId>
 			<version>2.8.4</version>
 		</dependency>
+		<dependency>
+			<groupId>jakarta.annotation</groupId>
+			<artifactId>jakarta.annotation-api</artifactId>
+			<version>3.0.0</version>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
@@ -115,13 +131,24 @@
 			<artifactId>java-jwt</artifactId>
 			<version>3.14.0</version>
 		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>slf4j-api</artifactId>
+			<version>${slf4j-version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>slf4j-simple</artifactId>
+			<version>${slf4j-version}</version>
+		</dependency>
 	</dependencies>
 
 	<build>
 		<plugins>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-jar-plugin</artifactId>
+				<version>3.4.1</version>
 				<configuration>
 					<archive>
 						<manifest>

src/main/java/io/swagger/api/core/BatchDeletesApi.java

@@ -23,7 +23,7 @@
 
 import java.util.ArrayList;
 
-@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
+@jakarta.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
 @Api(value = "batchDeletes", description = "the batch deletes API")
 public interface BatchDeletesApi {
 

src/main/java/io/swagger/api/core/CommonCropNamesApi.java

@@ -17,7 +17,7 @@
 import org.springframework.web.bind.annotation.RequestParam;
 
 
-@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
+@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
 @Api(value = "commoncropnames", description = "the commoncropnames API")
 public interface CommonCropNamesApi {
 

src/main/java/io/swagger/api/core/ListsApi.java

@@ -28,7 +28,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
+@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
 @Api(value = "lists", description = "the lists API")
 public interface ListsApi {
 

src/main/java/io/swagger/api/core/LocationsApi.java

@@ -25,7 +25,7 @@
 import jakarta.validation.Valid;
 import java.util.List;
 
-@javax.annotation.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
+@javax.annotation.processing.Generated(value = "io.swagger.codegen.v3.generators.java.SpringCodegen", date = "2020-03-20T16:31:52.030Z[GMT]")
 @Api(value = "locations", description = "the locations API")
 public interface LocationsApi {