Merge branch 'dev'

.github/workflows/ci.yml

@@ -0,0 +1,80 @@
+name: Java CI
+
+on: [push]
+
+jobs:
+  build:
+    name: Test, validate and build Java application
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK 11
+        uses: actions/setup-java@v1
+        with:
+          java-version: 11
+      - name: Cache local Maven repository
+        uses: actions/cache@v2
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
+      - name: Build with Maven
+        run: mvn verify
+      - name: Run Checkstyle
+        run: mvn checkstyle:check
+      - name: Run SpotBugs
+        run: mvn com.github.spotbugs:spotbugs-maven-plugin:check
+      - name: Run OWASP dependency-check (only on dev)
+        run: mvn org.owasp:dependency-check-maven:check
+        if: ${{ github.ref == 'refs/heads/dev' }}
+
+      - name: Extract Version
+        if: ${{ github.ref == 'refs/heads/master' }}
+        run: |
+          mvn help:evaluate -Dexpression=project.version -q -DforceStdout > version.txt
+      - name: Store artifacts
+        if: ${{ github.ref == 'refs/heads/master' }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: build-artifacts
+          path: |
+            version.txt
+            target/seqdb.api-*.jar
+            Dockerfile
+
+  push:
+    name: Build Docker Image and Push to DockerHub
+    needs: [build]
+    runs-on: ubuntu-latest
+    if: ${{ github.ref == 'refs/heads/master' }}
+
+    steps:
+      - name: Download artifacts from build job
+        uses: actions/download-artifact@v2
+        with:
+          name: build-artifacts
+
+      - name: Set VERSION_TAG ENV variable
+        run: |
+          echo "VERSION_TAG=$(cat version.txt)" >> $GITHUB_ENV
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Build Image and Push
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          push: true
+          tags: aafcbicoe/seqdb-api:${{ env.VERSION_TAG }}

.gitignore

@@ -4,4 +4,5 @@
 /target/
 .vscode
 .factorypath
-*.env
+*.env
+docker-compose.yml

Dockerfile

@@ -1,4 +1,5 @@
-FROM maven:3.6.3-jdk-11-slim
+FROM openjdk:11-jre-slim
+
 RUN useradd -s /bin/bash user
 USER user
 COPY --chown=644 target/seqdb.api-*.jar /seqdb-api.jar

README.md

@@ -9,6 +9,7 @@ seqdb-api is an implementation of the Sequence Module for the [DINA project](htt
 * Java 11
 * Maven 3.2+
 * PostgreSQL 10
+* Docker
 
 ## Run
 
@@ -27,20 +28,28 @@ mvn clean compile
 
 The single HTML page will be available at `target/generated-docs/index.html`
 
-## Testing
+## To Run
 
-For testing purpose or local development a [Docker Compose](https://docs.docker.com/compose/) file is available in the `local` folder.
+For testing purpose a [Docker Compose](https://docs.docker.com/compose/) example file is available in the `local` folder.
 
-**Please Note** : when running a local postgres database you will want to map your ports to something other then 5432 inside your `Docker Compose`:
+Create a new docker-compose.yml file and .env file from the example file in the local directory:
 
 ```
-ports:
-   - "5431:5432"
+cp local/docker-compose.yml.example docker-compose.yml
+cp local/*.env .
 ```
 
-And then you will want to update your `test-db-configuration` URLs to:
-````
-url: jdbc:postgresql://localhost:5431/seqdb_api_test?currentSchema=seqdb
-````
+Start the app (default port is 8084):
 
-This example would map your containers 5432 port to your Host machines 5431 port and the updated spring source url would allow your tests to connect to the newly mapped port.
+```
+docker-compose up
+```
+
+Once the services have started you can access the endpoints at http://localhost:8084/api/
+
+Cleanup:
+```
+docker-compose down
+```
+
+Automated tests are run using an embedded Docker container.

local/docker-compose.yml.example

@@ -1,13 +1,18 @@
-version: '3'
+version: '3.7'
 services:
-  db:
+  seqdb-db:
     image: "postgres:10"
-    container_name: "seqdbapi_test_postgres"
-    environment:
-      POSTGRES_DB: seqdb_api_test
-      POSTGRES_PASSWORD: mypassword
+    env_file:
+      - ${BASE_PATH_TO_SEQDB:-.}/pg.env
     volumes:
-      - ./src/test/resources/init-db.sql:/docker-entrypoint-initdb.d/1-init-schema.sql
+      - ${BASE_PATH_TO_SEQDB:-.}/src/test/resources/init-test-db.sql:/docker-entrypoint-initdb.d/1-init-schema.sql
+
+  seqdb-api:
+    build: ${BASE_PATH_TO_SEQDB:-.}
     ports:
-      - "5432:5432"
+      - "8084:8080"
+    env_file:
+      - ${BASE_PATH_TO_SEQDB:-.}/seqdb-api.env
+    networks:
+      default:      
 

local/pg.env

@@ -0,0 +1,2 @@
+POSTGRES_DB=seqdb_test
+POSTGRES_PASSWORD= mypassword

local/seqdb-api.env

@@ -0,0 +1,6 @@
+spring.datasource.url=jdbc:postgresql://seqdb-db/seqdb_test?currentSchema=seqdb
+spring.datasource.username=web_user
+spring.datasource.password=test
+spring.liquibase.user=migration_user
+spring.liquibase.password=test
+

pom.xml

@@ -3,33 +3,29 @@
 
   <groupId>ca.gc.aafc</groupId>
   <artifactId>seqdb.api</artifactId>
-  <version>1.5</version>
+  <version>2.0.0</version>
   <packaging>jar</packaging>
 
   <name>seqdb.api</name>
   <url>https://github.com/AAFC-BICoE/seqdb-api</url>
 
   <properties>
     <java.version>11</java.version>
-    <modelmapper.version>1.1.3</modelmapper.version>
     <guava.version>24.1.1-jre</guava.version>
     <javax.inject.version>1</javax.inject.version>
     <!-- Different from SpringBoot javax-jaxb.version since they don't manage jaxb-core and jaxb-impl-->
     <javax.interceptor-api>1.2.2</javax.interceptor-api>
 
     <spotbugs-maven-plugin.version>4.1.3</spotbugs-maven-plugin.version>
     <spotbugs.version>4.1.3</spotbugs.version>
-    <jcip-annotations.version>1.0</jcip-annotations.version>
+
     <!-- Override SpringBoot version (3.6) to avoid NoClassDefFoundError: org/apache/maven/doxia/siterenderer/DocumentContent -->
     <maven-site-plugin.version>3.7.1</maven-site-plugin.version>
     <dependency-check-maven.version>6.0.2</dependency-check-maven.version>
     <maven-checkstyle-plugin.version>3.1.1</maven-checkstyle-plugin.version>
     <jacoco-maven-plugin.version>0.8.5</jacoco-maven-plugin.version>
     <checkstyle.version>8.36</checkstyle.version>
     <asciidoctor-maven-plugin.version>2.1.0</asciidoctor-maven-plugin.version>
-    <justify.version>0.17.0</justify.version>    
-    <javax.json.version>1.1.3</javax.json.version>
-    <commons.beanutils.version>1.9.3</commons.beanutils.version>
     <hibernate-types-52.version>2.9.5</hibernate-types-52.version>
     <dina-base-api.version>0.42</dina-base-api.version>
 
@@ -74,9 +70,8 @@
       <groupId>org.liquibase</groupId>
       <artifactId>liquibase-core</artifactId>
     </dependency>
-
-	<!-- util -->
-	<dependency>
+    <!-- util -->
+    <dependency>
       <groupId>org.projectlombok</groupId>
       <artifactId>lombok</artifactId>
 	</dependency>
@@ -85,82 +80,27 @@
       <artifactId>guava</artifactId>
       <version>${guava.version}</version>
     </dependency>
-    <dependency>
-      <groupId>com.jayway.jsonpath</groupId>
-      <artifactId>json-path</artifactId>
-    </dependency>
 
 	<!-- Used by Spotbug annotation -->
-    <dependency>
-      <groupId>net.jcip</groupId>
-      <artifactId>jcip-annotations</artifactId>
-      <version>${jcip-annotations.version}</version>
-      <scope>provided</scope>
-    </dependency>
     <dependency>
       <groupId>com.github.spotbugs</groupId>
       <artifactId>spotbugs-annotations</artifactId>
       <version>${spotbugs.version}</version>
       <scope>provided</scope>
     </dependency>
 
-	<!-- Required support for JAXB annotations as of the latest version of liquibase. Redmine Issue: #18647-->
-	<dependency>
-		<groupId>com.fasterxml.jackson.module</groupId>
-		<artifactId>jackson-module-jaxb-annotations</artifactId>		
-	</dependency>
-
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-lang3</artifactId>
     </dependency>
-
-    <dependency>
-		<groupId>commons-beanutils</groupId>
-		<artifactId>commons-beanutils</artifactId>
-		<version>${commons.beanutils.version}</version>
-	</dependency>
 
     <!-- TEST Scope -->
     <dependency>
       <groupId>ca.gc.aafc</groupId>
       <artifactId>dina-test-support</artifactId>
       <version>${dina-base-api.version}</version>
       <scope>test</scope>
-    </dependency>  
-    <dependency>
-      <groupId>org.springframework.boot</groupId>
-      <artifactId>spring-boot-starter-test</artifactId>
-      <scope>test</scope>
     </dependency>
-    <dependency>
-      <groupId>io.rest-assured</groupId>
-      <artifactId>rest-assured</artifactId>
-      <scope>test</scope>
-	</dependency>
-	<dependency>
-      <groupId>io.rest-assured</groupId>
-      <artifactId>json-path</artifactId>
-      <scope>test</scope>
-	</dependency>
-    <dependency>
-      <groupId>io.rest-assured</groupId>
-	  <artifactId>rest-assured-all</artifactId>
-	  <version>${rest-assured.version}</version>
-	  <scope>test</scope>
-	</dependency>
-	<dependency>
-		<groupId>org.leadpony.justify</groupId>
-		<artifactId>justify</artifactId>
-		<version>${justify.version}</version>
-		<scope>test</scope>
-	</dependency>
-	<dependency>
-		<groupId>org.glassfish</groupId>
-		<artifactId>javax.json</artifactId>
-		<version>${javax.json.version}</version>
-		<scope>test</scope>
-	</dependency>
   </dependencies>
 
   <build>

src/main/java/ca/gc/aafc/seqdb/api/ResourceRepositoryConfig.java

@@ -68,7 +68,7 @@ public JpaDtoMapper dtoJpaMapper(BaseDAO baseDAO) {
 
     // Map all DTOs to their related Entities.
     Map<Class<?>, Class<?>> entitiesMap = ClassAnnotationHelper
-      .findAnnotatedClasses(ChainDto.class, RelatedEntity.class)
+      .findAnnotatedClasses(RegionDto.class, RelatedEntity.class)
       .stream()
       .collect(
         Collectors.toMap(

src/main/java/ca/gc/aafc/seqdb/api/dto/PcrPrimerDto.java

@@ -5,6 +5,11 @@
 import java.time.OffsetDateTime;
 import java.util.UUID;
 
+import org.javers.core.metamodel.annotation.Id;
+import org.javers.core.metamodel.annotation.PropertyName;
+import org.javers.core.metamodel.annotation.ShallowReference;
+import org.javers.core.metamodel.annotation.TypeName;
+
 import ca.gc.aafc.dina.dto.RelatedEntity;
 import ca.gc.aafc.seqdb.api.entities.PcrPrimer;
 import ca.gc.aafc.seqdb.api.entities.PcrPrimer.PrimerType;
@@ -15,12 +20,17 @@
 import lombok.Data;
 
 @Data
-@JsonApiResource(type = "pcrPrimer")
+@JsonApiResource(type = PcrPrimerDto.TYPENAME)
 @SuppressFBWarnings(value = "EI_EXPOSE_REP")
 @RelatedEntity(PcrPrimer.class)
+@TypeName(PcrPrimerDto.TYPENAME)
 public class PcrPrimerDto {
+
+  public static final String TYPENAME = "pcrPrimer";  
 
   @JsonApiId
+  @Id
+  @PropertyName("id")  
   private UUID uuid;
 
   private String createdBy;
@@ -32,6 +42,7 @@ public class PcrPrimerDto {
 
   private String name;
 
+  @ShallowReference  
   private PrimerType type;
 
   private String seq;
@@ -71,7 +82,7 @@ public class PcrPrimerDto {
   private String stockConcentration;
 
   // Optional relations
-
+  @ShallowReference
   @JsonApiRelation
   private RegionDto region;