adding receipt package from repository-lib

.github/workflows/build-biosamples-service.yml

@@ -27,7 +27,10 @@ jobs:
       - name: Build Docker image
         uses: docker/build-push-action@v6
         with:
-          context: repository-services
+          context: repository-services/isajson-biosamples
           file: repository-services/isajson-biosamples/Dockerfile
           push: false
           tags: user/app:latest
+          build-args: |
+            GPR_USER=${{ secrets.GPR_USER }}
+            GPR_TOKEN=${{ secrets.GPR_TOKEN }}

repository-services/docker-compose.yml

@@ -1,16 +1,22 @@
 services:
   isa_biosamples:
       build:
-        context: .
-        dockerfile: isajson-biosamples/Dockerfile
+        context: ./isajson-biosamples
+        dockerfile: Dockerfile
+        args:
+          GPR_USER: ${GPR_USER}
+          GPR_TOKEN: ${GPR_TOKEN}
       ports:
         - "8032:8032"
       restart: unless-stopped
 
   isa_sra:
       build:
-        context: .
-        dockerfile: isajson-ena/Dockerfile
+        context: ./isajson-ena
+        dockerfile: Dockerfile
+        args:
+          GPR_USER: ${GPR_USER}
+          GPR_TOKEN: ${GPR_TOKEN}
       ports:
         - "8042:8042"
       restart: unless-stopped

repository-services/isajson-biosamples/Dockerfile

@@ -1,26 +1,36 @@
-# Builder stage: Use gradle image to compile jar file
+# Builder stage
 FROM gradle:jdk11 AS builder
 
 WORKDIR /app
 
+# Copy everything from context (the service folder)
 COPY . .
 
-WORKDIR /app/receipt
-RUN ./gradlew build
-RUN ./gradlew publishToMavenLocal
+ARG GPR_USER
+ARG GPR_TOKEN
 
-WORKDIR /app/isajson-biosamples
-RUN ./gradlew build -x test -x spotlessApply --info --stacktrace "-Dorg.gradle.jvmargs=--add-exports jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED"
+# Make gradlew executable
+RUN chmod +x gradlew
+# Build the JAR
+RUN mkdir -p /root/.gradle && \
+    echo "gpr.user=${GPR_USER}" >> /root/.gradle/gradle.properties && \
+    echo "gpr.token=${GPR_TOKEN}" >> /root/.gradle/gradle.properties && \
+    ./gradlew build -x test -x spotlessApply --info --stacktrace \
+      "-Dorg.gradle.jvmargs=--add-exports jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED \
+       --add-exports jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED \
+       --add-exports jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED \
+       --add-exports jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED \
+       --add-exports jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED"
 
-# Use a lightweight base image to run the jar file
-FROM openjdk:11-jre-slim
-WORKDIR /app
 
-ARG JAR_FILE=/app/isajson-biosamples/build/libs/*.jar
+# Runtime stage           
+FROM eclipse-temurin:11-jre-alpine
+
+WORKDIR /app
 
-# Copy the JAR file from the builder stage
-COPY --from=builder ${JAR_FILE} app.jar
+# Copy the built JAR
+COPY --from=builder /app/build/libs/*.jar app.jar
 
-# Set the entry point for the application
 ENTRYPOINT ["java", "-jar", "app.jar"]
 
+

repository-services/isajson-biosamples/build.gradle

@@ -12,6 +12,13 @@ group = 'com.elixir.biohackaton'
 version = '0.0.1-SNAPSHOT'
 
 repositories {
+    maven {
+        url = uri("https://maven.pkg.github.com/elixir-europe/mars-repository-lib")
+        credentials {
+            username = project.findProperty("gpr.user") ?: System.getenv("GPR_USER")
+            password = project.findProperty("gpr.token") ?: System.getenv("GPR_TOKEN")
+        }
+    }
     mavenLocal()
     mavenCentral()
 }
@@ -27,8 +34,8 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-collections4', version: '4.1'
     implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5'
     implementation group: 'dom4j', name: 'dom4j', version: '1.6.1'
-    
-    implementation group: 'com.elixir.biohackaton', name: 'mars-receipt', version: '0.0.1'
+
+    implementation 'com.elixir.mars:mars-repository:0.0.1'
 
     compileOnly group: 'org.projectlombok', name: 'lombok', version: '1.18.24'
     annotationProcessor 'org.projectlombok:lombok:1.18.24'

repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java

@@ -16,9 +16,9 @@
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
 import com.elixir.biohackaton.ISAToSRA.biosamples.service.BioSamplesSubmitter;
 import com.elixir.biohackaton.ISAToSRA.biosamples.service.MarsReceiptService;
-import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.IsaJson;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Study;
+import com.elixir.mars.repository.MarsReceiptException;
+import com.elixir.mars.repository.models.isa.IsaJson;
+import com.elixir.mars.repository.models.isa.Study;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.ObjectMapper;
 

repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/model/BiosampleAccessionsMap.java

@@ -1,6 +1,6 @@
 package com.elixir.biohackaton.ISAToSRA.biosamples.model;
 
-import com.elixir.biohackaton.ISAToSRA.receipt.ReceiptAccessionsMap;
+import com.elixir.mars.repository.ReceiptAccessionsMap;
 
 public class BiosampleAccessionsMap {
     public ReceiptAccessionsMap sourceAccessionsMap = new ReceiptAccessionsMap();

repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java

@@ -22,14 +22,14 @@
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.BioSample;
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.Relationship;
-import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
-import com.elixir.biohackaton.ISAToSRA.receipt.ReceiptAccessionsMap;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Category;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Characteristic;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Sample;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Source;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Study;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Value;
+import com.elixir.mars.repository.MarsReceiptException;
+import com.elixir.mars.repository.ReceiptAccessionsMap;
+import com.elixir.mars.repository.models.isa.Category;
+import com.elixir.mars.repository.models.isa.Characteristic;
+import com.elixir.mars.repository.models.isa.Sample;
+import com.elixir.mars.repository.models.isa.Source;
+import com.elixir.mars.repository.models.isa.Study;
+import com.elixir.mars.repository.models.isa.Value;
 
 import lombok.extern.slf4j.Slf4j;
 

repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/MarsReceiptService.java

@@ -8,10 +8,10 @@
 import org.springframework.web.servlet.HandlerInterceptor;
 
 import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
-import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptProvider;
-import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.IsaJson;
-import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.MarsError;
-import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.MarsErrorType;
+import com.elixir.mars.repository.MarsReceiptProvider;
+import com.elixir.mars.repository.models.isa.IsaJson;
+import com.elixir.mars.repository.models.receipt.MarsError;
+import com.elixir.mars.repository.models.receipt.MarsErrorType;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;