Introduce sample batch domain model (#212)

Adds implementation and support for sample registration and batch registration.

Also includes a new domain dispatcher implementation backed by JobRunr, that allows for persistent
event management.

# Co-authored-by: KochTobi <[email protected]>

Author: sven1103

database-connector/src/main/java/life/qbic/projectmanagement/experiment/persistence/BatchJpaRepository.java

@@ -0,0 +1,54 @@
+package life.qbic.projectmanagement.experiment.persistence;
+
+import static life.qbic.logging.service.LoggerFactory.logger;
+
+import java.util.Optional;
+import life.qbic.application.commons.Result;
+import life.qbic.logging.api.Logger;
+import life.qbic.projectmanagement.domain.project.repository.BatchRepository;
+import life.qbic.projectmanagement.domain.project.sample.Batch;
+import life.qbic.projectmanagement.domain.project.sample.BatchId;
+import life.qbic.projectmanagement.domain.project.service.BatchDomainService.ResponseCode;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Repository;
+
+/**
+ * <b>Batch JPA Repository</b>
+ *
+ * <p>Implementation of the {@link BatchRepository} interface.</p>
+ *
+ * @since 1.0.0
+ */
+@Repository
+public class BatchJpaRepository implements BatchRepository {
+
+  private static final Logger log = logger(BatchJpaRepository.class);
+
+  private final QbicBatchRepo qbicBatchRepo;
+
+  @Autowired
+  public BatchJpaRepository(QbicBatchRepo qbicBatchRepo) {
+    this.qbicBatchRepo = qbicBatchRepo;
+  }
+
+  @Override
+  public Result<Batch, ResponseCode> add(Batch batch) {
+    try {
+      qbicBatchRepo.save(batch);
+    } catch (Exception e) {
+      log.error(e.getMessage(), e);
+      return Result.fromError(ResponseCode.BATCH_REGISTRATION_FAILED);
+    }
+    return Result.fromValue(batch);
+  }
+
+  @Override
+  public Optional<Batch> find(BatchId batchId) {
+    return this.qbicBatchRepo.findById(batchId);
+  }
+
+  @Override
+  public Result<Batch, ResponseCode> update(Batch batch) {
+    return Result.fromValue(this.qbicBatchRepo.save(batch));
+  }
+}

database-connector/src/main/java/life/qbic/projectmanagement/experiment/persistence/QbicBatchRepo.java

@@ -0,0 +1,11 @@
+package life.qbic.projectmanagement.experiment.persistence;
+
+import life.qbic.projectmanagement.domain.project.sample.Batch;
+import life.qbic.projectmanagement.domain.project.sample.BatchId;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface QbicBatchRepo extends JpaRepository<Batch, BatchId> {
+
+
+
+}

database-connector/src/main/java/life/qbic/projectmanagement/experiment/persistence/QbicSampleRepository.java

@@ -0,0 +1,9 @@
+package life.qbic.projectmanagement.experiment.persistence;
+
+import life.qbic.projectmanagement.domain.project.sample.Sample;
+import life.qbic.projectmanagement.domain.project.sample.SampleId;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface QbicSampleRepository extends JpaRepository<Sample, SampleId> {
+
+}

database-connector/src/main/java/life/qbic/projectmanagement/experiment/persistence/SampleJpaRepository.java

@@ -0,0 +1,42 @@
+package life.qbic.projectmanagement.experiment.persistence;
+
+import static life.qbic.logging.service.LoggerFactory.logger;
+
+import life.qbic.application.commons.Result;
+import life.qbic.logging.api.Logger;
+import life.qbic.projectmanagement.domain.project.repository.SampleRepository;
+import life.qbic.projectmanagement.domain.project.sample.Sample;
+import life.qbic.projectmanagement.domain.project.service.SampleDomainService.ResponseCode;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Repository;
+
+/**
+ * <b>Sample JPA Repository</b>
+ *
+ * <p>Implementation of the {@link SampleRepository} interface</p>
+ *
+ * @since 1.0.0
+ */
+@Repository
+public class SampleJpaRepository implements SampleRepository {
+
+  private static final Logger log = logger(SampleJpaRepository.class);
+
+  private final QbicSampleRepository qbicSampleRepository;
+
+  @Autowired
+  public SampleJpaRepository(QbicSampleRepository qbicSampleRepository) {
+    this.qbicSampleRepository = qbicSampleRepository;
+  }
+
+  @Override
+  public Result<Sample, ResponseCode> add(Sample sample) {
+    try {
+      this.qbicSampleRepository.save(sample);
+    } catch (Exception e) {
+      log.error("Saving sample with id failed:" + sample.sampleId(), e);
+      return Result.fromError(ResponseCode.REGISTRATION_FAILED);
+    }
+    return Result.fromValue(sample);
+  }
+}

pom.xml

@@ -131,6 +131,12 @@
         <version>2.4-M1-groovy-4.0</version>
         <scope>test</scope>
       </dependency>
+      <dependency>
+        <groupId>org.spockframework</groupId>
+        <artifactId>spock-spring</artifactId>
+        <version>2.4-M1-groovy-4.0</version>
+        <scope>test</scope>
+      </dependency>
       <dependency>
         <groupId>org.apache.groovy</groupId>
         <artifactId>groovy-all</artifactId>

projectmanagement/pom.xml

@@ -20,6 +20,16 @@
       <artifactId>spock-core</artifactId>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot</artifactId>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-starter-test</artifactId>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>finances</artifactId>
@@ -48,5 +58,24 @@
       <version>6.0.2</version>
       <scope>compile</scope>
     </dependency>
+    <dependency>
+      <groupId>life.qbic</groupId>
+      <artifactId>domain-concept</artifactId>
+      <version>0.15.1</version>
+      <scope>compile</scope>
+    </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-databind</artifactId>
+    </dependency>
+    <!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.datatype/jackson-datatype-jsr310 -->
+    <dependency>
+      <groupId>com.fasterxml.jackson.datatype</groupId>
+      <artifactId>jackson-datatype-jsr310</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.jobrunr</groupId>
+      <artifactId>jobrunr-spring-boot-3-starter</artifactId>
+    </dependency>
   </dependencies>
 </project>

projectmanagement/src/main/java/life/qbic/projectmanagement/application/batch/BatchRegistrationService.java

@@ -0,0 +1,52 @@
+package life.qbic.projectmanagement.application.batch;
+
+import life.qbic.application.commons.Result;
+import life.qbic.projectmanagement.domain.project.repository.BatchRepository;
+import life.qbic.projectmanagement.domain.project.sample.Batch;
+import life.qbic.projectmanagement.domain.project.sample.BatchId;
+import life.qbic.projectmanagement.domain.project.sample.SampleId;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+/**
+ * <b><class short description - 1 Line!></b>
+ *
+ * <p><More detailed description - When to use, what it solves, etc.></p>
+ *
+ * @since <version tag>
+ */
+@Service
+public class BatchRegistrationService {
+
+  private final BatchRepository batchRepository;
+
+  public BatchRegistrationService(@Autowired BatchRepository batchRepository) {
+    this.batchRepository = batchRepository;
+  }
+
+  public Result<BatchId, ResponseCode> registerBatch(String label, boolean isPilot) {
+    Batch batch = Batch.create(label, isPilot);
+    var result = batchRepository.add(batch);
+    if (result.isError()) {
+      return Result.fromError(ResponseCode.BATCH_CREATION_FAILED);
+    }
+    return Result.fromValue(batch.batchId());
+  }
+
+  public Result<BatchId, ResponseCode> addSampleToBatch(SampleId sampleId, BatchId batchId) {
+    var searchResult = batchRepository.find(batchId);
+    if (searchResult.isEmpty()) {
+      return Result.fromError(ResponseCode.BATCH_NOT_FOUND);
+    }
+    searchResult.ifPresent(batch -> {
+      batch.addSample(sampleId);
+      batchRepository.update(batch);
+    });
+    return Result.fromValue(batchId);
+  }
+
+  public enum ResponseCode {
+    BATCH_UPDATE_FAILED, BATCH_NOT_FOUND, BATCH_CREATION_FAILED
+  }
+
+}

projectmanagement/src/main/java/life/qbic/projectmanagement/application/policy/SampleRegisteredPolicy.java

@@ -0,0 +1,35 @@
+package life.qbic.projectmanagement.application.policy;
+
+import life.qbic.domain.concepts.DomainEventDispatcher;
+import life.qbic.projectmanagement.application.policy.directive.AddSampleToBatch;
+
+/**
+ * <b>Policy: Sample Registered</b>
+ * <p>
+ * A collection of all directives that need to be executed after a new sample has been registered
+ * for measurement.
+ * <p>
+ * The policy subscribes to events of type
+ * {@link life.qbic.projectmanagement.domain.project.sample.event.SampleRegistered} and ensures the
+ * registration of all business required directives.
+ *
+ * @since 1.0.0
+ */
+public class SampleRegisteredPolicy {
+
+  private final AddSampleToBatch addSampleToBatch;
+
+  /**
+   * Creates an instance of a {@link SampleRegisteredPolicy} object.
+   * <p>
+   * All directives will be created an subscribed upon instantiation.
+   *
+   * @param addSampleToBatch directive to update the affected sample
+   *                         {@link life.qbic.projectmanagement.domain.project.sample.Batch}
+   * @since 1.0.0
+   */
+  public SampleRegisteredPolicy(AddSampleToBatch addSampleToBatch) {
+    this.addSampleToBatch = addSampleToBatch;
+    DomainEventDispatcher.instance().subscribe(this.addSampleToBatch);
+  }
+}

projectmanagement/src/main/java/life/qbic/projectmanagement/application/policy/directive/AddSampleToBatch.java

@@ -0,0 +1,39 @@
+package life.qbic.projectmanagement.application.policy.directive;
+
+import life.qbic.domain.concepts.DomainEvent;
+import life.qbic.domain.concepts.DomainEventSubscriber;
+import life.qbic.projectmanagement.application.batch.BatchRegistrationService;
+import life.qbic.projectmanagement.domain.project.sample.event.SampleRegistered;
+import org.jobrunr.scheduling.JobScheduler;
+
+/**
+ * <b>Directive: Add Sample to Batch</b>
+ * <p>
+ * After a sample has been registered and assigned to a batch, we need to update the batch and add
+ * the sample reference of the newly registered sample.
+ *
+ * @since 1.0.0
+ */
+public class AddSampleToBatch implements DomainEventSubscriber<SampleRegistered> {
+
+  private final BatchRegistrationService batchRegistrationService;
+
+  private final JobScheduler jobScheduler;
+
+  public AddSampleToBatch(BatchRegistrationService batchRegistrationService,
+      JobScheduler jobScheduler) {
+    this.batchRegistrationService = batchRegistrationService;
+    this.jobScheduler = jobScheduler;
+  }
+
+  @Override
+  public Class<? extends DomainEvent> subscribedToEventType() {
+    return SampleRegistered.class;
+  }
+
+  @Override
+  public void handleEvent(SampleRegistered event) {
+    jobScheduler.enqueue(() -> batchRegistrationService.addSampleToBatch(event.registeredSample(),
+        event.assignedBatch()));
+  }
+}

projectmanagement/src/main/java/life/qbic/projectmanagement/domain/project/repository/BatchRepository.java

@@ -0,0 +1,31 @@
+package life.qbic.projectmanagement.domain.project.repository;
+
+import java.util.Optional;
+import life.qbic.application.commons.Result;
+import life.qbic.projectmanagement.domain.project.sample.Batch;
+import life.qbic.projectmanagement.domain.project.sample.BatchId;
+import life.qbic.projectmanagement.domain.project.service.BatchDomainService.ResponseCode;
+
+/**
+ * Batch data storage interface
+ * <p>
+ * Provides access to the persistence layer that handles the {@link Batch} data storage.
+ *
+ * @since 1.0.0
+ */
+public interface BatchRepository {
+
+  /**
+   * Saves a {@link Batch} entity persistently.
+   *
+   * @param batch the sample batch to register
+   * @return a {@link Result} with the batch as value or an error response code {@link ResponseCode}.
+   * @since 1.0.0
+   */
+  Result<Batch, ResponseCode> add(Batch batch);
+
+  Optional<Batch> find(BatchId batchId);
+
+  Result<Batch, ResponseCode> update(Batch batch);
+
+}

projectmanagement/src/main/java/life/qbic/projectmanagement/domain/project/repository/SampleRepository.java

@@ -0,0 +1,24 @@
+package life.qbic.projectmanagement.domain.project.repository;
+
+import life.qbic.application.commons.Result;
+import life.qbic.projectmanagement.domain.project.sample.Sample;
+import life.qbic.projectmanagement.domain.project.service.SampleDomainService.ResponseCode;
+
+/**
+ * Sample data storage interface
+ * <p>
+ * Provides access to the persistence layer that handles {@link Sample} data storage.
+ *
+ * @since 1.0.0
+ */
+public interface SampleRepository {
+
+  /**
+   * Saves a sample entity persistently.
+   *
+   * @param sample the sample to save.
+   * @since 1.0.0
+   */
+  Result<Sample, ResponseCode> add(Sample sample);
+
+}

projectmanagement/src/main/java/life/qbic/projectmanagement/domain/project/repository/jpa/BatchIdConverter.java

@@ -0,0 +1,24 @@
+package life.qbic.projectmanagement.domain.project.repository.jpa;
+
+import jakarta.persistence.AttributeConverter;
+import life.qbic.projectmanagement.domain.project.sample.BatchId;
+
+/**
+ * <b><class short description - 1 Line!></b>
+ *
+ * <p><More detailed description - When to use, what it solves, etc.></p>
+ *
+ * @since <version tag>
+ */
+public class BatchIdConverter implements AttributeConverter<BatchId, String> {
+
+  @Override
+  public String convertToDatabaseColumn(BatchId batchId) {
+    return batchId.value();
+  }
+
+  @Override
+  public BatchId convertToEntityAttribute(String s) {
+    return BatchId.parse(s);
+  }
+}