Refactor submission rejection process

src/main/java/com/insilicosoft/portal/svc/submission/exception/FileProcessingException.java

@@ -15,7 +15,7 @@ public class FileProcessingException extends Exception {
   /**
    * Initialising constructor.
    * 
-   * @param message
+   * @param message Exception message.
    */
   public FileProcessingException(final String message) {
     super(message);

src/main/java/com/insilicosoft/portal/svc/submission/persistence/entity/Simulation.java

@@ -46,34 +46,36 @@ public class Simulation {
   @GeneratedValue(strategy = IDENTITY)
   private Long entityId;
 
-  @Column(nullable = false)
+  @Column(nullable = false, updatable = false)
   private long submissionId;
 
   // Optional. How the client/user identifies the simulation
   @Column(name = "clientId")
   private String clientId;
 
-  @Column(nullable = false)
+  @Column(nullable = false, updatable = false)
   private int modelId;
 
-  @Column(nullable = false)
+  @Column(nullable = false, updatable = false)
   private BigDecimal pacingFrequency;
 
-  @Column(nullable = false)
+  @Column(nullable = false, updatable = false)
   private BigDecimal pacingMaxTime;
 
   @ElementCollection(fetch = FetchType.EAGER)
   @CollectionTable(name = "simulation_plasmapoints",
                    foreignKey = @ForeignKey(name = "simulation_fk"),
                    joinColumns = @JoinColumn(name = "entityId"))
   @Column(nullable = false)
+  // TODO : Find a way to prevent updating this collection
   private List<BigDecimal> plasmaPoints = new ArrayList<>();
 
   @ElementCollection(fetch = FetchType.EAGER)
   @CollectionTable(name = "simulation_message",
                    foreignKey = @ForeignKey(name = "simulation_fk"),
                    joinColumns = @JoinColumn(name = "entityId"))
   @Column(nullable = false)
+  // TODO : Find a way to prevent updating this collection
   private Set<Message> messages = new HashSet<>();
 
   // See JPA auditing
@@ -84,8 +86,9 @@ public class Simulation {
   @LastModifiedBy
   String lastModifiedBy;
 
+  // Optimistic locking concurrency control
   @Version
-  int version;
+  private Long lockVersion;
 
   // Default constructor.
   Simulation() {}
@@ -194,7 +197,7 @@ public String toString() {
     return "Simulation [entityId=" + entityId + ", submissionId=" + submissionId + ", modelId=" + modelId
         + ", pacingFrequency=" + pacingFrequency + ", pacingMaxTime=" + pacingMaxTime + ", plasmaPoints=" + plasmaPoints
         + ", messages=" + messages + ", lastModifiedDate=" + lastModifiedDate + ", lastModifiedBy=" + lastModifiedBy
-        + ", version=" + version + "]";
+        + ", lockVersion=" + lockVersion + "]";
   }
 
 }

src/main/java/com/insilicosoft/portal/svc/submission/persistence/entity/Submission.java

@@ -26,6 +26,7 @@
 import jakarta.persistence.Id;
 import jakarta.persistence.JoinColumn;
 import jakarta.persistence.Table;
+import jakarta.persistence.Version;
 
 /**
  * User submission entity.
@@ -59,6 +60,10 @@ public class Submission {
   @CreatedBy
   String createdBy;
 
+  // Optimistic locking concurrency control
+  @Version
+  private Long lockVersion;
+
   // Default constructor.
 
   /**
@@ -72,27 +77,14 @@ public Submission() {
 
   //
 
-  /**
-   * Reject the submission and populate with the problem as justification.
-   * <p>
-   * Assigns the state to {@link State.REJECTED}
-   * 
-   * @param problem Problem encountered.
-   */
-  public void rejectWithProblem(final Message problem) {
-    this.state = State.REJECTED;
-    this.messages.clear();
-    this.messages.add(problem);
-  }
-
   /**
    * Reject the submission and populate with the problems as justification.
    * <p>
    * Assigns the state to {@link State.REJECTED}
    * 
    * @param problems Problems encountered.
    */
-  public void rejectWithProblems(Map<String, Set<Message>> problems) {
+  public void rejectWithProblems(final Map<String, Set<Message>> problems) {
     this.state = State.REJECTED;
     this.messages.clear();
     for (Map.Entry<String, Set<Message>> mapEntry : problems.entrySet()) {
@@ -127,7 +119,7 @@ public State getState() {
   @Override
   public String toString() {
     return "Submission [entityId=" + entityId + ", state=" + state + ", messages=" + messages + ", createdDate="
-        + createdDate + ", createdBy=" + createdBy + "]";
+        + createdDate + ", createdBy=" + createdBy + ", lockVersion=" + lockVersion + "]";
   }
 
 }

src/main/java/com/insilicosoft/portal/svc/submission/service/InputProcessorServiceImpl.java

@@ -68,6 +68,7 @@ public InputProcessorServiceImpl(final SimulationRepository simulationRepository
     this.submissionService = submissionService;
   }
 
+  // Advice applied to this method to capture FileProcessingException
   @Override
   public void process(final long submissionId, final byte[] file) throws FileProcessingException,
                                                                          InputVerificationException {
@@ -116,20 +117,21 @@ public void process(final long submissionId, final byte[] file) throws FileProce
     if (simulations.isEmpty())
       throw new FileProcessingException("Could not generate any simulations");
 
-    Map<String, Set<Message>> problems = new HashMap<>();
-    int problemCnt = 1;
+    final Map<String, Set<Message>> problems = new HashMap<>();
+    int simulationCnt = 1;
     for (Simulation simulation: simulations) {
-      Set<Message> messages = simulation.getMessages(MessageLevel.WARN);
+      final Set<Message> messages = simulation.getMessages(MessageLevel.WARN);
       if (!messages.isEmpty()) {
+        // Simulations not yet persisted, so no entity id to use.
         problems.put(simulation.getClientId()
-                               .orElse(String.valueOf(submissionId).concat(".").concat(String.valueOf(problemCnt))),
+                               .orElse(String.valueOf(submissionId).concat(".").concat(String.valueOf(simulationCnt))),
                      messages);
-        problemCnt++;
+        simulationCnt++;
       }
     }
 
     if (!problems.isEmpty()) {
-      submissionService.rejectOnInvalidInput(submissionId, problems);
+      submissionService.reject(submissionId, problems);
       throw new InputVerificationException("Problems encountered translating the simulation input");
     }
 

src/main/java/com/insilicosoft/portal/svc/submission/service/SubmissionService.java

@@ -30,20 +30,20 @@ public interface SubmissionService {
   void delete(long submissionId) throws EntityNotAccessibleException;
 
   /**
-   * Reject the {@link Submission} due to file processing problems.
-   * 
-   * @param submissionId Affected submission identifier.
-   * @param problem Problem encountered.
-   */
-  void rejectOnFileProcessing(long submissionId, Message problem);
-
-  /**
-   * Reject the {@link Submission} due to input validation problems.
-   * 
+   * Reject the {@link Submission} due to problems.
+   * <p>
+   * The structure of {@code problems} is keyed on simulation identifier (preference for
+   * using optional client-defined identifier) , e.g. :
+   * <pre>
+   *   {
+   *     &lt;client simulation id | submission id(.&lt;sim 1&gt;)&gt; : [ &lt;Message&gt;, &ltMessage2&gt; ],
+   *     &lt;client simulation id | submission id(.&lt;sim 2&gt;)&gt; : [ &lt;Message&gt; ]
+   *   }
+   * </pre>
    * @param submissionId Affected submission identifier.
    * @param problems Collection of problems encountered.
    */
-  void rejectOnInvalidInput(long submissionId, Map<String, Set<Message>> problems);
+  void reject(long submissionId, Map<String, Set<Message>> problems);
 
   /**
    * Retrieve the {@link Submission} identified by the {@literal submissionId}.

src/main/java/com/insilicosoft/portal/svc/submission/service/SubmissionServiceImpl.java

@@ -60,17 +60,8 @@ public void delete(final long submissionId) throws EntityNotAccessibleException
   }
 
   @Override
-  public void rejectOnFileProcessing(final long submissionId, final Message problem) {
-    log.debug("~rejectOnFileProcessing() : Invoked for id {}", submissionId);
-
-    Submission submission = submissionRepository.getReferenceById(submissionId);
-    submission.rejectWithProblem(problem);
-    submissionRepository.save(submission);
-  }
-
-  @Override
-  public void rejectOnInvalidInput(final long submissionId, final Map<String, Set<Message>> problems) {
-    log.debug("~rejectOnInvalidInput() : Invoked for id {}", submissionId);
+  public void reject(final long submissionId, final Map<String, Set<Message>> problems) {
+    log.debug("~reject() : Invoked for id {}", submissionId);
 
     Submission submission = submissionRepository.getReferenceById(submissionId);
     submission.rejectWithProblems(problems);

src/main/java/com/insilicosoft/portal/svc/submission/service/advice/InputProcessorAdvice.java

@@ -1,5 +1,10 @@
 package com.insilicosoft.portal.svc.submission.service.advice;
 
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
 import org.aspectj.lang.JoinPoint;
 import org.aspectj.lang.annotation.AfterThrowing;
 import org.aspectj.lang.annotation.Aspect;
@@ -17,7 +22,7 @@
 @Component
 public class InputProcessorAdvice {
 
-  private SubmissionService submissionService;
+  private final SubmissionService submissionService;
 
   /**
    * Initialising constructor.
@@ -41,8 +46,13 @@ public class InputProcessorAdvice {
   public void handleFileProcessingException(JoinPoint joinPoint, FileProcessingException fpe)
                                             throws FileProcessingException {
     final long submissionId = Long.valueOf(joinPoint.getArgs()[0].toString());
-    submissionService.rejectOnFileProcessing(submissionId, new Message(MessageLevel.WARN,
-                                                                       fpe.getMessage()));
+
+    final Map<String, Set<Message>> problems = new HashMap<>();
+    final Set<Message> messages = new HashSet<>();
+    messages.add(new Message(MessageLevel.WARN, fpe.getMessage()));
+    problems.put(String.valueOf(submissionId), messages);
+
+    submissionService.reject(submissionId, problems);
     throw new FileProcessingException(fpe.getMessage());
   }
 

src/main/resources/application.yml

@@ -10,6 +10,8 @@ com:
       thread-name-prefix: ~simsvc-dflt-
 
 logging:
+  #file:
+  #  name: logs/submission-svc.log
   level:
     root: DEBUG
 

src/test-e2e/java/com/insilicosoft/portal/svc/submission/actuator/ActuatorE2E.java

@@ -1,22 +1,23 @@
 package com.insilicosoft.portal.svc.submission.actuator;
 
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.springframework.boot.test.context.SpringBootTest.WebEnvironment.RANDOM_PORT;
+
 
 import org.junit.jupiter.api.DisplayName;
 import org.junit.jupiter.api.Nested;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.boot.test.context.SpringBootTest.WebEnvironment;
 import org.springframework.boot.test.mock.mockito.MockBean;
 import org.springframework.boot.test.web.client.TestRestTemplate;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.security.oauth2.jwt.JwtDecoder;
 
-@SpringBootTest(webEnvironment = WebEnvironment.RANDOM_PORT)
+@SpringBootTest(webEnvironment = RANDOM_PORT)
 public class ActuatorE2E {
 
   private String actuatorUsername;

src/test-e2e/java/com/insilicosoft/portal/svc/submission/controller/SubmissionControllerE2E.java

@@ -188,6 +188,7 @@ void successOnSubmissionLifecycle() {
       var multipartBodyBuilder = new MultipartBodyBuilder();
       multipartBodyBuilder.part(SubmissionIdentifiers.PARAM_NAME_SIMULATION_FILE,
                                 new FileSystemResource(goodPath));
+
       webTestClient.post()
                    .uri(postUrl)
                    .headers(headers -> {