Refactor Simulation to Submission svc

flawmop · Sep 24, 2024 · 15b324e · 15b324e
1 parent d4cfdc1
commit 15b324e
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diff --git a/.github/workflows/acceptance-stage.yml b/.github/workflows/acceptance-stage.yml
@@ -9,7 +9,7 @@ concurrency: acceptance
 env:
   OWNER: flawmop
   REGISTRY: ghcr.io
-  APP_REPO: simulation-svc
+  APP_REPO: submission-svc
   DEPLOY_REPO: portal-deploy
   VERSION: ${{ github.sha }}
 

diff --git a/.github/workflows/commit-stage.yml b/.github/workflows/commit-stage.yml
@@ -4,8 +4,8 @@ on: push
 env:
   OWNER: flawmop
   REGISTRY: ghcr.io
-  IMAGE_NAME: flawmop/simulation-svc
-  APP_REPO: simulation-svc
+  IMAGE_NAME: flawmop/submission-svc
+  APP_REPO: submission-svc
   DEPLOY_REPO: portal-deploy
   VERSION: ${{ github.sha }}
 

diff --git a/README.md b/README.md
@@ -1 +1 @@
-Simulation Service
+Submission Service
diff --git a/k8s/deployment.yml b/k8s/deployment.yml
@@ -1,22 +1,22 @@
 apiVersion: apps/v1
 kind: Deployment
 metadata:
-  name: simulation-svc
+  name: submission-svc
   labels:
-    app: simulation-svc
+    app: submission-svc
 spec:
   replicas: 1
   selector:
     matchLabels:
-      app: simulation-svc
+      app: submission-svc
   template:
     metadata:
       labels:
-        app: simulation-svc
+        app: submission-svc
     spec:
       containers:
-        - name: simulation-svc
-          image: ghcr.io/flawmop/simulation-svc
+        - name: submission-svc
+          image: ghcr.io/flawmop/submission-svc
           imagePullPolicy: IfNotPresent
           lifecycle:
             preStop:
@@ -25,9 +25,9 @@ spec:
           ports:
             - containerPort: 9002
           volumeMounts:
-            - name: simulation-config-volume
+            - name: submission-config-volume
               mountPath: /workspace/config
       volumes:
-        - name: simulation-config-volume
+        - name: submission-config-volume
           configMap:
-            name: simulation-config
+            name: submission-config
diff --git a/k8s/kustomization.yml b/k8s/kustomization.yml
@@ -6,11 +6,11 @@ resources:
   - service.yml
 
 configMapGenerator:
-  - name: simulation-config
+  - name: submission-config
     files:
       - application.yml
 
 generatorOptions:
   #disableNameSuffixHash: true
   labels:
-    app: simulation-svc
+    app: submission-svc
diff --git a/k8s/service.yml b/k8s/service.yml
@@ -1,13 +1,13 @@
 apiVersion: v1
 kind: Service
 metadata:
-  name: simulation-svc
+  name: submission-svc
   labels:
-    app: simulation-svc
+    app: submission-svc
 spec:
   type: ClusterIP
   selector:
-    app: simulation-svc
+    app: submission-svc
   ports:
   - protocol: TCP
     port: 80

diff --git a/settings.gradle b/settings.gradle
@@ -1 +1 @@
-rootProject.name = 'simulation-svc'
+rootProject.name = 'submission-svc'
diff --git a/...svc/simulation/SimulationIdentifiers.java → ...svc/submission/SubmissionIdentifiers.java b/...svc/simulation/SimulationIdentifiers.java → ...svc/submission/SubmissionIdentifiers.java
@@ -1,13 +1,14 @@
-package com.insilicosoft.portal.svc.simulation;
+package com.insilicosoft.portal.svc.submission;
 
-public final class SimulationIdentifiers {
+public final class SubmissionIdentifiers {
 
   /** Also used in {@code application.yml} */
   public static final String BINDING_NAME_SIMULATION_INPUT = "simulation-input";
   public static final String PARAM_NAME_SIMULATION_FILE = "mpfile";
   public static final String REQUEST_MAPPING_SIMULATION = "/simulation";
+  public static final String REQUEST_MAPPING_SUBMISSION = "/submission";
   public static final String ROLE_USER = "user";
 
-  private SimulationIdentifiers() {}
+  private SubmissionIdentifiers() {}
 
 }
diff --git a/.../simulation/SimulationSvcApplication.java → .../submission/SubmissionSvcApplication.java b/.../simulation/SimulationSvcApplication.java → .../submission/SubmissionSvcApplication.java
@@ -1,13 +1,13 @@
-package com.insilicosoft.portal.svc.simulation;
+package com.insilicosoft.portal.svc.submission;
 
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 
 @SpringBootApplication
-public class SimulationSvcApplication {
+public class SubmissionSvcApplication {
 
   public static void main(String[] args) {
-    SpringApplication.run(SimulationSvcApplication.class, args);
+    SpringApplication.run(SubmissionSvcApplication.class, args);
   }
 
 }
diff --git a/...al/svc/simulation/config/AsyncConfig.java → ...al/svc/submission/config/AsyncConfig.java b/...al/svc/simulation/config/AsyncConfig.java → ...al/svc/submission/config/AsyncConfig.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.config;
+package com.insilicosoft.portal.svc.submission.config;
 
 import org.slf4j.Logger ;
 import org.slf4j.LoggerFactory ;

diff --git a/.../simulation/config/JpaAuditingConfig.java → .../submission/config/JpaAuditingConfig.java b/.../simulation/config/JpaAuditingConfig.java → .../submission/config/JpaAuditingConfig.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.config;
+package com.insilicosoft.portal.svc.submission.config;
 
 import java.util.Optional;
 

diff --git a/...svc/simulation/config/SecurityConfig.java → ...svc/submission/config/SecurityConfig.java b/...svc/simulation/config/SecurityConfig.java → ...svc/submission/config/SecurityConfig.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.config;
+package com.insilicosoft.portal.svc.submission.config;
 
 import static org.springframework.security.config.http.SessionCreationPolicy.STATELESS;
 import static org.springframework.security.config.Customizer.withDefaults;
@@ -22,7 +22,7 @@
 import org.springframework.security.provisioning.InMemoryUserDetailsManager;
 import org.springframework.security.web.SecurityFilterChain;
 
-import com.insilicosoft.portal.svc.simulation.SimulationIdentifiers;
+import com.insilicosoft.portal.svc.submission.SubmissionIdentifiers;
 
 /**
  * Security configuration.
@@ -53,8 +53,8 @@ SecurityFilterChain filterChain(HttpSecurity http) throws Exception {
     http.authorizeHttpRequests((authz) -> authz.requestMatchers(EndpointRequest.to(InfoEndpoint.class),
                                                                 EndpointRequest.to(MetricsEndpoint.class),
                                                                 EndpointRequest.to(PrometheusScrapeEndpoint.class)).authenticated()
-                                               .requestMatchers(SimulationIdentifiers.REQUEST_MAPPING_SIMULATION.concat("/**"))
-                                                               .hasRole(SimulationIdentifiers.ROLE_USER))
+                                               .requestMatchers(SubmissionIdentifiers.REQUEST_MAPPING_SUBMISSION.concat("/**"))
+                                                               .hasRole(SubmissionIdentifiers.ROLE_USER))
         .oauth2ResourceServer((oauth2) -> oauth2.jwt(withDefaults()))
         .sessionManagement(sessionManagement -> sessionManagement.sessionCreationPolicy(STATELESS))
         .csrf(AbstractHttpConfigurer::disable)

diff --git a/...tion/controller/SimulationController.java → ...sion/controller/SubmissionController.java b/...tion/controller/SimulationController.java → ...sion/controller/SubmissionController.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.controller;
+package com.insilicosoft.portal.svc.submission.controller;
 
 import java.io.IOException ;
 
@@ -12,11 +12,11 @@
 import org.springframework.web.bind.annotation.RequestPart ;
 import org.springframework.web.multipart.MultipartFile;
 
-import com.insilicosoft.portal.svc.simulation.SimulationIdentifiers;
-import com.insilicosoft.portal.svc.simulation.exception.FileProcessingException;
-import com.insilicosoft.portal.svc.simulation.exception.InputVerificationException;
-import com.insilicosoft.portal.svc.simulation.service.InputProcessorService;
-import com.insilicosoft.portal.svc.simulation.service.SubmissionService;
+import com.insilicosoft.portal.svc.submission.SubmissionIdentifiers;
+import com.insilicosoft.portal.svc.submission.exception.FileProcessingException;
+import com.insilicosoft.portal.svc.submission.exception.InputVerificationException;
+import com.insilicosoft.portal.svc.submission.service.InputProcessorService;
+import com.insilicosoft.portal.svc.submission.service.SubmissionService;
 
 import io.micrometer.core.annotation.Timed;
 
@@ -26,10 +26,10 @@
  * @author geoff
  */
 @Controller
-@RequestMapping(SimulationIdentifiers.REQUEST_MAPPING_SIMULATION)
-public class SimulationController {
+@RequestMapping(SubmissionIdentifiers.REQUEST_MAPPING_SUBMISSION)
+public class SubmissionController {
 
-  private static final Logger log = LoggerFactory.getLogger(SimulationController.class);
+  private static final Logger log = LoggerFactory.getLogger(SubmissionController.class);
 
   private final InputProcessorService inputProcessorService;
   private final SubmissionService submissionService;
@@ -40,14 +40,14 @@ public class SimulationController {
    * @param inputProcessorService Input processing implementation.
    * @param submissionService Submission service.
    */
-  public SimulationController(final InputProcessorService inputProcessorService,
+  public SubmissionController(final InputProcessorService inputProcessorService,
                               final SubmissionService submissionService) {
     this.inputProcessorService = inputProcessorService;
     this.submissionService = submissionService;
   }
 
   @GetMapping()
-  @Timed(value = "simulation.get", description = "GET request")
+  @Timed(value = "submission.get", description = "GET request")
   public ResponseEntity<String> get() {
     return ResponseEntity.ok(inputProcessorService.get());
   }
@@ -59,16 +59,16 @@ public ResponseEntity<String> get() {
    * @return Response entity.
    * @throws FileProcessingException If problems processing file.
    */
-  @PostMapping()
-  @Timed(value = "simulation.post", description = "Simulation POST Multipart request")
+  @PostMapping(value = SubmissionIdentifiers.REQUEST_MAPPING_SIMULATION)
+  @Timed(value = "submission.simulation.post", description = "Submit Simulation POST Multipart request")
   public ResponseEntity<String> createSimulation(final @RequestPart(required=false,
-                                                                    value=SimulationIdentifiers.PARAM_NAME_SIMULATION_FILE)
+                                                                    value=SubmissionIdentifiers.PARAM_NAME_SIMULATION_FILE)
                                                        MultipartFile file)
                                                  throws FileProcessingException,
                                                         InputVerificationException {
 
     if (file == null) {
-      final String message = "No Multipart file! Did you supply the parameter '" + SimulationIdentifiers.PARAM_NAME_SIMULATION_FILE + "' in the POST request?";
+      final String message = "No Multipart file! Did you supply the parameter '" + SubmissionIdentifiers.PARAM_NAME_SIMULATION_FILE + "' in the POST request?";
       log.warn("~createSimulation() : ".concat(message));
       throw new FileProcessingException(message);
     }

diff --git a/...n/controller/advice/ControllerAdvice.java → ...n/controller/advice/ControllerAdvice.java b/...n/controller/advice/ControllerAdvice.java → ...n/controller/advice/ControllerAdvice.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.controller.advice;
+package com.insilicosoft.portal.svc.submission.controller.advice;
 
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
@@ -7,8 +7,8 @@
 import org.springframework.web.multipart.MaxUploadSizeExceededException;
 import org.springframework.web.multipart.MultipartException;
 
-import com.insilicosoft.portal.svc.simulation.exception.FileProcessingException;
-import com.insilicosoft.portal.svc.simulation.exception.InputVerificationException;
+import com.insilicosoft.portal.svc.submission.exception.FileProcessingException;
+import com.insilicosoft.portal.svc.submission.exception.InputVerificationException;
 
 /**
  * REST controller advice.

diff --git a/...c/simulation/event/SimulationMessage.java → ...c/submission/event/SimulationMessage.java b/...c/simulation/event/SimulationMessage.java → ...c/submission/event/SimulationMessage.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.event;
+package com.insilicosoft.portal.svc.submission.event;
 
 import java.math.BigDecimal;
 import java.util.List;

diff --git a/...on/exception/FileProcessingException.java → ...on/exception/FileProcessingException.java b/...on/exception/FileProcessingException.java → ...on/exception/FileProcessingException.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.exception;
+package com.insilicosoft.portal.svc.submission.exception;
 
 /**
  * File processing exception.

diff --git a/...exception/InputVerificationException.java → ...exception/InputVerificationException.java b/...exception/InputVerificationException.java → ...exception/InputVerificationException.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.exception;
+package com.insilicosoft.portal.svc.submission.exception;
 
 /**
  * Input verification exception.

diff --git a/...tal/svc/simulation/persistence/State.java → ...tal/svc/submission/persistence/State.java b/...tal/svc/simulation/persistence/State.java → ...tal/svc/submission/persistence/State.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.persistence;
+package com.insilicosoft.portal.svc.submission.persistence;
 
 public enum State {
   APPROVED, COMPLETED, CREATED, FAILED, REJECTED

diff --git a/...imulation/persistence/entity/Message.java → ...ubmission/persistence/entity/Message.java b/...imulation/persistence/entity/Message.java → ...ubmission/persistence/entity/Message.java
@@ -1,6 +1,6 @@
-package com.insilicosoft.portal.svc.simulation.persistence.entity;
+package com.insilicosoft.portal.svc.submission.persistence.entity;
 
-import com.insilicosoft.portal.svc.simulation.value.MessageLevel;
+import com.insilicosoft.portal.svc.submission.value.MessageLevel;
 
 import jakarta.persistence.Embeddable;
 import jakarta.persistence.EnumType;

diff --git a/...lation/persistence/entity/Simulation.java → ...ission/persistence/entity/Simulation.java b/...lation/persistence/entity/Simulation.java → ...ission/persistence/entity/Simulation.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.persistence.entity;
+package com.insilicosoft.portal.svc.submission.persistence.entity;
 
 import static jakarta.persistence.GenerationType.IDENTITY;
 
@@ -12,8 +12,8 @@
 
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 
-import com.insilicosoft.portal.svc.simulation.event.SimulationMessage;
-import com.insilicosoft.portal.svc.simulation.value.MessageLevel;
+import com.insilicosoft.portal.svc.submission.event.SimulationMessage;
+import com.insilicosoft.portal.svc.submission.value.MessageLevel;
 
 import jakarta.persistence.CollectionTable;
 import jakarta.persistence.Column;
@@ -45,14 +45,14 @@ public class Simulation {
   @GeneratedValue(strategy = IDENTITY)
   private Long entityId;
 
-  @Column
+  @Column(nullable = false)
   private long submissionId;
 
   // Optional. How the client/user identifies the simulation
   @Column(name = "clientId")
   private String clientId;
 
-  @Column
+  @Column(nullable = false)
   private int modelId;
 
   @Column(nullable = false)
@@ -88,11 +88,11 @@ public class Simulation {
   /**
    * Initialising constructor.
    * 
-   * @param submissionId
-   * @param modelId
-   * @param pacingFrequency
-   * @param pacingMaxTime
-   * @param plasmaPoints
+   * @param submissionId Submission identifier.
+   * @param modelId Model identifier.
+   * @param pacingFrequency Pacing frequency (Hz)
+   * @param pacingMaxTime Pacing max time (Mins)
+   * @param plasmaPoints Plasma points / Concentrations (μM).
    */
   public Simulation(final long submissionId, final int modelId, final BigDecimal pacingFrequency,
                     final BigDecimal pacingMaxTime, final List<BigDecimal> plasmaPoints) {

diff --git a/...lation/persistence/entity/Submission.java → ...ission/persistence/entity/Submission.java b/...lation/persistence/entity/Submission.java → ...ission/persistence/entity/Submission.java
@@ -1,4 +1,4 @@
-package com.insilicosoft.portal.svc.simulation.persistence.entity;
+package com.insilicosoft.portal.svc.submission.persistence.entity;
 
 import static jakarta.persistence.GenerationType.IDENTITY;
 
@@ -11,7 +11,7 @@
 import org.springframework.data.annotation.CreatedDate;
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 
-import com.insilicosoft.portal.svc.simulation.persistence.State;
+import com.insilicosoft.portal.svc.submission.persistence.State;
 
 import jakarta.persistence.CollectionTable;
 import jakarta.persistence.Column;
@@ -70,6 +70,8 @@ public Submission() {
 
   /**
    * Reject the submission and populate with the problem as justification.
+   * <p>
+   * Assigns the state to {@link State.REJECTED}
    * 
    * @param problem Problem encountered.
    */
@@ -81,6 +83,8 @@ public void rejectWithProblem(final Message problem) {
 
   /**
    * Reject the submission and populate with the problems as justification.
+   * <p>
+   * Assigns the state to {@link State.REJECTED}
    * 
    * @param problems Problems encountered.
    */

diff --git a/...ence/repository/SimulationRepository.java → ...ence/repository/SimulationRepository.java b/...ence/repository/SimulationRepository.java → ...ence/repository/SimulationRepository.java
@@ -1,8 +1,8 @@
-package com.insilicosoft.portal.svc.simulation.persistence.repository;
+package com.insilicosoft.portal.svc.submission.persistence.repository;
 
 import org.springframework.data.jpa.repository.JpaRepository;
 
-import com.insilicosoft.portal.svc.simulation.persistence.entity.Simulation;
+import com.insilicosoft.portal.svc.submission.persistence.entity.Simulation;
 
 /**
  * Repository for {@link Simulation} objects.
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		rootProject.name = 'simulation-svc'
		rootProject.name = 'submission-svc'