fix: improve seedlot saving and audit information (#1405)

Co-authored-by: Derek Roberts <[email protected]>

.github/workflows/.deploy.yml

@@ -78,6 +78,7 @@ jobs:
             -p ORACLE_USER='${{ vars.ORACLE_USER }}'
             -p ORACLE_SYNC_USER='${{ vars.ORACLE_SYNC_USER }}'
             -p ORACLE_SYNC_PASSWORD='${{ secrets.ORACLE_SYNC_PASSWORD }}'
+            -p ORACLE_CERT_SECRET='${{ secrets.ORACLE_CERT_SECRET }}'
 
   database:
     name: Deploy (database)

.github/workflows/pr-open.yml

@@ -18,7 +18,7 @@ jobs:
       packages: write
     strategy:
       matrix:
-        package: [database, backend, frontend, oracle-api, sync]
+        package: [database, common, backend, frontend, oracle-api, sync]
     steps:
       - uses: bcgov-nr/[email protected]
         id: build

backend/Dockerfile

@@ -8,7 +8,7 @@ COPY src ./src
 COPY .mvn/ ./.mvn
 
 # Build
-RUN ./mvnw -B package -Pnative -DskipTests -Dspring-boot.run.profiles=prod
+RUN ./mvnw -B package -Pnative -DskipTests
 
 
 ### Deployer
@@ -25,4 +25,4 @@ EXPOSE ${PORT}
 HEALTHCHECK CMD timeout 10s bash -c 'true > /dev/tcp/127.0.0.1/8090'
 
 # Startup
-ENTRYPOINT ["/app/nr-spar-backend"]
+ENTRYPOINT ["/app/nr-spar-backend", "-Dspring.profiles.active=prod"]

backend/openshift.deploy.yml

@@ -35,9 +35,9 @@ parameters:
   - name: FORESTCLIENTAPI_ADDRESS
     value: "https://nr-forest-client-api-prod.api.gov.bc.ca/api"
   - name: CPU_REQUEST
-    value: 50m
+    value: 100m
   - name: CPU_LIMIT
-    value: 75m
+    value: 300m
   - name: MEMORY_REQUEST
     value: 100Mi
   - name: MEMORY_LIMIT

backend/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.3.0</version>
+    <version>3.3.1</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
   <groupId>ca.bc.gov</groupId>
@@ -39,6 +39,7 @@
     <sonar.organization>bcgov-sonarcloud</sonar.organization>
     <sonar.host.url>https://sonarcloud.io</sonar.host.url>
     <oci.revision>${project.version}</oci.revision>
+    <hibernate.version>6.5.2.Final</hibernate.version>
   </properties>
 
   <profiles>
@@ -215,6 +216,24 @@
 
   <build>
     <plugins>
+      <plugin>
+        <groupId>org.hibernate.orm.tooling</groupId>
+        <artifactId>hibernate-enhance-maven-plugin</artifactId>
+        <version>${hibernate.version}</version>
+        <executions>
+          <execution>
+            <id>enhance</id>
+            <goals>
+              <goal>enhance</goal>
+            </goals>
+            <configuration>
+              <enableLazyInitialization>true</enableLazyInitialization>
+              <enableDirtyTracking>true</enableDirtyTracking>
+              <enableAssociationManagement>true</enableAssociationManagement>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
 
       <plugin>
         <groupId>org.springframework.boot</groupId>

backend/src/main/java/ca/bc/gov/backendstartapi/config/NativeImageConfig.java

@@ -1,6 +1,6 @@
 package ca.bc.gov.backendstartapi.config;
 
-import ca.bc.gov.backendstartapi.dto.CaculatedParentTreeValsDto;
+import ca.bc.gov.backendstartapi.dto.CalculatedParentTreeValsDto;
 import ca.bc.gov.backendstartapi.dto.CodeDescriptionDto;
 import ca.bc.gov.backendstartapi.dto.DescribedEnumDto;
 import ca.bc.gov.backendstartapi.dto.FavouriteActivityCreateDto;
@@ -41,9 +41,9 @@
 import ca.bc.gov.backendstartapi.dto.SeedlotReviewElevationLatLongDto;
 import ca.bc.gov.backendstartapi.dto.SeedlotReviewGeoInformationDto;
 import ca.bc.gov.backendstartapi.dto.SeedlotReviewSeedPlanZoneDto;
+import ca.bc.gov.backendstartapi.dto.SeedlotSaveInMemoryDto;
 import ca.bc.gov.backendstartapi.dto.SeedlotSourceDto;
 import ca.bc.gov.backendstartapi.dto.SeedlotStatusResponseDto;
-import ca.bc.gov.backendstartapi.dto.UserDto;
 import ca.bc.gov.backendstartapi.dto.oracle.AreaOfUseDto;
 import ca.bc.gov.backendstartapi.dto.oracle.AreaOfUseSpuGeoDto;
 import ca.bc.gov.backendstartapi.dto.oracle.SpuDto;
@@ -79,7 +79,7 @@
     AreaOfUseDto.class,
     AreaOfUseSpuGeoDto.class,
     SpzDto.class,
-    CaculatedParentTreeValsDto.class,
+    CalculatedParentTreeValsDto.class,
     CodeDescriptionDto.class,
     DescribedEnumDto.class,
     FavouriteActivityCreateDto.class,
@@ -122,7 +122,6 @@
     SeedlotReviewSeedPlanZoneDto.class,
     SeedlotSourceDto.class,
     SeedlotStatusResponseDto.class,
-    UserDto.class,
     AreaOfUseDto.class,
     AreaOfUseSpuGeoDto.class,
     SpuDto.class,
@@ -135,7 +134,8 @@
     LongitudeCodeEnum.class,
     ConeAndPollenCountHeader.class,
     CsvParsingHeader.class,
-    SmpMixHeader.class
+    SmpMixHeader.class,
+    SeedlotSaveInMemoryDto.class,
 })
 @ImportRuntimeHints(value = {HttpServletRequestRuntimeHint.class})
 public class NativeImageConfig {

backend/src/main/java/ca/bc/gov/backendstartapi/dto/CaculatedParentTreeValsDto.java → backend/src/main/java/ca/bc/gov/backendstartapi/dto/CalculatedParentTreeValsDto.java

@@ -14,7 +14,7 @@
         """)
 @Getter
 @Setter
-public class CaculatedParentTreeValsDto {
+public class CalculatedParentTreeValsDto {
   private BigDecimal neValue;
   private GeospatialRespondDto geospatialData;
 }

backend/src/main/java/ca/bc/gov/backendstartapi/dto/PtCalculationResDto.java

@@ -14,6 +14,6 @@ public record PtCalculationResDto(
     @Schema(description = "Contains a list of calculated traits.")
         List<GeneticWorthTraitsDto> geneticTraits,
     @Schema(description = "Various calculated value for the orchard parent trees.")
-        CaculatedParentTreeValsDto calculatedPtVals,
+        CalculatedParentTreeValsDto calculatedPtVals,
     @Schema(description = "The calculated mean geospatial values for SMP mix.")
         GeospatialRespondDto smpMixMeanGeoData) {}

backend/src/main/java/ca/bc/gov/backendstartapi/dto/SeedlotSaveInMemoryDto.java

@@ -0,0 +1,12 @@
+package ca.bc.gov.backendstartapi.dto;
+
+import lombok.Getter;
+import lombok.Setter;
+
+/** This class contains values that are used in more than one place. */
+@Getter
+@Setter
+public class SeedlotSaveInMemoryDto {
+
+  private Integer primarySpuId;
+}

backend/src/main/java/ca/bc/gov/backendstartapi/interceptor/RoleAccessInterceptor.java

@@ -64,11 +64,11 @@ private boolean matchUserRoleWithResourceRoles(
       List<String> rolesRequired, List<String> userRoles) {
     for (String requiredRole : rolesRequired) {
       if (userRoles.contains(requiredRole)) {
-        SparLog.info("Request allowed by user role: {}", requiredRole);
+        SparLog.debug("Request allowed by user role: {}", requiredRole);
         return true;
       }
     }
-    SparLog.info("Request denied. No enough access levels!");
+    SparLog.debug("Request denied. No enough access levels!");
     return false;
   }
 
@@ -81,11 +81,11 @@ private boolean matchUserRoleWithResourceRoles(
   private List<String> getUserRoles(HttpServletRequest request) {
     if (request.getUserPrincipal() instanceof JwtAuthenticationToken jwtToken) {
       Set<String> roles = JwtSecurityUtil.getUserRolesFromJwt(jwtToken.getToken());
-      SparLog.info("User roles: {}", roles);
+      SparLog.debug("User roles: {}", roles);
       return new ArrayList<>(roles);
     }
 
-    // Test fix!
+    // Fix for unit testing
     SecurityContext context = SecurityContextHolder.getContext();
     if (context.getAuthentication().getName().equals("SPARTest")) {
       List<String> grantedList = new ArrayList<>();
@@ -96,7 +96,7 @@ private List<String> getUserRoles(HttpServletRequest request) {
           grantedList.add(grant.substring(5));
         }
       }
-      SparLog.info("SPAR Test User roles: {}", grantedList);
+      SparLog.debug("SPAR Test User roles: {}", grantedList);
       return grantedList;
     }
 
@@ -142,7 +142,7 @@ private List<String> getResourceRolesRequired(String[] classNameWithMethod, Stri
         }
 
         List<String> roles = Arrays.asList(annotation.value());
-        SparLog.info("Access level required for {}: {}", uri, roles);
+        SparLog.debug("Access level required for {}: {}", uri, roles);
         return roles;
       }
     } catch (Exception e) {

backend/src/main/java/ca/bc/gov/backendstartapi/service/ParentTreeService.java

@@ -1,7 +1,7 @@
 package ca.bc.gov.backendstartapi.service;
 
 import ca.bc.gov.backendstartapi.config.SparLog;
-import ca.bc.gov.backendstartapi.dto.CaculatedParentTreeValsDto;
+import ca.bc.gov.backendstartapi.dto.CalculatedParentTreeValsDto;
 import ca.bc.gov.backendstartapi.dto.GeneticWorthTraitsDto;
 import ca.bc.gov.backendstartapi.dto.GeospatialOracleResDto;
 import ca.bc.gov.backendstartapi.dto.GeospatialRequestDto;
@@ -57,8 +57,8 @@ public PtCalculationResDto calculatePtVals(PtValsCalReqDto ptVals) {
 
     BigDecimal neValue = geneticWorthService.calculateNe(ptVals.orchardPtVals());
 
-    CaculatedParentTreeValsDto calculatedVals = new CaculatedParentTreeValsDto();
-    calculatedVals.setNeValue(neValue); // <- review ne value being overwritten
+    CalculatedParentTreeValsDto calculatedVals = new CalculatedParentTreeValsDto();
+    calculatedVals.setNeValue(neValue);
 
     GeospatialRespondDto smpMixGeoData = calcMeanGeospatial(ptVals.smpMixIdAndProps());
     SparLog.info("SMP mix mean geospatial calculation complete.");

backend/src/main/java/ca/bc/gov/backendstartapi/service/SeedlotOrchardService.java

@@ -7,6 +7,7 @@
 import ca.bc.gov.backendstartapi.exception.SeedlotConflictDataException;
 import ca.bc.gov.backendstartapi.repository.SeedlotOrchardRepository;
 import ca.bc.gov.backendstartapi.security.LoggedUserService;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 import lombok.RequiredArgsConstructor;
@@ -71,23 +72,27 @@ public void saveSeedlotFormStep4(
   private void saveSeedlotOrchards(
       Seedlot seedlot, String primaryOrchardId, String secondaryOrchardId) {
 
+    List<SeedlotOrchard> seedlotsToSaveList = new ArrayList<>();
+
     SeedlotOrchard primary = new SeedlotOrchard(seedlot, true, primaryOrchardId);
     primary.setAuditInformation(loggedUserService.createAuditCurrentUser());
-    seedlotOrchardRepository.save(primary);
+    seedlotsToSaveList.add(primary);
     SparLog.info(
-        "Primary orchard id {} inserted on Seedlot_Orchard table for seedlot number {}",
+        "Primary orchard id {} to be saved for Seedlot number {}",
         primaryOrchardId,
         seedlot.getId());
 
     if (secondaryOrchardId != null) {
       SeedlotOrchard secondary = new SeedlotOrchard(seedlot, false, secondaryOrchardId);
       secondary.setAuditInformation(loggedUserService.createAuditCurrentUser());
-      seedlotOrchardRepository.save(secondary);
+      seedlotsToSaveList.add(secondary);
       SparLog.info(
-          "Secondary orchard id {} inserted on Seedlot_Orchard table for seedlot number {}",
+          "Secondary orchard id {} to be saved for Seedlot number {}",
           secondaryOrchardId,
           seedlot.getId());
     }
+
+    seedlotOrchardRepository.saveAll(seedlotsToSaveList);
   }
 
   /**

backend/src/main/java/ca/bc/gov/backendstartapi/service/SeedlotService.java

@@ -22,6 +22,7 @@
 import ca.bc.gov.backendstartapi.dto.SeedlotFormOwnershipDto;
 import ca.bc.gov.backendstartapi.dto.SeedlotFormParentTreeSmpDto;
 import ca.bc.gov.backendstartapi.dto.SeedlotFormSubmissionDto;
+import ca.bc.gov.backendstartapi.dto.SeedlotSaveInMemoryDto;
 import ca.bc.gov.backendstartapi.dto.SeedlotStatusResponseDto;
 import ca.bc.gov.backendstartapi.dto.oracle.AreaOfUseDto;
 import ca.bc.gov.backendstartapi.dto.oracle.SpuDto;
@@ -736,6 +737,9 @@ public SeedlotStatusResponseDto updateSeedlotWithForm(
      * 4. Add new ones
      */
 
+    // Object to hold data in memory, avoid querying same data
+    final SeedlotSaveInMemoryDto inMemoryDto = new SeedlotSaveInMemoryDto();
+
     // Step 1 (Collection methods)
     // Update the Seedlot instance and tables [seedlot_collection_method]
     seedlotCollectionMethodService.saveSeedlotFormStep1(
@@ -775,7 +779,7 @@ public SeedlotStatusResponseDto updateSeedlotWithForm(
 
     // Update the Seedlot instance only
     // Fetch data from Oracle to get the primary Seed Plan Unit id
-    setBecValues(seedlot, form.seedlotFormOrchardDto().primaryOrchardId());
+    setBecValues(seedlot, form.seedlotFormOrchardDto().primaryOrchardId(), inMemoryDto);
 
     if (isFromRegularForm) {
       // Update the Seedlot instance only
@@ -794,7 +798,7 @@ public SeedlotStatusResponseDto updateSeedlotWithForm(
       // Fetch data from Oracle to get the active Seed Plan Unit id
       if (!hasAreaOfUseData(seedlot)) {
         SparLog.info("Area of Use data has NOT been set previously, setting area of use data");
-        setAreaOfUse(seedlot, form.seedlotFormOrchardDto().primaryOrchardId());
+        setAreaOfUse(seedlot, form.seedlotFormOrchardDto().primaryOrchardId(), inMemoryDto);
       }
     } else {
       updateApplicantAndSeedlot(seedlot, form.applicantAndSeedlotInfo());
@@ -830,7 +834,8 @@ public SeedlotStatusResponseDto updateSeedlotWithForm(
         seedlotNumber, seedlot.getSeedlotStatus().getSeedlotStatusCode());
   }
 
-  private void setBecValues(Seedlot seedlot, String primaryOrchardId) {
+  private void setBecValues(
+      Seedlot seedlot, String primaryOrchardId, SeedlotSaveInMemoryDto inMemoryDto) {
     SparLog.info("Begin to set BEC values");
 
     OrchardDto orchardDto =
@@ -844,6 +849,7 @@ private void setBecValues(Seedlot seedlot, String primaryOrchardId) {
             .orElseThrow(NoSpuForOrchardException::new);
 
     Integer primarySpuId = primarySeedPlanUnit.getSeedPlanningUnitId();
+    inMemoryDto.setPrimarySpuId(primarySpuId);
 
     // Not sure why it's called Bgc in seedlot instead of Bec in orchard
     seedlot.setBgcZoneCode(orchardDto.becZoneCode());
@@ -970,13 +976,19 @@ private boolean hasAreaOfUseData(Seedlot seedlot) {
    * @param seedlot the seedlot object to set data to
    * @param primaryOrchardId the primary orchard Id to find the spu for
    */
-  private void setAreaOfUse(Seedlot seedlot, String primaryOrchardId) {
+  private void setAreaOfUse(
+      Seedlot seedlot, String primaryOrchardId, SeedlotSaveInMemoryDto inMemoryDto) {
     SparLog.info("Begin to set Area of Use values");
-    ActiveOrchardSpuEntity activeSpuEntity =
-        orchardService
-            .findSpuIdByOrchardWithActive(primaryOrchardId, true)
-            .orElseThrow(NoSpuForOrchardException::new);
-    Integer activeSpuId = activeSpuEntity.getSeedPlanningUnitId();
+
+    Integer activeSpuId = inMemoryDto.getPrimarySpuId();
+    if (Objects.isNull(activeSpuId)) {
+      ActiveOrchardSpuEntity activeSpuEntity =
+          orchardService
+              .findSpuIdByOrchardWithActive(primaryOrchardId, true)
+              .orElseThrow(NoSpuForOrchardException::new);
+      activeSpuId = activeSpuEntity.getSeedPlanningUnitId();
+    }
+
     AreaOfUseDto areaOfUseDto =
         oracleApiProvider
             .getAreaOfUseData(activeSpuId)
@@ -1038,6 +1050,7 @@ private void setAreaOfUse(Seedlot seedlot, String primaryOrchardId) {
     List<SeedlotSeedPlanZoneEntity> spzSaveList = new ArrayList<>();
     GeneticClassEntity genAclass =
         geneticClassRepository.findById("A").orElseThrow(GeneticClassNotFoundException::new);
+    AuditInformation currentUser = new AuditInformation(loggedUserService.getLoggedUserId());
     areaOfUseDto.getSpzList().stream()
         .forEach(
             spzDto -> {
@@ -1048,8 +1061,7 @@ private void setAreaOfUse(Seedlot seedlot, String primaryOrchardId) {
                       genAclass,
                       spzDto.getIsPrimary(),
                       spzDto.getDescription());
-              sspzToSave.setAuditInformation(
-                  new AuditInformation(loggedUserService.getLoggedUserId()));
+              sspzToSave.setAuditInformation(currentUser);
               spzSaveList.add(sspzToSave);
             });
     seedlotSeedPlanZoneRepository.saveAll(spzSaveList);