Merge pull request #229 from AAFC-BICoE/34080_update_to_Java_21

34080 update to java 21

.github/workflows/ci.yml

@@ -8,22 +8,22 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up JDK 17
-        uses: actions/setup-java@v3
+      - uses: actions/checkout@v4
+      - name: Set up JDK 21
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '17'
+          java-version: '21'
           cache: 'maven'
 
       - name: Build with Maven
-        run: mvn verify
+        run: mvn -B -q verify
       - name: Run Checkstyle
-        run: mvn checkstyle:check
+        run: mvn -q checkstyle:check
       - name: Run SpotBugs
-        run: mvn com.github.spotbugs:spotbugs-maven-plugin:check
+        run: mvn -q com.github.spotbugs:spotbugs-maven-plugin:check
       - name: Run OWASP dependency-check (only on dev)
-        run: mvn org.owasp:dependency-check-maven:check
+        run: mvn -q org.owasp:dependency-check-maven:check
         if: ${{ github.ref == 'refs/heads/dev' }}
 
       - name: Extract Version

Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:17-jre-jammy
+FROM eclipse-temurin:21-jre-jammy
 
 RUN useradd -s /bin/bash user
 USER user

pom.xml

@@ -16,28 +16,27 @@
   </parent>
 
   <properties>
-    <java.version>17</java.version>
+    <java.version>21</java.version>
     <javax.inject.version>1</javax.inject.version>
     <!-- Different from SpringBoot javax-jaxb.version since they don't manage jaxb-core and jaxb-impl-->
     <javax.interceptor-api>1.2.2</javax.interceptor-api>
-	
-    <spotbugs-maven-plugin.version>4.6.0.0</spotbugs-maven-plugin.version>
-    <spotbugs.version>4.7.1</spotbugs.version>
+
+    <spotbugs-maven-plugin.version>4.8.5.0</spotbugs-maven-plugin.version>
+    <spotbugs.version>4.8.5</spotbugs.version>
 
     <!-- Override SpringBoot version (3.6) to avoid NoClassDefFoundError: org/apache/maven/doxia/siterenderer/DocumentContent -->
     <maven-site-plugin.version>3.7.1</maven-site-plugin.version>
 
-    <dependency.check.version>8.3.1</dependency.check.version>
-    <jacoco-maven-plugin.version>0.8.8</jacoco-maven-plugin.version>
+    <dependency.check.version>8.4.3</dependency.check.version>
+    <jacoco-maven-plugin.version>0.8.12</jacoco-maven-plugin.version>
 
-    <maven-checkstyle-plugin.version>3.1.2</maven-checkstyle-plugin.version>
-    <checkstyle.version>9.3</checkstyle.version>
-    <checkstyle-antlr.version>4.9.3</checkstyle-antlr.version>
+    <maven-checkstyle-plugin.version>3.4.0</maven-checkstyle-plugin.version>
+    <checkstyle.version>10.17.0</checkstyle.version>
 
     <asciidoctor-maven-plugin.version>2.1.0</asciidoctor-maven-plugin.version>
     <dina-base-api.version>0.125</dina-base-api.version>
 
-    <postgresql.version>42.4.3</postgresql.version>
+    <postgresql.version>42.4.4</postgresql.version>
     <snakeyaml.version>1.33</snakeyaml.version>    
     <spring-boot-maven-plugin.fork>false</spring-boot-maven-plugin.fork>
 
@@ -171,11 +170,6 @@
             <artifactId>checkstyle</artifactId>
             <version>${checkstyle.version}</version>
           </dependency>
-          <dependency>
-            <groupId>org.antlr</groupId>
-            <artifactId>antlr4-runtime</artifactId>
-            <version>${checkstyle-antlr.version}</version>
-          </dependency>
         </dependencies>
         <configuration>
           <configLocation>checkstyle.xml</configLocation>

spotbugs-exclude.xml

@@ -12,4 +12,8 @@ See https://spotbugs.readthedocs.io/en/latest/filter.html
     <Bug pattern="EI_EXPOSE_REP2"/>
   </Match>
 
+  <Match>
+    <Bug pattern="CT_CONSTRUCTOR_THROW"/>
+  </Match>
+
 </FindBugsFilter>

src/main/java/ca/gc/aafc/seqdb/api/service/PcrBatchItemService.java

@@ -48,7 +48,7 @@ public <T> List<T> findAll(@NonNull Class<T> entityClass, @NonNull PredicateSupp
                              @NonNull Set<String> relationships)  {
 
     List<T> itemsList = super.findAll(entityClass, where, orderBy, startIndex, maxResult, includes, relationships);
-    if(PcrBatchItem.class == entityClass) {
+    if (PcrBatchItem.class == entityClass) {
       itemsList.forEach(t -> setCellNumber((PcrBatchItem) t));
     }
     return itemsList;

src/main/java/ca/gc/aafc/seqdb/api/service/SeqReactionService.java

@@ -43,7 +43,7 @@ public <T> List<T> findAll(@NonNull Class<T> entityClass, @NonNull PredicateSupp
                              @NonNull Set<String> relationships)  {
 
     List<T> itemsList = super.findAll(entityClass, where, orderBy, startIndex, maxResult, includes, relationships);
-    if(SeqReaction.class == entityClass) {
+    if (SeqReaction.class == entityClass) {
       itemsList.forEach(t -> setCellNumber((SeqReaction) t));
     }
     return itemsList;

src/main/java/ca/gc/aafc/seqdb/api/service/SeqSubmissionService.java

@@ -10,6 +10,8 @@
 import ca.gc.aafc.seqdb.api.entities.SeqSubmission;
 import lombok.NonNull;
 
+// CHECKSTYLE:OFF NoFinalizer
+// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class SeqSubmissionService extends DefaultDinaService<SeqSubmission> {
 
@@ -23,4 +25,9 @@ public SeqSubmissionService(
   protected void preCreate(SeqSubmission entity) {
     entity.setUuid(UUID.randomUUID());
   }
+
+  // Fixes CT_CONSTRUCTOR_THROW
+  protected final void finalize() {
+    // no-op
+  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/SequencingFacilityService.java

@@ -10,6 +10,8 @@
 
 import java.util.UUID;
 
+// CHECKSTYLE:OFF NoFinalizer
+// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class SequencingFacilityService extends DefaultDinaService<SequencingFacility> {
 
@@ -23,5 +25,10 @@ public SequencingFacilityService(
   protected void preCreate(SequencingFacility entity) {
     entity.setUuid(UUID.randomUUID());
   }
+
+  // Fixes CT_CONSTRUCTOR_THROW
+  protected final void finalize() {
+    // no-op
+  }
 }
 

src/main/java/ca/gc/aafc/seqdb/api/service/ThermocyclerProfileService.java

@@ -10,6 +10,8 @@
 import ca.gc.aafc.seqdb.api.entities.ThermocyclerProfile;
 import lombok.NonNull;
 
+// CHECKSTYLE:OFF NoFinalizer
+// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class ThermocyclerProfileService extends DefaultDinaService<ThermocyclerProfile> {
 
@@ -23,5 +25,9 @@ public ThermocyclerProfileService(
   protected void preCreate(ThermocyclerProfile entity) {
     entity.setUuid(UUID.randomUUID());
   }
-
+
+  // Fixes CT_CONSTRUCTOR_THROW
+  protected final void finalize() {
+    // no-op
+  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/libraryprep/IndexSetService.java

@@ -10,6 +10,8 @@
 import ca.gc.aafc.seqdb.api.entities.libraryprep.IndexSet;
 import lombok.NonNull;
 
+// CHECKSTYLE:OFF NoFinalizer
+// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class IndexSetService extends DefaultDinaService<IndexSet> {
 
@@ -23,5 +25,9 @@ public IndexSetService(
   protected void preCreate(IndexSet entity) {
     entity.setUuid(UUID.randomUUID());
   }
-
+
+  // Fixes CT_CONSTRUCTOR_THROW
+  protected final void finalize() {
+    // no-op
+  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/libraryprep/LibraryPrepBatchService.java

@@ -10,6 +10,8 @@
 import ca.gc.aafc.seqdb.api.entities.libraryprep.LibraryPrepBatch;
 import lombok.NonNull;
 
+// CHECKSTYLE:OFF NoFinalizer
+// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class LibraryPrepBatchService extends DefaultDinaService<LibraryPrepBatch> {
 
@@ -23,5 +25,9 @@ public LibraryPrepBatchService(
   protected void preCreate(LibraryPrepBatch entity) {
     entity.setUuid(UUID.randomUUID());
   }
-
+
+  // Fixes CT_CONSTRUCTOR_THROW
+  protected final void finalize() {
+    // no-op
+  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/libraryprep/LibraryPrepService.java

@@ -15,6 +15,8 @@
 import ca.gc.aafc.seqdb.api.validation.ContainerLocationValidator;
 import lombok.NonNull;
 
+// CHECKSTYLE:OFF NoFinalizer
+// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class LibraryPrepService extends DefaultDinaService<LibraryPrep> {
 
@@ -93,5 +95,10 @@ private void handleOverlap(LibraryPrep libraryPrep) {
       }
     }
   }
+
+  // Fixes CT_CONSTRUCTOR_THROW
+  protected final void finalize() {
+    // no-op
+  }
 
 }

src/main/java/ca/gc/aafc/seqdb/api/service/libraryprep/NgsIndexService.java

@@ -10,6 +10,8 @@
 import ca.gc.aafc.seqdb.api.entities.libraryprep.NgsIndex;
 import lombok.NonNull;
 
+// CHECKSTYLE:OFF NoFinalizer
+// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class NgsIndexService extends DefaultDinaService<NgsIndex> {
 
@@ -23,5 +25,9 @@ public NgsIndexService(
   protected void preCreate(NgsIndex entity) {
     entity.setUuid(UUID.randomUUID());
   }
-
+
+  // Fixes CT_CONSTRUCTOR_THROW
+  protected final void finalize() {
+    // no-op
+  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/pooledlibraries/LibraryPoolContentService.java

@@ -17,6 +17,8 @@
 import ca.gc.aafc.seqdb.api.entities.pooledlibraries.LibraryPoolContent;
 import lombok.NonNull;
 
+// CHECKSTYLE:OFF NoFinalizer
+// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class LibraryPoolContentService extends DefaultDinaService<LibraryPoolContent> {
 
@@ -94,5 +96,9 @@ private List<LibraryPrepBatch> getBatches(LibraryPool pool) {
 
     return batchs;
   }
-
+
+  // Fixes CT_CONSTRUCTOR_THROW
+  protected final void finalize() {
+    // no-op
+  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/pooledlibraries/LibraryPoolService.java

@@ -10,6 +10,8 @@
 import ca.gc.aafc.seqdb.api.entities.pooledlibraries.LibraryPool;
 import lombok.NonNull;
 
+// CHECKSTYLE:OFF NoFinalizer
+// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class LibraryPoolService extends DefaultDinaService<LibraryPool> {
 
@@ -23,5 +25,9 @@ public LibraryPoolService(
   protected void preCreate(LibraryPool entity) {
     entity.setUuid(UUID.randomUUID());
   }
-
+
+  // Fixes CT_CONSTRUCTOR_THROW
+  protected final void finalize() {
+    // no-op
+  }
 }

src/main/java/ca/gc/aafc/seqdb/api/validation/ContainerLocationValidator.java

@@ -47,7 +47,7 @@ public static class ContainerLocationArgs {
     private ContainerType containerType;
 
     public StorageGridLayout getStorageGridLayout() {
-      if(containerType == null) {
+      if (containerType == null) {
         return null;
       }
       return StorageGridLayout.builder()

src/main/java/ca/gc/aafc/seqdb/api/validation/PcrBatchItemValidator.java

@@ -35,7 +35,7 @@ public void validate(Object target, Errors errors) {
 
     // if there is no storage restriction defined, we can't validate.
     // we return and allow the location since we can't say for sure it's invalid
-    if(pcrBatchItem.getPcrBatch() == null || pcrBatchItem.getPcrBatch().getStorageRestriction() == null) {
+    if (pcrBatchItem.getPcrBatch() == null || pcrBatchItem.getPcrBatch().getStorageRestriction() == null) {
       return;
     }