updating field to make it nullable (#5982)

* updating field to make it nullable

* review fixes and test fixes

* review fixes

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_0/5981-make-poll-attempt-count-nullable.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 5981
+title: "Batch2WorkChunkEntity poll_attempt count is a nullable field, but was incorrectly
+        declared as a primitive.
+        This has been fixed.
+"

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java

@@ -78,7 +78,7 @@ public interface IBatch2WorkChunkRepository
 
 	@Modifying
 	@Query(
-			"UPDATE Batch2WorkChunkEntity e SET e.myStatus = :status, e.myNextPollTime = :nextPollTime, e.myPollAttempts = e.myPollAttempts + 1 WHERE e.myId = :id AND e.myStatus IN(:states)")
+			"UPDATE Batch2WorkChunkEntity e SET e.myStatus = :status, e.myNextPollTime = :nextPollTime, e.myPollAttempts = COALESCE(e.myPollAttempts, 0) + 1 WHERE e.myId = :id AND e.myStatus IN(:states)")
 	int updateWorkChunkNextPollTime(
 			@Param("id") String theChunkId,
 			@Param("status") WorkChunkStatusEnum theStatus,

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Batch2WorkChunkEntity.java

@@ -140,7 +140,7 @@ public class Batch2WorkChunkEntity implements Serializable {
 	 * The number of times the work chunk has had its state set back to POLL_WAITING.
 	 */
 	@Column(name = "POLL_ATTEMPTS", nullable = true)
-	private int myPollAttempts;
+	private Integer myPollAttempts;
 
 	/**
 	 * Default constructor for Hibernate.
@@ -352,7 +352,10 @@ public class Batch2WorkChunkEntity implements Serializable {
 		myNextPollTime = theNextPollTime;
 	}
 
-	public int getPollAttempts() {
+	public Integer getPollAttempts() {
+		if (myPollAttempts == null) {
+			return 0;
+		}
 		return myPollAttempts;
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/EntityTest.java

@@ -0,0 +1,76 @@
+package ca.uhn.fhir.jpa.entity;
+
+import com.google.common.reflect.ClassPath;
+import jakarta.persistence.Column;
+import org.junit.jupiter.api.Test;
+
+import java.io.IOException;
+import java.lang.reflect.Field;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static org.junit.jupiter.api.Assertions.fail;
+
+public class EntityTest {
+
+	private static final String PACKAGE_BASE = "ca.uhn.fhir.jpa.entity";
+
+	private static final Map<String, List<String>> CLASS_TO_FIELD_NAME_EXCEPTIONS = new HashMap<>();
+
+	static {
+		CLASS_TO_FIELD_NAME_EXCEPTIONS.put("TermValueSetConceptViewOracle",
+			List.of("myConceptOrder"));
+
+		CLASS_TO_FIELD_NAME_EXCEPTIONS.put("ResourceSearchView",
+			List.of("myHasTags"));
+
+		CLASS_TO_FIELD_NAME_EXCEPTIONS.put("HapiFhirEnversRevision",
+			List.of("myRev"));
+
+		CLASS_TO_FIELD_NAME_EXCEPTIONS.put("Batch2JobInstanceEntity",
+			List.of("myProgress", "myErrorCount"));
+
+		CLASS_TO_FIELD_NAME_EXCEPTIONS.put("TermValueSetConceptView",
+			List.of("myConceptOrder"));
+
+		CLASS_TO_FIELD_NAME_EXCEPTIONS.put("TermConcept",
+			List.of("myCodeSystemVersionPid"));
+	}
+
+	@SuppressWarnings("rawtypes")
+	@Test
+	public void nullableFieldsAreNotPrimitivesTest() throws IOException {
+		Set<Class> classes = ClassPath.from(ClassLoader.getSystemClassLoader())
+			.getAllClasses()
+			.stream()
+			.filter(clazz -> clazz.getPackageName().startsWith(PACKAGE_BASE))
+			.map(ClassPath.ClassInfo::load)
+			.collect(Collectors.toSet());
+
+		for (Class clazz : classes) {
+			String className = clazz.getName().replace(PACKAGE_BASE + ".", "");
+			for (Field field : clazz.getDeclaredFields()) {
+				Column column = field.getAnnotation(Column.class);
+				if (column == null) {
+					continue;
+				}
+
+				if (isPrimitiveFieldNullable(className, field, column)) {
+					fail(String.format("Column %s on Entity %s is nullable, but has been defined as primitive.",
+						field.getName(), className)
+						+ " If this is a new field on an existing Table, this can result in deserialization issues when reading old data."
+						+ " Either change to a nullable type (Object) or ensure existing data is migrated and add as an exception.");
+				}
+			}
+		}
+	}
+
+	private boolean isPrimitiveFieldNullable(String className, Field field, Column column) {
+		return column.nullable()
+			&& field.getType().isPrimitive()
+			&& !(CLASS_TO_FIELD_NAME_EXCEPTIONS.containsKey(className) && CLASS_TO_FIELD_NAME_EXCEPTIONS.get(className).contains(field.getName()));
+	}
+}

hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImplIT.java

@@ -0,0 +1,57 @@
+package ca.uhn.fhir.jpa.batch2;
+
+import ca.uhn.fhir.batch2.api.IJobPersistence;
+import ca.uhn.fhir.batch2.model.JobInstance;
+import ca.uhn.fhir.batch2.model.StatusEnum;
+import ca.uhn.fhir.batch2.model.WorkChunkStatusEnum;
+import ca.uhn.fhir.jpa.dao.data.IBatch2WorkChunkRepository;
+import ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity;
+import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.time.Instant;
+import java.time.temporal.ChronoUnit;
+import java.util.Date;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class JpaJobPersistenceImplIT extends BaseJpaR4Test {
+
+	@Autowired
+	private IBatch2WorkChunkRepository myWorkChunkRepository;
+	@Autowired
+	private IJobPersistence myJobPersistence;
+
+	@Test
+	public void onWorkChunkPollDelay_withValidData_updatesDeadlineAndPollAttemptCount() {
+		// setup
+		Date nextPollTime = Date.from(Instant.now().plus(1, ChronoUnit.HOURS));
+		JobInstance jobInstance = new JobInstance();
+		jobInstance.setJobDefinitionId("job-def-id");
+		jobInstance.setStatus(StatusEnum.IN_PROGRESS);
+		jobInstance.setJobDefinitionVersion(1);
+		String instanceId = myJobPersistence.storeNewInstance(jobInstance);
+
+		Batch2WorkChunkEntity workChunk = new Batch2WorkChunkEntity();
+		workChunk.setId("id");
+		workChunk.setInstanceId(instanceId);
+		workChunk.setJobDefinitionId(jobInstance.getJobDefinitionId());
+		workChunk.setJobDefinitionVersion(jobInstance.getJobDefinitionVersion());
+		workChunk.setStatus(WorkChunkStatusEnum.IN_PROGRESS);
+		workChunk.setCreateTime(new Date());
+		workChunk.setTargetStepId("step-id");
+		myWorkChunkRepository.save(workChunk);
+
+		// test
+		myJobPersistence.onWorkChunkPollDelay(workChunk.getId(), nextPollTime);
+
+		// verify
+		List<Batch2WorkChunkEntity> allChunks = myWorkChunkRepository.findAll();
+		assertEquals(1, allChunks.size());
+		Batch2WorkChunkEntity chunk = allChunks.get(0);
+		assertEquals(nextPollTime, chunk.getNextPollTime());
+		assertEquals(1, chunk.getPollAttempts());
+	}
+}

hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/WorkChunk.java

@@ -76,7 +76,7 @@ public class WorkChunk extends WorkChunkMetadata {
 	 * Total polling attempts done thus far.
 	 */
 	@JsonProperty("pollAttempts")
-	private int myPollAttempts;
+	private Integer myPollAttempts;
 
 	@JsonProperty(value = "recordsProcessed", access = JsonProperty.Access.READ_ONLY)
 	private Integer myRecordsProcessed;
@@ -214,7 +214,7 @@ public class WorkChunk extends WorkChunkMetadata {
 		myNextPollTime = theNextPollTime;
 	}
 
-	public int getPollAttempts() {
+	public Integer getPollAttempts() {
 		return myPollAttempts;
 	}