Fix JPA nullable primitive columns (#5926)

* Fix JPA nullable primitive columns * Add changelog * Spotless * License headers * Migration fix * Spotless * Cleanup * Cleanup * Add task skipping * Update docs * CLeanup * Spotless * Address review comments * Test fix * HAPI FHIR version bump
hapifhir · Jun 18, 2024 · 47d6e35 · 47d6e35
1 parent ec0021c
commit 47d6e35
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Showing 111 changed files with 721 additions and 352 deletions.
diff --git a/hapi-deployable-pom/pom.xml b/hapi-deployable-pom/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-android/pom.xml b/hapi-fhir-android/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-base/pom.xml b/hapi-fhir-base/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-bom/pom.xml b/hapi-fhir-bom/pom.xml
@@ -4,15 +4,15 @@
  <modelVersion>4.0.0</modelVersion>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-bom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <packaging>pom</packaging>
  <name>HAPI FHIR BOM</name>
 
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-checkstyle/pom.xml b/hapi-fhir-checkstyle/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/...cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseFlywayMigrateDatabaseCommand.java b/...cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseFlywayMigrateDatabaseCommand.java
@@ -26,8 +26,6 @@
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.lang3.StringUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import java.util.Arrays;
 import java.util.List;
@@ -40,12 +38,12 @@
  * NB since 2019-12-05: This class is kind of weirdly named now, since it can either use Flyway or not use Flyway
  */
 public abstract class BaseFlywayMigrateDatabaseCommand<T extends Enum> extends BaseCommand {
- private static final Logger ourLog = LoggerFactory.getLogger(BaseFlywayMigrateDatabaseCommand.class);
 
  public static final String MIGRATE_DATABASE = "migrate-database";
  public static final String NO_COLUMN_SHRINK = "no-column-shrink";
- public static final String STRICT_ORDER = "strict-order";
  public static final String SKIP_VERSIONS = "skip-versions";
+ public static final String ENABLE_HEAVYWEIGHT_MIGRATIONS = "enable-heavyweight-migrations";
+
  private Set<String> myFlags;
  private String myMigrationTableName;
 
@@ -100,6 +98,12 @@ public Options getOptions() {
  SKIP_VERSIONS,
  "Versions",
  "A comma separated list of schema versions to skip. E.g. 4_1_0.20191214.2,4_1_0.20191214.4");
+ addOptionalOption(
+ retVal,
+ null,
+ ENABLE_HEAVYWEIGHT_MIGRATIONS,
+ false,
+ "If this flag is set, additional migration tasks will be executed that are considered unnecessary to execute on a database with a significant amount of data loaded. This option is not generally necessary.");
 
  return retVal;
  }
@@ -125,6 +129,7 @@ public void run(CommandLine theCommandLine) throws ParseException {
 
  boolean dryRun = theCommandLine.hasOption("r");
  boolean noColumnShrink = theCommandLine.hasOption(BaseFlywayMigrateDatabaseCommand.NO_COLUMN_SHRINK);
+ boolean runHeavyweight = theCommandLine.hasOption(ENABLE_HEAVYWEIGHT_MIGRATIONS);
 
  String flags = theCommandLine.getOptionValue("x");
  myFlags = Arrays.stream(defaultString(flags).split(","))
@@ -139,6 +144,7 @@ public void run(CommandLine theCommandLine) throws ParseException {
 
  migrator.createMigrationTableIfRequired();
  migrator.setDryRun(dryRun);
+ migrator.setRunHeavyweightSkippableTasks(runHeavyweight);
  migrator.setNoColumnShrink(noColumnShrink);
  String skipVersions = theCommandLine.getOptionValue(BaseFlywayMigrateDatabaseCommand.SKIP_VERSIONS);
  addTasks(migrator, skipVersions);

diff --git a/hapi-fhir-cli/hapi-fhir-cli-app/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-cli</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-cli/pom.xml b/hapi-fhir-cli/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-client-okhttp/pom.xml b/hapi-fhir-client-okhttp/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-client/pom.xml b/hapi-fhir-client/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-converter/pom.xml b/hapi-fhir-converter/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-dist/pom.xml b/hapi-fhir-dist/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-docs/pom.xml b/hapi-fhir-docs/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/...n/resources/ca/uhn/hapi/fhir/changelog/7_4_0/5926-fix-jpa-nullable-primitive-columns.yaml b/...n/resources/ca/uhn/hapi/fhir/changelog/7_4_0/5926-fix-jpa-nullable-primitive-columns.yaml
@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 5926
+title: "A number of columns in the JPA schema use primitive types (and therefore can never have a null value) but aren't marked as non-null."
diff --git a/...ain/resources/ca/uhn/hapi/fhir/changelog/7_4_0/5926-skip-migrators-when-initializing.yaml b/...ain/resources/ca/uhn/hapi/fhir/changelog/7_4_0/5926-skip-migrators-when-initializing.yaml
@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 5926
+title: "A regression in HAPI FHIR 6.4.0 meant that ther JPA server schema migrator ran all tasks
+ even when the database was initially empty and the schema was being initialized by script. 
+ This did not produce any incorrect results, but did impact the amount of time taken to initialize
+ an empty database. This has been corrected."
diff --git a/hapi-fhir-jacoco/pom.xml b/hapi-fhir-jacoco/pom.xml
@@ -11,7 +11,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jaxrsserver-base/pom.xml b/hapi-fhir-jaxrsserver-base/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpa/pom.xml b/hapi-fhir-jpa/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-base/pom.xml b/hapi-fhir-jpaserver-base/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>7.3.7-SNAPSHOT</version>
+ <version>7.3.8-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Batch2JobInstanceEntity.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Batch2JobInstanceEntity.java
@@ -119,13 +119,13 @@ public class Batch2JobInstanceEntity implements Serializable {
  @Column(name = "WORK_CHUNKS_PURGED", nullable = false)
  private boolean myWorkChunksPurged;
 
- @Column(name = "PROGRESS_PCT")
+ @Column(name = "PROGRESS_PCT", nullable = false)
  private double myProgress;
 
  @Column(name = "ERROR_MSG", length = ERROR_MSG_MAX_LENGTH, nullable = true)
  private String myErrorMessage;
 
- @Column(name = "ERROR_COUNT")
+ @Column(name = "ERROR_COUNT", nullable = false)
  private int myErrorCount;
 
  @Column(name = "EST_REMAINING", length = TIME_REMAINING_LENGTH, nullable = true)

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Batch2WorkChunkEntity.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Batch2WorkChunkEntity.java
@@ -138,14 +138,20 @@ public class Batch2WorkChunkEntity implements Serializable {
 
  /**
  * The number of times the work chunk has had its state set back to POLL_WAITING.
+ * <p>
+ * TODO: Note that this column was added in 7.2.0, so it is nullable in order to
+ * account for existing rows that were added before the column was added. In
+ * the future we should make this non-null.
  */
  @Column(name = "POLL_ATTEMPTS", nullable = true)
  private Integer myPollAttempts;
 
  /**
  * Default constructor for Hibernate.
  */
- public Batch2WorkChunkEntity() {}
+ public Batch2WorkChunkEntity() {
+ myPollAttempts = 0;
+ }
 
  /**
  * Projection constructor for no-data path.
@@ -184,7 +190,7 @@ public Batch2WorkChunkEntity(
  myRecordsProcessed = theRecordsProcessed;
  myWarningMessage = theWarningMessage;
  myNextPollTime = theNextPollTime;
- myPollAttempts = thePollAttempts;
+ myPollAttempts = thePollAttempts != null ? thePollAttempts : 0;
  }
 
  public static Batch2WorkChunkEntity fromWorkChunk(WorkChunk theWorkChunk) {

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/HapiFhirEnversRevision.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/HapiFhirEnversRevision.java
@@ -58,7 +58,7 @@ public class HapiFhirEnversRevision implements Serializable {
  @SequenceGenerator(name = "SEQ_HFJ_REVINFO", sequenceName = "SEQ_HFJ_REVINFO")
  @GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_HFJ_REVINFO")
  @RevisionNumber
- @Column(name = "REV")
+ @Column(name = "REV", nullable = false)
  private long myRev;
 
  @RevisionTimestamp

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
@@ -117,11 +117,12 @@ public class TermConcept implements Serializable {
  @ManyToOne(fetch = FetchType.LAZY)
  @JoinColumn(
  name = "CODESYSTEM_PID",
+ nullable = false,
  referencedColumnName = "PID",
  foreignKey = @ForeignKey(name = "FK_CONCEPT_PID_CS_PID"))
  private TermCodeSystemVersion myCodeSystem;
 
- @Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
+ @Column(name = "CODESYSTEM_PID", insertable = false, updatable = false, nullable = false)
  @GenericField(name = "myCodeSystemVersionPid")
  private long myCodeSystemVersionPid;