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Start moving forced-id inline to ResourceTable (#4260) 

New fhir_id column in HFJ_RESOURCE.

Migration, changelog, and insert hook for inline fhir_id column.
This commit is contained in:
michaelabuckley 2022-11-16 13:38:52 -05:00 committed by GitHub
parent d8d8c5fa44
commit 6c4283e930
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7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_3_0/4260-inline-forcedid.yaml Normal file
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@ -0,0 +1,7 @@
---
type: add
issue: 4260
title: "The HFJ_RESOURCE table has a new column FHIR_ID which always contains the FHIR resource id,
both client-assigned and server-assigned.
This is parallel storage to allow gradual upgrade away from the current HFJ_FORCED_ID join table,
which should improve performance in a future release."

28
hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/config/HapiFhirLocalContainerEntityManagerFactoryBean.java
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@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.config;
* #L%
*/
import com.google.common.base.Strings;
import org.hibernate.cfg.AvailableSettings;
import org.hibernate.query.criteria.LiteralHandlingMode;
import org.hibernate.resource.jdbc.spi.PhysicalConnectionHandlingMode;
@ -27,6 +28,9 @@ import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.orm.hibernate5.SpringBeanContainer;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
/**
@ -46,6 +50,7 @@ public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContain
public Map<String, Object> getJpaPropertyMap() {
Map<String, Object> retVal = super.getJpaPropertyMap();
// SOMEDAY these defaults can be set in the constructor. setJpaProperties does a merge.
if (!retVal.containsKey(AvailableSettings.CRITERIA_LITERAL_HANDLING_MODE)) {
retVal.put(AvailableSettings.CRITERIA_LITERAL_HANDLING_MODE, LiteralHandlingMode.BIND);
}
@ -82,5 +87,28 @@ public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContain
return retVal;
}
/**
* Helper to add hook to property.
*
* Listener properties are comma-separated lists, so we can't just overwrite or default it.
*/
void addHibernateHook(String thePropertyName, String theHookFQCN) {
Map<String, Object> retVal = super.getJpaPropertyMap();
List<String> listeners = new ArrayList<>();
{
String currentListeners = (String) retVal.get(thePropertyName);
if (!Strings.isNullOrEmpty(currentListeners)) {
listeners.addAll(Arrays.asList(currentListeners.split(",")));
}
}
// add if missing
if (!listeners.contains(theHookFQCN)) {
listeners.add(theHookFQCN);
retVal.put(thePropertyName, String.join(",", listeners));
}
}
}

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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@ -321,6 +321,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
String resourceIdBeforeStorage = theResource.getIdElement().getIdPart();
boolean resourceHadIdBeforeStorage = isNotBlank(resourceIdBeforeStorage);
boolean resourceIdWasServerAssigned = theResource.getUserData(JpaConstants.RESOURCE_ID_SERVER_ASSIGNED) == Boolean.TRUE;
entity.setFhirId(resourceIdBeforeStorage);
HookParams hookParams;

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
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@ -86,6 +86,20 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
init600(); // 20211102 -
init610();
init620();
init630();
}
private void init630() {
Builder version = forVersion(VersionEnum.V6_3_0);
// start forced_id inline migration
version
.onTable("HFJ_RESOURCE")
.addColumn("20221108.1", "FHIR_ID")
.nullable()
// FHIR ids contain a subset of ascii, limited to 64 chars.
.type(ColumnTypeEnum.STRING, 64);
}
private void init620() {

50
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java
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@ -31,6 +31,9 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.Session;
import org.hibernate.annotations.GenerationTime;
import org.hibernate.annotations.GeneratorType;
import org.hibernate.annotations.OptimisticLock;
import org.hibernate.search.engine.backend.types.Projectable;
import org.hibernate.search.engine.backend.types.Searchable;
@ -43,6 +46,7 @@ import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDe
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.ObjectPath;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.PropertyBinding;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.PropertyValue;
import org.hibernate.tuple.ValueGenerator;
import org.hl7.fhir.instance.model.api.IIdType;
import javax.persistence.CascadeType;
@ -273,6 +277,38 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
@Transient
private transient boolean myUnchangedInCurrentOperation;
/**
* The id of the Resource.
* Will contain either the client-assigned id, or the sequence value.
* Will be null during insert time until the first read.
*
*/
@Column(name= "FHIR_ID",
// [A-Za-z0-9\-\.]{1,64} - https://www.hl7.org/fhir/datatypes.html#id
length = 64,
// we never update this after insert, and the Generator will otherwise "dirty" the object.
updatable = false)
// inject the pk for server-assigned sequence ids.
@GeneratorType(when = GenerationTime.INSERT, type = FhirIdGenerator.class)
// Make sure the generator doesn't bump the history version.
@OptimisticLock(excluded = true)
private String myFhirId;
/**
* Populate myFhirId with server-assigned sequence id when no client-id provided.
* We eat this complexity during insert to simplify query time with a uniform column.
* Server-assigned sequence ids aren't available until just before insertion.
* Hibernate calls insert Generators after the pk has been assigned, so we can use myId safely here.
*/
public static final class FhirIdGenerator implements ValueGenerator<String> {
@Override
public String generateValue(Session session, Object owner) {
ResourceTable that = (ResourceTable) owner;
return that.myFhirId != null ? that.myFhirId : that.myId.toString();
}
}
@Version
@Column(name = "RES_VER")
private long myVersion;
@ -782,4 +818,18 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
}
return mySearchParamPresents;
}
/**
* Get the FHIR resource id.
*
* @return the resource id, or null if the resource doesn't have a client-assigned id,
* and hasn't been saved to the db to get a server-assigned id yet.
*/
public String getFhirId() {
return myFhirId;
}
public void setFhirId(String theFhirId) {
myFhirId = theFhirId;
}
}

118
hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
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@ -2,11 +2,17 @@ package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.config.DaoConfig.ClientIdStrategyEnum;
import ca.uhn.fhir.jpa.api.config.DaoConfig.IdStrategyEnum;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.DaoTestUtils;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -87,7 +93,10 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvSource;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
@ -544,6 +553,115 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
obs = myObservationDao.read(obsId.toUnqualifiedVersionless(), mySrd);
}
/**
* We are starting a migration to inline forced_id into RESOURCE_TABLE.
* Verify we are populating the new field AND the old join table for a couple of releases to allow smooth upgrades.
*/
@Nested
class ForcedIdFieldPopulation {
DaoMethodOutcome myMethodOutcome;
String myExpectedId;
@AfterEach
void tearDown() {
myDaoConfig.setResourceClientIdStrategy(new DaoConfig().getResourceClientIdStrategy());
myDaoConfig.setResourceServerIdStrategy(new DaoConfig().getResourceServerIdStrategy());
}
@ParameterizedTest
@CsvSource({
"SEQUENTIAL_NUMERIC,NOT_ALLOWED,",
"SEQUENTIAL_NUMERIC,ANY,forcedId",
"SEQUENTIAL_NUMERIC,ANY,123",
"SEQUENTIAL_NUMERIC,ANY,",
"SEQUENTIAL_NUMERIC,ALPHANUMERIC,forcedId",
// illegal "SEQUENTIAL_NUMERIC,ALPHANUMERIC,123",
"SEQUENTIAL_NUMERIC,ALPHANUMERIC,",
"UUID,NOT_ALLOWED,",
"UUID,ANY,forcedId",
"UUID,ANY,123",
"UUID,ANY,", // uuid server-ids still use hfj_forced_id
"UUID,ALPHANUMERIC,forcedId",
// illegal "UUID,ALPHANUMERIC,123",
"UUID,ALPHANUMERIC,",
})
public void testCreateResource_populatesResourceTableFhirIdField(
IdStrategyEnum theServerIdStrategy,
ClientIdStrategyEnum theClientIdStrategy,
String theClientId
) {
// given id configuration settings
myDaoConfig.setResourceClientIdStrategy(theClientIdStrategy);
myDaoConfig.setResourceServerIdStrategy(theServerIdStrategy);
// create the resource with POST or PUT
Patient pat = new Patient();
runInTransaction(() -> {
if (theClientId != null) {
// PUT with id
pat.setId(theClientId);
myMethodOutcome = myPatientDao.update(pat, mySrd);
myExpectedId = theClientId;
} else {
// POST with server-assigned id
myMethodOutcome = myPatientDao.create(pat, mySrd);
myExpectedId = myMethodOutcome.getId().getIdPart();
}
assertEquals("Patient/" + myExpectedId,
myMethodOutcome.getId().toUnqualifiedVersionless().getValue(),
"the method returns the id");
// saving another resource in the same tx was causing a version bump.
// leaving it here to make sure that bug doesn't come back.
Condition condition = new Condition();
condition.getSubject().setReferenceElement(myMethodOutcome.getId());
myConditionDao.create(condition);
ourLog.info("about to flush");
});
// then verify the database contents
myEntityManager.clear();
// fetch the resource from the db and verify
ResourceTable readBackResource = myEntityManager
.find(ResourceTable.class, myMethodOutcome.getPersistentId().getId());
assertNotNull(readBackResource, "found entity");
assertEquals(1, readBackResource.getVersion(), "first version");
assertEquals(myExpectedId, readBackResource.getFhirId(), "inline column populated on readback");
ResourceHistoryTable readBackHistory = myEntityManager
.createQuery("select h from ResourceHistoryTable h where h.myResourceId = :resId and h.myResourceVersion = 1", ResourceHistoryTable.class)
.setParameter("resId", myMethodOutcome.getPersistentId().getId())
.getSingleResult();
assertNotNull(readBackHistory, "found history");
// no extra history
long historyCount = myEntityManager
.createQuery("select count(h) from ResourceHistoryTable h where h.myResourceId = :resId", Long.class)
.setParameter("resId", myMethodOutcome.getPersistentId().getId())
.getSingleResult();
assertEquals(1, historyCount, "only create one history version");
// make sure the search view works too
ResourceSearchView readBackView = myEntityManager
.createQuery("select v from ResourceSearchView v where v.myResourceId = :resId", ResourceSearchView.class)
.setParameter("resId", myMethodOutcome.getPersistentId().getId())
.getSingleResult();
assertNotNull(readBackView, "found search view");
// verify the forced id join still works
if (readBackResource.getForcedId() != null) {
assertEquals(myExpectedId, readBackResource.getForcedId().getForcedId(),
"legacy join populated");
assertEquals(myExpectedId, readBackView.getForcedId(),
"legacy join populated");
} else {
assertEquals(IdStrategyEnum.SEQUENTIAL_NUMERIC, theServerIdStrategy,
"hfj_forced_id join column is only empty when using server-assigned ids");
} }
}
@Test
public void testCreateDuplicateTagsDoesNotCauseDuplicates() {
Patient p = new Patient();

30
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/config/HapiFhirLocalContainerEntityManagerFactoryBeanTest.java Normal file
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@ -0,0 +1,30 @@
package ca.uhn.fhir.jpa.config;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.support.DefaultListableBeanFactory;
import static org.junit.jupiter.api.Assertions.*;
class HapiFhirLocalContainerEntityManagerFactoryBeanTest {
HapiFhirLocalContainerEntityManagerFactoryBean myBean = new HapiFhirLocalContainerEntityManagerFactoryBean(new DefaultListableBeanFactory());
@Test
void testAddHibernateHookToEmptyProperty() {
// start empty
myBean.addHibernateHook("theKey", "theHookClass");
assertEquals("theHookClass", myBean.getJpaPropertyMap().get("theKey"));
}
@Test
void testAddHibernateHookToSomeRegisteredHooks() {
// start with some hooks already registered
myBean.getJpaPropertyMap().put("theKey", "hook1,hook2");
myBean.addHibernateHook("theKey", "theHookClass");
assertEquals("hook1,hook2,theHookClass", myBean.getJpaPropertyMap().get("theKey"));
}
}