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Merge pull request #1505 from jamesagnew/1454-need-to-implement-the-ancestor-and-descendant-filters-for-loinc 

Resolve "Need to implement the ancestor and descendant filters for LOINC."
This commit is contained in:
Diederik Muylwyk 2019-09-30 09:39:32 -04:00 committed by GitHub
parent 557a8ccc66 ac9c10a4ee
commit 1b2892f475
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
39 changed files with 1146 additions and 299 deletions
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7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
View File

@ -9,7 +9,6 @@ import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.TransactionProcessor;
import ca.uhn.fhir.jpa.dao.dstu3.TransactionProcessorVersionAdapterDstu3;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu3;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryDstu3;
@ -21,6 +20,7 @@ import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
import ca.uhn.fhir.validation.IValidatorModule;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.CachingValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
@ -99,6 +99,11 @@ public class BaseDstu3Config extends BaseConfig {
return val;
}
@Bean
public DefaultProfileValidationSupport defaultProfileValidationSupport() {
return new DefaultProfileValidationSupport();
}
@Bean
public JpaValidationSupportChainDstu3 jpaValidationSupportChain() {
return new JpaValidationSupportChainDstu3();

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
View File

@ -8,7 +8,7 @@ import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.TransactionProcessor;
import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR4;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR4;
@ -20,14 +20,12 @@ import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR4;
import ca.uhn.fhir.validation.IValidatorModule;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import org.hl7.fhir.r4.hapi.validation.CachingValidationSupport;
import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.utils.GraphQLEngine;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@ -102,6 +100,11 @@ public class BaseR4Config extends BaseConfig {
return val;
}
@Bean
public DefaultProfileValidationSupport defaultProfileValidationSupport() {
return new DefaultProfileValidationSupport();
}
@Bean
public JpaValidationSupportChainR4 jpaValidationSupportChain() {
return new JpaValidationSupportChainR4();

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
View File

@ -20,6 +20,7 @@ import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR5;
import ca.uhn.fhir.validation.IValidatorModule;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.r5.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.hapi.validation.CachingValidationSupport;
import org.hl7.fhir.r5.hapi.validation.FhirInstanceValidator;
@ -99,6 +100,11 @@ public class BaseR5Config extends BaseConfig {
return val;
}
@Bean
public DefaultProfileValidationSupport defaultProfileValidationSupport() {
return new DefaultProfileValidationSupport();
}
@Bean
public JpaValidationSupportChainR5 jpaValidationSupportChain() {
return new JpaValidationSupportChainR5();

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -112,7 +112,7 @@ import static org.apache.commons.lang3.StringUtils.*;
@SuppressWarnings("WeakerAccess")
@Repository
public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao, ApplicationContextAware {
public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao, IJpaDao<T>, ApplicationContextAware {
public static final long INDEX_STATUS_INDEXED = 1L;
public static final long INDEX_STATUS_INDEXING_FAILED = 2L;
@ -1017,7 +1017,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
@SuppressWarnings("unchecked")
protected ResourceTable updateEntity(RequestDetails theRequest, final IBaseResource theResource, ResourceTable
@Override
public ResourceTable updateEntity(RequestDetails theRequest, final IBaseResource theResource, ResourceTable
theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
Validate.notNull(theEntity);
@ -1256,6 +1257,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
return theEntity;
}
@Override
public ResourceTable updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
ResourceTable theEntity, IIdType theResourceId, IBaseResource theOldResource) {

139
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
View File

@ -149,21 +149,29 @@ public class DaoConfig {
private boolean myFilterParameterEnabled = false;
private StoreMetaSourceInformationEnum myStoreMetaSourceInformation = StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code false}!
* Do not change default of {@code true}!
*
* @since 4.1.0
*/
private boolean myPreExpandValueSetsExperimental = false;
private boolean myPreExpandValueSets = true;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code 0}!
* Do not change default of {@code 0}!
*
* @since 4.1.0
*/
private int myPreExpandValueSetsDefaultOffsetExperimental = 0;
private int myPreExpandValueSetsDefaultOffset = 0;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code 1000}!
* Do not change default of {@code 1000}!
*
* @since 4.1.0
*/
private int myPreExpandValueSetsDefaultCountExperimental = 1000;
private int myPreExpandValueSetsDefaultCount = 1000;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code 1000}!
* Do not change default of {@code 1000}!
*
* @since 4.1.0
*/
private int myPreExpandValueSetsMaxCountExperimental = 1000;
private int myPreExpandValueSetsMaxCount = 1000;
/**
* Constructor
@ -920,7 +928,7 @@ public class DaoConfig {
* <p>
* Default is {@literal true} beginning in HAPI FHIR 2.4, since this
* feature is now specified in the FHIR specification. (Previously it
* was an experimental/rpposed feature)
* was an experimental/proposed feature)
* </p>
*
* @since 1.5
@ -1621,34 +1629,6 @@ public class DaoConfig {
myModelConfig.setWebsocketContextPath(theWebsocketContextPath);
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
* future optimization of the $expand operation on large ValueSets.
* </p>
* <p>
* The default value for this setting is {@code false}.
* </p>
*/
public boolean isPreExpandValueSetsExperimental() {
return myPreExpandValueSetsExperimental;
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
* future optimization of the $expand operation on large ValueSets.
* </p>
* <p>
* The default value for this setting is {@code false}.
* </p>
*/
public void setPreExpandValueSetsExperimental(boolean thePreExpandValueSetsExperimental) {
myPreExpandValueSetsExperimental = thePreExpandValueSetsExperimental;
}
/**
* If set to <code>true</code> the _filter search parameter will be enabled on this server. Note that _filter
* is very powerful, but also potentially dangerous as it can allow a user to create a query for which there
@ -1720,83 +1700,118 @@ public class DaoConfig {
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
* optimization of the $expand operation on large ValueSets.
* </p>
* <p>
* The default value for this setting is {@code true}.
* </p>
*
* @since 4.1.0
*/
public boolean isPreExpandValueSets() {
return myPreExpandValueSets;
}
/**
* <p>
* If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
* optimization of the $expand operation on large ValueSets.
* </p>
* <p>
* The default value for this setting is {@code true}.
* </p>
*
* @since 4.1.0
*/
public void setPreExpandValueSets(boolean thePreExpandValueSets) {
myPreExpandValueSets = thePreExpandValueSets;
}
/**
* <p>
* This is the default value of {@code offset} parameter for the ValueSet {@code $expand} operation when
* {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
* {@link DaoConfig#isPreExpandValueSets()} returns {@code true}.
* </p>
* <p>
* The default value for this setting is {@code 0}.
* </p>
*
* @since 4.1.0
*/
public int getPreExpandValueSetsDefaultOffsetExperimental() {
return myPreExpandValueSetsDefaultOffsetExperimental;
public int getPreExpandValueSetsDefaultOffset() {
return myPreExpandValueSetsDefaultOffset;
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* This is the default value of {@code count} parameter for the ValueSet {@code $expand} operation when
* {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
* {@link DaoConfig#isPreExpandValueSets()} returns {@code true}.
* </p>
* <p>
* The default value for this setting is {@code 1000}.
* </p>
*
* @since 4.1.0
*/
public int getPreExpandValueSetsDefaultCountExperimental() {
return myPreExpandValueSetsDefaultCountExperimental;
public int getPreExpandValueSetsDefaultCount() {
return myPreExpandValueSetsDefaultCount;
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* This is the default value of {@code count} parameter for the ValueSet {@code $expand} operation when
* {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
* {@link DaoConfig#isPreExpandValueSets()} returns {@code true}.
* </p>
* <p>
* If {@code thePreExpandValueSetsDefaultCountExperimental} is greater than
* {@link DaoConfig#getPreExpandValueSetsMaxCountExperimental()}, the lesser value is used.
* If {@code thePreExpandValueSetsDefaultCount} is greater than
* {@link DaoConfig#getPreExpandValueSetsMaxCount()}, the lesser value is used.
* </p>
* <p>
* The default value for this setting is {@code 1000}.
* </p>
*
* @since 4.1.0
*/
public void setPreExpandValueSetsDefaultCountExperimental(int thePreExpandValueSetsDefaultCountExperimental) {
myPreExpandValueSetsDefaultCountExperimental = Math.min(thePreExpandValueSetsDefaultCountExperimental, getPreExpandValueSetsMaxCountExperimental());
public void setPreExpandValueSetsDefaultCount(int thePreExpandValueSetsDefaultCount) {
myPreExpandValueSetsDefaultCount = Math.min(thePreExpandValueSetsDefaultCount, getPreExpandValueSetsMaxCount());
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* This is the max value of {@code count} parameter for the ValueSet {@code $expand} operation when
* {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
* {@link DaoConfig#isPreExpandValueSets()} returns {@code true}.
* </p>
* <p>
* The default value for this setting is {@code 1000}.
* </p>
*
* @since 4.1.0
*/
public int getPreExpandValueSetsMaxCountExperimental() {
return myPreExpandValueSetsMaxCountExperimental;
public int getPreExpandValueSetsMaxCount() {
return myPreExpandValueSetsMaxCount;
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* This is the max value of {@code count} parameter for the ValueSet {@code $expand} operation when
* {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
* {@link DaoConfig#isPreExpandValueSets()} returns {@code true}.
* </p>
* <p>
* If {@code thePreExpandValueSetsMaxCountExperimental} is lesser than
* {@link DaoConfig#getPreExpandValueSetsDefaultCountExperimental()}, the default {@code count} is lowered to the
* If {@code thePreExpandValueSetsMaxCount} is lesser than
* {@link DaoConfig#getPreExpandValueSetsDefaultCount()}, the default {@code count} is lowered to the
* new max {@code count}.
* </p>
* <p>
* The default value for this setting is {@code 1000}.
* </p>
*
* @since 4.1.0
*/
public void setPreExpandValueSetsMaxCountExperimental(int thePreExpandValueSetsMaxCountExperimental) {
myPreExpandValueSetsMaxCountExperimental = thePreExpandValueSetsMaxCountExperimental;
setPreExpandValueSetsDefaultCountExperimental(Math.min(getPreExpandValueSetsDefaultCountExperimental(), getPreExpandValueSetsMaxCountExperimental()));
public void setPreExpandValueSetsMaxCount(int thePreExpandValueSetsMaxCount) {
myPreExpandValueSetsMaxCount = thePreExpandValueSetsMaxCount;
setPreExpandValueSetsDefaultCount(Math.min(getPreExpandValueSetsDefaultCount(), getPreExpandValueSetsMaxCount()));
}
public enum IndexEnabledEnum {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java
View File

@ -73,8 +73,8 @@ public class FhirResourceDaoSubscriptionDstu2 extends FhirResourceDaoDstu2<Subsc
@Override
protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (theDeletedTimestampOrNull != null) {

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IJpaDao.java Normal file
View File

@ -0,0 +1,18 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import java.util.Date;
public interface IJpaDao<T extends IBaseResource> {
@SuppressWarnings("unchecked")
ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable
theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry);
ResourceTable updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
ResourceTable theEntity, IIdType theResourceId, IBaseResource theOldResource);
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java
View File

@ -909,10 +909,13 @@ public class TransactionProcessor<BUNDLE extends IBaseBundle, BUNDLEENTRY> {
IPrimitiveType<Date> deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
IFhirResourceDao<? extends IBaseResource> dao = myDaoRegistry.getResourceDao(nextResource.getClass());
IJpaDao jpaDao = (IJpaDao) dao;
if (updatedEntities.contains(nextOutcome.getEntity())) {
myDao.updateInternal(theRequest, nextResource, true, false, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource());
jpaDao.updateInternal(theRequest, nextResource, true, false, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource());
} else if (!nonUpdatedEntities.contains(nextOutcome.getEntity())) {
myDao.updateEntity(theRequest, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, theUpdateTime, false, true);
jpaDao.updateEntity(theRequest, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, theUpdateTime, false, true);
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -125,8 +125,8 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
CodeSystem csDstu3 = (CodeSystem) theResource;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
View File

@ -158,8 +158,8 @@ public class FhirResourceDaoConceptMapDstu3 extends FhirResourceDaoDstu3<Concept
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (retVal.getDeleted() == null) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSubscriptionDstu3.java
View File

@ -83,8 +83,8 @@ public class FhirResourceDaoSubscriptionDstu3 extends FhirResourceDaoDstu3<Subsc
@Override
protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (theDeletedTimestampOrNull != null) {

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -32,6 +32,7 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
@ -63,9 +64,13 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
@Autowired
@Qualifier("myJpaValidationSupportChainDstu3")
private IValidationSupport myValidationSupport;
@Autowired
private IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
@ -310,12 +315,18 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
boolean haveIdentifierParam = theValueSetIdentifier != null && theValueSetIdentifier.isEmpty() == false;
ValueSet vs = null;
boolean isBuiltInValueSet = false;
if (theId != null) {
vs = read(theId, theRequestDetails);
} else if (haveIdentifierParam) {
vs = myValidationSupport.fetchResource(getContext(), ValueSet.class, theValueSetIdentifier.getValue());
vs = myDefaultProfileValidationSupport.fetchValueSet(getContext(), theValueSetIdentifier.getValue());
if (vs == null) {
throw new InvalidRequestException("Unknown ValueSet identifier: " + theValueSetIdentifier.getValue());
vs = myValidationSupport.fetchValueSet(getContext(), theValueSetIdentifier.getValue());
if (vs == null) {
throw new InvalidRequestException("Unknown ValueSet identifier: " + theValueSetIdentifier.getValue());
}
} else {
isBuiltInValueSet = true;
}
} else {
if (theCode == null || theCode.isEmpty()) {
@ -332,7 +343,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSetsExperimental() && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
if (myDaoConfig.isPreExpandValueSets() && !isBuiltInValueSet && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);
@ -395,11 +406,11 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (myDaoConfig.isPreExpandValueSets()) {
if (retVal.getDeleted() == null) {
try {
ValueSet valueSet = (ValueSet) theResource;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
View File

@ -128,8 +128,8 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
CodeSystem cs = (CodeSystem) theResource;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java
View File

@ -158,8 +158,8 @@ public class FhirResourceDaoConceptMapR4 extends FhirResourceDaoR4<ConceptMap> i
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (retVal.getDeleted() == null) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSubscriptionR4.java
View File

@ -75,8 +75,8 @@ public class FhirResourceDaoSubscriptionR4 extends FhirResourceDaoR4<Subscriptio
@Override
protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (theDeletedTimestampOrNull != null) {

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -33,6 +33,7 @@ import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.*;
@ -57,6 +58,9 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
@Autowired
@Qualifier("myJpaValidationSupportChainR4")
private IValidationSupport myValidationSupport;
@ -306,12 +310,18 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
boolean haveIdentifierParam = theValueSetIdentifier != null && !theValueSetIdentifier.isEmpty();
ValueSet vs = null;
boolean isBuiltInValueSet = false;
if (theId != null) {
vs = read(theId, theRequestDetails);
} else if (haveIdentifierParam) {
vs = myValidationSupport.fetchResource(getContext(), ValueSet.class, theValueSetIdentifier.getValue());
vs = myDefaultProfileValidationSupport.fetchValueSet(getContext(), theValueSetIdentifier.getValue());
if (vs == null) {
throw new InvalidRequestException("Unknown ValueSet identifier: " + theValueSetIdentifier.getValue());
vs = myValidationSupport.fetchValueSet(getContext(), theValueSetIdentifier.getValue());
if (vs == null) {
throw new InvalidRequestException("Unknown ValueSet identifier: " + theValueSetIdentifier.getValue());
}
} else {
isBuiltInValueSet = true;
}
} else {
if (theCode == null || theCode.isEmpty()) {
@ -328,7 +338,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSetsExperimental() && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
if (myDaoConfig.isPreExpandValueSets() && !isBuiltInValueSet && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);
@ -391,11 +401,11 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (myDaoConfig.isPreExpandValueSets()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSet(retVal, valueSet);
@ -407,4 +417,5 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
return retVal;
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -128,8 +128,8 @@ public class FhirResourceDaoCodeSystemR5 extends FhirResourceDaoR5<CodeSystem> i
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
CodeSystem cs = (CodeSystem) theResource;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java
View File

@ -157,7 +157,7 @@ public class FhirResourceDaoConceptMapR5 extends FhirResourceDaoR5<ConceptMap> i
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoSubscriptionR5.java
View File

@ -73,8 +73,8 @@ public class FhirResourceDaoSubscriptionR5 extends FhirResourceDaoR5<Subscriptio
@Override
protected ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (theDeletedTimestampOrNull != null) {

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -33,6 +33,7 @@ import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r5.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r5.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.model.*;
@ -57,6 +58,9 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
@Autowired
@Qualifier("myJpaValidationSupportChainR5")
private IValidationSupport myValidationSupport;
@ -312,12 +316,18 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
boolean haveIdentifierParam = theValueSetIdentifier != null && theValueSetIdentifier.isEmpty() == false;
ValueSet vs = null;
boolean isBuiltInValueSet = false;
if (theId != null) {
vs = read(theId, theRequestDetails);
} else if (haveIdentifierParam) {
vs = myValidationSupport.fetchResource(getContext(), ValueSet.class, theValueSetIdentifier.getValue());
vs = myDefaultProfileValidationSupport.fetchValueSet(getContext(), theValueSetIdentifier.getValue());
if (vs == null) {
throw new InvalidRequestException("Unknown ValueSet identifier: " + theValueSetIdentifier.getValue());
vs = myValidationSupport.fetchValueSet(getContext(), theValueSetIdentifier.getValue());
if (vs == null) {
throw new InvalidRequestException("Unknown ValueSet identifier: " + theValueSetIdentifier.getValue());
}
} else {
isBuiltInValueSet = true;
}
} else {
if (theCode == null || theCode.isEmpty()) {
@ -334,7 +344,7 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSetsExperimental() && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
if (myDaoConfig.isPreExpandValueSets() && !isBuiltInValueSet && myTerminologySvc.isValueSetPreExpandedForCodeValidation(vs)) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);
@ -397,11 +407,11 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (myDaoConfig.isPreExpandValueSets()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet));

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java
View File

@ -68,7 +68,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.");
}
int offset = myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental();
int offset = myDaoConfig.getPreExpandValueSetsDefaultOffset();
if (theOffset != null && theOffset.hasValue()) {
if (theOffset.getValue() >= 0) {
offset = theOffset.getValue();
@ -77,7 +77,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
}
}
int count = myDaoConfig.getPreExpandValueSetsDefaultCountExperimental();
int count = myDaoConfig.getPreExpandValueSetsDefaultCount();
if (theCount != null && theCount.hasValue()) {
if (theCount.getValue() >= 0) {
count = theCount.getValue();
@ -85,7 +85,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
}
}
int countMax = myDaoConfig.getPreExpandValueSetsMaxCountExperimental();
int countMax = myDaoConfig.getPreExpandValueSetsMaxCount();
if (count > countMax) {
ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
count = countMax;
@ -94,7 +94,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (myDaoConfig.isPreExpandValueSets()) {
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
} else if (haveIdentifier) {

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderValueSetR4.java
View File

@ -60,7 +60,7 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have a url specified, or have a ValueSet specified. Can not combine these options.");
}
int offset = myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental();
int offset = myDaoConfig.getPreExpandValueSetsDefaultOffset();
if (theOffset != null && theOffset.hasValue()) {
if (theOffset.getValue() >= 0) {
offset = theOffset.getValue();
@ -69,7 +69,7 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
}
}
int count = myDaoConfig.getPreExpandValueSetsDefaultCountExperimental();
int count = myDaoConfig.getPreExpandValueSetsDefaultCount();
if (theCount != null && theCount.hasValue()) {
if (theCount.getValue() >= 0) {
count = theCount.getValue();
@ -77,7 +77,7 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
}
}
int countMax = myDaoConfig.getPreExpandValueSetsMaxCountExperimental();
int countMax = myDaoConfig.getPreExpandValueSetsMaxCount();
if (count > countMax) {
ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
count = countMax;
@ -86,7 +86,7 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (myDaoConfig.isPreExpandValueSets()) {
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
} else if (haveIdentifier) {

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderValueSetR5.java
View File

@ -60,7 +60,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have a url specified, or have a ValueSet specified. Can not combine these options.");
}
int offset = myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental();
int offset = myDaoConfig.getPreExpandValueSetsDefaultOffset();
if (theOffset != null && theOffset.hasValue()) {
if (theOffset.getValue() >= 0) {
offset = theOffset.getValue();
@ -69,7 +69,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
}
}
int count = myDaoConfig.getPreExpandValueSetsDefaultCountExperimental();
int count = myDaoConfig.getPreExpandValueSetsDefaultCount();
if (theCount != null && theCount.hasValue()) {
if (theCount.getValue() >= 0) {
count = theCount.getValue();
@ -77,7 +77,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
}
}
int countMax = myDaoConfig.getPreExpandValueSetsMaxCountExperimental();
int countMax = myDaoConfig.getPreExpandValueSetsMaxCount();
if (count > countMax) {
ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
count = countMax;
@ -86,7 +86,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (myDaoConfig.isPreExpandValueSets()) {
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
} else if (haveIdentifier) {

163
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
View File

@ -63,9 +63,9 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
import org.quartz.Job;
import org.quartz.JobExecutionContext;
import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
@ -204,22 +204,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ValueSet.ConceptSetFilterComponent nextFilter) {
bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
}
private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ValueSet.ConceptSetFilterComponent nextFilter) {
Query textQuery = qb
.phrase()
.withSlop(2)
.onField("myDisplay").boostedTo(4.0f)
.andField("myDisplayEdgeNGram").boostedTo(2.0f)
// .andField("myDisplayNGram").boostedTo(1.0f)
// .andField("myDisplayPhonetic").boostedTo(0.5f)
.sentence(nextFilter.getValue().toLowerCase()).createQuery();
bool.must(textQuery);
}
private boolean addToSet(Set<TermConcept> theSetToPopulate, TermConcept theConcept) {
boolean retVal = theSetToPopulate.add(theConcept);
if (retVal) {
@ -888,18 +872,20 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
break;
case "parent":
case "child":
if (isCodeSystemLoinc(theSystem)) {
handleFilterLoincParentChild(theQb, theBool, theFilter);
} else {
throw new InvalidRequestException("Invalid filter, property " + theFilter.getProperty() + " is LOINC-specific and cannot be used with system: " + theSystem);
}
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
handleFilterLoincParentChild(theQb, theBool, theFilter);
break;
case "ancestor":
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
handleFilterLoincAncestor(theSystem, theQb, theBool, theFilter);
break;
case "descendant":
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
handleFilterLoincDescendant(theSystem, theQb, theBool, theFilter);
break;
case "copyright":
if (isCodeSystemLoinc(theSystem)) {
handleFilterLoincCopyright(theQb, theBool, theFilter);
} else {
throw new InvalidRequestException("Invalid filter, property " + theFilter.getProperty() + " is LOINC-specific and cannot be used with system: " + theSystem);
}
isCodeSystemLoingOrThrowInvalidRequestException(theSystem, theFilter.getProperty());
handleFilterLoincCopyright(theQb, theBool, theFilter);
break;
default:
handleFilterRegex(theBool, theFilter);
@ -907,6 +893,13 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
private boolean isCodeSystemLoingOrThrowInvalidRequestException(String theSystem, String theProperty) {
if (!isCodeSystemLoinc(theSystem)) {
throw new InvalidRequestException("Invalid filter, property " + theProperty + " is LOINC-specific and cannot be used with system: " + theSystem);
}
return true;
}
private boolean isCodeSystemLoinc(String theSystem) {
return IHapiTerminologyLoaderSvc.LOINC_URI.equals(theSystem);
}
@ -923,6 +916,22 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ValueSet.ConceptSetFilterComponent nextFilter) {
bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
}
private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ValueSet.ConceptSetFilterComponent nextFilter) {
Query textQuery = qb
.phrase()
.withSlop(2)
.onField("myDisplay").boostedTo(4.0f)
.andField("myDisplayEdgeNGram").boostedTo(2.0f)
// .andField("myDisplayNGram").boostedTo(1.0f)
// .andField("myDisplayPhonetic").boostedTo(0.5f)
.sentence(nextFilter.getValue().toLowerCase()).createQuery();
bool.must(textQuery);
}
private void handleFilterConceptAndCode(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
TermConcept code = findCode(theSystem, theFilter.getValue())
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + theSystem + "}" + theFilter.getValue()));
@ -936,12 +945,15 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
private void handleFilterLoincParentChild(QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
if (theFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
addLoincFilterParentChildEqual(theBool, theFilter.getProperty(), theFilter.getValue());
} else if (theFilter.getOp() == ValueSet.FilterOperator.IN) {
addLoincFilterParentChildIn(theBool, theFilter);
} else {
throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
switch (theFilter.getOp()) {
case EQUAL:
addLoincFilterParentChildEqual(theBool, theFilter.getProperty(), theFilter.getValue());
break;
case IN:
addLoincFilterParentChildIn(theBool, theFilter);
break;
default:
throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
}
}
@ -964,6 +976,83 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
return new Term(TermConceptPropertyFieldBridge.CONCEPT_FIELD_PROPERTY_PREFIX + theProperty, theValue);
}
private void handleFilterLoincAncestor(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
switch (theFilter.getOp()) {
case EQUAL:
addLoincFilterAncestorEqual(theSystem, theQb, theBool, theFilter);
break;
case IN:
addLoincFilterAncestorIn(theSystem, theQb, theBool, theFilter);
break;
default:
throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
}
}
private void addLoincFilterAncestorEqual(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
TermConcept code = findCode(theSystem, theFilter.getValue())
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + theSystem + "}" + theFilter.getValue()));
logFilteringValueOnProperty(theFilter.getValue(), theFilter.getProperty());
theBool.must(theQb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
}
private void addLoincFilterAncestorIn(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
throw new UnsupportedOperationException();
// FIXME: DM 2019-09-25 - Filter with op=IN on ancestor; see #1512 in GitHub.
// FIXME: DM 2019-09-26 - Once implemented, fix changelog entry for #1454 in changes.xml
// String[] values = theFilter.getValue().split(",");
// for (String value : values) {
// logFilteringValueOnProperty(value, theFilter.getProperty());
// }
}
private void handleFilterLoincDescendant(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
switch (theFilter.getOp()) {
case EQUAL:
addLoincFilterDescendantEqual(theSystem, theBool, theFilter);
break;
case IN:
addLoincFilterDescendantIn(theSystem, theQb, theBool, theFilter);
break;
default:
throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
}
}
private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
addLoincFilterDescendantEqual(theSystem, theBool, theFilter.getProperty(), theFilter.getValue());
}
private void addLoincFilterDescendantEqual(String theSystem, BooleanJunction<?> theBool, String theProperty, String theValue) {
List<Term> terms = getDescendantTerms(theSystem, theProperty, theValue);
theBool.must(new TermsQuery(terms));
}
private void addLoincFilterDescendantIn(String theSystem, QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
String[] values = theFilter.getValue().split(",");
List<Term> terms = new ArrayList<>();
for (String value : values) {
terms.addAll(getDescendantTerms(theSystem, theFilter.getProperty(), value));
}
theBool.must(new TermsQuery(terms));
}
private List<Term> getDescendantTerms(String theSystem, String theProperty, String theValue) {
List<Term> retVal = new ArrayList<>();
TermConcept code = findCode(theSystem, theValue)
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + theSystem + "}" + theValue));
String[] parentPids = code.getParentPidsAsString().split(" ");
for (String parentPid : parentPids) {
retVal.add(new Term("myId", parentPid));
}
logFilteringValueOnProperty(theValue, theProperty);
return retVal;
}
private void handleFilterLoincCopyright(QueryBuilder theQb, BooleanJunction<?> theBool, ValueSet.ConceptSetFilterComponent theFilter) {
if (theFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
@ -1870,7 +1959,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Override
@Transactional
public void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap) {
ourLog.info("Storing TermConceptMap {}", theConceptMap.getIdElement().getValue());
ourLog.info("Storing TermConceptMap for {}", theConceptMap.getIdElement().toVersionless().getValueAsString());
ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theConceptMap.getUrl(), "ConceptMap has no value for ConceptMap.url");
@ -1981,7 +2070,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
throw new UnprocessableEntityException(msg);
}
ourLog.info("Done storing TermConceptMap[{}]", termConceptMap.getId());
ourLog.info("Done storing TermConceptMap[{}] for {}", termConceptMap.getId(), theConceptMap.getIdElement().toVersionless().getValueAsString());
}
@Override
@ -2077,7 +2166,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Override
@Transactional
public void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet) {
ourLog.info("Storing TermValueSet {}", theValueSet.getIdElement().getValue());
ourLog.info("Storing TermValueSet for {}", theValueSet.getIdElement().toVersionless().getValueAsString());
ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theValueSet.getUrl(), "ValueSet has no value for ValueSet.url");
@ -2111,7 +2200,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
throw new UnprocessableEntityException(msg);
}
ourLog.info("Done storing TermValueSet[{}]", termValueSet.getId());
ourLog.info("Done storing TermValueSet[{}] for {}", termValueSet.getId(), theValueSet.getIdElement().toVersionless().getValueAsString());
}
@Override

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincPartRelatedCodeMappingHandler.java
View File

@ -42,8 +42,8 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
public static final String LOINC_SCT_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-snomed-ct";
private static final String LOINC_SCT_PART_MAP_NAME = "LOINC Part Map to SNOMED CT";
public static final String LOINC_TERM_TO_RPID_PART_MAP_ID = "loinc-term-to-rpids";
public static final String LOINC_TERM_TO_RPID_PART_MAP_URI = "http://loinc.org/cm/loinc-term-to-rpids";
public static final String LOINC_TERM_TO_RPID_PART_MAP_ID = "loinc-to-rpids";
public static final String LOINC_TERM_TO_RPID_PART_MAP_URI = "http://loinc.org/cm/loinc-to-rpids";
public static final String LOINC_TERM_TO_RPID_PART_MAP_NAME = "LOINC Terms to RadLex RPIDs";
public static final String LOINC_PART_TO_RID_PART_MAP_ID = "loinc-part-to-rids";

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChainDstu3.java
View File

@ -38,7 +38,8 @@ public class JpaValidationSupportChainDstu3 extends ValidationSupportChain {
@Autowired
@Qualifier("myJpaValidationSupportDstu3")
public ca.uhn.fhir.jpa.dao.dstu3.IJpaValidationSupportDstu3 myJpaValidationSupportDstu3;
private DefaultProfileValidationSupport myDefaultProfileValidationSupport = new DefaultProfileValidationSupport();
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
@Autowired
private IHapiTerminologySvcDstu3 myTerminologyService;
@Autowired

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChainR4.java
View File

@ -20,10 +20,8 @@ package ca.uhn.fhir.jpa.validation;
* #L%
*/
import javax.annotation.PostConstruct;
import javax.annotation.PreDestroy;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r4.hapi.validation.SnapshotGeneratingValidationSupport;
@ -32,11 +30,13 @@ import org.hl7.fhir.r4.model.StructureDefinition;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
import javax.annotation.PostConstruct;
import javax.annotation.PreDestroy;
public class JpaValidationSupportChainR4 extends ValidationSupportChain {
private DefaultProfileValidationSupport myDefaultProfileValidationSupport = new DefaultProfileValidationSupport();
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
@Autowired
private FhirContext myFhirContext;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChainR5.java
View File

@ -35,7 +35,8 @@ import javax.annotation.PreDestroy;
public class JpaValidationSupportChainR5 extends ValidationSupportChain {
private DefaultProfileValidationSupport myDefaultProfileValidationSupport = new DefaultProfileValidationSupport();
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
@Autowired
private FhirContext myFhirContext;

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java
View File

@ -537,6 +537,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
@Test
public void testIndexNoDuplicatesUri() {
ValueSet res = new ValueSet();
res.setUrl("http://www.example.org/vs");
res.getCompose().addInclude().setSystem("http://foo");
res.getCompose().addInclude().setSystem("http://bar");
res.getCompose().addInclude().setSystem("http://foo");
@ -549,7 +550,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
Class<ResourceIndexedSearchParamUri> type = ResourceIndexedSearchParamUri.class;
List<?> results = myEntityManager.createQuery("SELECT i FROM " + type.getSimpleName() + " i WHERE i.myMissing = false", type).getResultList();
ourLog.info(toStringMultiline(results));
assertEquals(2, results.size());
assertEquals(3, results.size());
List<IIdType> actual = toUnqualifiedVersionlessIds(myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(ValueSet.SP_REFERENCE, new UriParam("http://foo"))));
assertThat(actual, contains(id));
@ -2161,13 +2162,14 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
}
@Test
public void testSearchUriWrongParam() throws Exception {
public void testSearchUriWrongParam() {
ValueSet v1 = new ValueSet();
v1.getUrlElement().setValue("http://foo");
String id1 = myValueSetDao.create(v1).getId().toUnqualifiedVersionless().getValue();
ValueSet v2 = new ValueSet();
v2.getExpansion().getIdentifierElement().setValue("http://foo");
v2.getUrlElement().setValue("http://www.example.org/vs");
String id2 = myValueSetDao.create(v2).getId().toUnqualifiedVersionless().getValue();
{

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValueSetTest.java
View File

@ -229,7 +229,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
}
@Test
public void testValiedateCodeAgainstBuiltInValueSetAndCodeSystemWithValidCode() {
public void testValidateCodeAgainstBuiltInValueSetAndCodeSystemWithValidCode() {
IPrimitiveType<String> display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -914,6 +914,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
@Test
public void testIndexNoDuplicatesUri() {
ValueSet res = new ValueSet();
res.setUrl("http://www.example.org/vs");
res.getCompose().addInclude().setSystem("http://foo");
res.getCompose().addInclude().setSystem("http://bar");
res.getCompose().addInclude().setSystem("http://foo");
@ -927,7 +928,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
Class<ResourceIndexedSearchParamUri> type = ResourceIndexedSearchParamUri.class;
List<?> results = myEntityManager.createQuery("SELECT i FROM " + type.getSimpleName() + " i WHERE i.myMissing = false", type).getResultList();
ourLog.info(toStringMultiline(results));
assertEquals(2, results.size());
assertEquals(3, results.size());
});
List<IIdType> actual = toUnqualifiedVersionlessIds(myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(ValueSet.SP_REFERENCE, new UriParam("http://foo"))));
@ -2951,6 +2952,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
ValueSet v2 = new ValueSet();
v2.getExpansion().getIdentifierElement().setValue("http://foo");
v2.getUrlElement().setValue("http://www.example.org/vs");
String id2 = myValueSetDao.create(v2).getId().toUnqualifiedVersionless().getValue();
{

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoHashesTest.java
View File

@ -772,6 +772,7 @@ public class FhirResourceDaoR4SearchNoHashesTest extends BaseJpaR4Test {
@Test
public void testIndexNoDuplicatesUri() {
ValueSet res = new ValueSet();
res.setUrl("http://www.example.org/vs");
res.getCompose().addInclude().setSystem("http://foo");
res.getCompose().addInclude().setSystem("http://bar");
res.getCompose().addInclude().setSystem("http://foo");
@ -785,7 +786,7 @@ public class FhirResourceDaoR4SearchNoHashesTest extends BaseJpaR4Test {
Class<ResourceIndexedSearchParamUri> type = ResourceIndexedSearchParamUri.class;
List<?> results = myEntityManager.createQuery("SELECT i FROM " + type.getSimpleName() + " i WHERE i.myMissing = false", type).getResultList();
ourLog.info(toStringMultiline(results));
assertEquals(2, results.size());
assertEquals(3, results.size());
});
List<IIdType> actual = toUnqualifiedVersionlessIds(myValueSetDao.search(new SearchParameterMap().setLoadSynchronous(true).add(ValueSet.SP_REFERENCE, new UriParam("http://foo"))));

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValueSetTest.java
View File

@ -22,7 +22,7 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
@After
public void after() {
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
myDaoConfig.setPreExpandValueSets(new DaoConfig().isPreExpandValueSets());
}
@AfterClass
@ -128,7 +128,7 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
@Test
public void testValidateCodeOperationByResourceIdAndCodeableConceptWithExistingValueSetAndPreExpansionEnabled() {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
UriType valueSetIdentifier = null;
IIdType id = myExtensionalVsId;
@ -169,7 +169,7 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
@Test
public void testValidateCodeOperationByResourceIdAndCodeAndSystemWithExistingValueSetAndPreExpansionEnabled() {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
UriType valueSetIdentifier = null;
IIdType id = myExtensionalVsId;

20
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
View File

@ -140,7 +140,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
createLocalVsWithUnknownCode(codeSystem);
}
private void createLocalCsAndVs() {
private void createLocalCs() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
@ -155,8 +155,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
.addConcept(new ConceptDefinitionComponent().setCode("BA").setDisplay("Code BA"))
.addConcept(new ConceptDefinitionComponent().setCode("BB").setDisplay("Code BB"));
myCodeSystemDao.create(codeSystem, mySrd);
createLocalVs(codeSystem);
}
@ -242,6 +240,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
// Include
vs = new ValueSet();
vs.setUrl("http://www.example.org/vs");
vs.getCompose()
.addInclude()
.setSystem(CS_URL);
@ -282,6 +281,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
// Include
vs = new ValueSet();
vs.setUrl("http://www.example.org/vs");
vs.getCompose()
.addInclude()
.setSystem(CS_URL);
@ -329,7 +329,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@Test
public void testExpandByIdWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
@ -445,7 +445,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@Test
public void testExpandByUrlWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
@ -468,7 +468,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@Test
public void testExpandByUrlWithPreExpansionAndBogusUrl() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
@ -746,7 +746,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
public void testValidateCodeOperationByCodeAndSystemInstanceOnInstance() throws IOException {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
createLocalCsAndVs();
createLocalCs();
createLocalVsWithIncludeConcept();
String url = ourServerBase +
@ -789,7 +789,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
* Technically this is the wrong param name
*/
@Test
public void testValiedateCodeAgainstBuiltInSystem() throws Exception {
public void testValidateCodeAgainstBuiltInSystem() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
Parameters respParam = ourClient
@ -819,7 +819,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
* Technically this is the right param name
*/
@Test
public void testValiedateCodeAgainstBuiltInSystemByUrl() throws Exception {
public void testValidateCodeAgainstBuiltInSystemByUrl() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
Parameters respParam = ourClient
@ -847,7 +847,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@After
public void afterResetPreExpansionDefault() {
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
myDaoConfig.setPreExpandValueSets(new DaoConfig().isPreExpandValueSets());
}
@AfterClass

15
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
View File

@ -70,6 +70,7 @@ import java.nio.charset.StandardCharsets;
import java.util.*;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
import static ca.uhn.fhir.jpa.util.TestUtil.sleepOneClick;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hamcrest.Matchers.*;
@ -846,7 +847,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
@Override
public void interceptResponse(IHttpResponse theResponse) { // TODO Auto-generated method stu
public void interceptResponse(IHttpResponse theResponse) { // TODO Auto-generated method stub
}
});
@ -3900,10 +3901,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
ourClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
/*
* First, make sure that we don't reuse a search if
* it's not marked with an expiry
*/
{
myDaoConfig.setReuseCachedSearchResultsForMillis(10L);
Bundle result1 = ourClient
@ -3912,7 +3910,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.returnBundle(Bundle.class)
.execute();
final String uuid1 = toSearchUuidFromLinkNext(result1);
sleepOneClick();
sleepAtLeast(11L);
Bundle result2 = ourClient
.search()
.forResource("Organization")
@ -3922,10 +3920,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
assertNotEquals(uuid1, uuid2);
}
/*
* Now try one but mark it with an expiry time
* in the future
*/
{
myDaoConfig.setReuseCachedSearchResultsForMillis(1000L);
Bundle result1 = ourClient
@ -3946,7 +3940,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.returnBundle(Bundle.class)
.execute();
// Expiry doesn't affect reusablility
final String uuid2 = toSearchUuidFromLinkNext(result2);
assertEquals(uuid1, uuid2);

202
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
View File

@ -3,8 +3,7 @@ package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
@ -36,6 +35,7 @@ import org.springframework.transaction.support.TransactionTemplate;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.Optional;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_VALUE_SET;
@ -57,12 +57,28 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
loadAndPersistValueSet(theVerb);
}
private void loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb theVerb) throws IOException {
loadAndPersistCodeSystemWithDesignations(theVerb);
loadAndPersistValueSet(theVerb);
}
private void loadAndPersistCodeSystemAndValueSetWithDesignationsAndExclude(HttpVerb theVerb) throws IOException {
loadAndPersistCodeSystemWithDesignations(theVerb);
loadAndPersistValueSetWithExclude(theVerb);
}
private void loadAndPersistCodeSystem(HttpVerb theVerb) throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
codeSystem.setId("CodeSystem/cs");
persistCodeSystem(codeSystem, theVerb);
}
private void loadAndPersistCodeSystemWithDesignations(HttpVerb theVerb) throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs-with-designations.xml");
codeSystem.setId("CodeSystem/cs");
persistCodeSystem(codeSystem, theVerb);
}
private void persistCodeSystem(CodeSystem theCodeSystem, HttpVerb theVerb) {
switch (theVerb) {
case POST:
@ -93,6 +109,12 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
persistValueSet(valueSet, theVerb);
}
private void loadAndPersistValueSetWithExclude(HttpVerb theVerb) throws IOException {
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs-with-exclude.xml");
valueSet.setId("ValueSet/vs");
persistValueSet(valueSet, theVerb);
}
private void persistValueSet(ValueSet theValueSet, HttpVerb theVerb) {
switch (theVerb) {
case POST:
@ -222,7 +244,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@Test
public void testExpandByIdWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
@ -274,7 +296,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@Test
public void testExpandByIdWithFilterWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
@ -333,7 +355,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@Test
public void testExpandByUrlWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
@ -356,7 +378,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@Test
public void testExpandByUrlWithPreExpansionAndBogusUrl() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
@ -398,7 +420,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@Test
public void testExpandByValueSetWithPreExpansion() throws IOException {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystem(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
@ -687,6 +709,168 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
}
@Test
public void testUpdateValueSetTriggersAnotherPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
String initialValueSetName = valueSet.getName();
validateTermValueSetNotExpanded(initialValueSetName);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildren(initialValueSetName, codeSystem);
ValueSet updatedValueSet = valueSet;
updatedValueSet.setName(valueSet.getName().concat(" - MODIFIED"));
persistValueSet(updatedValueSet, HttpVerb.PUT);
updatedValueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("Updated ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedValueSet));
String updatedValueSetName = valueSet.getName();
validateTermValueSetNotExpanded(updatedValueSetName);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildren(updatedValueSetName, codeSystem);
}
@Test
public void testUpdateValueSetTriggersAnotherPreExpansionUsingTransactionBundle() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
String initialValueSetName = valueSet.getName();
validateTermValueSetNotExpanded(initialValueSetName);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildren(initialValueSetName, codeSystem);
ValueSet updatedValueSet = valueSet;
updatedValueSet.setName(valueSet.getName().concat(" - MODIFIED"));
String url = ourClient.getServerBase().concat("/").concat(myExtensionalVsId.getValueAsString());
Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.TRANSACTION);
bundle
.addEntry()
.setFullUrl(url)
.setResource(updatedValueSet)
.getRequest()
.setMethod(Bundle.HTTPVerb.PUT)
.setUrl(url);
ourLog.info("Transaction Bundle:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
ourClient.transaction().withBundle(bundle).execute();
updatedValueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("Updated ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedValueSet));
String updatedValueSetName = valueSet.getName();
validateTermValueSetNotExpanded(updatedValueSetName);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
validateTermValueSetExpandedAndChildren(updatedValueSetName, codeSystem);
}
private void validateTermValueSetNotExpanded(String theValueSetName) {
runInTransaction(()->{
Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable);
assertTrue(optionalValueSetByResourcePid.isPresent());
Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
assertTrue(optionalValueSetByUrl.isPresent());
TermValueSet termValueSet = optionalValueSetByUrl.get();
assertSame(optionalValueSetByResourcePid.get(), termValueSet);
ourLog.info("ValueSet:\n" + termValueSet.toString());
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals(theValueSetName, termValueSet.getName());
assertEquals(0, termValueSet.getConcepts().size());
assertEquals(TermValueSetPreExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
});
}
private void validateTermValueSetExpandedAndChildren(String theValueSetName, CodeSystem theCodeSystem) {
runInTransaction(()->{
Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable);
assertTrue(optionalValueSetByResourcePid.isPresent());
Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
assertTrue(optionalValueSetByUrl.isPresent());
TermValueSet termValueSet = optionalValueSetByUrl.get();
assertSame(optionalValueSetByResourcePid.get(), termValueSet);
ourLog.info("ValueSet:\n" + termValueSet.toString());
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals(theValueSetName, termValueSet.getName());
assertEquals(theCodeSystem.getConcept().size(), termValueSet.getConcepts().size());
assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("8450-9", concept.getCode());
assertEquals("Systolic blood pressure--expiration", concept.getDisplay());
assertEquals(2, concept.getDesignations().size());
assertEquals(0, concept.getOrder());
TermValueSetConceptDesignation designation = concept.getDesignations().get(0);
assertEquals("nl", designation.getLanguage());
assertEquals("http://snomed.info/sct", designation.getUseSystem());
assertEquals("900000000000013009", designation.getUseCode());
assertEquals("Synonym", designation.getUseDisplay());
assertEquals("Systolische bloeddruk - expiratie", designation.getValue());
designation = concept.getDesignations().get(1);
assertEquals("sv", designation.getLanguage());
assertEquals("http://snomed.info/sct", designation.getUseSystem());
assertEquals("900000000000013009", designation.getUseCode());
assertEquals("Synonym", designation.getUseDisplay());
assertEquals("Systoliskt blodtryck - utgång", designation.getValue());
concept = termValueSet.getConcepts().get(1);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("11378-7", concept.getCode());
assertEquals("Systolic blood pressure at First encounter", concept.getDisplay());
assertEquals(0, concept.getDesignations().size());
assertEquals(1, concept.getOrder());
// ...
concept = termValueSet.getConcepts().get(22);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("8491-3", concept.getCode());
assertEquals("Systolic blood pressure 1 hour minimum", concept.getDisplay());
assertEquals(1, concept.getDesignations().size());
assertEquals(22, concept.getOrder());
designation = concept.getDesignations().get(0);
assertEquals("nl", designation.getLanguage());
assertEquals("http://snomed.info/sct", designation.getUseSystem());
assertEquals("900000000000013009", designation.getUseCode());
assertEquals("Synonym", designation.getUseDisplay());
assertEquals("Systolische bloeddruk minimaal 1 uur", designation.getValue());
concept = termValueSet.getConcepts().get(23);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("8492-1", concept.getCode());
assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
assertEquals(0, concept.getDesignations().size());
assertEquals(23, concept.getOrder());
});
}
@Test
public void testValidateCodeOperationByCodeAndSystemInstance() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
@ -767,7 +951,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
}
@Test
public void testValiedateCodeAgainstBuiltInSystem() {
public void testValidateCodeAgainstBuiltInSystem() {
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
@ -839,7 +1023,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@After
public void afterResetPreExpansionDefault() {
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
myDaoConfig.setPreExpandValueSets(new DaoConfig().isPreExpandValueSets());
}
@AfterClass

554
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
View File

@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -17,9 +18,8 @@ import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Test;
import org.junit.*;
import org.junit.rules.ExpectedException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.transaction.TransactionStatus;
@ -38,6 +38,9 @@ import static org.junit.Assert.*;
public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
private static final Logger ourLog = LoggerFactory.getLogger(TerminologySvcImplDstu3Test.class);
@Rule
public final ExpectedException expectedException = ExpectedException.none();
private static final String CS_URL = "http://example.com/my_code_system";
private static final String CS_URL_2 = "http://example.com/my_code_system2";
@ -145,6 +148,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
LOINC_URI,
code2.getCode(),
code2.getDisplay());
code1.addChild(code2, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
cs.getConcepts().add(code1);
code2.addPropertyString("SYSTEM", "Ser");
@ -159,11 +163,13 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
LOINC_URI,
code3.getCode(),
code3.getDisplay());
code2.addChild(code3, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
code2.addPropertyCoding(
"child",
LOINC_URI,
code4.getCode(),
code4.getDisplay());
code2.addChild(code4, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
cs.getConcepts().add(code2);
code3.addPropertyString("SYSTEM", "Ser");
@ -306,7 +312,6 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, empty());
}
@Test
@ -485,12 +490,10 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("copyright")
.setOp(ValueSet.FilterOperator.ISA)
.setValue("LOINC");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Don't know how to handle op=ISA on property copyright", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle op=ISA on property copyright");
myTermSvc.expandValueSet(vs);
}
@Test
@ -504,18 +507,16 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include.setSystem(CS_URL);
include
.addFilter()
.setProperty("copyright")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("LOINC");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Invalid filter, property copyright is LOINC-specific and cannot be used with system: http://example.com/my_code_system", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Invalid filter, property copyright is LOINC-specific and cannot be used with system: http://example.com/my_code_system");
myTermSvc.expandValueSet(vs);
}
@Test
@ -534,12 +535,245 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("copyright")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("bogus");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Don't know how to handle value=bogus on property copyright", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle value=bogus on property copyright");
myTermSvc.expandValueSet(vs);
}
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithExcludeAndEqual() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-3");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-4");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4", "47239-9"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4", "47239-9"));
}
@Ignore("Not yet implemented; see #1512 in GitHub.")
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithExcludeAndIn() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.IN)
.setValue("50015-7,43343-3,43343-4,47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7"));
}
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithIncludeAndEqual() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-3", "43343-4", "47239-9"));
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-3");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-4", "47239-9"));
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-4");
outcome = myTermSvc.expandValueSet(vs);
assertEquals(0, outcome.getExpansion().getContains().size());
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("47239-9");
outcome = myTermSvc.expandValueSet(vs);
assertEquals(0, outcome.getExpansion().getContains().size());
}
@Ignore("Not yet implemented; see #1512 in GitHub.")
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithIncludeAndIn() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.IN)
.setValue("50015-7,43343-3,43343-4,47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-3", "43343-4", "47239-9"));
}
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithUnsupportedOp() {
createLoincSystemWithSomeCodes();
ValueSet vs;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.ISA)
.setValue("50015-7");
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle op=ISA on property ancestor");
myTermSvc.expandValueSet(vs);
}
@Test
public void testExpandValueSetPropertyFilterLoincAncestorWithUnsupportedSystem() {
createCodeSystem();
createLoincSystemWithSomeCodes();
ValueSet vs;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(CS_URL);
include
.addFilter()
.setProperty("ancestor")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Invalid filter, property ancestor is LOINC-specific and cannot be used with system: http://example.com/my_code_system");
myTermSvc.expandValueSet(vs);
}
@Test
@ -747,12 +981,10 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("child")
.setOp(ValueSet.FilterOperator.ISA)
.setValue("50015-7");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Don't know how to handle op=ISA on property child", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle op=ISA on property child");
myTermSvc.expandValueSet(vs);
}
@Test
@ -772,12 +1004,244 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("child")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Invalid filter, property child is LOINC-specific and cannot be used with system: http://example.com/my_code_system", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Invalid filter, property child is LOINC-specific and cannot be used with system: http://example.com/my_code_system");
myTermSvc.expandValueSet(vs);
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithExcludeAndEqual() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4", "47239-9"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-3");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-3", "43343-4", "47239-9"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-4");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-4", "47239-9"));
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-4", "47239-9"));
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithExcludeAndIn() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(LOINC_URI);
// Exclude
exclude = vs.getCompose().addExclude();
exclude.setSystem(LOINC_URI);
exclude
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.IN)
.setValue("50015-7,43343-3,43343-4,47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-4", "47239-9"));
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithIncludeAndEqual() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
outcome = myTermSvc.expandValueSet(vs);
assertEquals(0, outcome.getExpansion().getContains().size());
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-3");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7"));
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("43343-4");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3"));
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3"));
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithIncludeAndIn() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.IN)
.setValue("50015-7,43343-3,43343-4,47239-9");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3"));
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithUnsupportedOp() {
createLoincSystemWithSomeCodes();
ValueSet vs;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(LOINC_URI);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.ISA)
.setValue("50015-7");
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle op=ISA on property descendant");
myTermSvc.expandValueSet(vs);
}
@Test
public void testExpandValueSetPropertyFilterLoincDescendantWithUnsupportedSystem() {
createCodeSystem();
createLoincSystemWithSomeCodes();
ValueSet vs;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(CS_URL);
include
.addFilter()
.setProperty("descendant")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Invalid filter, property descendant is LOINC-specific and cannot be used with system: http://example.com/my_code_system");
myTermSvc.expandValueSet(vs);
}
@Test
@ -984,12 +1448,10 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("parent")
.setOp(ValueSet.FilterOperator.ISA)
.setValue("50015-7");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Don't know how to handle op=ISA on property parent", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Don't know how to handle op=ISA on property parent");
myTermSvc.expandValueSet(vs);
}
@Test
@ -1009,12 +1471,10 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.setProperty("parent")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("50015-7");
try {
myTermSvc.expandValueSet(vs);
} catch (InvalidRequestException e) {
assertEquals(400, e.getStatusCode());
assertEquals("Invalid filter, property parent is LOINC-specific and cannot be used with system: http://example.com/my_code_system", e.getMessage());
}
expectedException.expect(InvalidRequestException.class);
expectedException.expectMessage("Invalid filter, property parent is LOINC-specific and cannot be used with system: http://example.com/my_code_system");
myTermSvc.expandValueSet(vs);
}
@Test

82
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
View File

@ -65,7 +65,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@After
public void after() {
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
myDaoConfig.setPreExpandValueSets(new DaoConfig().isPreExpandValueSets());
}
private IIdType createCodeSystem() {
@ -629,7 +629,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testDeleteValueSet() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
@ -641,7 +641,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffset(), myDaoConfig.getPreExpandValueSetsDefaultCount());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
TermValueSet termValueSet = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable).get();
@ -666,7 +666,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testDeleteValueSetWithClientAssignedId() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.PUT);
@ -678,7 +678,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffset(), myDaoConfig.getPreExpandValueSetsDefaultCount());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
TermValueSet termValueSet = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable).get();
@ -723,7 +723,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testDuplicateValueSetUrls() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
// DM 2019-03-05 - We pre-load our custom CodeSystem otherwise pre-expansion of the ValueSet will fail.
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
@ -736,7 +736,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testExpandTermValueSetAndChildren() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
@ -750,7 +750,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
myCaptureQueriesListener.clear();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffset(), myDaoConfig.getPreExpandValueSetsDefaultCount());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
@ -760,7 +760,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertThat(myCaptureQueriesListener.getDeleteQueriesForCurrentThread(), empty());
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffset(), expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
@ -821,7 +821,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
public void testExpandExistingValueSetNotPreExpanded() throws Exception {
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
@ -829,11 +829,11 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffset(), myDaoConfig.getPreExpandValueSetsDefaultCount());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffset(), expandedValueSet.getExpansion().getOffset());
assertEquals(0, expandedValueSet.getExpansion().getParameter().size());
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getContains().size());
@ -885,11 +885,11 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("Systolic blood pressure 8 hour minimum", containsComponent.getDisplay());
assertFalse(containsComponent.hasDesignation());
expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffset(), myDaoConfig.getPreExpandValueSetsDefaultCount());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffset(), expandedValueSet.getExpansion().getOffset());
assertEquals(0, expandedValueSet.getExpansion().getParameter().size());
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getContains().size());
@ -944,7 +944,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testExpandTermValueSetAndChildrenWithClientAssignedId() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.PUT);
@ -956,11 +956,11 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffset(), myDaoConfig.getPreExpandValueSetsDefaultCount());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffset(), expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
@ -1019,7 +1019,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testExpandTermValueSetAndChildrenWithCount() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
@ -1031,11 +1031,11 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), 23);
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffset(), 23);
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffset(), expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
@ -1088,7 +1088,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testExpandTermValueSetAndChildrenWithCountWithClientAssignedId() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.PUT);
@ -1100,11 +1100,11 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), 23);
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffset(), 23);
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffset(), expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
@ -1157,7 +1157,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testExpandTermValueSetAndChildrenWithCountOfZero() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
@ -1169,11 +1169,11 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), 0);
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffset(), 0);
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffset(), expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
@ -1185,7 +1185,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testExpandTermValueSetAndChildrenWithCountOfZeroWithClientAssignedId() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.PUT);
@ -1197,11 +1197,11 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), 0);
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffset(), 0);
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffset(), expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
@ -1213,7 +1213,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testExpandTermValueSetAndChildrenWithOffset() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
@ -1225,7 +1225,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, 1, myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, 1, myDaoConfig.getPreExpandValueSetsDefaultCount());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
@ -1274,7 +1274,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testExpandTermValueSetAndChildrenWithOffsetWithClientAssignedId() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.PUT);
@ -1286,7 +1286,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, 1, myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, 1, myDaoConfig.getPreExpandValueSetsDefaultCount());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
@ -1335,7 +1335,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testExpandTermValueSetAndChildrenWithOffsetAndCount() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
@ -1390,7 +1390,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testExpandTermValueSetAndChildrenWithOffsetAndCountWithClientAssignedId() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.PUT);
@ -2046,7 +2046,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testStoreTermValueSetAndChildren() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
@ -2148,7 +2148,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testStoreTermValueSetAndChildrenWithClientAssignedId() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.PUT);
@ -2250,7 +2250,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testStoreTermValueSetAndChildrenWithExclude() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignationsAndExclude(HttpVerb.POST);
@ -2352,7 +2352,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testStoreTermValueSetAndChildrenWithExcludeWithClientAssignedId() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignationsAndExclude(HttpVerb.PUT);
@ -3600,7 +3600,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testValidateCodeIsInPreExpandedValueSet() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
@ -3650,7 +3650,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Test
public void testValidateCodeIsInPreExpandedValueSetWithClientAssignedId() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.PUT);

44
src/changes/changes.xml
View File

@ -43,7 +43,7 @@
</action>
<action type="add" issue="1489">
<![CDATA[
<b>Improovement</b>:
<b>Improvement</b>:
A significant performance improvement was made to the parsers (particularly the Json Parser)
when serializing resources. This work yields improvements of 20-50% in raw encode speed when
encoding large resources. Thanks to David Maplesden for the pull request!
@ -91,11 +91,11 @@
The informational message returned in an OperationOutcome when a delete failed due to cascades not being enabled
contained an incorrect example. This has been corrected.
</action>
<action type="fix">
In some cases, deleting a CodeSystem resource would fail because the underlying
codes were not correctly deleted from the terminology service tables. This is
fixed.
</action>
<action type="fix">
In some cases, deleting a CodeSystem resource would fail because the underlying
codes were not correctly deleted from the terminology service tables. This is
fixed.
</action>
<action type="change">
Two foreign keys have been dropped from the HFJ_SEARCH_RESULT table used by the FHIR search query cache. These
constraints did not add value and caused unneccessary contention when used under high load.
@ -115,7 +115,7 @@
leaving the Bundle.entry.request.method blank in DSTU3 transactions and setting the request payload
as a Binary resource containing a valid patch.
</action>
<action type="change" issue="1366">
<action type="change">
The HAPI FHIR CLI server now uses H2 as its database platform instead of Derby.
Note that this means that data in any existing installations will need to be
re-uploaded to the new database platform.
@ -219,6 +219,36 @@
handled by method implementations that did not have any <![CDATA[<code>@IncludeParam</code>]]> defined. This
is now corrected. Thanks to Tuomo Ala-Vannesluoma for reporting and providing a test case!
</action>
<action type="add" issue="1366">
The ValueSet operation <![CDATA[<code>$expand</code>]]> has been optimized for large ValueSets. ValueSets are
now persistence-backed by the terminology tables, which are populated by a scheduled pre-expansion process.
A ValueSet previously stored in an existing FHIR repository will need to be re-created or updated to make
it a candidate for pre-expansion. ValueSets that have yet to be pre-expanded will continue to be expanded
in-memory.
</action>
<action type="add" issue="1431">
The ValueSet operation <![CDATA[<code>$validate-code</code>]]> has been optimized for large ValueSets.
Codes in ValueSets that have yet to be pre-expanded will continue to be validated in-memory.
</action>
<action type="add" issue="1447">
LOINC filenames for terminology upload are now configurable using the
<![CDATA[<code>loincupload.properties</code>]]> file.
</action>
<action type="add" issue="1451">
Support for the LOINC <![CDATA[<code>EXTERNAL_COPYRIGHT_NOTICE</code>]]> property and
<![CDATA[<code>copyright</code>]]> filter has been added.
</action>
<action type="add" issue="1453">
Support for the LOINC <![CDATA[<code>parent</code>]]> and <![CDATA[<code>child</code>]]> filters has been
added. Both filters can be used with either of the <![CDATA[<code>=</code>]]> or
<![CDATA[<code>in</code>]]> operators.
</action>
<action type="add" issue="1454">
Support for the LOINC <![CDATA[<code>ancestor</code>]]> and <![CDATA[<code>descendant</code>]]> filters has
been added. The <![CDATA[<code>descendant</code>]]> filter can be used with either of the
<![CDATA[<code>=</code>]]> or <![CDATA[<code>in</code>]]> operators. At present, the
<![CDATA[<code>ancestor</code>]]> filter can only be used with the <![CDATA[<code>=</code>]]> operator.
</action>
<action type="fix">
The JPA server failed to find codes defined in not-present codesystems in some cases, and reported
that the CodeSystem did not exist. This has been corrected.