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

Resolve "Need to implement the ancestor and descendant filters for LOINC."
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@dmuylwyk
dmuylwyk committed Sep 30, 2019
2 parents 557a8cc + ac9c10a commit 1b2892f
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Showing 39 changed files with 1,146 additions and 299 deletions.
7 changes: 6 additions & 1 deletion hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
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Expand Up @@ -9,7 +9,6 @@
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;
Expand All @@ -21,6 +20,7 @@
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;
Expand Down Expand Up @@ -99,6 +99,11 @@ public IValidatorModule instanceValidatorDstu3() {
return val;
}

@Bean
public DefaultProfileValidationSupport defaultProfileValidationSupport() {
return new DefaultProfileValidationSupport();
}

@Bean
public JpaValidationSupportChainDstu3 jpaValidationSupportChain() {
return new JpaValidationSupportChainDstu3();
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11 changes: 7 additions & 4 deletions hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
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Expand Up @@ -8,7 +8,7 @@
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;
Expand All @@ -20,14 +20,12 @@
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;
Expand Down Expand Up @@ -102,6 +100,11 @@ public IValidatorModule instanceValidatorR4() {
return val;
}

@Bean
public DefaultProfileValidationSupport defaultProfileValidationSupport() {
return new DefaultProfileValidationSupport();
}

@Bean
public JpaValidationSupportChainR4 jpaValidationSupportChain() {
return new JpaValidationSupportChainR4();
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6 changes: 6 additions & 0 deletions hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
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Expand Up @@ -20,6 +20,7 @@
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;
Expand Down Expand Up @@ -99,6 +100,11 @@ public IValidatorModule instanceValidatorR5() {
return val;
}

@Bean
public DefaultProfileValidationSupport defaultProfileValidationSupport() {
return new DefaultProfileValidationSupport();
}

@Bean
public JpaValidationSupportChainR5 jpaValidationSupportChain() {
return new JpaValidationSupportChainR5();
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6 changes: 4 additions & 2 deletions hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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Expand Up @@ -112,7 +112,7 @@

@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;
Expand Down Expand Up @@ -1017,7 +1017,8 @@ protected ResourceTable updateEntityForDelete(RequestDetails theRequest, Resourc
}

@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);
Expand Down Expand Up @@ -1256,6 +1257,7 @@ protected ResourceTable updateEntity(RequestDetails theRequest, final IBaseResou
return theEntity;
}

@Override
public ResourceTable updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
ResourceTable theEntity, IIdType theResourceId, IBaseResource theOldResource) {

Expand Down
139 changes: 77 additions & 62 deletions hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
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Expand Up @@ -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
Expand Down Expand Up @@ -920,7 +928,7 @@ public boolean isAllowInlineMatchUrlReferences() {
* <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
Expand Down Expand Up @@ -1621,34 +1629,6 @@ public void setWebsocketContextPath(String theWebsocketContextPath) {
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
Expand Down Expand Up @@ -1720,83 +1700,118 @@ public boolean isStoreRequestId() {
}

/**
* 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 {
Expand Down
4 changes: 2 additions & 2 deletions ...ir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java
View file
Expand Up @@ -73,8 +73,8 @@ protected void postPersist(ResourceTable theEntity, Subscription theSubscription


@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) {
Expand Down
18 changes: 18 additions & 0 deletions hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IJpaDao.java
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 changes: 5 additions & 2 deletions hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java
View file
Expand Up @@ -909,10 +909,13 @@ private Map<BUNDLEENTRY, ResourceTable> doTransactionWriteOperations(final Servl
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);
}
}

Expand Down
4 changes: 2 additions & 2 deletions ...paserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View file
Expand Up @@ -125,8 +125,8 @@ protected void preDelete(CodeSystem theResourceToDelete, ResourceTable theEntity
}

@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;
Expand Down

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